CDS 1 - 864 /gene="1" /product="gp1" /function="Hypothetical Protein" /locus tag="FlyingTortilla_1" /note=Original Glimmer call @bp 1 has strength 13.47; Genemark calls start at 1 /note=SSC: 1-864 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp001 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.268, -4.422065872383915, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp001 [Gordonia phage ChisanaKitsune] ],,YP_010675648,94.4056,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 1 has strength 13.47 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) no gap/overlap /note=(3) GeneMark most coding potential /note=(4) negative final score (start #16 less neg), Z score above 2 /note=(5) All 10 BLASTp S1:Q1 /note=(6) All Pham members same start (7 MAs) /note= /note=DECISION : NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: most of the top hits don`t have good coverage, functional calls are not conserved /note=Pham: (Chidi & Schomber): neither of their feature 1`s have a functional call /note=BLASTp: of the S1:Q1 hits (non-drafts), only 1 makes a functional call (Hanem=DNA binding protein); others have `function unknown` /note= /note=CALL: unknown function CDS 898 - 2271 /gene="2" /product="gp2" /function="Hypothetical Protein" /locus tag="FlyingTortilla_2" /note=Original Glimmer call @bp 898 has strength 8.59; Genemark calls start at 898 /note=SSC: 898-2271 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_GRAY_2 [Gordonia phage Gray] ],,NCBI, q1:s1 26.9147% 5.42089E-12 GAP: 33 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.635, -5.465638252962307, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_GRAY_2 [Gordonia phage Gray] ],,AZS07857,21.9941,5.42089E-12 SIF-HHPRED: SIF-Syn: /note=FUNCTIONAL CALL: /note=HHpred:low coverage of top hits, fun call not conserved /note=Pham: gene 2 for comp phage not same as gene for FlyingTortilla. Small pham (3 members, 2 of which are drafts with no func call) /note=BLASTp: Top hits same pham, drafts with no func /note=DECISION: Unknown Function /note= /note=Original Glimmer call @bp 898 has strength 8.59 /note= /note=ORF CALL /note=(1) Glimmer and GM agree /note=(2) +34bp gap /note=(3) Longest ORF possible, GM most coding potential /note=(4) Not least neg final, Z score not 2 * /note=(5) 9/10 S1:Q1 match /note=(6) no MA to compare (small Pham, other 2 members drafts) /note= /note=DECISION: NO CHANGE /note= /note=*GeneMark report, there is a region ~1300bp where the coding potentisl goes does then back up; appears to be another good start candidate, but no upstream stop (4 - recognizing that potential start around potential starts 7 & 8) /note= /note=FUNCTIONAL CALL: /note=HHpred: lo coverage of top hits, functional call not conserved /note=Pham: gene 2 for comparison phage not the same as gene 2 for FlyingTortilla, small pham with 3 members, other 2 members are drafts with no functional calls /note=BLASTp: all top hits (from same pham) have unknown function /note= /note=CALL: unknown function CDS 2268 - 2726 /gene="3" /product="gp3" /function="Hypothetical Protein" /locus tag="FlyingTortilla_3" /note=Original Glimmer call @bp 2268 has strength 8.33; Genemark calls start at 2268 /note=SSC: 2268-2726 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp003 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 4.19836E-81 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -2.827683592113848, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp003 [Gordonia phage Chidiebere] ],,YP_010675521,88.8889,4.19836E-81 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 2268 has strength 8.33 /note= /note=ORF CALL: /note=(frame window, 2 potential starts - ps2 autoannotated) /note=(1) Glimmer and GM agree /note=(2) bp2268 start -3bp overlap (upstream start too large overlap?) /note=(3) while upstream start exists, does not encompass any additional coding potential compared to 2268bp start /note=(4) RBS final score least neg, Z score above 2 (final score more negative than 2262bp potential) /note=(5) 10/10 S1:Q1 match /note=(6) all 6 MA members of Pham choose 2268bp as start /note= /note=DECISION: no change CDS 2726 - 3439 /gene="4" /product="gp4" /function="Hypothetical Protein" /locus tag="FlyingTortilla_4" /note=Original Glimmer call @bp 2726 has strength 10.1; Genemark calls start at 2726 /note=SSC: 2726-3439 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp004 [Gordonia phage Chidiebere] ],,NCBI, q126:s42 46.4135% 4.45505E-13 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.283, -4.390754385080681, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp004 [Gordonia phage Chidiebere] ],,YP_010675522,38.7435,4.45505E-13 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] Glimmer and GeneMark agree /note=[2] Overlap of -1 between 3 & 4 /note=[3] GeneMark most coding potential /note=[4] Negative Final Score. Z-Score above 2 /note=[5] 2/10 Starts are 1 to 1 /note=[6] No manual annotations reporting this start /note= /note=Decision: No change. /note= /note=FUNCTIONAL CALLS: /note=HHpred: Hits have low coverage. Functional calls not conserved. /note=Pham: gene 4 for comparison phages not the same as gene 4 for FlyingTortilla. Small pgame with 3 other members, other 2 members are drafts with no functional calls. /note=Blastp: All one to one matches in Blastp have unknown functions. Other good hits are all drafts that are not annotated. /note= /note=CALL: Unknown function CDS 3456 - 4178 /gene="5" /product="gp5" /function="Hypothetical Protein" /locus tag="FlyingTortilla_5" /note=Original Glimmer call @bp 3456 has strength 9.34; Genemark calls start at 3456 /note=SSC: 3456-4178 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp005 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 2.13003E-77 GAP: 16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.12, -3.1837611541087343, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp005 [Gordonia phage Chidiebere] ],,YP_010675523,62.0968,2.13003E-77 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] GeneMark calls an earlier start at basepair 3447. /note=[2] Gap of 16 base pairs between ORF 4 and ORF 5 for the Glimmer sequence and a gap of 7 base pairs between ORF 4 and ORF 5 for the GeneMark sequence. /note=[3] GeneMark displays the most coding potential compared to Glimmer. /note=[4] Negative final score, z-score above 2 /note=[5] 10/10 one to one matches for Glimmer start. /note=[6] Same start found in 6 manual annotations. /note= /note=Decsion: No change. /note= /note=FUNCTIONAL CALLS /note=HHpred: Very low coverage of gene. Function remains unknown. /note=Pham: Gene 5 appears to be the same as the other two comparison samples, showing a good chance for a match. Unknown function for all three though with no functional calls. /note=Blastp: Function unknown for all one to one matches in Blastp. /note= /note=Call: Unknown Function. CDS 4178 - 4528 /gene="6" /product="gp6" /function="Hypothetical Protein" /locus tag="FlyingTortilla_6" /note=Original Glimmer call @bp 4178 has strength 5.25; Genemark calls start at 4178 /note=SSC: 4178-4528 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp006 [Gordonia phage ChisanaKitsune] ],,NCBI, q3:s6 59.4828% 2.13112E-15 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.04, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp006 [Gordonia phage ChisanaKitsune] ],,YP_010675653,58.4416,2.13112E-15 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 4178 has strength 5.25 /note= /note=ORF Calls /note=(1) Glimmer and GM agrees /note=(2) No Gap /note=(3) Longest ORF possible, GM most coding potential /note=(4) Negative final score(start#4178 less neg), Z score above 2 /note=(5) 3/10 S1:Q1 Matches /note=(6) no MA to compare [small Pham, other member is a draft] /note= /note=DECISION, NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred low coverage of top hits functional call not covered /note=Pham: gene 2 not the same gene as comparison to Flying Tortilla, not the same gene, other pham member are drafts with no functional call /note=BLASTp: top hit (from the same pham) have unkown function /note= /note=Call: Unknown function CDS 4589 - 4936 /gene="7" /product="gp7" /function="Hypothetical Protein" /locus tag="FlyingTortilla_7" /note=Original Glimmer call @bp 4637 has strength 6.77; Genemark calls start at 4583 /note=SSC: 4589-4936 CP: no SCS: both-cs ST: NI BLAST-Start: [hypothetical protein PQD14_gp009 [Gordonia phage Chidiebere] ],,NCBI, q50:s4 57.3913% 3.51365E-27 GAP: 60 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.565, -5.631526093152131, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp009 [Gordonia phage Chidiebere] ],,YP_010675527,86.9565,3.51365E-27 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 4637 has strength 6.77; GeneMark calls start at 4589 /note= /note=ORF Calls for bp@4637: /note=(1) Glimmer and GM disagree /note=(2) Gap of +109 for 4637 /note=(3) GeneMark does not encode all coding potential, and not longest ORF /note=(4) Least negative final score start at #4637, Z Score above 2 /note=(5) bp @ 4637 S1:Q1 1/10 /note=(6) no MA to compare [small Pham, other 2 members are drafts] /note= /note=ORF Call bp@ 4589: /note=(1) Glimmer and GM disagree /note=(2) Gap of +61 /note=(3) Most coding potential /note=(4) Z score not greater then 2, not least negative final score /note=(5) S1:Q1 for 2/10 /note=(6):no MA to compare [small Pham, other 2 members are drafts] /note= /note=ORF CALLbp@4583 /note=(1) GeneMark start on PECAAN /note=(2) Gap of +55 /note=(3) Most coding potential longest ORF /note=(4) Z score not greater then 2 and not least final score /note=(5) no S1:q1 hits /note=(6) no MA to compare [small Pham, other 2 members are drafts] /note= /note=Change start to bp@ 4589 /note= /note=Both of the starts were not clear enough to formulate thorough examination of which one to choose. If functional calls don`t help, then proceed to send to headquarters. /note= /note=Functional Call: /note=HHpred low coverage of top hits functional call not covered /note=Pham: gene 2 not the same gene as comparison to Flying Tortilla, not the same gene, other pham member are drafts with no functional call /note=BLASTp: top hit (from the same pham) have unkown function /note= /note=Call: Unknown function CDS 4936 - 5217 /gene="8" /product="gp8" /function="Hypothetical Protein" /locus tag="FlyingTortilla_8" /note=Original Glimmer call @bp 4936 has strength 10.74; Genemark calls start at 4936 /note=SSC: 4936-5217 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_SCHOMBER_10 [Gordonia Phage Schomber]],,NCBI, q1:s1 100.0% 1.6354E-30 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.191, -4.373866523711432, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SCHOMBER_10 [Gordonia Phage Schomber]],,WNM67031,67.6471,1.6354E-30 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 4936 has strength 10.74 /note= /note=FUNCTIONAL CALL /note= /note=1. No top hits; Best hit has a probability of 67.6% and is Yced /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), but these genes have no functional calls /note=3. All S1Q1 have unknown functions /note= /note=Decision: Unknown Function CDS 5210 - 5593 /gene="9" /product="gp9" /function="Hypothetical Protein" /locus tag="FlyingTortilla_9" /note=Original Glimmer call @bp 5210 has strength 11.65; Genemark calls start at 5210 /note=SSC: 5210-5593 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp011 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 99.2126% 2.18653E-63 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.04, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp011 [Gordonia phage Chidiebere] ],,YP_010675529,84.8,2.18653E-63 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 5210 has strength 11.65 /note= /note=FUNCTIONAL CALL /note= /note=1. No top hits; Best hit has a probability of 25.4% and is DUF3826 /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), but these genes have no functional calls /note=3. All S1Q1 have unknown functions /note= /note=Decision: Unknown Function CDS 5590 - 5949 /gene="10" /product="gp10" /function="Hypothetical Protein" /locus tag="FlyingTortilla_10" /note=Original Glimmer call @bp 5590 has strength 8.61; Genemark calls start at 5590 /note=SSC: 5590-5949 CP: no SCS: both ST: SS BLAST-Start: GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.562, -3.4515614587161716, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 5590 has strength 8.61 /note= /note=ORF CALL: /note=[1] Glimmer and GenMark agree /note=[2] overlap -3bp /note=[3] Longest coding potential and Longest ORF /note=[4] Start 2 has a "z" score >2 & least negative score /note=[5] 1/10 BLASTp hits Q1:S1 /note=[6] Startt 2@5590 has 0 MAs (none at all) /note= /note=Decision no change to start /note= /note=Functional Call /note=[1] HHpred=no close calls /note=[2] Pham=two comparison phages have a different gene in position 10, no direct matches-function unknown /note=[3] BLASTp= no Q1:S1 matches no function /note= /note=Call unknown function CDS 5946 - 6230 /gene="11" /product="gp11" /function="Hypothetical Protein" /locus tag="FlyingTortilla_11" /note=Original Glimmer call @bp 5946 has strength 9.89; Genemark calls start at 5946 /note=SSC: 5946-6230 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PQD15_gp010 [Gordonia phage ChisanaKitsune] ],,NCBI, q3:s8 97.8723% 1.86196E-48 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.843, -2.9392830384527056, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp010 [Gordonia phage ChisanaKitsune] ],,YP_010675657,86.8687,1.86196E-48 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 5946 has strength 9.89 /note= /note=ORF CALL /note=[1] Glimmer and GenMark agree /note=[2] overlap -3BP /note=[3] Longest coding potential and Longest ORF /note=[4]Start 1 has a "z" score >2 & least negative score /note=[5] 2/10 BLASTp hits Q1:S1 /note=[6] Start 1@5946 has 0 MAs (none at all) /note= /note=Decision no change to start /note= /note=FUNCTIONAL CALL /note=[1] HHpred=no close calls, might be "Luciferase catalytic domain" probability of "Luciferase_cat" 83.1% /note=[2] Pham= position 11 is a match to position 12 of both Schomber and Chidiebere, function unknown /note=[3] BLASTp= no Q1:S1 matches, Q1:S1 match with ScarletRaider Draft no function /note= /note=Call Unknown Function CDS 6471 - 6677 /gene="12" /product="gp12" /function="Hypothetical Protein" /locus tag="FlyingTortilla_12" /note=Original Glimmer call @bp 6471 has strength 8.14; Genemark calls start at 6471 /note=SSC: 6471-6677 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp011 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 3.12346E-38 GAP: 240 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.04, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp011 [Gordonia phage ChisanaKitsune] ],,YP_010675658,95.5882,3.12346E-38 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 6471 has strength 8.14 /note= /note=ORF CALLS: /note=(1) Glimmer and GeneMark Agree /note=(2) Bp Gap of +241 /note=(3) Longest possible ORF, GM most coding potential despite the gap /note=(4) Highest Z-value & least negative score /note=(5) 4/10 S1:Q1 Match /note=(6) All 6 MA members of PHAM chose 6471 as start /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: Low coverage of top hits, functional call not conserved /note=Pham: Comparable gene for Chidiebere and Schomber gene 14 for FlyingTortilla`s gene 12, have no functional call /note=BLASTp: All comparable S1:Q1 members have unknown function /note= /note=CALL: Unknown CDS 6674 - 6952 /gene="13" /product="gp13" /function="Hypothetical Protein" /locus tag="FlyingTortilla_13" /note=Original Glimmer call @bp 6674 has strength 7.25; Genemark calls start at 6674 /note=SSC: 6674-6952 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp015 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 9.74649E-44 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.035, -4.702334767722353, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp015 [Gordonia phage Chidiebere] ],,YP_010675533,89.1304,9.74649E-44 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 6674 has strength 7.25 /note= /note=ORF CALLS: /note=(1) Glimmer and GeneMark Agree /note=(2) Bp of -3 overlap /note=(3) Longest possible ORF, low coding potential but other starts cut off tons of the genome and create huge gaps /note=(4) Z-score value is greater than 2 and has a low score. Other starts have better z-scores and lower scores but significantly lower lengths /note=(5) 10/10 S1:Q1 match /note=(6) All manual annotations agree /note= /note=DECISION: NO CHANGE /note= /note= /note=FUNCTIONAL CALL: /note=HHpred: No coverage of top hits; functional call not conserved /note=Pham: FlyingTortilla gene 13 comparable to Chidiebere`s gene 15 and no comparable gene to Schomber; no functional calls /note=BLASTp: All comparable S1:Q1 members have unknown function /note= /note=CALL: unknown CDS 6945 - 8417 /gene="14" /product="gp14" /function="terminase, large subunit" /locus tag="FlyingTortilla_14" /note=Original Glimmer call @bp 6945 has strength 12.14; Genemark calls start at 6945 /note=SSC: 6945-8417 CP: no SCS: both ST: NI BLAST-Start: [terminase large subunit [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.04, -2.583959800616441, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Gordonia phage ChisanaKitsune] ],,YP_010675659,97.7551,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 6945 has strength 12.14 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) Overlap of 5 /note=(3) GeneMark most coding potential /note=(4) negative final score (#1 least neg), Z score above 2 /note=(5) 6/10 BLASTp S1:Q1 /note=(6) Start 4 has 2 MAs, Not most common MA /note= /note=DECISION: INVESTIGATE LATER START (@bp 6960) /note=(2) Gap of 10 /note=(3a) Longest possible ORF w/o overlap /note=(3b) Cuts off some coding potential /note=(4) Negative final score (-6.496), Z score NOT above 2 (1.415) /note=(5) 0/10 BLASTp S1:Q1 /note=(6) No MAs for start 6 /note= /note=DECISION: NO CHANGE? /note= /note=FUNCTIONAL CALL /note=HHpred: most top hits have good coverage, functional calls conserved for large subunit terminase /note=Pham: both (Chidi & Schomber) both have functional calls; terminase function /note=BLASTp: all S1:Q1 top hits (non-drafts) have their function as either terminase or large subunit terminase /note= /note=CALL: terminase, large subunit CDS 8500 - 8718 /gene="15" /product="gp15" /function="Hypothetical Protein" /locus tag="FlyingTortilla_15" /note=Original Glimmer call @bp 8500 has strength 11.21; Genemark calls start at 8410 /note=SSC: 8500-8718 CP: no SCS: both-gl ST: NI BLAST-Start: GAP: 82 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.614, -3.3418724531147843, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 8500 has strength 11.21; GeneMark calls start at 8410 /note= /note=ORF CALLS (8500 start) /note=(1) Glimmer and GM do NOT agree /note=(2) Gap of 83 /note=(3a) Not longest possible ORF /note=(3b) Glimmer does not ecompass all coding potential /note=(4) negative final score, Z score above 2 (not least negative score) /note=(5) 2/4 BLASTp S1:Q1 /note=(6) No MAs for start 12 /note= /note=DECISION: INVESTIGATE EARLIER START (@bp 8431) /note=(2) Gap of 14 /note=(3a) Longest possible ORF w/o overlap /note=(3b) Glimmer does not encompass all coding potential (better than bp 8500) /note=(4) high negative final score, Z score not above 2 /note=(5) 0/4 BLASTp S1:Q1 /note=(6) No MAs for start 9 /note= /note=DECISION: INVESTIGATE EARLIER START (@bp 8410) /note=(2) Overlap of 7 /note=(3a) Longest possible ORF w/ overlap /note=(3b) Genemark most coding potential /note=(4) negative final score (#8 less neg), Z score above 2 (#8 higher Z score) /note=(5) 0/4 BLASTp S1:Q1 /note=(6) No MAs for start 8 /note= /note=DECISION: SEEKING TO RESOLVE FURTHER (@BP 8410) /note= /note=FUNCTIONAL CALL /note=HHpred: low