CDS 197 - 994
  /gene="1"
  /product="gp1"
  /function="thymidylate synthase"
  /locus tag="Madraxi_1"
    /note=Original Glimmer call @bp 197 has strength 10.53
    /note=SSC: 197-994 CP: yes SCS: glimmer ST: SS BLAST-Start: [thymidylate synthase [Prescottella equi] ],,NCBI, q1:s1 100.0% 2.80151E-175 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.81, -3.3252317253000454, no F: thymidylate synthase SIF-BLAST: ,,[thymidylate synthase [Prescottella equi] ],,MBM4613742,95.3846,2.80151E-175 SIF-HHPRED: Thymidylate synthase; SSGCID, Structural Genomics, Elizabethkingia anophelis, Seattle Structural Genomics Center for Infectious Disease, TRANSFERASE; HET: PGE, M0H; 1.7A {Elizabethkingia anophelis NUHP1} SCOP: d.117.1.1,,,6AUJ_C,98.8679,100.0 SIF-Syn: also first gene in Jflix2;
    /note=Start shared by multiple genes and captures all CP; no ThyX domain; very strong hits to domain and BLAST hits; commonly called start

CDS 1008 - 1280
  /gene="2"
  /product="gp2"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_2"
    /note=Original Glimmer call @bp 1008 has strength 10.7; Genemark calls start at 1008
    /note=SSC: 1008-1280 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 5.04835E-57 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.155, -2.604595770381943, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4569322,98.8889,5.04835E-57 SIF-HHPRED: Virion-associated phage protein; Complex, VIRAL PROTEIN;{Ralstonia phage GP4},,,8JOU_C,98.8889,100.0 SIF-Syn: same gene is also #2 in Jflix2
    /note=does not have most annotated start, but same start is shared with Jflix2 (only).

CDS 1301 - 2092
  /gene="3"
  /product="gp3"
  /function="minor tail protein"
  /locus tag="Madraxi_3"
    /note=Original Glimmer call @bp 1301 has strength 16.56; Genemark calls start at 1301
    /note=SSC: 1301-2092 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 4.09965E-124 GAP: 20 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.164, -4.85287563363746, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4569321,85.3282,4.09965E-124 SIF-HHPRED:  SIF-Syn: a minor tail protein sits in the same position in Jflix2; different gene though
    /note=start is not present in other members of pham; has HHPred hits to kallikrein and peptidase activity; has synteny but not homology with minor tail protein in same position in Jflix2; 
    /note=NOTE THAT THIS GENE IS ALSO FOUND IN DORIN AND FRANCESCA: gene 40 near larger genes that could be minor tail proteins even though they are in front of tape measure gene

CDS complement (2147 - 2263)
  /gene="4"
  /product="gp4"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_4"
    /note=Original Glimmer call @bp 2263 has strength 13.14; Genemark calls start at 2257
    /note=SSC: 2263-2147 CP: yes SCS: both-gl ST: NA BLAST-Start: [hypothetical protein RE0327_47950 [Prescottella equi]],,NCBI, q1:s20 92.1053% 1.68824E-5 GAP: 269 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.066, -4.530674820099623, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein RE0327_47950 [Prescottella equi]],,BCN76196,39.6825,1.68824E-5 SIF-HHPRED:  SIF-Syn: other CF genomes do not have reverse genes at beginning of genome;
    /note=small for a gene but CP good enough to keep gene; not much coding potential elsewhere

CDS 2533 - 3120
  /gene="5"
  /product="gp5"
  /function="minor tail protein"
  /locus tag="Madraxi_5"
    /note=Original Glimmer call @bp 2533 has strength 16.96; Genemark calls start at 2533
    /note=SSC: 2533-3120 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 98.9744% 1.02832E-115 GAP: 269 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.5052746077145835, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4569320,96.3731,1.02832E-115 SIF-HHPRED: Gp105; bacteriophage baseplate protein, VIRAL PROTEIN; HET: MSE; 2.38A {Listeria phage A511},,,6HHK_B,72.8205,98.2 SIF-Syn: same gene is near beginning of Shagrat genome, near other probable and larger minor tail proteins
    /note=top HHPred hit is baseplate protein, which is considered a tail protein (most distal part of the tail); same call in Shagrat (CF)

CDS complement (2357 - 2548)
  /gene="6"
  /product="gp6"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_6"
    /note=Original Glimmer call @bp 2548 has strength 3.43; Genemark calls start at 2449
    /note=SSC: 2548-2357 CP: yes SCS: both-gl ST: NA BLAST-Start:  GAP: 671 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.777, -5.2756940258553, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED: Conserved Hypothetical Protein MTH1598; MTH1598, hypothetical protein, structural genomics, Protein Structure Initiative, OCSP, NESG, beta-alpha-beta sandwich fold, PSI, Northeast Structural; NMR {Methanothermobacter thermautotrophicus} SCOP: d.208.1.1,,,1JW3_A,49.2063,54.9 SIF-Syn: the other CF genomes do not have reverse genes in the beginning of the genome
    /note=CP supports as real gene; orpham; not much coding potential elsewhere; 2nd start doesn`t capture CP even though RBS scores are better;

CDS 3220 - 4257
  /gene="7"
  /product="gp7"
  /function="minor tail protein"
  /locus tag="Madraxi_7"
    /note=Original Glimmer call @bp 3220 has strength 12.32; Genemark calls start at 3220
    /note=SSC: 3220-4257 CP: yes SCS: both ST: SS BLAST-Start: [peptidoglycan DD-metalloendopeptidase family protein [Prescottella equi]],,NCBI, q1:s1 100.0% 0.0 GAP: 671 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.968, -2.707694805492614, yes F: minor tail protein SIF-BLAST: ,,[peptidoglycan DD-metalloendopeptidase family protein [Prescottella equi]],,NKS33111,92.5287,0.0 SIF-HHPRED:  SIF-Syn: minor tail protein in similar position in Jflix2
    /note=Start 3220, Stop 4257; CP: good, yes; LO: no, but best option; Gap: 99; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: metalloendopeptidase, tail protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: minor tail protein; HHPred: possible resuscitation promotion factor, couple of hits for peptidase M-23
    /note=FUNCTION: possibly metallopeptidase, lysine motif, or lysosome-like domain, minor tail protein
    /note=
    /note=WE WILL LIKELY END UP SAYING MINOR TAIL PROTEIN, BUT WE NEED TO UNDERSTAND WHY THIS WAS THE CALL FOR JFLIX2. Called minor tail protein because has cell wall activity (i.e. peptidase)

CDS 4327 - 4521
  /gene="8"
  /product="gp8"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_8"
    /note=Original Glimmer call @bp 4327 has strength 5.42; Genemark calls start at 4327
    /note=SSC: 4327-4521 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 7.79976E-35 GAP: 69 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.995, -5.2064707039754765, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4569318,95.3125,7.79976E-35 SIF-HHPRED: Vacuolar-sorting protein SNF7; ESCRT, Snf7, Active, Core, PROTEIN TRANSPORT; 1.6A {Saccharomyces cerevisiae (strain ATCC 204508 / S288c)},,,5FD9_A,48.4375,36.7 SIF-Syn: this gene is in between minor tail proteins in Jflix2 also
    /note=Start 4237, Stop 4521; CP: good, yes; LO: yes; Gap: 69; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS 4532 - 6715
  /gene="9"
  /product="gp9"
  /function="minor tail protein"
  /locus tag="Madraxi_9"
    /note=Original Glimmer call @bp 4532 has strength 11.17; Genemark calls start at 4532
    /note=SSC: 4532-6715 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.477, -4.197870532213559, no F: minor tail protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33113,94.3604,0.0 SIF-HHPRED:  SIF-Syn: large gene in similar position in Jflix2 (which should have been called a minor tail protein probably)
    /note=Start 4532, Stop 6715; CP: good, yes; LO: yes; Gap: 10; RBS: best score; BLAST-start: Q1:T1; Starterator: orpham;
    /note=BLAST-function: hypothetical protein; Synteny: yes, orpham in similar place in Jflix2; Conserved domain: none; HHPred: glycosidic hydrolase hits

CDS 6717 - 7079
  /gene="10"
  /product="gp10"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_10"
    /note=Original Glimmer call @bp 6717 has strength 10.33; Genemark calls start at 6717
    /note=SSC: 6717-7079 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 9.0316E-73 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.144, -2.8035499123971284, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4569316,98.3471,9.0316E-73 SIF-HHPRED:  SIF-Syn: in Shagrat and Jflix2 in similar position
    /note=Start 6716, Stop 7079; CP: good, yes; LO: yes; Gap: 1; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits

CDS 7082 - 8635
  /gene="11"
  /product="gp11"
  /function="terminase"
  /locus tag="Madraxi_11"
    /note=Original Glimmer call @bp 7082 has strength 14.83; Genemark calls start at 7082
    /note=SSC: 7082-8635 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.873, -5.014101562099983, no F: terminase SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4613734,98.2592,0.0 SIF-HHPRED: Large terminase protein; DNA-packaging, Large terminase, Small terminase, nuclease fold, endonuclease, DNA, DNA-packaging motor, HYDROLASE; HET: SO4; 2.02A {Enterobacteria phage P22},,,4DKW_C,39.6518,98.9 SIF-Syn: 
    /note=Start 7082, Stop 8635; CP: good, yes; LO: yes; Gap: 2; RBS: best score; BLAST-start: Q1:T1; Starterator: called 92.5% of the time when present;
    /note=BLAST-function: terminase; Synteny: yes, terminase in similar place in Jflix2; Conserved domain: terminase-like protein; HHPred: terminase large subunit
    /note=FUNCTION: terminase, potentially large subunit
    /note=
    /note=MR: I would call terminase, there is no small subunit found in other sections, plus the match to the large subunit covers only 1/3 of the gene, and the gene matches with terminase units with anywhere from 60-70% coverage.

CDS 8649 - 8795
  /gene="12"
  /product="gp12"
  /function="membrane protein"
  /locus tag="Madraxi_12"
    /note=Original Glimmer call @bp 8649 has strength 14.33; Genemark calls start at 8649
    /note=SSC: 8649-8795 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 4.49779E-18 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.711, -3.243963255891538, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Rhodococcus phage Jflix2]],,WIF20500,91.6667,4.49779E-18 SIF-HHPRED:  SIF-Syn: 
    /note=Start 8649, Stop 8795; CP: good, yes; LO: yes; Gap: 13; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: membrane protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: major capsid protein; DeepTMHMM: 2 transmembrane regions
    /note=FUNCTION: membrane protein

CDS 8795 - 10309
  /gene="13"
  /product="gp13"
  /function="portal protein"
  /locus tag="Madraxi_13"
    /note=Original Glimmer call @bp 8795 has strength 17.51; Genemark calls start at 8795
    /note=SSC: 8795-10309 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.477, -3.8116689268127657, no F: portal protein SIF-BLAST: ,,[portal protein [Rhodococcus phage Jflix2]],,WIF20501,90.7816,0.0 SIF-HHPRED: Portal protein, gp7; Myophage, redox trigger, VIRUS; 4.5A {Agrobacterium phage Milano},,,8FXR_AJ,84.3254,100.0 SIF-Syn: yes!
    /note=Start 8795, Stop 10309; CP: good, yes; LO: yes; Gap: 0; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: portal protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: portal protein, phage portal; HHPred: portal protein
    /note=FUNCTION: portal protein