coverage of top hits, functional call not conserved (highest has 56% probability) /note=Pham: gene 15 for comparison phage not the same as gene 15 for FlyingTortilla, small pham with 3 members, other 2 members are drafts with no functional calls /note=BLASTp: all top hits (from same pham) have unknown function (all are drafts) /note= /note=CALL: unknown function CDS 8787 - 8981 /gene="16" /product="gp16" /function="Hypothetical Protein" /locus tag="FlyingTortilla_16" /note=Original Glimmer call @bp 8787 has strength 6.97; Genemark calls start at 8739 /note=SSC: 8787-8981 CP: yes SCS: both-gl ST: NI BLAST-Start: [membrane protein [Gordonia phage Chidiebere] ],,NCBI, q4:s26 95.3125% 3.71612E-13 GAP: 68 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.12, -2.338663114094478, yes F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Gordonia phage Chidiebere] ],,YP_010675536,61.7978,3.71612E-13 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 8787 has strength 6.97; GeneMark calls start at 8739 /note= /note=[1] Glimmer and Genemark do not agree /note=[2] Gap +69 bp /note=[3] longest ORF possible; Has most coding potiential but there could be more in the previous start points (coding potiential cut off) /note=[4] z-value over 2 and least negative final score /note=[5] S1:Q1=2/10 /note=[6] at bp 8715 there are 7 MA`s; all pham members have 7 MA`s at start 3 /note= /note=DESCISION MADE: NO CHANGE? /note= /note=FUNCTIONAL CALLS: /note=HHpred: Low coverage of top hits. Little consistency. /note=Pham: (Shomber-17) function unknown /note=BLAST p: all in pham say function unknown /note= /note=CALL: Unknown function CDS 8978 - 9136 /gene="17" /product="gp17" /function="Hypothetical Protein" /locus tag="FlyingTortilla_17" /note=Original Glimmer call @bp 8978 has strength 1.64 /note=SSC: 8978-9136 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein [Blastococcus carthaginiensis] ],,NCBI, q7:s14 80.7692% 0.00416581 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.56, -5.641543284616902, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Blastococcus carthaginiensis] ],,WP_305998851,42.8571,0.00416581 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 8978 has strength 1.64 ** not called by GeneMark /note=[1] Glimmer and GeneMark do not agree. GeneMark is not called at all /note=[2] Longest ORF possible; Overlap -3 bp /note=[3] Does not have most coding potiential at 8978 bp /note=[4] z-value less than 2 and final score is not the least negative (at bp=8978) /note=[5] S1:Q1= 3/10 /note=[6] no MA`s for any pham members /note= /note=DECISION MADE: NO CHANGE? /note= /note=FUNCTIONAL CALLS /note=HHpred: Low coverage of top hits. Little consistency. /note=Pham: (Shomber-16) function unknown /note=BLAST p: all in pham say function unknown /note= /note=CALL: Unknown function CDS 9133 - 9321 /gene="18" /product="gp18" /function="Hypothetical Protein" /locus tag="FlyingTortilla_18" /note=Original Glimmer call @bp 9133 has strength 3.46; Genemark calls start at 9151 /note=SSC: 9133-9321 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_SCHOMBER_18 [Gordonia Phage Schomber]],,NCBI, q1:s1 100.0% 1.74223E-19 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.631, -5.411464006628378, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SCHOMBER_18 [Gordonia Phage Schomber]],,WNM67039,72.5806,1.74223E-19 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 9133 has strength 3.46; GeneMark calls start at 9151 /note= /note=ORF CALLS /note=(1) Glimmer and GM do not agree /note=(2) -4 bp overlap /note=(3) GeneMark most coding potential /note=(4) RBS final score is not the least negative; Z value is not above 2(start#7) but at start #1 the Z value is above 2 and has the least negative final score /note=(5) 2/4 are S1:Q1 match /note=(6) One MA @bp 9133 /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: no top hits and no good coverage, functional calls are not consistent /note=Pham (Chidi and Schomber): same feature 18 as Schomber, but both do not have a functional call /note=BLASTp: all hits have an unknown function /note= /note=CALL: unknown function CDS 9321 - 9617 /gene="19" /product="gp19" /function="Hypothetical Protein" /locus tag="FlyingTortilla_19" /note=Original Glimmer call @bp 9321 has strength 11.21; Genemark calls start at 9321 /note=SSC: 9321-9617 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp016 [Gordonia phage ChisanaKitsune] ],,NCBI, q4:s7 92.8571% 9.85887E-42 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.965, -2.66371296573402, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp016 [Gordonia phage ChisanaKitsune] ],,YP_010675663,81.6327,9.85887E-42 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 9321 has strength 11.21 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) +1 bp gap /note=(3) Longest ORF possible, GM best coding potential /note=(4) RBS final score is the least negative (start #3). Z value above 2. /note=(5) 3/10 are S1:Q1 match /note=(6) 2 MAs @ bp 9318; 4 MAs @ bp 9321 /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHPred: there are no top hits and no good coverage, functional calls are not consistent /note=Pham (Chidi and Schomber): feature 19 matches Schombers feature 19 and Chidi`s feature 20, but none have a functional call /note=BLASTp: all top hits have unknown functions /note= /note=CALL: unknown function CDS 9598 - 9897 /gene="20" /product="gp20" /function="Hypothetical Protein" /locus tag="FlyingTortilla_20" /note=Original Glimmer call @bp 9598 has strength 11.01; Genemark calls start at 9598 /note=SSC: 9598-9897 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp017 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 1.69959E-48 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.791, -3.494990588194529, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp017 [Gordonia phage ChisanaKitsune] ],,YP_010675664,84.8485,1.69959E-48 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 9598 has strength 11.01 /note= /note=(1) Genemark and glimmer agree /note=(2) -19 bp overlap /note=(3) Longest ORF possible GM most coding potential /note=(4)Least negative final score - highest z score above 2 /note=(5) 10/10 x S1Q1 match /note=(6) 6 MA`s /note= /note=DECISION: MADE. keep start /note= /note=FUNCTIONAL CALL: /note=HHpred: most of the top hits do not have good coverage. Functional calls are not conserved. (there is no red) /note=Pham: None of the comparisons have a functional call and only 2/3 of them match in color (flying tortilla and schomber) but chidi has a different color (much darker purple) /note=BLAST p: All 10 S1/Q1 matches listed are function unknown /note= /note=CALL: UNKNOWN FUNCTION CDS 9872 - 10078 /gene="21" /product="gp21" /function="Hypothetical Protein" /locus tag="FlyingTortilla_21" /note=Original Glimmer call @bp 9860 has strength 6.93; Genemark calls start at 9872 /note=SSC: 9872-10078 CP: no SCS: both-gm ST: NI BLAST-Start: [hypothetical protein PQD14_gp022 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 8.82994E-40 GAP: -26 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.084, -6.916087465240288, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp022 [Gordonia phage Chidiebere] ],,YP_010675540,100.0,8.82994E-40 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 9860 has strength 6.93; GeneMark calls start at 9872 /note= /note=(1) Genemark and glimmer do not agree /note=(2) -37 bp overlap /note=(3) Longest ORF possible most GM coding potential /note=(4) not least negative, not highest z score (still above 2) /note=(5) 1/10 S1Q1 match /note=(6) @ start 9860 there are no MA`s but start at 9872 has 6 MA`s /note= /note=(2) -25 bp overlap (smaller thn the other start) /note=(3) Good GM coding potential /note=(4) Not least negative final (-6.916) ... Z score below 2 (1.072) /note=(5) 9/10 S1Q1 match /note=(6) 6 MA`s /note= /note=DECISION: CHANGE START to 9872 /note= /note=Functional Call: /note=HHpred: Top hits have good coverage but there is no red so the functional calls are not conserved /note=PHAM: All 3 comparissons have different colors and none of them have a function /note=BLAST: 10/10 S1Q1 is function unknown /note= /note=DECISION: Unknown function CDS 10228 - 12855 /gene="22" /product="gp22" /function="portal protein" /locus tag="FlyingTortilla_22" /note=Original Glimmer call @bp 10228 has strength 10.32; Genemark calls start at 10228 /note=SSC: 10228-12855 CP: no SCS: both ST: NI BLAST-Start: [portal protein [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 99.8857% 0.0 GAP: 149 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.04, -2.442961286954254, no F: portal protein SIF-BLAST: ,,[portal protein [Gordonia phage ChisanaKitsune] ],,YP_010675666,92.1946,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 10228 has strength 10.32 /note=(1) gene mark and glimmer agree /note=(2)+150 gap /note=(3) not longest ORF possible GM most coding potential /note=(4) least negative final score... highest Z score above 2 /note=(5) 9/10 S1Q1 match /note=(6) 6 MAs /note=ORF CALL: NO CHANGE /note= /note=FUNCTIONAL CALL /note=Pham: (Chidi and Schomber): both of their feature 22`s have a portal protein functional call /note=Blastp: of the S1Q1 hits, 4 make a portal protein functional call /note=HHpred: high coverage top hits, others have portal protein /note=FUNCTIONAL CALL: PORTAL PROTEIN CDS 12855 - 13073 /gene="23" /product="gp23" /function="Hypothetical Protein" /locus tag="FlyingTortilla_23" /note=Original Glimmer call @bp 12855 has strength 12.99; Genemark calls start at 12855 /note=SSC: 12855-13073 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein [Slackia piriformis]],,NCBI, q6:s4 88.8889% 9.76151E-18 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.959, -4.862260131515226, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Slackia piriformis]],,WP_276684927,77.6119,9.76151E-18 SIF-HHPRED: SIF-Syn: /note=Original GIimmer call @bp 12855 has strength 12.99 /note=ORF CALL /note=(1) gene mark and glimmer agree /note=(2) no overlap or gap /note=(3) Longest ORF but not GM most coding potential /note=(4) least negative final score... no Z score value above 2 /note=(5) 4/10 S1Q1 match /note=(6) 8 MAs /note=ORF CALL: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=PHAM (Chidi and Schomber) neither of their feature 23`s have a functional call /note=BLASTp: of the S1:Q1 hits, none make a functional call /note=HHpred: low coverage top hits, mostly unknown function /note=CALL: hypothetical protein CDS 13066 - 14064 /gene="24" /product="gp24" /function="RNA ligase" /locus tag="FlyingTortilla_24" /note=Original Glimmer call @bp 13066 has strength 11.74; Genemark calls start at 13066 /note=SSC: 13066-14064 CP: no SCS: both ST: NI BLAST-Start: [RNA ligase [Gordonia phage Chidiebere] ],,NCBI, q4:s6 99.0964% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.786, -5.166207523958222, no F: RNA ligase SIF-BLAST: ,,[RNA ligase [Gordonia phage Chidiebere] ],,YP_010675543,88.8218,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 13066 has strength 11.74 /note= /note=ORF CALLS /note=[1] Glimmer and GM agree /note=[2] -8 bp overlap /note=[3] GeneMark most coding potential /note=[4] negative final score (start #3). Z score not above 2 /note=[5] 3/10 BLAST p S1:Q1 /note=[6] 6 MAs @bp 13066 /note= /note=DECISION MADE; NO CHANGE /note= /note=FUNCTION CALLS /note=HHpred: high coverage of top hits, little consistency, also found hydrolase /note=Pham: (DalanDe-19 & Schomber-24) RNA ligase /note=BLASTp: most in pham say RNA Ligase /note= /note=CALL: RNA Ligase CDS 14061 - 15158 /gene="25" /product="gp25" /function="VIP2-like ADP-ribosyltransferase toxin" /locus tag="FlyingTortilla_25" /note=Original Glimmer call @bp 14061 has strength 14.52; Genemark calls start at 14061 /note=SSC: 14061-15158 CP: no SCS: both ST: NI BLAST-Start: [VIP2-like ADP-ribosyltransferase toxin [Gordonia phage Kabocha] ],,NCBI, q1:s1 99.726% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.791, -3.0478325568523097, yes F: VIP2-like ADP-ribosyltransferase toxin SIF-BLAST: ,,[VIP2-like ADP-ribosyltransferase toxin [Gordonia phage Kabocha] ],,WAA19814,87.5691,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 14061 has strength 14.52 /note= /note=ORF CALLS /note=[1] Glimmer and GM agree /note=[2] -4 bp overlap /note=[3] GeneMark most coding potential /note=[4] negative final score (start #1). Z score above 2 /note=[5] ALL 12 BLAST p S1:Q1 /note=[6] 6 MAs at bp @14061 /note= /note=DECISION MADE; NO CHANGE /note= /note=FUNCTION CALLS /note=HHpred: high coverage of top hits, 8/10 - high consistency of ADP-ribosyltransferase /note=Pham: (Schomber-25) ADP-ribosyltransferase; (Kabocha-27 & Chidiebere-26) VIP2-like ADP-ribosyltransferase toxin /note=BLASTp: 4 in pham say ADP-ribosyltransferase toxin; 6 in pham say VIP2-like ADP-ribosyltransferase toxin /note= /note=CALL: VIP2-like ADP-ribosyltransferase toxin CDS 15158 - 18106 /gene="26" /product="gp26" /function="Hypothetical Protein" /locus tag="FlyingTortilla_26" /note=Original Glimmer call @bp 15158 has strength 13.23; Genemark calls start at 15158 /note=SSC: 15158-18106 CP: no SCS: both ST: NI BLAST-Start: [helix-turn-helix DNA binding domain protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.821, -3.0457372370466467, no F: Hypothetical Protein SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Gordonia phage Chidiebere] ],,YP_010675545,84.655,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 15158 has strength 13.23 /note= /note=ORF CALLS /note=(1) Glimmer and GeneMark agree /note=(2) No gap/overlap /note=(3) GeneMark most coding potential /note=(4) Negative final score (start #1 less neg), Z score above 2 /note=(5) All 10 BLAST p S1:Q1 /note=(6) Start 2 has 6 MA`s @15158 /note= /note=DECISION: NO CHANGE IN ORF CALLS /note= /note=FUNCTIONAL CALL: /note=HHpred: most of the top its don`t have good coverage, functional calls are no conserved /note=Pham: Schomber has feature 26 that are similar while Chidi does not match /note=BLASTp: of the S1:Q1 hits (non-drafts), only 2 make a functional call (Chidi & Gray=helix-turn-helix DNA binding domain protein); others have `function unknown` /note= /note=CALL: unknown function CDS 18106 - 18762 /gene="27" /product="gp27" /function="Hypothetical Protein" /locus tag="FlyingTortilla_27" /note=Original Glimmer call @bp 18106 has strength 10.13; Genemark calls start at 18106 /note=SSC: 18106-18762 CP: no SCS: both ST: NI BLAST-Start: [head maturation protease [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 1.64112E-118 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.023, -2.4787699911121788, yes F: Hypothetical Protein SIF-BLAST: ,,[head maturation protease [Gordonia phage Chidiebere] ],,YP_010675546,87.156,1.64112E-118 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 18106 has strength 10.13 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) No gap/overlap /note=(3) GeneMark most coding potential /note=(4) Negative final score (start #1 less neg), Z score above 2 /note=(5) All 10 BLAST p S1:Q1 /note=(6) Start 3 @18106 has 6 MAs /note= /note=DECISION: NO CHANGE IN ORF CALLS /note= /note=FUNCTIONAL CALL: /note=HHpred: Most of the top hits don`t have good coverage, functional calls are not conserved /note=Pham: No functional calls and Chidi does not match the numbers and Schomber has the same color but no functional call /note=BlASTp: of the S1:Q1 none of the 10 BLASTs have a function /note= /note=CALL: Unknown function CDS 18759 - 21599 /gene="28" /product="gp28" /function="Hypothetical Protein" /locus tag="FlyingTortilla_28" /note=Original Glimmer call @bp 18759 has strength 8.68; Genemark calls start at 18759 /note=SSC: 18759-21599 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Gordonia phage Pupper] ],,NCBI, q387:s1146 52.6427% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.97, -4.7784408226142965, no F: Hypothetical Protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Pupper] ],,YP_010058886,20.577,0.0 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) +3 bp gap /note=(3) longest possible ORF /note=(4) start 2, least neg, Z value above 2 /note=(5) 3/10 S1:Q1 match /note=(6) NO pham to compare to /note=Descision: (undecided) /note= /note=FUNCTIONAL CALL: /note=HHpred : most of the top hits don`t have good coverage, functional calls are not conserved /note=Pham:(Chidi and schomber): neither of their features have a functional call /note=BLAST p : of the S1:Q1 hits 3/10, only all have `functional unknown` /note= /note=CALL: unknown function CDS 21608 - 24448 /gene="29" /product="gp29" /function="minor tail protein" /locus tag="FlyingTortilla_29" /note=Original Glimmer call @bp 21608 has strength 11.42; Genemark calls start at 21725 /note=SSC: 21608-24448 CP: no SCS: both-gl ST: NI BLAST-Start: [minor tail protein [Gordonia phage DalanDe]],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.737, -5.268820064297846, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Gordonia phage DalanDe]],,UVF61439,75.8253,0.0 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=(1) Glimmer and GM DONT agree /note=(2) -9 bp gap /note=(3) longest ORF possible /note=(4) start 2, least neg score, above 2 Z value /note=(5) 10/10 S1:SQ /note=(6) 2/15 pham /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred : most of the top hits have good coverage /note=Pham:(Chidi and schomber): some similar features, 2 labeled as minor tail protein /note=BLAST p: of the S1:Q1 hits 10/10, 5: minor tail protein, 5: `functional unknown` /note= /note=CALL: Minor tail protein CDS 24461 - 25141 /gene="30" /product="gp30" /function="lysin B" /locus tag="FlyingTortilla_30" /note=Original Glimmer call @bp 24461 has strength 10.56; Genemark calls start at 24461 /note=SSC: 24461-25141 CP: no SCS: both ST: NI BLAST-Start: [endolysin [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 6.62756E-107 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.791, -2.967790469131549, yes F: lysin B SIF-BLAST: ,,[endolysin [Gordonia phage ChisanaKitsune] ],,YP_010675674,76.7241,6.62756E-107 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] Glimmer and GeneMark Agree /note=[2] Gap of 12 gene positions between the end of ORF 29 and the beginning of ORF 30. /note=[3] Highest GeneMark coding potential. /note=[4] Z score is above 2 and the final score is the least negative. /note=[5] 9/10 one to one matches for the BLAST sequence for predermined ORF start. /note=[6] 11 Manual Annotations for the 24461 Start. /note= /note=Decision: No change. /note= /note=FUNCTIONAL CALLS: /note=HHpred: Good coverage, but still not the entire gene. Closest match would be coding for Lysin B. /note=Pham: FlyingTortilla have the same number of family members within the 30th ORF. Neither have a known function. /note=Blastp: 5 one to one Blastp matches list the function as coding for lysin B /note= /note=CALL: Still unkown, but likely to be Lysin B. CDS 25138 - 25962 /gene="31" /product="gp31" /function="minor tail protein" /locus tag="FlyingTortilla_31" /note=Original Glimmer call @bp 25138 has strength 12.47; Genemark calls start at 25138 /note=SSC: 25138-25962 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_GRAY_32 [Gordonia phage Gray]],,NCBI, q1:s1 100.0% 2.20289E-142 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.939, -4.904754965500383, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein PBI_GRAY_32 [Gordonia phage Gray]],,AZS07886,86.7647,2.20289E-142 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] GeneMark and Glimmer Agree. /note=[2] Overlap of 4 between the end of ORF 30 at 25142 and the beginning of ORF 31 at 25138 /note=[3] GeneMark Most Coding Potential. /note=[4] Z Value just beneath 2 (1.928) /note=[5] 10/10 one to one BLAST matches at predetermiend ORF start. /note=[6] 6 Manual Annotations for start 1 at base pair 25138. /note= /note=Decision: No Change. /note= /note=FUNCTIONAL