CDS 10316 - 12640
  /gene="14"
  /product="gp14"
  /function="major capsid and protease fusion protein"
  /locus tag="Madraxi_14"
    /note=Original Glimmer call @bp 10316 has strength 17.37; Genemark calls start at 10316
    /note=SSC: 10316-12640 CP: yes SCS: both ST: SS BLAST-Start: [phage major capsid protein [Prescottella equi] ],,NCBI, q1:s1 99.8708% 0.0 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.298, -2.305049668942183, yes F: major capsid and protease fusion protein SIF-BLAST: ,,[phage major capsid protein [Prescottella equi] ],,MBM4613724,94.2857,0.0 SIF-HHPRED: Major capsid protein; HK97-like fold, capsid size redirection, major capsid protein, VIRUS; 4.0A {Staphylococcus aureus},,,7RWZ_C,61.8863,100.0 SIF-Syn: 
    /note=Start 10316, Stop 12640; CP: good, yes; LO: yes; Gap: 6; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: major capsid and protease fusion protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: major capsid protein, caudovirus prohead serine protease; HHPred: major capsid protein
    /note=FUNCTION: major capsid and protease fusion protein

CDS 12660 - 12917
  /gene="15"
  /product="gp15"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_15"
    /note=Original Glimmer call @bp 12660 has strength 11.71; Genemark calls start at 12660
    /note=SSC: 12660-12917 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q7:s8 92.9412% 9.97701E-28 GAP: 19 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.91, -2.7653702713535186, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570264,75.8242,9.97701E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Start 12660, Stop 12917; CP: good, yes; LO: yes; Gap: 19; RBS: best score; BLAST-start: Q7:T8; Starterator: orpham;
    /note=BLAST-function: hypothetical protein; Synteny: orpham; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS 12994 - 13167
  /gene="16"
  /product="gp16"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_16"
    /note=Original Glimmer call @bp 12994 has strength 11.69; Genemark calls start at 12994
    /note=SSC: 12994-13167 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 3.79091E-30 GAP: 76 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.491, -5.875567920036636, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570265,94.7368,3.79091E-30 SIF-HHPRED:  SIF-Syn: 
    /note=Start 12994, Stop 13167; CP: passable, yes; LO: no, but other options return worse scores and add nothing; Gap: 76; RBS: best score; BLAST-start: Q1:T1; Starterator: orpham;
    /note=BLAST-function: hypothetical protein; Synteny: orpham; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS 13177 - 13794
  /gene="17"
  /product="gp17"
  /function="head-to-tail adaptor"
  /locus tag="Madraxi_17"
    /note=Original Glimmer call @bp 13177 has strength 12.74; Genemark calls start at 13171
    /note=SSC: 13177-13794 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 4.6792E-132 GAP: 9 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.92, -5.186767100221219, no F: head-to-tail adaptor SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570266,96.0784,4.6792E-132 SIF-HHPRED: Adaptor protein Rcc01688; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_D,98.0488,99.9 SIF-Syn: 
    /note=Start: 13177; Stop: 13794; Gap: 9; CP: Yes, start includes all CP; LO: Yes; RBS: Other starts has worse scores; BLAST-Start: Q1:T1 for all blast results; BLAST-function: head-to-tail adaptor/connector; Synteny: Shared gene in similar area, near start, shared with other CF phages; HHPred: significant hit for Adapter protein, including SPP1 gp15 and HK97 gp6; Starterator: This Gene is only found in cluster CF, but this start is the most common start for this gene within the 4 members of the cluster; FUNCTION: head-to-tail adaptor protein

CDS 13798 - 14229
  /gene="18"
  /product="gp18"
  /function="tail terminator"
  /locus tag="Madraxi_18"
    /note=Original Glimmer call @bp 13798 has strength 13.21; Genemark calls start at 13798
    /note=SSC: 13798-14229 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.25492E-93 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.133, -4.742415228075981, no F: tail terminator SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570267,95.8042,1.25492E-93 SIF-HHPRED: Terminator protein; Marine bacteriophage, Cryo-EM, Siphophage, Stopper protein, Terminator protein, Head-to-tail interface, VIRUS; 6.6A {Dinoroseobacter phage vB_DshS-R4C},,,8GTF_o,96.5035,99.3 SIF-Syn: 
    /note=Start: 13798; Stop: 14229; Gap = 3; CP: includes start; good; LO: Yes; RBS: Other scores were not good/shortened gene; BLAST-Start: q1:t1 in multiple genes; Starterator: start present in all members of pham; called 100% when present; Synteny: Yes shared with other members of the cluster around this number of gene, other ones closer to 13 or 14; HHPred: terminator protein, prob=99.5%, align=91.30%, significant hit including SPP1 gp17; FUNCTION: tail terminator
    /note=
    /note=*NOTE: The function results in HHPred could fit the criteria of a tail terminator protein, but it is unclear, should be looked at again and in consideration with it otherwise being a minor tail protein*

CDS 14251 - 14661
  /gene="19"
  /product="gp19"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_19"
    /note=Original Glimmer call @bp 14251 has strength 6.44; Genemark calls start at 14251
    /note=SSC: 14251-14661 CP: yes SCS: both ST: NA BLAST-Start:  GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.857, -4.968394496817548, no F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start: 14251; Stop: 14661; Gap: 20; CP: Yes, start includes all CP; LO: Yes; RBS: Other starts had worse scores; BLAST-Start: No Q1:T1; Synteny: Orpham; HHPred: no significant hits; Starterator: orpham; FUNCTION: hypothetical protein

CDS 14693 - 15040
  /gene="20"
  /product="gp20"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_20"
    /note=Original Glimmer call @bp 14693 has strength 13.48; Genemark calls start at 14693
    /note=SSC: 14693-15040 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_14 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 5.80813E-46 GAP: 31 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.583959800616441, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_14 [Rhodococcus phage Jflix2]],,WIF20505,83.9286,5.80813E-46 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 14693; Stop: 15040; Gap: 31; CP: includes start; good; LO: Yes; RBS: Other scores were not good/shortened gene; BLAST Result: multiple q1:t1; Starterator: start present in all members of pham; called 100% when present; HHPred: best hit not significant; prob= 81.5%, align= 82.81%; Synteny: JFlix2: 20, REQ1: 78, Shagrat: 21, yes; FUNCTION: Hypothetical protein

CDS 15040 - 15282
  /gene="21"
  /product="gp21"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_21"
    /note=Original Glimmer call @bp 15040 has strength 7.68; Genemark calls start at 15040
    /note=SSC: 15040-15282 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_15 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 7.06137E-20 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.777, -5.214737599913874, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_15 [Rhodococcus phage Jflix2]],,WIF20506,71.0843,7.06137E-20 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 15040; Stop: 15282; Gap: -1; CP: coding potential does not include start; LO: Yes; RBS: other starts had worse scores; BLAST-Start: Q1:T1; Blast-Function: hypothetical protein; Starterator: only one start called, in same pham, but aligns with our start; HHPred: hits were not significant; Synteny: Seen in two other CF cluster phages; FUNCTION: Hypothetical Protein

CDS 15288 - 15704
  /gene="22"
  /product="gp22"
  /function="major tail protein"
  /locus tag="Madraxi_22"
    /note=Original Glimmer call @bp 15288 has strength 14.35; Genemark calls start at 15288
    /note=SSC: 15288-15704 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 2.69456E-89 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.583959800616441, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Rhodococcus phage Jflix2]],,WIF20507,95.6522,2.69456E-89 SIF-HHPRED: Major tail protein; Marine bacteriophage, Cryo-EM, Siphophage, Baseplate, Megatron protein, Tail fibre protein, Distal tail protein, Hub protein, VIRAL; 4.5A {Dinoroseobacter phage vB_DshS-R4C},,,8GTC_F,96.3768,99.7 SIF-Syn: 
    /note=Start: 15288; Stop: 15704; Gap: 5; CP: includes start; good; LO: Yes; RBS: Other scores were not good/shortened gene; BLAST-Start: q1:t1 in multiple genes; BLAST-Function: Major tail protein; Starterator: start present in all members of pham called 100% when present; HHPred: tail protein; Synteny: Yes synteny; similar to JFlix gene 16; FUNCTION: Major tail protein

CDS 15718 - 16221
  /gene="23"
  /product="gp23"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_23"
    /note=Original Glimmer call @bp 15718 has strength 13.93; Genemark calls start at 15718
    /note=SSC: 15718-16221 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 7.43045E-115 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.316, -6.161291040112473, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570271,98.8024,7.43045E-115 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.12,69.4611,98.2 SIF-Syn: 
    /note=Start:15718; Stop:1622; Gap: 13; CP: Decent CP, start includes all CP; LO: Yes; RBS: Start #2 has better scores, but shortens the gene in half: Starterator: same start called in JFlix2 and REQ1; BLAST-Start: q1:t1 in three genes; BLAST-Function: Hypothetical protein; HHPred: not sig hit; Synteny: Seen in order CF phages, in similar area, but in genes 16; FUNCTION: hypothetical protein

CDS 16345 - 16743
  /gene="24"
  /product="gp24"
  /function="tail assembly chaperone"
  /locus tag="Madraxi_24"
    /note=Original Glimmer call @bp 16345 has strength 15.29; Genemark calls start at 16345
    /note=SSC: 16345-16743 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.03182E-82 GAP: 123 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.201, -2.8084998623841946, yes F: tail assembly chaperone SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570272,95.4545,1.03182E-82 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 16345; Stop: 16743; Gap: 23; CP: CP includes start; good; LO: Yes; RBS: Other scores were not good/shortened gene; BLAST-Start: Q1:T1 in multiple genes; BLAST-Function: hypothetical protein and tail assembly chaperone; Starterator: start present in 13/15 members of pham;  called in 10 of the 11 non-draft genes in the pham; HHPred: phage tail assembly chaperone; Synteny: Yes, similar to other genes in Jflix, Req1, and Shagrat; FUNCTION: tail assembly chaperone

CDS 16758 - 17039
  /gene="25"
  /product="gp25"
  /function="tail assembly chaperone (frameshift)"
  /locus tag="Madraxi_25"
    /note=Original Glimmer call @bp 16758 has strength 10.74; Genemark calls start at 16758
    /note=SSC: 16758-17039 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 3.11131E-53 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.711, -3.1816499351312086, yes F: tail assembly chaperone (frameshift) SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617993,93.5484,3.11131E-53 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 16758; Stop: 282; Gap: 14; CP: Good, start includes all CP; LO: Yes; RBS: Best start, the only other one which is comparable would shorten the gene significantly; BLAST-Start: Q1:T1; BLAST-Function: Hypothetical protein; Starterator: Only shared by other members of the cluster Shagrat and REQ1, REQ1 has a similar start but is not called, still seems promising based on other evidence; HHPred: no hits were significant; Synteny: Shared by other cluster members Shagrat and REQ1; FUNCTION: Hypothetical Protein
    /note=
    /note=*NOTE:Hits Jflix2 tail assembly chaperone(this gene is related to the one before it)*
    /note=MR: No known slippery sequence detected, likely not a translational frameshift although it is probably an assembly chaperone based off of blast and synteny
    /note=DeJong and MR: Found slippery sequence in both madraxi and shagrat that corresponds to the one found and correctly annotated in Jflix2, definitely can call this a translational frameshift. Coordinates are 16704 (T base is read twice, same as in Jflix2)