CALLS /note=HHpred: Very poor coverage by potential coding purposes. Function remains unknown. /note=Pham: FlyingTortilla and Schomber have the same number of family members in the 31st ORF. Function listed as Mtd_N but has very poor coverage. Function remains unknown. /note=Blastp: 2 of the one to one matches list the protein as coding for a minor tail protein. Other eight remain as function unknown. /note= /note=CALL: Unknown Function. Could be minor tail protein. CDS 25962 - 26633 /gene="32" /product="gp32" /function="Hypothetical Protein" /locus tag="FlyingTortilla_32" /note=Original Glimmer call @bp 25962 has strength 10.97; Genemark calls start at 25962 /note=SSC: 25962-26633 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp029 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 99.5516% 4.82352E-43 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.989, -5.4868071391403275, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp029 [Gordonia phage ChisanaKitsune] ],,YP_010675676,59.1111,4.82352E-43 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 25962 has strength 10.97 /note= /note=ORF CALL: /note=(1) Glimmer and GM agree /note=(2) no gap /note=(3) GeneMark does not account for most coding potential. Most coding potential starts at the start before but overlap would take place. /note=(4) Not least negative final score, and Z score below 2 /note=(5) S1:Q1 10/10 match /note=(6) 6 MA`s @25962 /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred no coverage and functional call not covered /note=Phamarater: Chidiebere does not have the same gene compared to Flying Tortilla and Schomber which have the same for gene 32, however no function /note=BLASTp: top hit from same pham have unkown function /note= /note=Call: Unknown function CDS 26668 - 28026 /gene="33" /product="gp33" /function="capsid maturation protease" /locus tag="FlyingTortilla_33" /note=Original Glimmer call @bp 26668 has strength 17.98; Genemark calls start at 26668 /note=SSC: 26668-28026 CP: no SCS: both ST: NI BLAST-Start: [capsid maturation protease [Gordonia phage Gray]],,NCBI, q11:s4 97.5664% 0.0 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.966, -5.535726432718978, no F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Gordonia phage Gray]],,AZS07888,89.011,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 26668 has strength 17.98 /note= /note=ORF CALL @bp 26668: /note=(1) Glimmer and GM agree /note=(2) gap +35 /note=(3) Genemark most coding potential /note=(4) Not least final score, Z score below 2 /note=(5) S1:Q1 2/10 match /note=(6) No MA`s at this bp /note= /note=ORF CALL bp@ 26698: /note=(1) GM and Glimmer agree /note=(2) gap+65 /note=(3) Most coding potenial other then start 1 /note=(4) Z score above 2 and least negative final score compared to bp@26668 /note=(5) S1:Q1 no match /note=(6) 1 MA`s /note= /note=DECISION: NO CHANGE /note= /note=Fuctional Call: /note=HHpred:top hit number 3 is capsid maturation protease and probability is 99.75% /note=Phamarater: gene in schomber and chidiebere is capsid maturation protease /note=BLASTp: S1:Q1 functions are unkown but other queries have a capsid maturation protease function /note= /note=Function: capsid maturation protease CDS 28161 - 29570 /gene="34" /product="gp34" /function="major capsid protein" /locus tag="FlyingTortilla_34" /note=Original Glimmer call @bp 28161 has strength 17.56; Genemark calls start at 28161 /note=SSC: 28161-29570 CP: no SCS: both ST: NI BLAST-Start: [major head protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: 134 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.944, -3.5527928455068705, yes F: major capsid protein SIF-BLAST: ,,[major head protein [Gordonia phage Chidiebere] ],,YP_010675553,92.8421,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 28161 has strength 17.56 /note= /note=FUNCTIONAL CALL /note= /note=1. Several top hits; Best hit has a probability of 100%. Most common functional call is major capsid protein. /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), and these genes both have functional calls. Chidiebere gene 35 and Schomber gene 34 has a functional call as major capsid protein. /note=3. >30 top hiits in BLASTp all have manual annotated fuctions of `major capsid protein` /note= /note=Decision: Major Capsid Protein CDS 29610 - 29801 /gene="35" /product="gp35" /function="Hypothetical Protein" /locus tag="FlyingTortilla_35" /note=Original Glimmer call @bp 29610 has strength 3.53; Genemark calls start at 29610 /note=SSC: 29610-29801 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp032 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 98.4127% 1.76677E-32 GAP: 39 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.863, -2.8793565916978188, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp032 [Gordonia phage ChisanaKitsune] ],,YP_010675679,90.625,1.76677E-32 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 29610 has strength 3.53 ** not called by GeneMark /note= /note=FUNCTIONAL CALL /note= /note=1. No top hits; Best hit has a probability of 90.83% and is DUF5810 /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), but these genes have no functional calls /note=3. All S1Q1 have unknown functions /note= /note=Decision: Unknown Function CDS 29798 - 30100 /gene="36" /product="gp36" /function="Hypothetical Protein" /locus tag="FlyingTortilla_36" /note=Original Glimmer call @bp 29798 has strength 8.21; Genemark calls start at 29798 /note=SSC: 29798-30100 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp037 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 2.379E-53 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.965, -2.6814417326944517, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp037 [Gordonia phage Chidiebere] ],,YP_010675555,92.0,2.379E-53 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 29798 has strength 8.21 /note= /note=ORF CALL /note=[1] Glimmer and GenMark agree /note=[2] Overlap-3 Bp /note=[3] Longest coding potential and Longest ORF /note=[4] Start 1has a "z" score >2 and least negative score /note=[5] 10/10 BLASTp hits Q1:S1 /note=[6] Start 4 @ 29798 has 6 MAs /note= /note=Decision no change to start /note=Original Glimmer call @bp 29798 has strength 8.21 /note= /note=Functional Call /note=[1]Pham= Chi /note=diebere (37) and Schombere (38) have similarities but no functional call /note=[2] HHpred=no close calls /note=[3] BLASTp= 8 q1:S1 " Unknown Function Calls" /note= /note=Functional Call Unknown CDS 30101 - 30541 /gene="37" /product="gp37" /function="Hypothetical Protein" /locus tag="FlyingTortilla_37" /note=Original Glimmer call @bp 30101 has strength 7.28; Genemark calls start at 30101 /note=SSC: 30101-30541 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp038 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 2.1026E-93 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.246, -4.117143323918745, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp038 [Gordonia phage Chidiebere] ],,YP_010675556,96.5753,2.1026E-93 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 1 has strength 13.47 /note= /note=ORF Calls /note=[1] Glimmer and GM agrees /note=[2] No Gap/ overlap /note=[3]GeneMark most coding period /note=[4] Negative final score[start#16 less neg], Z score above 2 /note=[5] All 10 Blastp S1:Q1 /note=[6] All Pham memeber same start[7MAs] MA= Manual Annotation /note= /note=DECISION, NO CHANGE /note= /note=Functional Call /note= /note=[1] HHpred- might be a "Baseplate upper protein immunoglobulin like domain" probability with "BppU_IgG Basepla" 88.3 % /note=[2] Pham- has similarities but unknown function with: Chidiebere (38) and Schomber (37) /note=[3] BLASTp- 6 Q1:S1 "Unkown Function" /note= /note=Functional Call- Unknown Function CDS 30557 - 31465 /gene="38" /product="gp38" /function="Hypothetical Protein" /locus tag="FlyingTortilla_38" /note=Original Glimmer call @bp 30557 has strength 17.39; Genemark calls start at 30557 /note=SSC: 30557-31465 CP: no SCS: both ST: NI BLAST-Start: [head decoration [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.273, -2.305049668942183, yes F: Hypothetical Protein SIF-BLAST: ,,[head decoration [Gordonia phage ChisanaKitsune] ],,YP_010675682,90.7285,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 30557 has strength 17.39 /note= /note=ORF CALL: /note=(1) Glimmer and GeneMark Agree /note=(2) The bp gap is +16 /note=(3) Longest ORF possible, with highest coding potential* /note=(4) Has least negative score and greatest Z-score value /note=(5) S1:Q1 10/10 members agree /note=(6) Start 11 has 173 MA`s; called 99.5% of time when present /note= /note=DECISION: NO CHANGE /note= /note=* Did notice previous ORF has massive drop in coding potential but does not split the ORF, for gene 37 /note= /note=FUNCTIONAL CALL: /note=HHpred: No coverage of top hits; functional call not preserved. /note=Pham: FlyingTortilla`s gene 38 comparable to Schomber`s gene 38 and comparable to Chidiebere`s gene 39; no functional calls. /note=BLASTp: Most members are unknown function; however, there is one member that has a functional call called "capsid decoration protein". And another member that has a "putative tail fiber" but could not find it in the functional call excel database. /note= /note=CALL: Unknown CDS 31503 - 32126 /gene="39" /product="gp39" /function="Hypothetical Protein" /locus tag="FlyingTortilla_39" /note=Original Glimmer call @bp 31503 has strength 14.5; Genemark calls start at 31503 /note=SSC: 31503-32126 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp036 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 98.5507% 1.61158E-101 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.04, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp036 [Gordonia phage ChisanaKitsune] ],,YP_010675683,87.6238,1.61158E-101 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 31503 has strength 14.50 /note= /note=ORF CALL: /note=(1) Glimmer and GeneMark agree /note=(2) Bp gap of +47 /note=(3) Longest ORF possible, despite the drop in coding potential /note=(4) Least negative score and highest Z-score /note=(5) S1:Q1 10/10 agree on start position /note=(6) Start 1 has 6 MA`s; found in 12 of 12 genes in pham(100%) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALLS: /note=HHpred: No coverage of top hits; functional call not preserved /note=Pham: FlyingTortilla`s gene 39 is comparable to that of Schomber`s gene 39 and Chidiebere`s gene 40; no functional call /note=BLASTp: All comparable S1:Q1 members have no functional call. /note= /note=CALL: Unknown CDS 32130 - 32687 /gene="40" /product="gp40" /function="head-to-tail adaptor" /locus tag="FlyingTortilla_40" /note=Original Glimmer call @bp 32130 has strength 10.21; Genemark calls start at 32130 /note=SSC: 32130-32687 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_GRAY_41 [Gordonia phage Gray] ],,NCBI, q1:s1 100.0% 1.65887E-111 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.999, -4.637072905118042, no F: head-to-tail adaptor SIF-BLAST: ,,[hypothetical protein PBI_GRAY_41 [Gordonia phage Gray] ],,AZS07895,91.3979,1.65887E-111 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 32130 has strength 10.21 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) Gap of 6 /note=(3a) Longest possible ORF /note=(3b) GeneMark most coding potential (no drop in coding potential with orf 39) /note=(4) Negative final score, Z value NOT above 2 (1.998) (close enough) /note=(5) 10/10 BLASTp S1:Q1 /note=(6) Start 1 has 8 MAs, most common MA /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL /note=HHpred: most top hits have good coverage, functional calls conserved for head completion protein, and adaptor protein. HHpred is consistant with the rules/notes listed on the functional calls excel file (gp15, HK97) /note=Pham: only Schomber has a functional call, Chidbi does not have a funtional call, 40 for FlyingTortilla and Schomber is not the same for Chidbi which does not have a functional call; Schomber calls as `head-to-tail adaptor` /note=BLASTp: all S1:Q1 top hits (non-drafts) have their function as either head-to-tail adaptor or function unknown /note= /note=CALL: head-to-tail adaptor CDS 32692 - 33147 /gene="41" /product="gp41" /function="Hypothetical Protein" /locus tag="FlyingTortilla_41" /note=Original Glimmer call @bp 32692 has strength 9.13; Genemark calls start at 32692 /note=SSC: 32692-33147 CP: no SCS: both ST: NI BLAST-Start: [tail completion or Neck1 protein [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 1.5405E-89 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.063, -5.155002627644538, no F: Hypothetical Protein SIF-BLAST: ,,[tail completion or Neck1 protein [Gordonia phage ChisanaKitsune] ],,YP_010675685,93.3775,1.5405E-89 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 32692 has strength 9.13 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) Gap of 7 /note=(3a) Longest possible ORF /note=(3b) GeneMark most coding potential /note=(4) Negative final score (#3 less neg), Z score above 2 (#3 higher Z score) /note=(5) 10/10 BLASTp S1:Q1 /note=(6) Start 5 has 7 MAs, most common MA /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL /note=HHpred: some top hits have good coverage, functional calls are conserved (most has 99.91%) for Putative capsid assembly protein /note=Pham: gene 41 for comparison phage (Chibi) not the same as gene 41 for FlyingTortilla, however Schomber same as gene 41 for FlyingTortilla. /note=BLASTp: Most top hist from (from same phame) have unknown function, only 1 makes functional call (that is S1:Q1) (Cantare=minor tail protein) /note= /note=CALL: Function unknown? /note=Note: all comparison phages call for function unknown, however HHpred has great coverage for this protein and calls for a putative capsid protein. CDS 33144 - 33806 /gene="42" /product="gp42" /function="tail terminator" /locus tag="FlyingTortilla_42" /note=Original Glimmer call @bp 33144 has strength 6.74; Genemark calls start at 33144 /note=SSC: 33144-33806 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp043 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 6.80164E-143 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.71, -3.219494343057515, no F: tail terminator SIF-BLAST: ,,[hypothetical protein PQD14_gp043 [Gordonia phage Chidiebere] ],,YP_010675561,95.4545,6.80164E-143 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 33144 has strength 6.74 /note=[1]Glimmer and GeneMark agreed at bp 33144 /note=[2] Overlap -3 bp /note=[3] longest ORF possible; greatest start potiential at 33144 bp /note=[4] z-value greater than 2 and final score is the least negative (at bp=33144) /note=[5] S1:Q1= all 12 blast /note=[6] 6 MA`s for all pham members /note= /note=DESCISION MADE: NO CHANGES /note= /note=FUNCTIONAL CALLS /note=HHpred: High coverage of top hits. High consistency of tail terminator. /note=Pham: (Shomber-46) tail assembly chaperone /note=BLAST p: all in pham say tail terminator /note= /note=CALL: Tail Terminator CDS 33816 - 34145 /gene="43" /product="gp43" /function="Hypothetical Protein" /locus tag="FlyingTortilla_43" /note=Original Glimmer call @bp 33816 has strength 9.44; Genemark calls start at 33813 /note=SSC: 33816-34145 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PQD14_gp044 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 2.94531E-58 GAP: 9 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.283, -2.0111200136961407, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp044 [Gordonia phage Chidiebere] ],,YP_010675562,89.9083,2.94531E-58 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 33816 has strength 9.44 /note=[1] Glimmer and GeneMark agree. Glimmer called at bp 33816. /note=[2] Gap +10 bp. /note=[3] GeneMaster recognizes start position at 33816 and there is no seperate stop indicated in GeneMaster. GeneMaster does not recognize seperate gene. Greatest ORF potiential at bp=33816. /note=[4] z-value graeter than 2 and final score is the least negative (at bp=33816). /note=[5] S1:Q1= 14/10 /note=[6] 6 MA`s for all pham members /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: Low coverage of top hits. Low consistency. /note=Pham: (Shomber-43) unknown function /note=BLAST p: all in pham say unknown function /note= /note=CALL: Function Unknown CDS 34149 - 35597 /gene="44" /product="gp44" /function="tail sheath protein" /locus tag="FlyingTortilla_44" /note=Original Glimmer call @bp 34149 has strength 15.58; Genemark calls start at 34149 /note=SSC: 34149-35597 CP: no SCS: both ST: NI BLAST-Start: [tail sheath protein [Gordonia Phage Schomber]],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.04, -2.794070146961553, yes F: tail sheath protein SIF-BLAST: ,,[tail sheath protein [Gordonia Phage Schomber]],,WNM67065,97.5104,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 34149 has strength 15.58 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) +3bp gap /note=(3) Longest ORF possible, GM best coding potential /note=(4) RBS final score is the least negative (start #1). Z score is above 2 /note=(5) 10/10 are S1:Q1 match /note=(6) 58 MAs @bp 34149 /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHPred: High coverage of top hits, high consistency of a tail sheath protein /note=Pham (Chidi-45 and Schomber-44) : both say tail sheath protein /note=BLASTp: most of the top hits state tail sheath protein /note= /note=CALL: tail sheath protein CDS 35634 - 36041 /gene="45" /product="gp45" /function="tail tube protein" /locus tag="FlyingTortilla_45" /note=Original Glimmer call @bp 35634 has strength 13.33; Genemark calls start at 35634 /note=SSC: 35634-36041 CP: no SCS: both ST: NI BLAST-Start: [tail tube protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 1.76156E-88 GAP: 36 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.177, -2.2186743274732437, yes F: tail tube protein SIF-BLAST: ,,[tail tube protein [Gordonia phage Chidiebere] ],,YP_010675564,98.5185,1.76156E-88 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 35634 has strength 13.33 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) +36bp gap /note=(3) Longest ORF possible, GM best coding potential /note=(4) RBS final score is the leat negative (start #1). Z value above 2 /note=(5) 10/10 are S1:Q1 match /note=(6) 10 MAs @bp 35634 /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHPred: high coverage of top hits, not very consistent with functions /note=Pham (Chidi-46 and Schomber-45) : both say tail tube protein /note=BLASTp: 5/10 S1:Q1 are tail tube protein /note= /note=CALL: tail tube protein CDS 36136 - 36711 /gene="46" /product="gp46" /function="tail assembly chaperone" /locus tag="FlyingTortilla_46" /note=Original Glimmer call @bp 36136 has strength 16.93; Genemark calls start at 36136 /note=SSC: 36136-36711 CP: no SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Gordonia phage Chidiebere] ],,NCBI, q1:s1 99.4764% 2.10941E-100 GAP: 94 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.13, -2.394485424036831, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Gordonia phage Chidiebere] ],,YP_010675565,87.5,2.10941E-100 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 36136 has strength 16.93 /note= /note=(1) GeneMark and GLIMMER agree /note=(2) +95 bp gap /note=(3) Longest possible ORF and most GM coding potential /note=(4) Least negative final score (-2.394)... High z value above 2 (3.121) /note=(5) 10/10 S1Q1 Match /note=(6) Start at 36136 has 8 MA`s /note= /note=(looks like this is the best start!) /note= /note= /note=FUNCTIONAL CALL: /note= /note=HHpred: Top hits have good coverage and functional calls are conserved (lots of red) *lots of calls for 46 call its functionas a tail assembly chaperone /note=PHAM: majority of members in PHAM call for assembly chaperone /note=BLASTp: 6/8 S1Q1 members (not including drafts) has function listed as a tail assembly chaperone /note= /note=DECISION: Called