CDS 17119 - 21537
  /gene="26"
  /product="gp26"
  /function="tape measure protein"
  /locus tag="Madraxi_26"
    /note=Original Glimmer call @bp 17119 has strength 13.61; Genemark calls start at 17119
    /note=SSC: 17119-21537 CP: yes SCS: both ST: SS BLAST-Start: [tail length tape measure protein [Rhodococcus phage REQ1] ],,NCBI, q1:s1 100.0% 0.0 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.5052746077145835, yes F: tape measure protein SIF-BLAST: ,,[tail length tape measure protein [Rhodococcus phage REQ1] ],,YP_005087330,89.3573,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start 17119 Stop 21357
    /note=Pham 17047
    /note=Covers all CP
    /note=Yes LPO
    /note=Best ORF: Could stop one site sooner
    /note=79 bp Gap
    /note=RBS: Good scores for this start
    /note=Q1:T1
    /note=Starterator: do not have the "most annotated" start, found in 2 of 3 phams members, called 100%
    /note=>>> Keep start for now, but there are possibly better options.
    /note=
    /note=Blast: "tail length tape measure protien" in phages and "transglycosylase SLT domain-contianing-protien" in bacteria (E=0 but not always great alignment)
    /note=Phamerator: All CF have it as tape measure protien
    /note=Synteny: Very good syntent in all CF. Different areas of genome but next to lots of other similar genes in all CF
    /note=Conserved Domains: Many domains. None are necessary for determining function...
    /note=--- No TM domains ---
    /note=HHPred: Didn`t do cause DeJong said it wasn`t necessary 
    /note=Approved Funtion list: 
    /note=>>> Very confident this is the Tape measure protien cause its the longest one in the genome and matches very well with other CF phages

CDS 21604 - 25605
  /gene="27"
  /product="gp27"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_27"
    /note=Original Glimmer call @bp 21604 has strength 18.08; Genemark calls start at 21604
    /note=SSC: 21604-25605 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 0.0 GAP: 66 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.286, -4.150999100097377, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570274,97.6744,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start 21604 Stop 25605
    /note=Pham 25803
    /note=CP quality: Good
    /note=Yes, longest ORF, could stop one site sooner
    /note=66bp gap
    /note=RBS: Best score
    /note=BlastStart Q1:T1
    /note=Starterator: called one of most annotated start, found in start 1
    /note=>>> Keep start
    /note=
    /note=Blast function: hypothetical protien
    /note=Phamerator: Minor tail protien in all CF except REQ1
    /note=Synteny: very good synteny for all CF, always next to phams 17407 and 140206
    /note=--- No conserved Domains ---
    /note=--- No TM Domains ---
    /note=HHPred: (One hit with probablility of 90%, terrible E value) Carbohydrate enzyme stability/Endo 1-4 beta-xylanase
    /note=Approved List: 
    /note=>>> No good evidence to call the function, but possibly involved in tail formation

CDS 25619 - 26752
  /gene="28"
  /product="gp28"
  /function="minor tail protein"
  /locus tag="Madraxi_28"
    /note=Original Glimmer call @bp 25619 has strength 17.85; Genemark calls start at 25619
    /note=SSC: 25619-26752 CP: yes SCS: both ST: SS BLAST-Start: [DUF5047 domain-containing protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 0.0 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.442961286954254, yes F: minor tail protein SIF-BLAST: ,,[DUF5047 domain-containing protein [Prescottella equi] ],,MBM4570275,98.6737,0.0 SIF-HHPRED: Tail protein, 43 kDa; tail protein, structural genomics, PSI, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics, UNKNOWN FUNCTION; 2.1A {Neisseria meningitidis MC58} SCOP: b.106.1.1,,,3D37_B,88.3289,99.9 SIF-Syn: 
    /note=> start, stop: 25619, 26752
    /note=> gene#: 28 in both
    /note=> pham#: 140206
    /note=> phamMember#: 12 (all CF phages, singletons Footloose, Samy_Draft, Wollypog, and phiAsp2, BA VWB, and BL phages AbbeyMikolon, Nesbitt, and Rowa)
    /note=> cpQuality: Good (sizeable gap around 25800)
    /note=> longestORF: Yes
    /note=> bestORF: Coil stop 2 sites shorter - DO YOU MEAN COULD CHOOSE 2 STARTS SHORTER? SEEMS LIKE EVIDENCE IS SUGGESTING KEEPING THIS START
    /note=> gap/overlap: 13n gap
    /note=> RBS: best score 
    /note=> BLAST Start: Q1:T1
    /note=> BLAST Function: domain containing protein, minor tail protein, tail protein 
    /note=> Starterator: does not have most annotated, found start 41, also found in Jflix2
    /note=>>> Keep start, could possibly start one sooner  -- WHY?
    /note=
    /note=BLAST Function: domain containing protein, minor tail protein, tail protein 
    /note=Phamerator: "minor tail protien" in Shagrat and JFlix2
    /note=Synteny: Vary good synteny; consistent with other "tail protien genes" in CF
    /note=Conserved Domain: unknown function, "N-terminal of uncharacterized protiens and peptidases
    /note=--- NO TM domains ---
    /note=HHPred: Strong hits to tail protien, "baseplate hub", and "secretion system"
    /note=Approved Funtion List: 
    /note=>>> Mostl likely a tail protien involved near the baseplate of the tail.
    /note=
    /note=SAME HERE; MINOR TAIL PROTEINS ARE USUALLY FOUND RIGHT HERE