function, TAIL ASSEMBLY CHAPERONE CDS 36708 - 36905 /gene="47" /product="gp47" /function="Hypothetical Protein" /locus tag="FlyingTortilla_47" /note=Original Glimmer call @bp 36708 has strength 3.85; Genemark calls start at 36708 /note=SSC: 36708-36905 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp048 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 96.9231% 6.29972E-26 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.864, -6.227794898055632, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp048 [Gordonia phage Chidiebere] ],,YP_010675566,87.5,6.29972E-26 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 36708 has strength 3.85 /note= /note=(1) Genemark and GLIMMER agree /note=(2) -3 bp overlap /note=(3) Longest possible ORF and most GM coding potential /note=(4) Final score is NOT the least negative (-6.228)... Z value is under 2 (1.853) - but no z value is above 2 on the list /note=(5) 10/10 S1Q1 match /note=(6) start at 36708 has 4 MA`s /note= /note=FUNCTIONAL CALL: /note= /note=HHpred: One has good coverage but not conserved (no red) /note=PHAM: Comparrisons have no function call for 47 /note=BLASTp: All members of S1Q1 have unknown function /note= /note=DECISION: UNKNOWN FUNCTION CDS 36938 - 40285 /gene="48" /product="gp48" /function="tape measure protein" /locus tag="FlyingTortilla_48" /note=Original Glimmer call @bp 36938 has strength 12.91; Genemark calls start at 36938 /note=SSC: 36938-40285 CP: no SCS: both ST: NI BLAST-Start: [tail length tape measure protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: 32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.535, -3.50848394673489, no F: tape measure protein SIF-BLAST: ,,[tail length tape measure protein [Gordonia phage Chidiebere] ],,YP_010675567,84.319,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 36938 has strength 12.91 /note=(1) gene mark and glimmer agree /note=(2) +33 gap /note=(3) not longest ORF... not GM most coding potential /note=(4) least negative final score... not highest Z score above 2 /note=(5) 10/10 S1Q1 match /note=(6) 7 MA /note=ORF CALL: NO CHANGE /note=FUNCTIONAL CALL: /note=(1) HHpred: high coverage top hits, lots of red, mostly tape measure protein /note=(2) Pham: two comparison phage have tape measure protein gene for position /note=(3) BLASTp: 7 S1Q1 matches for tape measure protein CDS 40285 - 40998 /gene="49" /product="gp49" /function="Hypothetical Protein" /locus tag="FlyingTortilla_49" /note=Original Glimmer call @bp 40285 has strength 8.18; Genemark calls start at 40285 /note=SSC: 40285-40998 CP: no SCS: both ST: NI BLAST-Start: [HNH endonuclease [Antarcticirhabdus aurantiaca]],,NCBI, q54:s49 57.384% 5.70864E-34 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.04, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[HNH endonuclease [Antarcticirhabdus aurantiaca]],,WP_199266656,42.7808,5.70864E-34 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 40285 has strength 8.18 /note=(1) gene mark and glimmer agree /note=(2) no gap or overlap /note=(3) longest ORF possible and GM most coding potential /note=(4) least negative final score and highest Z score above 2 /note=(5) 2/10 S1Q1 match /note=(6) no MA /note=ORF CALL: no change /note= /note=Functional call /note=(1) HHpred: low coverage top hits, little red, only two that match are drafts /note=(2) Pham: two comparison phage do not match /note=(3) BLASTp: 0 S1Q1 matches /note=CALL: hypothetical protein CDS 41004 - 41774 /gene="50" /product="gp50" /function="Hypothetical Protein" /locus tag="FlyingTortilla_50" /note=Original Glimmer call @bp 41004 has strength 14.88; Genemark calls start at 41004 /note=SSC: 41004-41774 CP: no SCS: both ST: NI BLAST-Start: [LysM-like peptidoglycan binding protein [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 1.68144E-163 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.159, -4.36137266396122, no F: Hypothetical Protein SIF-BLAST: ,,[LysM-like peptidoglycan binding protein [Gordonia phage ChisanaKitsune] ],,YP_010675693,94.5098,1.68144E-163 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 41004 has strength 14.88 /note= /note=ORF CALLS /note=[1] Glimmer and GM agree /note=[2] 5bp gap /note=[3] GeneMark most coding potential /note=[4] not least negative final score @bp 41004 (start #1), Z score above 2 /note=[5] ALL 14 BLAST p S1:Q1 /note=[6] 1 MA @ bp 41004 /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTION CALLS: /note=HHpred: high coverage of top hits, little consistency /note=Pham: (DalanDe-45, GMA6-44) unknown function, (Kabocha-51) LysM-like peptidoglycan binding protein), (Schomber-49) minor tail protein /note=BLASTp: 3/14 in pham say LysM-like peptidoglycan binding protein, 9/14 unknown, 1/14 putative lysin, 1/14 minor tail protein /note= /note=CALL: Unknown function CDS 41776 - 43140 /gene="51" /product="gp51" /function="minor tail protein" /locus tag="FlyingTortilla_51" /note=Original Glimmer call @bp 41776 has strength 8.8; Genemark calls start at 41776 /note=SSC: 41776-43140 CP: no SCS: both ST: NI BLAST-Start: [virion structural protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.284, -4.1774766973090856, no F: minor tail protein SIF-BLAST: ,,[virion structural protein [Gordonia phage Chidiebere] ],,YP_010675569,93.8053,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 41776 has strength 8.80 /note= /note=ORF CALLS /note=[1] Glimmer and GM agree /note=[2] 1 bp gap /note=[3] GeneMark most coding potential /note=[4] not least negative final score @bp 41776 (start #1). Z score above 2 /note=[5] ALL 12 BLAST p S1:Q1 /note=[6] 6 MAs @bp 41776 /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTION CALLS /note=HHpred: high coverage of top hits, little consistency /note=Pham:(Schomber-50, Kabocha-52, DalanDe-46) minor tail protein /note=BLASTp: 6/12 in pham say minor tail protein; 6/12 in pham say function unknown /note= /note=CALL: minor tail protein CDS 43151 - 44503 /gene="52" /product="gp52" /function="Hypothetical Protein" /locus tag="FlyingTortilla_52" /note=Original Glimmer call @bp 43151 has strength 8.72; Genemark calls start at 43151 /note=SSC: 43151-44503 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.13, -2.253486910374644, yes F: Hypothetical Protein SIF-BLAST: ,,[minor tail protein [Gordonia phage Chidiebere] ],,YP_010675570,96.0,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 43151 has strength 8.72 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) Gap by +11 base pairs /note=(3) Not the longest possible ORF and does not encompass all coding potential /note=(4) Most negative final score (start #3 least neg), Z score above 2 /note=(5) All 10 BLAST p S1:Q1 /note=(6) All 6 MA`s same start @43151 /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: most of the top hits don`t have good coverage, functional calls are not conserved /note=Pham: Chidi has feature 52 that are similar while Schomber does not match /note=BLASTp: of the S1:Q1 is (non-drafts), only 1 makes a functional call (Hanem=DNA binding protein); others have `function unknown` /note= /note=CALL: unknown function CDS 44513 - 44956 /gene="53" /product="gp53" /function="Hypothetical Protein" /locus tag="FlyingTortilla_53" /note=Original Glimmer call @bp 44513 has strength 9.98; Genemark calls start at 44513 /note=SSC: 44513-44956 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp053 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 6.86965E-85 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.682, -3.8493754792411874, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp053 [Gordonia phage Chidiebere] ],,YP_010675571,89.7959,6.86965E-85 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 44513 has strength 9.98 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) Gap by +10 base pairs /note=(3) Most coding potential and longest possible ORF /note=(4) Negative final score (start #1 least neg), Z score above 2 /note=(5) All 10 BLAST p S1:Q1 /note=(6) All Pham member same start (6 MAs) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: Most of the top hits have good coverage, functional calls are not conserved /note=Pham: Chidi matches but there is no functional call and Schomber does not match at all /note=BLASTp: of the S1:Q1 its (non-drafts), there are unknown functions /note= /note=CALL: Unknown function CDS 44953 - 45342 /gene="54" /product="gp54" /function="baseplate wedge protein" /locus tag="FlyingTortilla_54" /note=Original Glimmer call @bp 44953 has strength 11.82; Genemark calls start at 44953 /note=SSC: 44953-45342 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp054 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 2.70333E-79 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.251, -5.014632449993951, yes F: baseplate wedge protein SIF-BLAST: ,,[hypothetical protein PQD14_gp054 [Gordonia phage Chidiebere] ],,YP_010675572,96.124,2.70333E-79 SIF-HHPRED: SIF-Syn: /note=ORF CALLS: /note=(1) Glimmer and GM agree /note=(2) - 3 bp gap /note=(3) longest orf possible /note=(4) start 1, least neg, 2+ Z value /note=(5) S1:Q1 10/10 match /note=(6) 14/14 All Pham members same start (7 MAs) /note= /note=Descision: NO Change /note= /note=FUNCTIONAL CALL: /note=HHpred : most of the top hits have poor coverage /note=Pham:(Chidi and schomber): chi.(baseplate wedge protien), sch(hydrolasbaseplate wedge protien) /note=BLAST p: of the S1:Q1 hits 10/10 match (5 wedge protein: others have `functional unknown`) /note= /note=CALL: wedge protein CDS 45339 - 45671 /gene="55" /product="gp55" /function="baseplate wedge protein" /locus tag="FlyingTortilla_55" /note=Original Glimmer call @bp 45339 has strength 5.77; Genemark calls start at 45339 /note=SSC: 45339-45671 CP: no SCS: both ST: NI BLAST-Start: [baseplate protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 9.59628E-68 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -2.8454123590742793, yes F: baseplate wedge protein SIF-BLAST: ,,[baseplate protein [Gordonia phage Chidiebere] ],,YP_010675573,93.6364,9.59628E-68 SIF-HHPRED: SIF-Syn: /note=(1) Glimmer and GM agree /note=(2) +3 bp gap /note=(3) longest orf possible /note=(4) start 2, least neg, 2+ Z value /note=(5) S1:Q1 10/10 match /note=(6) 14/15 All Pham members same start (7/8 MAs) /note= /note=DESCISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred : majority of the top hits have good coverage /note=Pham:(Chidi and schomber):chi.(baseplate wedge protein), sch(hydrolasbaseplate wedge protein) /note=BLAST p: of the S1:Q1 hits 10/10 ( baseplate wedge protein, other 5 unknown function) /note= /note=CALL: baseplate wedge protein CDS 45668 - 46828 /gene="56" /product="gp56" /function="baseplate J protein" /locus tag="FlyingTortilla_56" /note=Original Glimmer call @bp 45668 has strength 11.38; Genemark calls start at 45668 /note=SSC: 45668-46828 CP: no SCS: both ST: NI BLAST-Start: [baseplate wedge subunit [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.267, -4.134629096801125, no F: baseplate J protein SIF-BLAST: ,,[baseplate wedge subunit [Gordonia phage ChisanaKitsune] ],,YP_010675699,98.1818,0.0 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] GeneMark and Glimmer agree on start. /note=[2] Overlap of 4 between the end of ORF 55 at BP 45672 and the beginning of ORF 56 and BP 45668 /note=[3] GeneMark Most coding potential. /note=[4] Z score is above 2 and the final score is the least negative. /note=[5] 4/10 one to one matches for BLAST sequence at default start of BP 45668 /note=[6] Start 9 at BP 45668 has 6 Manual Annotations /note= /note=Decision: No Change. /note= /note=FUNCTIONAL CALLS /note=HHpred: Not complete coverage but still excellent coverage that likely codes for a baseplate coding. /note=Pham: FlyingTortilla and Chidiebere appear to have the same ORF 56, with both having the same number of family members. Function listed as hypotehtical_protein_s /note=Blastp: 5 of the one to one matches show that the coding is called as baseplate J protein. /note= /note=CALL: Likely baseplate J protein. CDS 46821 - 47993 /gene="57" /product="gp57" /function="Hypothetical Protein" /locus tag="FlyingTortilla_57" /note=Original Glimmer call @bp 46821 has strength 9.09; Genemark calls start at 46821 /note=SSC: 46821-47993 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp057 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.014, -5.133363921001095, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp057 [Gordonia phage Chidiebere] ],,YP_010675575,91.5385,0.0 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] Glimmer and GeneMark agree on start. /note=[2] Overlap of eight basepairs between the end of ORF 56 at 46829 and the beginning of ORF 57 at 46821 /note=[3] Most GeneMark coding potenntial. /note=[4] Z-score is above two and the final score is the least negative option. /note=[5] 10/10 one to one matches for default BLAST sequence. /note=[6] 6 Manual annotations for start 6 at basepair 46821 /note= /note=Decision: No change. /note= /note=FUNCTIONAL CALLS /note=HHpred:Poor coverage overall, with the most likely match covering only about half of the full length of the feature. Function remains unknown. /note=Pham: FlytingTortilla and Chidibere appear to have matching genes for feature 3, while Schomber has a different feature 57. Function is unknown between the two. /note=Blastp: Schomber annotates the function of feature 57 as a minor tail protein but the rest of the one to one matches in blast do not have a function listed. /note= /note=CALL: Unknown function. Could be a structural protein for a baseplate. CDS 48003 - 49985 /gene="58" /product="gp58" /function="Hypothetical Protein" /locus tag="FlyingTortilla_58" /note=Original Glimmer call @bp 48003 has strength 9.64; Genemark calls start at 48003 /note=SSC: 48003-49985 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp058 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.147, -4.325675514574479, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp058 [Gordonia phage Chidiebere] ],,YP_010675576,90.8953,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 48003 has strength 9.64 /note= /note=ORF CALL: /note=(1) Glimmer and GM agree /note=(2) gap +10 /note=(3) Longest coding potential, longest ORF /note=(4) Not least final score, Z score above 2 (start @48195 least negative, and Z score above 2 /note=(5) 10/10 S1:Q1 match /note=(6) 7MA`s at this start /note= /note=DECISION: NO CHANGE /note= /note=Functional Call: /note=HHpred low coverage of top hits functional call not covered /note=Pham: gene 58 is the same for cidiebere but not schomber, however no function is called /note=BLASTp: all tops hits (from the same pham) have unkown function /note= /note=CALL: UNKOWN FUNCTION CDS 50003 - 50374 /gene="59" /product="gp59" /function="Hypothetical Protein" /locus tag="FlyingTortilla_59" /note=Original Glimmer call @bp 50003 has strength 10.66; Genemark calls start at 50003 /note=SSC: 50003-50374 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp055 [Gordonia phage ChisanaKitsune] ],,NCBI, q25:s13 80.4878% 1.9373E-35 GAP: 17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.177, -2.5074698667202133, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp055 [Gordonia phage ChisanaKitsune] ],,YP_010675702,68.4685,1.9373E-35 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 50003 has strength 10.66 /note= /note=ORF CALL: /note=(1) Glimmer and GM agree /note=(2) gap +18 /note=(3) most coding potential /note=(4) Least final score, Z score above 2 /note=(5) 3/10 S1:Q1 Match /note=(6) 6 MA`s start @50003 /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred low coverage of top hits functional call not covered /note=Pham: gene 59 is the same for cidiebere but not schomber, however no function is called. /note=BLASTp: all tops hits have unknown function. /note= /note=CALL: UNKOWN FUNCTION CDS 50367 - 53561 /gene="60" /product="gp60" /function="lysin A" /locus tag="FlyingTortilla_60" /note=Original Glimmer call @bp 50367 has strength 9.09; Genemark calls start at 50367 /note=SSC: 50367-53561 CP: no SCS: both ST: NI BLAST-Start: [endolysin [Gordonia phage Chidiebere] ],,NCBI, q1:s1 99.1541% 0.0 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.864, -3.1667933672806092, no F: lysin A SIF-BLAST: ,,[endolysin [Gordonia phage Chidiebere] ],,YP_010675578,90.6867,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 50367 has strength 9.09 /note= /note=FUNCTIONAL CALL /note= /note=1. Several top hits; Best hit has a probability of 100%. The hits at %100 are DUF4185, Mycobacterium tuberculosis H37Rv, and Microbacterium arabinogalactanolyticum. /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), and these genes both have functional calls. Chidiebere gene 60 and Schomber gene 59 has a functional call as lysin A. /note=3. >60 top hiits in BLASTp all have manual annotated fuctions of `lysin A` /note= /note=Decision: lysin A CDS 53558 - 54097 /gene="61" /product="gp61" /function="holin" /locus tag="FlyingTortilla_61" /note=Original Glimmer call @bp 53558 has strength 11.87; Genemark calls start at 53558 /note=SSC: 53558-54097 CP: no SCS: both ST: NI BLAST-Start: [holin [Gordonia phage ChisanaKitsune] ],,NCBI, q4:s3 98.324% 5.59151E-83 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.04, -2.583959800616441, yes F: holin SIF-BLAST: ,,[holin [Gordonia phage ChisanaKitsune] ],,YP_010675704,80.4469,5.59151E-83 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 53558 has strength 11.87 /note= /note= /note=FUNCTIONAL CALL /note= /note=1. Has a top hit that has a probability of 95% and is Halogen_Hydrol. /note=2.Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), but these genes have no functional calls. /note=3. >40 top hiits in BLASTp all have manual annotated fuctions of `holin` /note= /note=Decision: holin /note= /note=The excel file states to not call this a holin, but to refer to it as a membrane protein unless we have biochemical data to say otherwise. CDS 54094 - 54468 /gene="62" /product="gp62" /function="Hypothetical Protein" /locus tag="FlyingTortilla_62" /note=Original Glimmer call @bp 54094 has strength 6.28; Genemark calls start at 54094 /note=SSC: 54094-54468 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PQD15_gp058 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 2.62304E-67 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.219, -4.236379132697792, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp058 [Gordonia phage ChisanaKitsune] ],,YP_010675705,87.0968,2.62304E-67 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 54094 has strength 6.28 /note= /note= /note=ORF CALL /note=[1] Glimmer and GenMark agree /note=[2] Overlap -3 BP /note=[3] Longest coding potential and longes ORF (tail end appears to lack coding potential) /note=[4] Start 2 is favored and does not have the least negative "z" score>2 /note=[5] 10/10 BLASTp hits Q1:S1 /note=[6] Phamerator report not found /note= /note=Decision no change to start /note= /note=FUNCTIONAL CALL /note=[1] HHpred= several strong matches, function: "Ryanodine receptor" /note=[2] Pham= position 62 predicted to be a "Dna B-like dsDNA helicase", it was a match to Chidiebere position 62 and Schomber position 61/ both had unknown functions /note=[3] BLASTp= 7 Q1:S1 matches, function unknown /note= /note=Functional Call- Ryanodine Receptor CDS 54543 - 54986 /gene="63" /product="gp63" /function="Hypothetical Protein" /locus tag="FlyingTortilla_63" /note=Original Glimmer call @bp 54543 has strength 8.95; Genemark calls start at 54543 /note=SSC: 54543-54986 CP: yes SCS: both ST: NI BLAST-Start: [membrane protein [Gordonia phage ChisanaKitsune] ],,NCBI, q3:s20 97.9592% 6.68215E-82 GAP: 74 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.73, -5.856194091974515, no F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Gordonia phage ChisanaKitsune] ],,YP_010675706,81.0976,6.68215E-82 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 33816 has strength 9.44 /note=[1] Glimmer and GeneMark agree. Glimmer called at bp 33816. /note=[2] Gap +10 bp. /note=[3] GeneMaster recognizes start position at 33816 and there is no seperate stop indicated in GeneMaster. GeneMaster does not recognize seperate gene. Greatest ORF potiential at bp=33816. /note=[4] z-value graeter than 2 and final score is the least negative (at bp=33816). /note=[5] S1:Q1= 14/10 /note=[6] 6 MA`s for all pham members /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: Low coverage of top hits. Low consistency. /note=Pham: (Shomber-43) unknown function /note=BLAST p: all in pham say unknown function /note= /note=CALL: Function Unknown CDS 54986 - 55324 /gene="64" /product="gp64" /function="Hypothetical Protein" /locus tag="FlyingTortilla_64" /note=Original Glimmer call @bp 54986 has strength 6.51; Genemark calls start at 54986 /note=SSC: 54986-55324 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp064 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 99.1071% 3.66947E-63 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.562, -3.513874779476501, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp064 [Gordonia phage Chidiebere] ],,YP_010675582,91.9643,3.66947E-63 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 54986 has strength 6.51 /note= /note=ORF CALL: /note=(1) Glimmer and Genemark agree /note=(2) No gap /note=(3) Longest ORF possible; highest coding potential /note=(4) Greatest Z-score; and lowest final score /note=(5) S1:Q1 10/10 members agree /note=(6) Has 6 MA`s; start 4 found in 12 of 12 of genes in pham(100%) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: Top three hits called were Phage shock protein B, Spanin, inner membrane subunit, and Cell division protein FtsB. Full coverage of top hits. /note=Pham: FlyingTortilla`s gene 64 comparable to Chidiebere`s gene 64 and Schomber`s gene 63; no functional calls. /note=BLASTp: All comparable S1:Q1 members have no functional calls. /note= /note=CALL: Function unknown CDS complement (55417 - 56355) /gene="65" /product="gp65" /function="DNA primase" /locus tag="FlyingTortilla_65" /note=Original Glimmer call @bp 56268 has strength 9.81; Genemark calls start at 56268 /note=SSC: 56355-55417 CP: no SCS: both-cs ST: NI BLAST-Start: [DNA primase [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.572, -3.430952136556091, no F: DNA primase SIF-BLAST: ,,[DNA primase [Gordonia phage ChisanaKitsune] ],,YP_010675709,93.9103,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 56268 has strength 9.81 /note= /note=ORF CALLS: /note=1) GLIMMER and GeneMark agree on start at 56268 /note=2) 87 bp gap /note=3) GeneMark start covers all likely coding potential /note=4) RBS- Final score is -3.182, lowest possible; Z-score good (2.47>2) /note=5) S1:Q1- 3/10 /note=6) Phamerator: 2 MA @56268 /note= /note=DECISION:CHANGE START to 56355 /note= /note=START @ 56355 /note=RBS- Final score -3.421, second lowest; Z-score 2.561 (>2) /note=S1:Q1 7/10 matches /note=Phamerator 5 MAs @56355 /note= /note=FUNCTION CALLS-@ start 56355 /note=1) HHpred- High coverage, high similarity of DNA primases, 99.96% for top hit, several at 99.9- /note=2)Phamerator- Schomber (64) and Chidiebere (66) declare DNA primase /note=3) BLASTp- many in Pham declared DNA primase /note= /note=DECISION- DNA PRIMASE /note=(DNA Primase is functional call when feature with start @ 56268 is BLASTed as well) CDS complement (56355 - 57749) /gene="66" /product="gp66" /function="DnaB-like dsDNA helicase" /locus tag="FlyingTortilla_66" /note=Original Glimmer call @bp 57749 has strength 15.21; Genemark calls start at 57749 /note=SSC: 57749-56355 CP: no SCS: both ST: NI BLAST-Start: [DnaB-like replicative helicase [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 99.7845% 0.0 GAP: 288 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.535, -4.609715333525589, no F: DnaB-like dsDNA helicase SIF-BLAST: ,,[DnaB-like replicative helicase [Gordonia phage ChisanaKitsune] ],,YP_010675710,98.0645,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 57749 has strength 15.21 /note= /note= /note=ORF CALLS: /note=1) GLIMMER and GeneMark agree /note=2) 289 bp gap between feature 66 and 67 /note=3) start at 57749 encompasses most coding potential /note=4) RBS: least neg score (-4.610) that doesn`t cut off coding potential. Z score > 2 (2.5252). --> best RBS /note=5) S1:Q1 10/10 match /note=6) 7 MA`s at 57749 /note= /note=DECISION: No Change /note= /note=FUNC CALLS: /note=1) 100% matches to DNA helicases (replicative helicase, DnaB, etc.) /note=2)Pham: correspond to gene 67 of Chiedebere and 65 of Schomber, both say DnaB-like dsDNA helicase /note=3)BLASTp- several non-draft BLAST results declare DnaB-like dsDNA helicase /note= /note=DECISION: DnaB-like dsDNA helicase CDS complement (58038 - 58274) /gene="67" /product="gp67" /function="Hypothetical Protein" /locus tag="FlyingTortilla_67" /note=Original Glimmer call @bp 58274 has strength 13.3; Genemark calls start at 58274 /note=SSC: 58274-58038 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp068 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 9.1403E-31 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.137, -4.487636275856737, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp068 [Gordonia phage Chidiebere] ],,YP_010675586,74.3902,9.1403E-31 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 58274 has strength 13.30 /note= /note=ORF Call: /note=1. GeneMark and GLIMMER agree /note=2. -3bp overlap /note=3. some coding potential is not encompassed, however the stop causes some cutoff and there are no upstream starts that do not cause major overlap /note=4. RBS is least negative final score and z-score over 2 /note=5. No S1:Q1 hits /note=6. There are no MA`s for start 2, however the most annotated MA is start 3, which does not exist in this gene. /note= /note=DECISION: no change to ORF /note= /note=Functional Call: /note=1. no top hits, closest hit is at 84.34% and it is cd14797 (uncharacterized domain family DUF302) /note=2. Schomber gene 66 seems to be the same, but no known function /note=3. No S1:Q1 hits and most genes seem to have unknown function /note= /note=DECISION: function unknown CDS complement (58271 - 58768) /gene="68" /product="gp68" /function="Hypothetical Protein" /locus tag="FlyingTortilla_68" /note=Original Glimmer call @bp 58768 has strength 14.22; Genemark calls start at 58768 /note=SSC: 58768-58271 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp069 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 8.57166E-73 GAP: 485 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.944, -2.707694805492614, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp069 [Gordonia phage Chidiebere] ],,YP_010675587,88.4848,8.57166E-73 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 58768 has strength 14.22 /note= /note=ORF Call: /note= /note=1. Glimmer and genemark agree /note=2. 486 bp gap /note=3. longest possible ORF (there is a stop directly upstream) and encompasses all possible coding potential /note=4. least negative final score and highest Z score (over 2) /note=5. 8/10 S1:Q1 matches /note=6. 3 MA`s, other most annotated start is at start 3, which is not an option in flying tortilla /note= /note=Decision: no change to ORF /note= /note=Functional Call: /note= /note=1. There are no top hits on HHphred /note=2. the gene in Schomber and DalanDe has function unknown /note=3. most S1:Q1 have function unknown /note= /note=DECISION: function unknown CDS 59254 - 59391 /gene="69" /product="gp69" /function="Hypothetical Protein" /locus tag="FlyingTortilla_69" /note=Original Glimmer call @bp 59254 has strength 0.74 /note=SSC: 59254-59391 CP: no SCS: glimmer ST: SS BLAST-Start: GAP: 485 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.556, -6.62067764433794, no F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 59254 has strength 0.74 ** not called by GeneMark /note= /note=ORF CALL /note=[1] Glimmer and GenMark Agree /note=[2] +486 BP gap, (59254-58768 /note=[3] Longest ORF possible. GM most coding potentia /note=[4] start 1 was predicted, start 2 (position: 59266) seems better it has the least negative final score (-3.467) and "z" score above 2 ("z"=2.544) /note=[5] BLASTp 0/10 had Q1:S1 match /note=[6] No MA to compare [small Pham, other 2 members are drafts] /note= /note=DECISION, NO CHANGE /note= /note=FUNCTIONAL CALL /note=[1] HHpred-no close calls, function unknown /note=[2] Pham- no similarities, function unknown /note=[3] BLASTp- no Q1:S1 match, function unknown /note= /note=FUNCTION UNKNOWN /note= /note= /note=ORF CALL CDS 59943 - 60479 /gene="70" /product="gp70" /function="Hypothetical Protein" /locus tag="FlyingTortilla_70" /note=Original Glimmer call @bp 59943 has strength 12.51; Genemark calls start at 59943 /note=SSC: 59943-60479 CP: no SCS: both ST: NI BLAST-Start: GAP: 551 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.177, -3.0637723674875006, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 59943 has strength 12.51 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) +551bp gap /note=(3) Not the longest ORF possible; 3 other start potentials, but GM shows that all the coding potential is covered /note=(4) RBS final score is the least negative (start #4). Z score above 2 /note=(5) 3/10 are S1:Q1 match /note=(6) No MAs /note= /note=DECISION MADE: NO CHANGE? /note= /note=FUNCTIONAL CALLS /note=HHPred: low coverage of top hits, functional call not consistent /note=Pham: neither Chidi or Schomber had similar genes for comparison /note=BLASTp: all top hits have unknown function /note= /note=CALL: unknown function CDS 60565 - 60780 /gene="71" /product="gp71" /function="Hypothetical Protein" /locus tag="FlyingTortilla_71" /note=Original Glimmer call @bp 60565 has strength 15.69; Genemark calls start at 60565 /note=SSC: 60565-60780 CP: no SCS: both ST: NI BLAST-Start: GAP: 85 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.177, -2.5074698667202133, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 60565 has strength 15.69 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) +85bp gap /note=(3) Longest ORF possibe, GM best coding potential /note=(4) RBS final score is the least negative (start #3). Z score is above 2 /note=(5) 3/3 are S1:Q1 match /note=(6) No MAs /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: low coverage of top hits, functional calls are not consistent /note=Pham: Chidi 75 and Schomber 73; all are drafts with no functional calls /note=BLASTp: all top hits have unknown function /note= /note=CALL: Unknown function CDS 60870 - 61325 /gene="72" /product="gp72" /function="Hypothetical Protein" /locus tag="FlyingTortilla_72" /note=Original Glimmer call @bp 60870 has strength 11.08; Genemark calls start at 60870 /note=SSC: 60870-61325 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp071 [Gordonia phage Chidiebere] ],,NCBI, q31:s8 80.1325% 3.23907E-35 GAP: 89 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.187, -2.484606983760709, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp071 [Gordonia phage Chidiebere] ],,YP_010675589,65.8537,3.23907E-35 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 60870 has strength 11.08 /note= /note=(1) GeneMark and GLIMMER agree /note=(2) +90 bp gap /note=(3) Longest possible ORF and most GM coding potential /note=(4) Least negative final score (-2.485) and highest z-value (3.178) /note=(5) 2/10 S1Q1 match /note=(6) No MA`s...? /note= /note=DECISION: MADE, Keep start /note= /note=Functional Call: /note=HHpred: Good coverage but no red (not conserved) /note=PHAM: Comparissons call for unknown function (Hanem and Schomber) /note=BLAST p: members in S1Q1 call function as unknown /note= /note=Decision: UNKNOWN FUNCTION CDS 61445 - 62680 /gene="73" /product="gp73" /function="AAA-ATPase" /locus tag="FlyingTortilla_73" /note=Original Glimmer call @bp 61445 has strength 20.51; Genemark calls start at 61445 /note=SSC: 61445-62680 CP: no SCS: both ST: NI BLAST-Start: [porphyrin biosynthesis [Gordonia phage Chidiebere] ],,NCBI, q1:s1 94.6472% 0.0 GAP: 119 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.023, -2.4787699911121788, yes F: AAA-ATPase SIF-BLAST: ,,[porphyrin biosynthesis [Gordonia phage Chidiebere] ],,YP_010675590,91.4425,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 61445 has strength 20.51 /note= /note=(1) Glimmer and Gene Mark agree /note=(2) +120 bp gap /note=(3) Longest possible ORF and Most GM coding potential /note=(4) Least negative Final score (-2.479) ... greatest z-value (3.014) /note=(5) 10/10 S1Q1 Match /note=(6) start at 61445 has 6 MA`s /note= /note=DECISION: MADE /note= /note=FUNCTIONAL CALL: /note=HHpred: good coverage and lots of red /note=PHAM: Comparisons both call for function as AAA ATPase /note=BLAST p: PHAM members call for function of 73 as AAA-ATPase /note= /note=Decision: FUNCTIONAL CALL AAA-ATPase CDS 62719 - 64512 /gene="74" /product="gp74" /function="CobT-like cobalamin biosynthesis protein" /locus tag="FlyingTortilla_74" /note=Original Glimmer call @bp 62719 has strength 15.51; Genemark calls start at 62719 /note=SSC: 62719-64512 CP: no SCS: both ST: NI BLAST-Start: [CobT-like cobalamin biosynthesis protein [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: 38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.177, -2.2186743274732437, yes F: CobT-like cobalamin biosynthesis protein SIF-BLAST: ,,[CobT-like cobalamin biosynthesis protein [Gordonia phage ChisanaKitsune] ],,YP_010675717,79.3388,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 62719 has strength 15.51 /note=(1) gene mark and glimmer agree /note=(2) +39 gap /note=(3) longest ORF but not GM most coding potential /note=(4) least negative final score and highest Z score above 2 /note=(5) 10/10 S1Q1 match /note=(6) 6 MAs /note=ORF CALL: no change /note= /note=Functional Call: /note=HHpred: one high coverage top hit, red, CobT-like cobalamin biosynthesis protein /note=Pham: one comparison phage matches for CobT-like cobalamin biosynthesis protein /note=BLASTp: 2 S1Q1 matches for CobT-like cobalamin biosynthesis protein /note=FUNCTIONAL CALL: CobT-like cobalamin biosynthesis protein CDS 64516 - 64818 /gene="75" /product="gp75" /function="Hypothetical Protein" /locus tag="FlyingTortilla_75" /note=Original Glimmer call @bp 64516 has strength 4.21; Genemark calls start at 64516 /note=SSC: 64516-64818 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp071 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 92.0% 1.18992E-50 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.631, -3.3060637489568596, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp071 [Gordonia phage ChisanaKitsune] ],,YP_010675718,77.8846,1.18992E-50 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 64516 has strength 4.21 /note= /note=(1) gene mark and glimmer agree /note=(2) +4 gap /note=(3) longest ORF... Most GM coding potential /note=(4) least negative final score... highest Z score above 2 /note=(5) 10/10 S1Q1 match /note=(6) 6 MAs /note=ORF CALL: no change /note= /note=Functional Call: /note=HHpred: low coverage top hits, no red, mostly unknown /note=Pham: two comparison genes have unknown function /note=BLASTp: all S1Q1 matches have unknown function /note=FUNCTIONAL CALL: hypothetical protein CDS 64781 - 64993 /gene="76" /product="gp76" /function="Hypothetical Protein" /locus tag="FlyingTortilla_76" /note=Original Glimmer call @bp 64781 has strength 1.0 /note=SSC: 64781-64993 CP: no SCS: glimmer ST: NI BLAST-Start: [hypothetical protein PQD15_gp072 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 4.30327E-22 GAP: -38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.791, -3.108788982793736, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp072 [Gordonia phage ChisanaKitsune] ],,YP_010675719,70.0,4.30327E-22 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 64781 has strength 1.00 ** not called by GeneMark /note= /note=ORF CALLS 64781 /note=[1] Glimmer and GeneMark do not agree. No call made by GeneMark. /note=[2] -38 bp overlap /note=[3] GeneMark low coding potential. Not reported on GeneMark report. /note=[4] least negative final score (start #1), Z score above 2 /note=[5] 2/10 BLAST p S1: Q1 /note=[6] No MAs /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCION CALLS: 64781 /note=HHpred: low coverage of top hits, little consistency /note=Pham: (Chidiebere-75 & Schomber-73) Unknown function /note=BLASTp: all in pham say function unknown /note= /note=CALL: Unknown function CDS 64993 - 65328 /gene="77" /product="gp77" /function="Hypothetical Protein" /locus tag="FlyingTortilla_77" /note=Original Glimmer call @bp 64993 has strength 5.28; Genemark calls start at 64993 /note=SSC: 64993-65328 CP: no SCS: both ST: NI BLAST-Start: GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.197, -2.17469248771465, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 64993 has strength 5.28 /note= /note=ORF CALLS /note=[1] Glimmer and GeneMark agree /note=[2] -1 bp overlap /note=[3] GeneMark most coding potential /note=[4] least negative final score (start#2), Z score above 2 /note=[5] 2/10 BLAST p S1: Q1 /note=[6] No MAs /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTION CALL: /note=HHpred: low coverage of top hits. little consistency /note=Pham: (DalanDe & Schomber) Unknown function /note=BLASTp: all in pham say unknown function /note= /note=CALL: Unknown function CDS 65328 - 65501 /gene="78" /product="gp78" /function="Hypothetical Protein" /locus tag="FlyingTortilla_78" /note=Original Glimmer call @bp 65328 has strength 18.36; Genemark calls start at 65328 /note=SSC: 65328-65501 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein KHQ85_gp045 [Gordonia phage Skog] ],,NCBI, q3:s2 80.7018% 1.30251E-6 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.101, -2.3771126854926803, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein KHQ85_gp045 [Gordonia phage Skog] ],,YP_010059295,33.6066,1.30251E-6 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 65328 has strength 18.36 /note= /note=ORF CALLS /note=(1) Glimmer and GeneMark agree /note=(2) No overlap/gaps /note=(3) GeneMark most coding potential and the longest possible ORF /note=(4) Negative final score (start #1 least neg), Z score above 2 /note=(5) 3 BLAST p S1:Q1 /note=(6) All Pham members same start (3 MAs) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALLS: /note=HHpred: Most of the top hits don`t have good coverage, functional calls are not conserved /note=Pham: neither of their feature 78`s have a functional call /note=BLASTp: of the S1:Q1 none make a functional call /note= /note=CALL: Unknown function CDS 65803 - 66264 /gene="79" /product="gp79" /function="Hypothetical Protein" /locus tag="FlyingTortilla_79" /note=Original Glimmer call @bp 65803 has strength 11.57; Genemark calls start at 65803 /note=SSC: 65803-66264 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp077 [Gordonia phage Chidiebere] ],,NCBI, q11:s16 85.6209% 2.21488E-36 GAP: 301 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.04, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp077 [Gordonia phage Chidiebere] ],,YP_010675595,58.2822,2.21488E-36 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 65803 has strength 11.57 /note= /note=ORF CALLS /note=(1) Glimmer and GeneMark agree /note=(2) Gap by +302 base pairs /note=(3) GeneMark most coding potential and longest possible ORF /note=(4) Negative final score (start #3 least neg), Z score above 2 /note=(5) All 4 BLAST p S1:Q1 /note=(6) All Pham member same start (5 MAs) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALLS: /note=HHpred: There were no top hits and they do not have good coverage, functional calls are not conserved /note=Pham: Neither of their features do not have functional calls /note=BLASTp: of the S1:Q1 there are no hits that make a functional call /note= /note=CALL: Unknown function CDS 