CDS 26749 - 27633
  /gene="29"
  /product="gp29"
  /function="minor tail protein"
  /locus tag="Madraxi_29"
    /note=Original Glimmer call @bp 26791 has strength 14.34; Genemark calls start at 26749
    /note=SSC: 26749-27633 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.764, -3.0713502170045657, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33131,94.898,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=> start, stop: 26791, 27633
    /note=> gene#: 29 (in both)
    /note=> pham#:20121
    /note=> phamMember#: 4 (all CF phages)
    /note=> cpQuality: Yes (covers all cp)
    /note=> longestORF: Yes
    /note=> bestORF: Yes - DOES THIS MEAN BEST START CONSIDERING ALL THE EVIDENCE OR IS THIS A SPECIFIC PIECE OF EVIDENCE BEING LISTED? 
    /note=> gap/overlap: 39n gap
    /note=> RBS: Best Score 
    /note=> BLAST Start: 1st Q23:T37, many other hits are more or less as short 
    /note=> Starterator: suggests Jflix and REQ1 start at start 1 which is more lengthy than Madraxi, but Madraxi can be lengthened to start 2 making it more similar to the others
    /note=>>> Keep start 
    /note=DID YOU CHANGE THE START? THE BEST RBS SCORE IS ACTUALLY START 1 - COMBINED WITH STARTERATOR AND BLAST SUGGESTING A LONGER START, START 1 MAY BE BEST?
    /note=
    /note=> Blast Funtion: "Hypothetical protien" and "minor tail protien" (in phages) most common
    /note=> Phamerator: Minor Tail protien (Shagrat, JFlix); Only found in  CF
    /note=> Synteny: Good syntney, follows 142465 with other minor tail protiens within CF
    /note=> Conserved Domain: N/A
    /note=> Transmembrane Domain: N/A
    /note=> HHPred: Not the best hit, but top was "Gp15 protien receptor binding protien" (E=0.000035)
    /note=> Approved Funtion List: 
    /note=>>> Phamerator info says somethinng about this being a minor tail protien, but nothing conclusive

CDS 27765 - 28058
  /gene="30"
  /product="gp30"
  /function="endonuclease VII"
  /locus tag="Madraxi_30"
    /note=Original Glimmer call @bp 27765 has strength 4.8; Genemark calls start at 27630
    /note=SSC: 27765-28058 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 8.64187E-58 GAP: 131 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.479, -4.972273674200951, no F: endonuclease VII SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33132,95.8763,8.64187E-58 SIF-HHPRED: RECOMBINATION ENDONUCLEASE VII; ENDONUCLEASE, RESOLVASE, HOLLIDAY JUNCTION, DNASE; HET: SO4; 1.32A {BACTERIOPHAGE T4} SCOP: a.140.4.1, d.4.1.5,,,1E7L_A,90.7216,99.8 SIF-Syn: 
    /note=> start, stop: 27765, 28058
    /note=> pham#:138552
    /note=> cpQuality: Moderate, covers all cp but cp is limited
    /note=> longestORF: Yes, too long
    /note=> bestORF: No, could stop way sooner and still cover all cp
    /note=> gap/overlap: 66n overlap
    /note=> RBS: couple other good RBS, but chosen start also good RBS 
    /note=> BLAST Start: Q1:T1
    /note=> Starterator: start 10, found in 5 out of 17, "most annotated" but not called 
    /note=>>> could start one site sooner, but keeping start
    /note=
    /note=> Blast Funtion: "Hypothetical protien", Endonuclease
    /note=> Phamerator: (gene #30) 
    /note=> Synteny: Only found in REQ1, at the end of the gene but with other tail protien sections
    /note=> Conserved Domain: recombination endonuclease VII; Provisional; and Recombination endonuclease VII.
    /note=> Transmembrane Domain: N/A
    /note=> HHPred: Many 99%+ hits on Recombination endonuclease VII; lots of mentions of being used in CRISPR!
    /note=> Approved Funtion List: 1 approved match
    /note=>>> Good evidence to be a possible endonuclease gene
    /note=WHAT ARE THE CRITERIA IN THE OFFICIAL FUNCTION LIST FOR DIFFERENTIATING AMONG THE DIFFERENT KINDS OF ENDONUCLEASES?

CDS 28062 - 29615
  /gene="31"
  /product="gp31"
  /function="endolysin"
  /locus tag="Madraxi_31"
    /note=Original Glimmer call @bp 28062 has strength 13.54; Genemark calls start at 28062
    /note=SSC: 28062-29615 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q2:s1 99.8066% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.673, -3.6131959421438604, yes F: endolysin SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570279,98.0507,0.0 SIF-HHPRED: Protein PS1; Mycoloyltransferase, TRANSFERASE, Mycolic acid, cell wall; HET: ACT, MSE; 2.796A {Corynebacterium glutamicum},,,6SX4_CCC,41.0058,99.1 SIF-Syn: 
    /note=> start, stop: 28062-29615
    /note=> Pham#:141986 (gene 31)
    /note=> cpQuality: Good, covers all cp
    /note=> longestORF: Yes
    /note=> bestORF: Yes
    /note=> gap/overlap: 3n gap
    /note=> RBS: best score 
    /note=> BLAST Start: Q2:T1
    /note=> Starterator: called one of the most annotated, found in start 2 along with Jflix2 and REQ1
    /note=>>> Keep start
    /note=
    /note=> Blast Funtion: "hypothetical protien"
    /note=> Phamerator: No good funtion, only found in one other singleton "Trogglehumper" where it is a "endolysin" gene
    /note=> Synteny: Gene seems to be swapped into place with Pham138266 (lysin gene) in between other genes with synteny within CF
    /note=> Conserved Domain: 6 smaller conserved domains: seem to do something with "peptidoglycan" "and "transglycolase"
    /note=> Transmembrane Domain: N/A
    /note=> HHPred: 98%+ Hits on Alanine Amidase and Endolysin
    /note=> Approved Funtion List: N/A
    /note=>>> Best, but not strong guess would be a endolysin protien or alanin amidase because its the best matches. Need to compare the conserved domains agaisnt the HHpred functions. Also this gene appears to be swapped in position with another gene that is supposedly an endolysin gene in phamerator. 
    /note=ENDOLYSIN (OF A DIFFERENT TYPE) SITS IN THE SAME POSITION IN JFLIX2
    /note=
    /note=MR: I would agree with this call due to no other lysin being found and the match with the N-acetylmuramoyl-L-alanine amidase domain that is typically found in lysins
    /note=RDJ: Agree, it has that domain but since there is not another endolysin in the genome, this should not be listed as just the domain. Also, the size of the gene and the presence of other domains suggest that this is the whole endolysin gene.

CDS 29647 - 29919
  /gene="32"
  /product="gp32"
  /function="holin"
  /locus tag="Madraxi_32"
    /note=Original Glimmer call @bp 29647 has strength 16.89; Genemark calls start at 29647
    /note=SSC: 29647-29919 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 1.69546E-42 GAP: 31 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.064, -2.442961286954254, yes F: holin SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,MBM4570280,87.9121,1.69546E-42 SIF-HHPRED: Phage_holin_1 ; Bacteriophage holin,,,PF04531.17,78.8889,92.3 SIF-Syn: 
    /note=> start, stop: 29647-29919
    /note=>Pham#138743; only found in CF
    /note=> cpQuality: Good, covers most cp
    /note=> longestORF: No
    /note=> bestORF: Starts sooner, unclear with cutoff on Genemark
    /note=> gap/overlap: 31n gap
    /note=> RBS: other good RBS, but chosen start good 
    /note=> BLAST Start: Q1:T1
    /note=> Starterator: does not have most annotated, found in start 33
    /note=>>> Keep Start
    /note=
    /note=
    /note=> Blast Funtion: "hypothetical protien"
    /note=> Phamerator: "holin" in Jflix2
    /note=> Synteny: decent. Matches with the block pattern but seems to be at the end of it.
    /note=> Conserved Domain: N/A
    /note=> Transmembrane Domain: has 2 membrane domains
    /note=> HHPred: 4 Hits on mycobacterium phage Holin
    /note=> Approved Funtion List: N/A
    /note=>>> evidence for Holin protien but not much to call off of.
    /note=OFFICIAL FUNCTION LIST CRITERIA FOR HOLIN. JFLIX2 HAS HOLIN IN SAME LOCATION

CDS 29919 - 30368
  /gene="33"
  /product="gp33"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_33"
    /note=Original Glimmer call @bp 29919 has strength 13.17; Genemark calls start at 29919
    /note=SSC: 29919-30368 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q15:s1 90.604% 3.14825E-86 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.438, -5.985256925638024, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617965,98.5185,3.14825E-86 SIF-HHPRED:  SIF-Syn: 
    /note=> start, stop: 29919-30368
    /note=> Pham#140969 (233 others)
    /note=> cpQuality: Good
    /note=> longestORF: No (earlier start would have huge overlap)
    /note=> bestORF: Yes (covers all important cp)
    /note=> gap/overlap: 1n overlap
    /note=> RBS: other good RBS, but chosen start good 
    /note=> BLAST Start: Q15:T1, many other hits are more or less as short 
    /note=> Starterator: NA, orpham
    /note=
    /note=> Blast Funtion: "hypothetical protien "
    /note=> Phamerator: function not found
    /note=> Synteny: Not the greatest, not much correlation within CF. Seems to be tacked on to the end of some forward genes but other phages switch to reverse genes. Similar to a couple nearby reverse genes in Jflix2
    /note=> Conserved Domain: N/A
    /note=> Transmembrane Domain: N/A
    /note=> HHPred: no good hits
    /note=> Approved Funtion List: N/A
    /note=>>> No good info or evidence for function

CDS 30365 - 30688
  /gene="34"
  /product="gp34"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_34"
    /note=Original Glimmer call @bp 30365 has strength 10.0; Genemark calls start at 30365
    /note=SSC: 30365-30688 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.32509E-67 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.985, -5.0518135660984065, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617964,100.0,1.32509E-67 SIF-HHPRED:  SIF-Syn: 
    /note=> start, stop: 30365-30688
    /note=> pham 139272, ORPham
    /note=> cpQuality: Good (covers most cp)
    /note=> longestORF: No
    /note=> bestORF: Unsure, an earlier start to cover slightly more cp would have more overlap
    /note=> gap/overlap: 2n overlap
    /note=> RBS: Not the best start
    /note=> BLAST Start: Q1:T1
    /note=> Starterator: NA
    /note=>>> Keep start for now, but there is a slightly better
    /note=
    /note=> Blast Funtion: "hypothetical protien"
    /note=> Phamerator: N/A
    /note=> Synteny: tacked on to the end of the forward genes like many of the other phages. this and gene 34 seem to be replacing other genes in this position for other phages
    /note=> Conserved Domain: N/A
    /note=> Transmembrane Domain: N/A
    /note=> HHPred: 96%+ Hits on cell division protein and cell membrane protein
    /note=> Approved Funtion List: N/A
    /note=>>> Not much info except for HHPred hits. Can`t really call