66349 - 66543 /gene="80" /product="gp80" /function="Hypothetical Protein" /locus tag="FlyingTortilla_80" /note=Original Glimmer call @bp 66349 has strength 15.29; Genemark calls start at 66349 /note=SSC: 66349-66543 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp079 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 2.76848E-19 GAP: 84 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.944, -2.996490344739583, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp079 [Gordonia phage Chidiebere] ],,YP_010675597,81.25,2.76848E-19 SIF-HHPRED: SIF-Syn: /note=ORF CALL: /note=(1) Glimmer and GM agree /note=(2) -85 bp gap /note=(3) longest orf possible, not sure about start /note=(4) RBS final score least neg. Z score above 2 (final score), /note=(5) S1:Q1 10/10 /note=(6) All Pham members same start (6 MAs) /note= /note=NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred : No hits, none have that good of coverage /note=Pham:(Chidi and schomber): neither of their features have a functional call, none match perfectly but some are similar /note=BLAST p: of the S1:Q1 hits, all 10 match "function unknown" /note= /note=CALL: Function Unknown CDS 66540 - 67136 /gene="81" /product="gp81" /function="Hypothetical Protein" /locus tag="FlyingTortilla_81" /note=Original Glimmer call @bp 66540 has strength 10.94; Genemark calls start at 66540 /note=SSC: 66540-67136 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp080 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 98.9899% 3.18821E-67 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.458, -3.75071250087134, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp080 [Gordonia phage Chidiebere] ],,YP_010675598,71.5789,3.18821E-67 SIF-HHPRED: SIF-Syn: /note=ORF CALLS: /note=(1) Glimmer and GM agree /note=(2) +3 bp gap /note=(3) longest orf possible /note=(4) start 2, least neg, 2+ Z value /note=(5) S1:Q1 10/10 /note=(6) 12/12 All Pham members same start (6 MAs) /note= /note=DESCISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred : poor top coverage /note=Pham:(Chidi and schomber): neither of their features have a fuctional call, none match /note=BLAST p: of the S1:Q1 hits (non-drafts), 10/10 match /note= `functional unknown` /note= /note=CALL: Function unknown CDS 67136 - 67600 /gene="82" /product="gp82" /function="Hypothetical Protein" /locus tag="FlyingTortilla_82" /note=Original Glimmer call @bp 67136 has strength 11.92; Genemark calls start at 67136 /note=SSC: 67136-67600 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp081 [Gordonia phage Chidiebere] ],,NCBI, q5:s10 97.4026% 4.1133E-72 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -2.827683592113848, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp081 [Gordonia phage Chidiebere] ],,YP_010675599,83.5443,4.1133E-72 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 67136 has strength 11.92 /note= /note=ORF CALL: /note=(1) Glimmer and GeneMark agree /note=(2) No Gap/Overlap /note=(3) High coding potential and longest ORF possible /note=(4) Lowest final score; second highest Z-score and greater than 2 /note=(5) S1:Q1 1 out of 10 match /note=(6) Has 6 MAs at that start /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALLS: /note=HHpred: Moderate top coverage; closest match is siphovirus Gp157 /note=Pham: FlyingTortilla`s gene 82 comparable to Chidiebere`s gene 81 and Schomber`s gene 79; no functional calls. /note=BLASTp: All comparable S1:Q1 members have no functional calls; however gene 79 of Schomber`s has a function of host nuclease inhibitor. /note= /note=CALL: Unknown function CDS 67605 - 67916 /gene="83" /product="gp83" /function="Hypothetical Protein" /locus tag="FlyingTortilla_83" /note=Original Glimmer call @bp 67605 has strength 10.15; Genemark calls start at 67605 /note=SSC: 67605-67916 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp082 [Gordonia phage Chidiebere] ],,NCBI, q10:s11 86.4078% 6.16291E-39 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.791, -3.108788982793736, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp082 [Gordonia phage Chidiebere] ],,YP_010675600,68.932,6.16291E-39 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 67605 has strength 10.15 /note= /note=ORF CALLS (@bp 67605) /note=(1) Glimmer and GM agree /note=(2) Gap of 7 /note=(3a) Longest possible ORF /note=(3b) GeneMark most coding potential /note=(4) Negative final score (least negative), Z value above 2 /note=(5) 3/10 BLASTp S1:Q1 /note=(6) Start 18 has 1 MA, Not most common MA (start 14 has 54 MAs; FlyingTortilla does not have an MA at 14) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: most of the top hits don`t have great coverage , functional calls are not conserved. /note=Pham: Gene 83 for both comparison phages not the same as gene 83 for FlyingTortilla (83 for FT = 82 for Chidi and 80 for Schomber), neither have functional calls /note=BLASTp: all top hits (from same pham) have unknown function (all are drafts). /note= /note=CALL: function unknown CDS 67913 - 68119 /gene="84" /product="gp84" /function="Hypothetical Protein" /locus tag="FlyingTortilla_84" /note=Original Glimmer call @bp 67913 has strength 6.82; Genemark calls start at 67913 /note=SSC: 67913-68119 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp080 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 6.57934E-21 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.273, -2.0162541296952132, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp080 [Gordonia phage ChisanaKitsune] ],,YP_010675727,81.4286,6.57934E-21 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 67913 has strength 6.82 /note= /note=ORF CALLS (@bp 67913) /note=(1) Glimmer and GM agree /note=(2) Overlap of 1 /note=(3a) Longest possible ORF (overlap) /note=(3b) GeneMark most coding potential /note=(4) Negative final score (least negative), Z value above 2 /note=(5) 10/10 BLASTp S1:Q1 (4/10 S1:Q1)(6/10 4S:Q1) /note=(6) Start 8 has 6 MAs, Most common MA /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL /note=HHpred: most of the top hits don`t have great coverage , functional calls are not conserved. /note=Pham: Gene 84 for both comparison phages not the same as gene 84 for FlyingTortilla (84 for FT = 83 for Chidi and 81 for Schomber), neither have functional calls /note=BLASTp: of the S1:Q1 hits (non-drafts) only one is present and calls for unknown function /note= /note=CALL: unknown function CDS 68116 - 68277 /gene="85" /product="gp85" /function="Hypothetical Protein" /locus tag="FlyingTortilla_85" /note=Original Glimmer call @bp 68116 has strength 18.67; Genemark calls start at 68116 /note=SSC: 68116-68277 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_GRAY_84 [Gordonia phage Gray] ],,NCBI, q1:s1 100.0% 0.00298962 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.023, -2.8298788511194775, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_GRAY_84 [Gordonia phage Gray] ],,AZS07937,54.5455,0.00298962 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 33816 has strength 9.44 /note=[1] Glimmer and GeneMark agree. Glimmer called at bp 33816. /note=[2] Gap +10 bp. /note=[3] GeneMaster recognizes start position at 33816 and there is no seperate stop indicated in GeneMaster. GeneMaster does not recognize seperate gene. Greatest ORF potiential at bp=33816. /note=[4] z-value graeter than 2 and final score is the least negative (at bp=33816). /note=[5] S1:Q1= 14/10 /note=[6] 6 MA`s for all pham members /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: Low coverage of top hits. Low consistency. /note=Pham: (Shomber-84) unknown function /note=BLAST p: all in pham say unknown function /note= /note=CALL: Function Unknown CDS 68310 - 69086 /gene="86" /product="gp86" /function="Hypothetical Protein" /locus tag="FlyingTortilla_86" /note=Original Glimmer call @bp 68310 has strength 10.63; Genemark calls start at 68310 /note=SSC: 68310-69086 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp085 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 99.6124% 3.07301E-126 GAP: 32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.177, -2.5074698667202133, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp085 [Gordonia phage Chidiebere] ],,YP_010675603,83.2031,3.07301E-126 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] Glimmer and GeneMark agree /note=[2] Gap of +28 base pairs between the end of ORF 85 and the beginning of ORF 86 /note=[3] Most GeneMark coding potential. /note=[4] Z-Score is well above 2 and the final score is the least negative option. /note=[5] 10/10 one to one matches for the default BLAST sequence. /note=[6] 6 Manual annotations for start 5 at basepair 68310 /note= /note=Decision: No change. /note= /note=FUNCTIONAL CALLS /note=HHpred: Very poor coverage, function remains unknown. /note=Pham: Featrue 86 in FlyingTortilla is different than the other two comparison phages. No function listed for FlyingTortilla feature 86. /note=BLASTp: None of the BLASTp matches have any knon function, and most are unannotated drafts. /note= /note=CALL: Unknown Function. CDS 69098 - 69604 /gene="87" /product="gp87" /function="Hypothetical Protein" /locus tag="FlyingTortilla_87" /note=Original Glimmer call @bp 69098 has strength 8.56; Genemark calls start at 69089 /note=SSC: 69098-69604 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PQD15_gp083 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s4 100.0% 2.38959E-81 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.39, -3.954790667257792, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp083 [Gordonia phage ChisanaKitsune] ],,YP_010675730,81.2866,2.38959E-81 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] Glimmer and GeneMark do not agree. Glimmer claims the best start is at 69038 and GeneMark claims the best start is at 69089 /note=[2] Gap of 11 basepairs between the end of ORF 86 and the beginning of the Glimer start of ORF 87 and a gap of 2 basepairs between the end of the ORF 86 and the GeneMark start for ORF 87 /note=[3] Most GeneMark coding potential. Too close to tell the difference between the Glimmer and GeneMark start. /note=[4] Glimmer Z-Score is above 2 and has one of the less negative final scores, but the GeneMark Z-score is higher and it`s final score is less negative than the Glimmer scores. /note=[5] 7/10 one to one matches for the Glimmer sequence start BLAST sequence. 5/10 one to one matches for the GeneMark start Blast Sequence. /note=[6] 5 manual MA`s for start 4 at basepair 69098 and one MA for start 5 at basepair 69089 /note= /note=Decision: No change. /note= /note=FUNCTIONAL CALLS /note=HHpred: Very poor coverage. Unknown function. /note=Pham: None of the feature 87`s match each other when comabred between Chidiebere, Schomber, and FlyingTortilla. No function listed. /note=BLASTp: Only matches to feature 87 in BLASTp are drafts and have no function listed. /note= /note=CALL: Unknown Function. CDS 69601 - 69861 /gene="88" /product="gp88" /function="helix-turn-helix DNA binding domain" /locus tag="FlyingTortilla_88" /note=Original Glimmer call @bp 69601 has strength 6.98; Genemark calls start at 69601 /note=SSC: 69601-69861 CP: no SCS: both ST: NI BLAST-Start: [MerR-like transcriptional regulator [Gordonia phage Chidiebere] ],,NCBI, q4:s3 96.5116% 1.17653E-51 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.187, -2.213540211474171, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[MerR-like transcriptional regulator [Gordonia phage Chidiebere] ],,YP_010675605,96.4706,1.17653E-51 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 69601 has strength 6.98; GeneMark calls start at 69613 /note= /note=ORF CALL @bp96901: /note=(1) Glimmer and GeneMark disagree /note=(2) there is a 3bp overlap /note=(3) most coding potential, longest ORF /note=(4) least negative score and z score above 2 /note=(5) 1/10 S1Q1 match (the match found is its own draft) /note=(6) 6MA`s at 69601 /note= /note=DECISION: Start at bp96901 /note= /note=Functioal Call: /note=HHpred: high coverage, functional calls very from winged helix-turn-helix, sup, helix-turn-helix, DNA binding, VIRAL PROTEIN, and MerR-like; Helix-Turn-Helix DNA binding domain all with high probabilities. /note=Phamarater: gene 88 on Flying tortilla not same for two other phams, however similar gene on Schomber is helix-turn-helix DNA binding domain protein /note=BLASTp: top hits function unkown, however S3:Q4 queries all have the function as MerR-like helix-turn-helix DNA binding domain /note= /note=Function: From the given different functions, can`t distingiush which function to choose CDS 69862 - 70245 /gene="89" /product="gp89" /function="Hypothetical Protein" /locus tag="FlyingTortilla_89" /note=Original Glimmer call @bp 69862 has strength 8.34; Genemark calls start at 69862 /note=SSC: 69862-70245 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp085 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 7.61616E-66 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.04, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp085 [Gordonia phage ChisanaKitsune] ],,YP_010675732,86.4,7.61616E-66 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 69862 has strength 8.34 /note= /note=ORF CALL: /note=(1) Glimmer and GM agree /note=(2) gap of +1 /note=(3) longest ORF and most coding potential /note=(4) least negative final score and z score aboove 2 /note=(5) 10/10 S1:Q1 Match /note=(6) 6MA`s bp@69862 /note= /note=DECISION: NO CHANGE /note= /note=Fuctional Call: /note=HHpred: Low coverage of top hits functional call unknown /note=Phamarater: Similar gene on Chidiebere and Schomber has no given function /note=BLASTp: S1:Q1 top hits have a function unknown /note= /note=Function: Unknown CDS 70317 - 71081 /gene="90" /product="gp90" /function="SSB protein" /locus tag="FlyingTortilla_90" /note=Original Glimmer call @bp 70317 has strength 18.01; Genemark calls start at 70317 /note=SSC: 70317-71081 CP: no SCS: both ST: NI BLAST-Start: [ssDNA binding protein [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 8.64618E-117 GAP: 71 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.04, -2.523003374675015, yes F: SSB protein SIF-BLAST: ,,[ssDNA binding protein [Gordonia phage Chidiebere] ],,YP_010675607,89.7233,8.64618E-117 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 70317 has strength 18.01 /note= /note=FUNCTIONAL CALL /note= /note=1. HHpred calls highest prob. of it being ssDNA-binding protein at 99.8% /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), and these genes both have functional calls. Chidiebere gene 89 and Schomber gene 90 has a functional call as ssDNA binding protein. /note=3. >30 top hiits in BLASTp all have manual annotated fuctions of `ssDNA binding protein` /note= /note=Decision: SSB protein CDS 71239 - 72009 /gene="91" /product="gp91" /function="Hypothetical Protein" /locus tag="FlyingTortilla_91" /note=Original Glimmer call @bp 71239 has strength 20.67; Genemark calls start at 71239 /note=SSC: 71239-72009 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp090 [Gordonia phage Chidiebere] ],,NCBI, q3:s2 95.3125% 1.0589E-96 GAP: 157 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.04, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp090 [Gordonia phage Chidiebere] ],,YP_010675608,78.022,1.0589E-96 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 71239 has strength 20.67 /note= /note=FUNCTIONAL CALL /note= /note=1. HHpred calls highest prob. of it being Putative ubiquitin thioesterase at 98.76% /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), but these genes have no functional calls. /note=3. All/Most S1Q1 have unknown functions /note= /note=Decision: Unknown Function CDS 72116 - 72529 /gene="92" /product="gp92" /function="membrane protein" /locus tag="FlyingTortilla_92" /note=Original Glimmer call @bp 72116 has strength 13.85; Genemark calls start at 72116 /note=SSC: 72116-72529 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp088 [Gordonia phage ChisanaKitsune] ],,NCBI, q19:s53 86.1314% 3.91442E-67 GAP: 106 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.911, -4.902434413078284, no F: membrane protein SIF-BLAST: ,,[hypothetical protein PQD15_gp088 [Gordonia phage ChisanaKitsune] ],,YP_010675735,62.3529,3.91442E-67 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 72116 has strength 13.85 /note= /note=ORF CALL /note=[1] Glimmer and GenMark agree /note=[2] +107 BP gap, (72116-72009) /note=[3] Longest ORF possible. GM most coding potential. /note=[4] Start 2 predicted but not least negative Final Score and lacks "z"score above 2, Start 2(position:72062) has least negative Final Score and a "z"score of >2 /note=[5] BLASTp 4/10 had Q1:S1 match /note=[6] No MA to compare /note= /note=DECISION, NO CHANGE /note= /note=FUNCTIONAL CALL /note=[1] HHpred-membrane protein /note=[2] Pham-no similarities between comparison phages, unknown function /note=[3] BLASTp-4/10 Q1:S1, unknown function /note= /note=CALL, membrane protein CDS 72771 - 73049 /gene="93" /product="gp93" /function="Hypothetical Protein" /locus tag="FlyingTortilla_93" /note=Original Glimmer call @bp 72771 has strength 7.54; Genemark calls start at 72771 /note=SSC: 72771-73049 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp092 [Gordonia phage Chidiebere] ],,NCBI, q7:s4 93.4783% 1.76342E-33 GAP: 241 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.5, -4.886359045494357, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp092 [Gordonia phage Chidiebere] ],,YP_010675610,77.5281,1.76342E-33 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 72771 has strength 7.54 /note= /note=ORF CALLS: /note=1) GeneMark and GLIMMER agree /note=2) 242 bp gap between 92 STOP and 93 start @72771 /note=3) this is longest ORF, covers all coding potential in GeneMark /note=4) RBS- Final score -4.886 (almost least negative), Z-score=2.5 (> 2) /note=5) S1:Q1- 1 match /note=6) no MA`s at any start /note= /note=DECISION: No change to start /note= /note=FUNC CALLS: /note=1)HHPred- closest match at 82%-not useful /note=2)Phamerator- corresponds to 92 on Chiedibere and 94 on Kabocha (both unknown function) /note=3)BLASTp- function unknown /note= /note=DECISION: Unknown function /note=Original Glimmer call @bp 72771 has strength 7.54 /note= /note=ORF CALL /note=[1] Glimmer and GenMark agree /note=[2] +242 BP gap (72771-72529) /note=[3] Longest ORF possible. GM most coding potential /note=[4] Start 1 was favored (2771) , not the least negative final score but has the highest "z"score above 2 /note=[5] BLASTp had 0/10 Q1:S1 matches, matches were SEA-phage drafts /note=[6] No MA to compare /note= /note=DECISION NO CHANGE /note= /note=FUNCTIONAL CALL /note=[1] HHpred= no close calls /note=[2] Pham= Chidiebere (92) and Schomber (90) have similarities but no functional call /note=[3] BLASTp= 0/10 Q1:S1 matches, "unknown function" /note= /note=FUNCTIONAL CALL "Unkown Function" CDS 73030 - 73251 /gene="94" /product="gp94" /function="Hypothetical Protein" /locus tag="FlyingTortilla_94" /note=Genemark calls start at 73030 /note=SSC: 73030-73251 CP: no SCS: genemark ST: NI BLAST-Start: [membrane protein [Gordonia phage Kabocha] ],,NCBI, q1:s1 100.0% 4.50257E-16 GAP: -20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.788, -2.9754816289569264, yes F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Gordonia phage Kabocha] ],,WAA19880,66.6667,4.50257E-16 SIF-HHPRED: SIF-Syn: /note=ORF CALL: /note=(1) DNA Master did not recognize it as a feature; appeared in GeneMar report but did not have any coding potential. /note=(2) 19 +BP overlap /note=(3) GeneMark has no coding potential for the feature. Longest ORF possible without cutting a large amount of BP out /note=(4) Highest Z-score value greater than 2 and lowest final score /note=(5) 5/10 S1:Q1 match /note=(6) Has 4 MA`s /note= /note=DECISION: UNKNOWN /note= /note=HHpred: Has no top coverage; functional call not preserved /note=Pham: FlyingTortilla gene 94 comparable to Chidiebere`s gene 93 and Schomber`s 91; unknown function /note=Blastp: All S1:Q1 members agree it is unknown function. /note= /note= /note=CALL: Unknown Function CDS 73248 - 73457 /gene="95" /product="gp95" /function="Hypothetical Protein" /locus tag="FlyingTortilla_95" /note=Original Glimmer call @bp 73248 has strength 14.79; Genemark calls start at 73248 /note=SSC: 73248-73457 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp094 [Gordonia phage Chidiebere] ],,NCBI, q2:s3 98.5507% 6.25991E-20 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.023, -2.4787699911121788, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp094 [Gordonia phage Chidiebere] ],,YP_010675612,75.3623,6.25991E-20 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 73248 has strength 14.79` /note= /note=ORF CALL: /note=(1) Glimmer and GeneMark agree /note=(2) 199 BP gap /note=(3) Coding potential highest; Longest ORF possible* /note=(4) Highest Z-value, greater than 2 and lowest final score /note=(5) 1/10 S1:Q1 Match /note=(6) Has 6 MAs /note= /note=DECISION: NO CHANGE /note= /note=*GeneMark suggests a gene between 93 and 94; however there is low coding potential on the GeneMark report. Although DNA master does not find this feature in flyingtortilla, we found that closely related phage do have a feature identified between 93 and 94. /note= /note=FUNCTIONAL CALLS: /note=HHpred: Good top coverage; top match is 93% so function is likely unknown. /note=Pham: FlyingTortilla`s gene 95 in phamerator(shift because of extra gene) is comparable to Chidiebere`s gene 94 and Schomber`s gene 92; no functional calls. /note=BLASTp: All comparable S1:Q1 members have no functional call. /note= /note=CALL: Unknown function CDS 73457 - 73663 /gene="96" /product="gp96" /function="Hypothetical Protein" /locus tag="FlyingTortilla_96" /note=Original Glimmer call @bp 73457 has strength 9.85; Genemark calls start at 73457 /note=SSC: 73457-73663 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp095 [Gordonia phage Chidiebere] ],,NCBI, q4:s2 95.5882% 9.26763E-22 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.639, -7.503299120564459, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp095 [Gordonia phage Chidiebere] ],,YP_010675613,77.2727,9.26763E-22 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 73457 has strength 9.85 /note= /note=ORF CALL @ 73457: /note=(1) Glimmer and GeneMark Agree /note=(2) No gap/overlap /note=(3) Highest coding potential with a slight drop towards the end; longest ORF possible without losing coding potential, gaps, and overlaps /note=(4) Z-score less than 2 and highest final score; /note=(5) 3/10 S1:Q1 match /note=(6) Has no MA`s /note= /note=ORF CALL @ 73502: /note=(1) NOT APPLICABLE /note=(2) Has a +47bp gap /note=(3) Not longest ORF possible; /note=(4) Highest Z-score with a value of 2.181; lowest final score /note=(5) 0/10 S1:Q1 match /note=(6) 0 MA`s /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALLS: /note=HHpred: No top coverage; functional call not preserved. /note=Pham: FlyingTortilla`s gene 96 comparable to Chidiebere`s gene 95 and Schomber`s gene 93; DNaE-like DNA polymerase III alpha is called on Schomber`s gene 96; other than that no functional calls. /note=BLASTp: All comparable S1:Q1 members have no functional call. /note= /note=CALL: Unknown Function CDS 73663 - 74055 /gene="97" /product="gp97" /function="Hypothetical Protein" /locus tag="FlyingTortilla_97" /note=Original Glimmer call @bp 73747 has strength 2.93; Genemark calls start at 73663 /note=SSC: 73663-74055 CP: no SCS: both-gm ST: NI BLAST-Start: [hypothetical protein PBI_GRAY_96 [Gordonia phage Gray]],,NCBI, q1:s1 99.2308% 7.34548E-58 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.402, -3.787175982222016, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_GRAY_96 [Gordonia phage Gray]],,AZS07948,77.4436,7.34548E-58 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 73747 has strength 2.93; GeneMark calls start at 73663 /note= /note=ORF CALLS (@bp 73747) /note=(1) Glimmer and GM do NOT agree /note=(2) Gap of 86 /note=(3a) Not longest possible ORF /note=(3b) Glimmer does not encompass all coding potential /note=(4) Negative final score (most negative score), Z score NOT above 2 /note=(5) 1/10 BLASTp S1:Q1 /note=(6) Start 11 has 0 MAs, NOT most common MA /note= /note=DECISION: INVESTIGATE EARLIER START (@bp 73663) /note=(2) Gap of 2 /note=(3a) Longest possible ORF /note=(3b) Genemark most coding potential /note=(4) Negative final score, Z value above 2 /note=(5) 4/10 BLASTp S1:Q1 /note=(6) Start 4 has 2 MAs, most common MA /note= /note=DECISION: CHANGE START POSITION TO bp 73663 /note= /note=FUNCTIONAL CALL /note=HHpred: most hits do not have good coverage, functional calls not conserved, however HHpred calls for function = family of unknown function (99.93%) /note=Pham: gene 96 on FlyingTortilla (97 on Pham) does not correlate to any of the comparison genes best comparison would be to gene 94 for Schomber and gene 96 for Chidbi. Other than that there are no good comparisons. /note=BLASTp: all S1:Q1 top hits (non-drafts) have their function as unknown /note= /note=CALL: unknown function CDS 74166 - 76973 /gene="98" /product="gp98" /function="DNA polymerase" /locus tag="FlyingTortilla_98" /note=Original Glimmer call @bp 74166 has strength 11.42; Genemark calls start at 74166 /note=SSC: 74166-76973 CP: yes SCS: both ST: NI BLAST-Start: [DnaE-like DNA polymerase III [Gordonia phage Gray]],,NCBI, q2:s3 99.8931% 0.0 GAP: 110 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.13, -2.3158002311349737, yes F: DNA polymerase SIF-BLAST: ,,[DnaE-like DNA polymerase III [Gordonia phage Gray]],,AZS07949,94.6638,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 76970 has strength 8.75; GeneMark calls start at 76973 /note=[1] Glimmer and GeneMark do not agree /note=[2] Overlap -3 bp /note=[3] has the greatest coding potiential at bp=76970 /note=[4] z-value is less than 2 and the final score is not the least negative value /note=[5] S1:Q1= 3/10 /note=[6] All pham members have 44 MA`s at start 11. /note= /note=FINAL DECISION: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: High coverage of top hits. High consistency of tail terminator. /note=Pham: (Shomber-100) DNA Polymerase /note=BLAST p: all in pham say DNA Polymerase. /note=FINAL DECISION: DNA Polymerase. CDS 76970 - 77227 /gene="99" /product="gp99" /function="DNA polymerase" /locus tag="FlyingTortilla_99" /note=Original Glimmer call @bp 76970 has strength 8.75; Genemark calls start at 76973 /note=SSC: 76970-77227 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PQD14_gp100 [Gordonia phage Chidiebere] ],,NCBI, q14:s11 80.0% 1.48839E-11 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.727, -6.117693456646997, no F: DNA polymerase SIF-BLAST: ,,[hypothetical protein PQD14_gp100 [Gordonia phage Chidiebere] ],,YP_010675618,62.3377,1.48839E-11 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 76970 has strength 8.75; GeneMark calls start at 76973 /note=[1] Glimmer and GeneMark do not agree /note=[2] Overlap -3 bp /note=[3] has the greatest coding potiential at bp=76970 /note=[4] z-value is less than 2 and the final score is not the least negative value /note=[5] S1:Q1= 3/10 /note=[6] All pham members have 44 MA`s at start 11. /note= /note=FINAL DECISION: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: High coverage of top hits. High consistency of tail terminator. /note=Pham: (Shomber-100) DNA Polymerase /note=BLAST p: all in pham say DNA Polymerase. /note=FINAL DECISION: DNA Polymerase. CDS 77220 - 77477 /gene="100" /product="gp100" /function="Hypothetical Protein" /locus tag="FlyingTortilla_100" /note=Original Glimmer call @bp 77220 has strength 7.94; Genemark calls start at 77220 /note=SSC: 77220-77477 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp101 [Gordonia phage Chidiebere] ],,NCBI, q12:s15 76.4706% 1.31384E-16 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.208, -2.1518296047551457, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp101 [Gordonia phage Chidiebere] ],,YP_010675619,51.6129,1.31384E-16 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 77220 has strength 7.94 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) -8bp overlap /note=(3) Longest ORF possible, GM best coding potential /note=(4) RBS final score is the least negative (start #1). Z score is above 2 /note=(5) 3/10 are S1:Q1 match /note=(6) No MAs /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: low coverage of top hits, fuctional calls are not consistent /note=Pham: Chidi-100 and Schomber-98; members are all drafts without functional calls /note=BLASTp: all top hits are unknown function /note= /note=CALL: Unknown function CDS 77822 - 78235 /gene="101" /product="gp101" /function="Hypothetical Protein" /locus tag="FlyingTortilla_101" /note=Original Glimmer call @bp 77822 has strength 2.12; Genemark calls start at 77822 /note=SSC: 77822-78235 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp103 [Gordonia phage Chidiebere] ],,NCBI, q6:s5 96.3504% 2.22942E-46 GAP: 344 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.46, -3.7469643924750877, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp103 [Gordonia phage Chidiebere] ],,YP_010675621,71.1111,2.22942E-46 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 77822 has strength 2.12 /note= /note=ORF CALLS /note= /note=(1) Glimmer and GM agree /note=(2) +344bp gap /note=(3) Longest ORF possible, GM encompasses all coding potential /note=(4) RBS final score is the least negative (start #1). Z score above 2 /note=(5) 3/10 are S1:Q1 match /note=(6) No MAs /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTIONAL CALLS /note=HHpred: very low coverage of top hits, functional calls are not consistent /note=Pham: Chidi-101 and Schomber-99; members are all drafts without functional calls /note=BLASTp: all top hits are function unknown /note= /note=CALL: Unknown function CDS 78219 - 79325 /gene="102" /product="gp102" /function="RecA-like DNA recombinase" /locus tag="FlyingTortilla_102" /note=Original Glimmer call @bp 78219 has strength 14.3; Genemark calls start at 78219 /note=SSC: 78219-79325 CP: no SCS: both ST: NI BLAST-Start: [RecA-like DNA recombinase [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.13, -2.7806870294376242, yes F: RecA-like DNA recombinase SIF-BLAST: ,,[RecA-like DNA recombinase [Gordonia phage ChisanaKitsune] ],,YP_010675749,97.0109,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 78219 has strength 14.30 /note= /note=(1) GM and GLIMMER agree /note=(2) -16 bp overlap /note=(3) Longest possible ORF and most GM coding potential /note=(4) Least negative final score (-2.781) and has z value above 2 (3.121) /note=(5) 10/10 S1Q1 match /note=(6) Start at 78219 bp has 7 MA`s... /note= /note= /note=DECISION: MADE... keep start where it is. /note= /note= /note=FUNCTIONAL CALL: /note=HHpred: Good coverage and conservation (lots of red) many members have function listed as DNA recombinase /note=PHAM: comparrisons (Hanem and Schober) have unknown function /note=BLAST p: Most S1Q1 members (excluding drafts) have 102 as a RecA-Like DNA recombinase /note= /note=DECISION: RecA-like DNA recombinase (DNA recombinase) CDS 79557 - 79796 /gene="103" /product="gp103" /function="Hypothetical Protein" /locus tag="FlyingTortilla_103" /note=Original Glimmer call @bp 79557 has strength 6.18; Genemark calls start at 79557 /note=SSC: 79557-79796 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp106 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 87.3418% 1.19701E-28 GAP: 231 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.46, -5.273303669864932, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp106 [Gordonia phage Chidiebere] ],,YP_010675624,50.8475,1.19701E-28 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 79557 has strength 6.18 /note= /note=(1) GLIMMER and GM agree /note=(2) +232 bp overlap /note=(3) Longest possible ORF and most GM coding potential /note=(4) NOT least negative final score (-5.273) but has a z value above 2 (2.449) however it is not the highest z value above 2... /note=(5) 9/10 S1Q1 matches /note=(6) The start at 79557 bp has 1 MA`s /note= /note=Functional call: /note=HHpred: Good coverage but not conserved (no red) /note=PHAM: Hanem and Schomber comparrison has 103 listed as DNA recombinase... /note=BLAST p: 7/7 S1Q1 (excluding drafts) are listed as unknown function /note= /note=DECISION: UNKNOWN FUNCTION CDS 79766 - 80056 /gene="104" /product="gp104" /function="Hypothetical Protein" /locus tag="FlyingTortilla_104" /note=Original Glimmer call @bp 79766 has strength 6.9; Genemark calls start at 79766 /note=SSC: 79766-80056 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp107 [Gordonia phage Chidiebere] ],,NCBI, q38:s2 61.4583% 1.97356E-21 GAP: -31 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.725, -3.7606820078281067, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp107 [Gordonia phage Chidiebere] ],,YP_010675625,86.6667,1.97356E-21 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 79766 has strength 6.90 /note= /note=(1) gene mark and glimmer agree /note=(2) -30 overlap /note=(3) not longest ORF without overlapping... not most coding potential /note=(4) not least negative final score... not highest Z score above 2 /note=(5) 3/10 S1Q1 match /note=(6) No MAs /note=ORF CALL: no change /note= /note=Functional Call: /note=HHpred: high coverage, no red, most calls do not match /note=Pham:two comparison phage do not match /note=BLASTp: no S1Q1 matches with functional call /note=FUNCTIONAL CALL: hypothetical protein CDS 80053 - 80211 /gene="105" /product="gp105" /function="Hypothetical Protein" /locus tag="FlyingTortilla_105" /note=Original Glimmer call @bp 80053 has strength 9.38; Genemark calls start at 80053 /note=SSC: 80053-80211 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp108 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 86.5385% 5.01823E-7 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.843, -3.0002394643941313, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp108 [Gordonia phage Chidiebere] ],,YP_010675626,55.5556,5.01823E-7 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 80053 has strength 9.38 /note= /note=(1) glimmer and gene mark agree /note=(2) -3 overlap /note=(3) longest ORF possible... most GM coding potential /note=(4) least negative final score... highest Z score above 2 /note=(5) 0/10 S1Q1 match /note=(6) 5 MAs /note=ORF CALL: no change /note= /note=Functional Call: /note=HHpred: low coverage top hits and no red /note=Pham: both comparison phage have function unknown /note=BLASTp: all S1Q1 matches have function unknown /note=FUNCTIONAL CALL: hypothetical protein CDS 80198 - 80335 /gene="106" /product="gp106" /function="Hypothetical Protein" /locus tag="FlyingTortilla_106" /note=Original Glimmer call @bp 80198 has strength 2.92; Genemark calls start at 80198 /note=SSC: 80198-80335 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp107 [Gordonia phage ChisanaKitsune] ],,NCBI, q2:s1 95.5556% 8.5434E-7 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.492, -3.597563630176197, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp107 [Gordonia phage ChisanaKitsune] ],,YP_010675754,71.7391,8.5434E-7 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 80198 has strength 2.92 ** not called by GeneMark /note= /note=ORF CALLS /note=[1] Glimmer and GeneMark do not agree. No call made by GeneMark. /note=[2] -14 bp overlap /note=[3] GeneMark most coding potential /note=[4] least negative final score @ bp 80198 (start #2), Z score above 2 /note=[5] 3/10 BLAST p S1: Q1 /note=[6] 5 MAs @bp 80053 /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTION CALLS: /note=HHpred: low coverage of top hits, little consistency /note=Pham: (DalanDe- 97) RuvC- like resolvase /note=BLASTp: all in pham say function unknown /note= /note=CALL: Unknown function CDS 80522 - 81343 /gene="107" /product="gp107" /function="exonuclease" /locus tag="FlyingTortilla_107" /note=Original Glimmer call @bp 80522 has strength 13.23; Genemark calls start at 80522 /note=SSC: 80522-81343 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp111 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: 186 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.458, -3.75071250087134, no F: exonuclease SIF-BLAST: ,,[hypothetical protein PQD14_gp111 [Gordonia phage Chidiebere] ],,YP_010675629,97.0696,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 80522 has strength 13.23 /note= /note=ORF CALLS /note=[1] Glimmer and GeneMark do not agree. /note=[2] 186 bp gap /note=[3] GeneMark most coding potential /note=[4] not least negative final score @bp 80522, Z score above 2 /note=[5] All 11 BLAST p S1: Q1 /note=[6] 0 MAs /note= /note=DECISION MADE: NO CHANGE /note= /note=FUNCTION CALLS: /note=HHpred: high coverage of top hits, some consistency /note=Pham: (Schomber-107 & Chidiebere-109) unknown function /note=BLASTp: some in pham say exonuclease /note= /note=CALL: exonuclease CDS 81340 - 81468 /gene="108" /product="gp108" /function="Hypothetical Protein" /locus tag="FlyingTortilla_108" /note=Original Glimmer call @bp 81340 has strength 7.89; Genemark calls start at 81340 /note=SSC: 81340-81468 CP: no SCS: both ST: NI BLAST-Start: GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.04, -3.3503726477288405, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 81340 has strength 7.89 /note= /note=ORF CALLS /note=(1) Glimmer and GeneMark agree /note=(2) Overlap by -3 /note=(3) Longest possible ORF and GeneMark has most coding potential /note=(4) Negative final score (start #1 least neg), Z-score above 2 /note=(5) All 2 BLAST p S1:Q1 /note=(6) All Pham member same start (8 MAs) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: there are no top its and it does not have good coverage /note=Pham: Neither Chidi nor Schomber have functional calls at 108 /note=BLASTp: of the S1:Q1 it does not have any functional calls /note= /note=CALL: Unknown function CDS 81465 - 81674 /gene="109" /product="gp109" /function="Hypothetical Protein" /locus tag="FlyingTortilla_109" /note=Original Glimmer call @bp 81465 has strength 5.88; Genemark calls start at 81450 /note=SSC: 81465-81674 CP: no SCS: both-gl ST: NI BLAST-Start: [membrane protein [Gordonia phage Gray]],,NCBI, q1:s1 98.5507% 8.80454E-25 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.54, -5.684423281098294, no F: Hypothetical Protein SIF-BLAST: ,,[membrane protein [Gordonia phage Gray]],,AZS07959,82.6087,8.80454E-25 SIF-HHPRED: SIF-Syn: CDS 81677 - 82117 /gene="110" /product="gp110" /function="Hypothetical Protein" /locus tag="FlyingTortilla_110" /note=Original Glimmer call @bp 81677 has strength 2.83; Genemark calls start at 81677 /note=SSC: 81677-82117 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PBI_GRAY_110 [Gordonia phage Gray]],,NCBI, q1:s13 99.3151% 4.74949E-79 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.631, -3.3060637489568596, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_GRAY_110 [Gordonia phage Gray]],,AZS07960,84.7134,4.74949E-79 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 81677 has strength 2.83 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) -3 bp gap /note=(3) longest ORF possible /note=(4) start 4, least neg, 2 Z value /note=(5) 4/10 S1:Q1 /note=(6)13/15 genes in pham match (5 MA) /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred : No hits, poor top coverage /note=Pham:(Chidi and schomber): neither of their features have a fuctional call, none match perfectly but some are similar in different numbers /note=BLAST p: of the S1:Q1 hits (non-drafts) 4/10, all "function unknown" /note= /note= /note=CALL: Function Unknown CDS 82104 - 82703 /gene="111" /product="gp111" /function="Hypothetical Protein" /locus tag="FlyingTortilla_111" /note=Original Glimmer call @bp 82104 has strength 8.47; Genemark calls start at 82104 /note=SSC: 82104-82703 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp113 [Gordonia phage ChisanaKitsune] ],,NCBI, q4:s7 98.4925% 3.70123E-115 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.046, -6.645415752238343, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp113 [Gordonia phage ChisanaKitsune] ],,YP_010675760,86.5672,3.70123E-115 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 82104 has strength 8.47 /note= /note=ORF CALLS /note=(1) Glimmer and GM agree /note=(2) + 13 bp gap /note=(3) longest orf possible with coding potential /note=(4) start 2, least neg, 2+ /note=(5)1/10 S!:Q1 /note=(6) 1/12 pham no MA /note= /note=Descision: undecided /note= /note=FUNCTIONAL CALL: /note=HHpred : No hits, none have that good of coverage /note=Pham:(Chidi and schomber): neither of their features have a functional call, none match perfectly but some are similar in different numbers /note=BLAST p: of the S1:Q1 hits (non-drafts), 1/10 match "function unknown" /note= /note=CALL: Function unknown CDS 82708 - 83283 /gene="112" /product="gp112" /function="RuvC-like resolvase" /locus tag="FlyingTortilla_112" /note=Original Glimmer call @bp 82708 has strength 11.13; Genemark calls start at 82708 /note=SSC: 82708-83283 CP: no SCS: both ST: NI BLAST-Start: [RuvC-like Holliday junction resolvase [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 3.48931E-101 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.236, -6.307407324449475, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like Holliday junction resolvase [Gordonia phage Chidiebere] ],,YP_010675633,86.3874,3.48931E-101 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] Glimmer and GeneMark agree /note=[2] Gap of +4 between the end of ORF 111 and the beginning of ORF 112 /note=[3] GeneMark most coding potential. /note=[4] Z-score for default start is not above 2 (1.224) and the final score is not the least negative option. /note=[5] 10/10 one to one matches for the BLAST squence. /note=[6] No manual annotations for any start in the FlyingTortialla Pham report. /note= /note=Decision: No change. /note= /note=FUNCTIONAL CALLS /note=HHpred: Nearly full coverage. Function likely to be RuvC-like resolvase. /note=Pham: Feature 113 (because everything after 94 is shifted one) match across all comparison phages and FlyingTortilla. Function listed as RuvC. /note=BLASTp: A number of matches list the function as RuvC-like resolvase. Function likely. /note= /note=CALL: RuvC-like Resolvase. CDS 83270 - 84850 /gene="113" /product="gp113" /function="ParB-like nuclease domain" /locus tag="FlyingTortilla_113" /note=Original Glimmer call @bp 83270 has strength 13.36; Genemark calls start at 83270 /note=SSC: 83270-84850 CP: no SCS: both ST: NI BLAST-Start: [ParB-like nuclease domain protein [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 98.0989% 0.0 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.594, -3.384070132909239, yes F: ParB-like nuclease domain SIF-BLAST: ,,[ParB-like nuclease domain protein [Gordonia phage ChisanaKitsune] ],,YP_010675762,94.3074,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 83270 has strength 13.36 /note= /note=ORF CALL: /note=(1) Glimme and GM agree /note=(2) overlap of 13bp /note=(3) encomposes all coding potential and longest ORF /note=(4) least negative final score, Z score above 2 /note=(5) 10/10 S1:Q1 match /note=(6) 6MA`s at bp83270 /note= /note=DECISION:NO CHANGE /note= /note=Functional Call: /note=HHpred: Most top hits are listed as a Par B Proteins /note=Phamarater: All similar genes are the same within similar phams (Schomber and Cidiebere), function is listed as ParB-like nuclease domain protein /note=BLASTp: S1:Q1 top hits have a function of ParB-like nuclease domain protein /note= /note=Function:ParB-like nuclease domain protein CDS 84976 - 85263 /gene="114" /product="gp114" /function="Hypothetical Protein" /locus tag="FlyingTortilla_114" /note=Original Glimmer call @bp 84976 has strength 15.7; Genemark calls start at 84976 /note=SSC: 84976-85263 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD15_gp116 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s51 93.6842% 1.15662E-13 GAP: 125 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.742, -3.5985503360675457, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp116 [Gordonia phage ChisanaKitsune] ],,YP_010675763,43.871,1.15662E-13 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 84976 has strength 15.70 /note= /note=FUNCTIONAL CALL /note= /note=1. HHpred calls highest prob. of it being Structural protein VP2; helical symmetry, archaeal pilus, STRUCTURAL PROTEIN, VIRUS at 95.03% /note=2. Phamerator has similar genes on 2 different phages (Chidiebere and Schomber), but these genes have no functional calls. /note=3. All/Most S1Q1 have unknown functions /note= /note=Decision: Unknown Function CDS 85349 - 86254 /gene="115" /product="gp115" /function="Hypothetical Protein" /locus tag="FlyingTortilla_115" /note=Original Glimmer call @bp 85349 has strength 12.77; Genemark calls start at 85349 /note=SSC: 85349-86254 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp118 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 100.0% 0.0 GAP: 85 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.905, -5.186767100221219, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp118 [Gordonia phage Chidiebere] ],,YP_010675636,89.3688,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 85349 has strength 12.77 /note= /note=ORF CALLS: /note=1)GLIMMER and GeneMark agree /note=2)86 bp gap /note=3) start covers longest coding potential in GeneMark /note=4) RBS- Final Score -5.187 (not least negative), Z-score=1.905 (not >2), better RBS would have a large gap /note=5) S1:Q1- 9 1:1 matches /note=6) 5 MAs @ start 85349 /note= /note=FUNC CALLS: /note=1)HHPred-99.9% match to protein of unknown function /note=2) Phamerator- match to 117 on Chiedibere and 118 on Kabocha (both unknown function) /note=3) BLASTp- unknown function /note= /note=DECISION: Hypothetical protein /note= /note=Original Glimmer call @bp 85349 has strength 12.77 /note= /note=ORF CALL /note=[1] Glimmer and GenMark agree /note=[2] +86 BP (85349-85263) /note=[3] Longest ORF possible. GM most coding potential /note=[4] Start 1 is favored, Start 11(position: 86081) appears to be better as it has the least negative final score (-3.796) and largest "z" score above 2 /note=[5] BLASTp 5/10 Q1:S1 matches, several draft matches as well /note=[6] no MAs to compare /note= /note=DECISON NO CHANGE /note= /note=FUNCTIONAL CALL /note=[1] HHpred= 2 strong matches, unknown function /note=[2] Pham= same as Schomber (115) and Chidiebere (117) /note=[3]BLASTp= 5/10 unknown function /note= /note=FUNCTIONAL CALL, "Unknown Function" CDS 86256 - 86732 /gene="116" /product="gp116" /function="Hypothetical Protein" /locus tag="FlyingTortilla_116" /note=Original Glimmer call @bp 86256 has strength 6.72; Genemark calls start at 86256 /note=SSC: 86256-86732 CP: no SCS: both ST: NI BLAST-Start: [minor tail protein [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 7.8449E-69 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.152, -4.841864039781758, no F: Hypothetical Protein SIF-BLAST: ,,[minor tail protein [Gordonia phage ChisanaKitsune] ],,YP_010675765,77.5641,7.8449E-69 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 86256 has strength 6.72 /note= /note=ORF CALL: /note=(1) Glimmer and GeneMark agree /note=(2) There is a +2 gap /note=(3) Longest ORF possible without overlap. There was a slight drop in coding potential but it was fairly consistent other than that. /note=(4) Z-score greater than 2 and is the highest out of all of them. And has the lowest final score at -4.842 /note=(5) 10/10 S1:Q1 match /note=(6) Has 6 MA`s /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: Has great top coverage; unknown function /note=Pham: FlyingTortilla`s gene 117(shifted because of extra gene) is comparable to Chidiebere`s gene 119 and is the same for Schomber`s 117; no functional calls. /note=BLASTp: 1/11 S1:Q1 members have a functional call "metalloprotease"; overall consensus unknown function. /note= /note=CALL: UNKNOWN FUNCTION CDS 86830 - 87570 /gene="117" /product="gp117" /function="Hypothetical Protein" /locus tag="FlyingTortilla_117" /note=Original Glimmer call @bp 86830 has strength 14.95; Genemark calls start at 86830 /note=SSC: 86830-87570 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp120 [Gordonia phage Chidiebere] ],,NCBI, q1:s10 100.0% 3.71837E-160 GAP: 97 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.965, -2.6814417326944517, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp120 [Gordonia phage Chidiebere] ],,YP_010675638,90.1961,3.71837E-160 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 86830 has strength 14.95 /note= /note=ORF CALLS (@bp 86830) /note=(1) Glimmer and GM agree /note=(2) Gap of 100 /note=(3a) Not longest possible ORF /note=(3b) GeneMark NOT most coding poetential /note=(4) Negative final score, Z score above 2 /note=(5) 5/10 BLASTp S1:Q1 /note=(6) Start 4 has 1 MA, NOT most common MA /note= /note=DECISION: INVESTIGATE EARLIER START (@bp 86794) /note=(2) Gap of 64 /note=(3a) longest possible ORF /note=(3b) GeneMark most coding potential /note=(4) Negative final score (bp 86830 better score), Z score above 2 (1.977) (close enough) /note=(5) 0/10 BLASTp S1:Q1 /note=(6) Start 1 has 0 MAs, NOT most common MA /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL /note=HHpred: most hits do not have good coverage, functional calls not conserved /note=Pham: gene 117 for comparison phage (Chibi) not the same as gene 117 for FlyingTortilla (listed as gene 118 on pham), however Schomber same as gene 118 for FlyingTortilla. /note=BLASTp: all S1:Q1 top hits (non-drafts) have their function as function unknown /note= /note=CALL: Function unknown CDS 87580 - 88707 /gene="118" /product="gp118" /function="Hypothetical Protein" /locus tag="FlyingTortilla_118" /note=Original Glimmer call @bp 87580 has strength 14.64; Genemark calls start at 87580 /note=SSC: 87580-88707 CP: yes SCS: both ST: NI BLAST-Start: [tail fiber protein [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 100.0% 0.0 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.379, -3.8366550365551095, no F: Hypothetical Protein SIF-BLAST: ,,[tail fiber protein [Gordonia phage ChisanaKitsune] ],,YP_010675767,91.9571,0.0 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 87580 has strength 14.64 /note=[1] Glimmer and GeneMArk agree at bp=87580 /note=[2] Gap +10 bp /note=[3] Has the greatest coding potiential at bp=57580 /note=[4] z-value is greater than 2 and the final score is the least negative value /note=[5] S1:Q1= 8/10 /note=[6] All pham mebers have 6 MA`s at start 2. /note= /note=FINAL DECISION= NO CHANGE /note= /note= /note=FUNCTIONAL CALLS /note=HHpred: Low coverage of top hits. /note=Pham: All phages show unknown function. /note=BLAST p: All show unknown function. /note= /note=FINAL DECISION: Unknown Function CDS 88841 - 90307 /gene="119" /product="gp119" /function="Hypothetical Protein" /locus tag="FlyingTortilla_119" /note=Original Glimmer call @bp 88841 has strength 7.12; Genemark calls start at 88739 /note=SSC: 88841-90307 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PQD14_gp123 [Gordonia phage Chidiebere] ],,NCBI, q1:s35 67.418% 3.0207E-132 GAP: 133 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.164, -7.224343665540421, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp123 [Gordonia phage Chidiebere] ],,YP_010675641,48.4461,3.0207E-132 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 88841 has strength 7.12; GeneMark calls start at 88739 /note= /note=ORF CALLS /note=(1) Glimmer and GM do not agree /note=(2) + 133 bp gap /note=(3) Longest ORF possible, GM encompasses all coding potential /note=(4) RBS final score is not the least negative. Z score is not above 2. /note=(5) 1/10 is S1:Q1 match /note=(6) No MAs /note= /note=DECISION MADE: NO CHANGE? /note= /note=FUNCTIONAL CALLS: /note=HHpred: low coverage on top hihts, functional calls are not consistent /note=Pham: Chidi-121 and Schomber-119; all drafts do not have functional calls for comparison /note=BLASTp: all top hits are function unknown /note= /note=CALL: Unknown Function CDS 90338 - 90814 /gene="120" /product="gp120" /function="Hypothetical Protein" /locus tag="FlyingTortilla_120" /note=Original Glimmer call @bp 90338 has strength 2.99; Genemark calls start at 90332 /note=SSC: 90338-90814 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PQD14_gp124 [Gordonia phage Chidiebere] ],,NCBI, q1:s1 94.9367% 3.7517E-81 GAP: 30 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.641, -3.4259484787582526, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp124 [Gordonia phage Chidiebere] ],,YP_010675642,86.0,3.7517E-81 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 90338 has strength 2.99; GeneMark calls start at 90332 /note= /note=(1) Glimmer and genemark do NOT agree /note=(2) +31 bp gap /note=(3) Longest possible ORF and most GM coding potential /note=(4) Least negative final score (-3.426) and high z value above 2 (2.631) /note=(5) 2/10 S1Q1 match /note=(6) Start @ 90338 has 5 MA`s /note= /note=DECISION: MADE (keep start) /note= /note=FUNCTIONAL CALL: /note= /note=HHpred: mostly good coverage and lots of red /note=PHAM: Comparrisons call for unknown function ( Hanem and kambocha) /note=BLASTp: 1 S1/Q1 match lists as unknown function (all other non drafts that are not S1/Q1 have unknown function listed /note= /note=DECISION: UNKNOWN FUNCTION CDS 90792 - 90935 /gene="121" /product="gp121" /function="Hypothetical Protein" /locus tag="FlyingTortilla_121" /note=Original Glimmer call @bp 90792 has strength 12.07; Genemark calls start at 90846 /note=SSC: 90792-90935 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PQD14_gp125 [Gordonia phage Chidiebere] ],,NCBI, q1:s29 100.0% 1.07181E-20 GAP: -23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.267, -4.072315776040796, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp125 [Gordonia phage Chidiebere] ],,YP_010675643,61.3333,1.07181E-20 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 90792 has strength 12.07; GeneMark calls start at 90846 /note= /note=(1) glimmer and gene mark do not agree /note=(2) -22 overlap /note=(3) not longest ORF without overlap... most GM coding potential /note=(4) not least final score... not highest Z score /note=(5) 0/10 S1Q1 match /note=(6) No MAs /note=ORF CALL: no change /note= /note=Functional Call: /note=HHpred: medium coverage, only blue, unknown function /note=Pham: two comparison phage do not match /note=BLASTp: no S1Q1 matches with call /note=FUNCTIONAL CALL: hypothetical protein CDS 91022 - 91498 /gene="122" /product="gp122" /function="Hypothetical Protein" /locus tag="FlyingTortilla_122" /note=Original Glimmer call @bp 91022 has strength 12.53; Genemark calls start at 91109 /note=SSC: 91022-91498 CP: no SCS: both-gl ST: NI BLAST-Start: [hypothetical protein SEA_KABOCHA_127 [Gordonia phage Kabocha]],,NCBI, q1:s12 89.2405% 4.75058E-56 GAP: 86 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.237, -4.662288835884043, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_KABOCHA_127 [Gordonia phage Kabocha]],,WAA19913,68.6747,4.75058E-56 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 91022 has strength 12.53; GeneMark calls start at 91109 /note= /note=ORF CALLS /note=[1] Glimmer and GeneMark agree /note=[2] 86 bp overlap /note=[3] GeneMark most coding potential /note=[4] not least negative final score (start #4), Z score above 2 /note=[5] 3/10 BLAST p S1: Q1 /note=[6] 0 MAs /note= /note=DECISION MADE: NO CHANGE /note= /note=FUUNCTION CALLS: /note=HHpred: mild coverage of top hits, little consistency /note=Pham: Genome too long to compare to others /note=BLASTp: all in pham say function unknown /note= /note=CALL: Unknown Function CDS 91581 - 92147 /gene="123" /product="gp123" /function="Hypothetical Protein" /locus tag="FlyingTortilla_123" /note=Original Glimmer call @bp 91581 has strength 13.2; Genemark calls start at 91581 /note=SSC: 91581-92147 CP: no SCS: both ST: NI BLAST-Start: GAP: 82 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.283, -2.0111200136961407, yes F: Hypothetical Protein SIF-BLAST: SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 91581 has strength 13.20; GeneMark calls start at 91668 /note= /note=ORF CALLS /note=(1) Glimmer and GeneMark do not agree /note=(2) Gap by +83 /note=(3) Not longest possible ORF, GeneMark does not have coding potential /note=(4) Neg final score (start #1 least neg), Z-score above 2 /note=(5) 2 out of 10 BLAST p S1:Q1 /note=(6) Start 3 has 6 MAs /note= /note=DECISION: NO CHANGE /note= /note=FUNCTIONAL CALL: /note=HHpred: there are no top hits and it does not have good coverage /note=Pham: Neither have functional calls /note=BLASTp: Unknown function when comparing S1:Q1 /note= /note=FUNCTION: UNKNOWN CDS 92296 - 92478 /gene="124" /product="gp124" /function="Hypothetical Protein" /locus tag="FlyingTortilla_124" /note=Original Glimmer call @bp 92296 has strength 8.1; Genemark calls start at 92296 /note=SSC: 92296-92478 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein PQD14_gp127 [Gordonia phage Chidiebere] ],,NCBI, q1:s20 96.6667% 2.507E-17 GAP: 148 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.887, -2.9063687850157054, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD14_gp127 [Gordonia phage Chidiebere] ],,YP_010675645,56.962,2.507E-17 SIF-HHPRED: SIF-Syn: /note=Original Glimmer call @bp 92296 has strength 8.10 /note= /note=ORF CALL /note=(1) Glimmer and GM agree /note=(2) -149 bp gap /note=(3) longest orf possible /note=(4) start 2 , 2+ Z value, least neg /note=(5) 2/10 S1:Q1 /note=(6) All phams match, no MA /note= /note=Descision: undecided /note= /note= /note=FUNCTIONAL CALL: /note=HHpred : poor top coverage /note=Pham:(Chidi and schomber): neither of their features have a fuctional call, none match /note=BLAST p: of the S1:Q1 hits (non-drafts), 2/10 hits /note=`functional unknown` /note= /note=CALL: unknown function CDS 92479 - 92871 /gene="125" /product="gp125" /function="Hypothetical Protein" /locus tag="FlyingTortilla_125" /note=Original Glimmer call @bp 92530 has strength 3.14; Genemark calls start at 92479 /note=SSC: 92479-92871 CP: no SCS: both-gm ST: NI BLAST-Start: [hypothetical protein PQD15_gp126 [Gordonia phage ChisanaKitsune] ],,NCBI, q1:s1 97.6923% 3.15854E-46 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.326, -4.856194091974515, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PQD15_gp126 [Gordonia phage ChisanaKitsune] ],,YP_010675773,74.8092,3.15854E-46 SIF-HHPRED: SIF-Syn: /note=ORF CALLS /note=[1] Glimmer and GeneMark do not agree. /note=[2] Gap of +51 basepairs between the end of ORF 124 and the beginning of the Glimmer called ORF 125. Gap of 0 between the start of the end of ORF 124 and the beginning of the GeneMark called ORF of 125 /note=[3] GeneMark ORF has the most coding potential. /note=[4] Glimmer start does not have a Z-value above 2 (1.588) and its final score is not the least negative. The GeneMark start has a Z-value above 2 and does have a less negative score, but not THE least negative. /note=[5] 3/10 one to one matches for the BLAST sequence for the Glimmer start. 7/10 one to one matches for the BLAST sequence for the GeneMark start. /note=[6] 6 MA`s for start 1 at basepair 92479 /note= /note=Decision: Change to GeneMark start of 92479 /note= /note=FUNCTIONAL CALLS /note=HHpred: Very poor coverage. No known function. /note=Pham: Only Schomber has a matching feature 126 to feature 126 to FlyingTortilla. No known function listed. /note=BLASTp: All other comparison phages in BLASTp are unannotated drafts and do not have a listed function. /note= /note=CALL: Unknown Function.