CDS complement (30775 - 30930)
  /gene="35"
  /product="gp35"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_35"
    /note=Original Glimmer call @bp 30930 has strength 4.18; Genemark calls start at 30930
    /note=SSC: 30930-30775 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s5 98.0392% 7.93783E-20 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.004, -4.80230064365488, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,WP_175278746,78.1818,7.93783E-20 SIF-HHPRED: g.41.9.0 (L:) automated matches {Sus scrofa [TaxId: 9825]} | CLASS: Small proteins, FOLD: Rubredoxin-like, SUPFAM: RNA polymerase subunits, FAM: automated matches,,,SCOP_d7b7ul_,82.3529,97.2 SIF-Syn: 
    /note=Gap: -4
    /note=Completely covers CP: Yes
    /note=Longest Possible ORF: No, but longer would provide significant overlap w. gene 37
    /note=SD score: Best score of the options. Though shorter than the other choice, as mentioned above this would be too much overlap. 
    /note=BLAST-start: Rhodococcus equi, 72% identity, e-value=8.1E–20, Q1:T5 
    /note=Starterator: NA
    /note=Function: Hypothetical protein
    /note=Synteny: NA
    /note=HHPred: closest match was “DUF1451,” however likelihood is very low (e value > 0)
    /note=Conserved Domain: NA
    /note=TMHMM: NA

CDS complement (30927 - 31277)
  /gene="36"
  /product="gp36"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_36"
    /note=Original Glimmer call @bp 31277 has strength 15.42; Genemark calls start at 31277
    /note=SSC: 31277-30927 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 96.5517% 7.85576E-61 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.789, -3.099505556436281, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617962,85.3448,7.85576E-61 SIF-HHPRED:  SIF-Syn: 
    /note=CP: Yes, good cp 
    /note=LP ORF: No, but longer would mean massive overlap w. Gene 38. 
    /note=Gap: 11
    /note=RBS: Yes, other good scores but chosen start has best RBS score.
    /note=BLAST-Start: Q1:T1
    /note=Starterator: start found in all 8 of pham, called 7/8 times. Called twice each in Madraxi and Jflix2.
    /note=BLAST-Funtion: A couple of blast hits in phages and bacteria - Hypothetical protein: no function in phamerator.
    /note=Phamerator Function: NA
    /note=Synteny: Gene not in same location in Jflix2&Shagrat (not same number, but similar area?)
    /note=HHPred: no good hits
    /note=TMHMM: no good calls
    /note=
    /note=MR: I would call this a hypothetical protein as well, although it is located in the syntenic region of minor tail proteins.

CDS complement (31289 - 31438)
  /gene="37"
  /product="gp37"
  /function="membrane protein"
  /locus tag="Madraxi_37"
    /note=Original Glimmer call @bp 31438 has strength 8.58; Genemark calls start at 31438
    /note=SSC: 31438-31289 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 1.88377E-25 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.775, -5.790822999612066, no F: membrane protein SIF-BLAST: ,,[membrane protein [Rhodococcus phage Jflix2]],,WIF20522,97.9592,1.88377E-25 SIF-HHPRED:  SIF-Syn: 
    /note=CP: Yes, good cp 
    /note=LP ORF: No, but longer would mean massive overlap w. Gene 38. 
    /note=Gap: 11
    /note=RBS: Yes, other good scores but chosen start has best RBS score.
    /note=BLAST-Start: Q1:T1
    /note=Starterator: start found in all 8 of pham, called 7/8 times. Called twice each in Madraxi and Jflix2.
    /note=BLAST-Funtion: A couple of blast hits in phages and bacteria - Hypothetical protein: no function in phamerator.
    /note=Phamerator Function: NA
    /note=Synteny: Gene not in same location in Jflix2&Shagrat (not same number, but similar area?)
    /note=HHPred: no good hits
    /note=TMHMM: no good calls
    /note=
    /note=MR:Make sure your notes contain the correct gap, and reason for the start (I`m guessing its due to the length but make sure you note it) Membrane protein looks like a good call to me

CDS complement (31442 - 31717)
  /gene="38"
  /product="gp38"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_38"
    /note=Original Glimmer call @bp 31717 has strength 12.73; Genemark calls start at 31717
    /note=SSC: 31717-31442 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_32 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 2.21976E-43 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.144, -2.356391881054909, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_32 [Rhodococcus phage Jflix2]],,WIF20523,83.5165,2.21976E-43 SIF-HHPRED:  SIF-Syn: 
    /note=CP: Good CP
    /note=ORF: not longest ORF, there are 3 other ORFs that are longer but have worse final scores.
    /note=Gap: 11
    /note=RBS Scores: Best score! 
    /note=BLAST-Start: Hypothetical protein SEA_JFLIX_32, Rhodococcus equi, 74.73%, e-value=2.3e-43 Q1:T1
    /note=Starterator: Start found in Jflix2 as well, both called it. 
    /note=Synteny: Found in same gene sequence as Jflix2, but not exactly lined up in gene #. 
    /note=HHPred: no good hits
    /note=CD/TMHMM: NA

CDS complement (31729 - 32109)
  /gene="39"
  /product="gp39"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_39"
    /note=Original Glimmer call @bp 32109 has strength 7.66; Genemark calls start at 32109
    /note=SSC: 32109-31729 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_33 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 6.91773E-86 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.625, -4.189437364676697, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_33 [Rhodococcus phage Jflix2]],,WIF20524,99.2064,6.91773E-86 SIF-HHPRED:  SIF-Syn: 
    /note=CP: Good CP
    /note=ORF: not longest possible ORF- rbs shoes one longer but overlaps with the next gene
    /note=Gap: 2
    /note=RBS Scores: Z-value= 2.620 Final Score=-4.189
    /note=BLAST-Start: Q1:T1
    /note=BLAST-Function: hypothetical protein SEA_JFLIX_33, Rhodococcus equi
    /note=Starterator: does not have most annotated start, chosen start also called for Jflix2.
    /note=Function: Hypothetical protein
    /note=Synteny: NA
    /note=HHPred: inconclusive/unreliable- closest hit was “DUF6083”, but %prob= 87.85%. Many of the other hits were ribosomal proteins but not enough evidence to support those
    /note=CD: NA; 
    /note=TMHMM: none

CDS complement (32112 - 32336)
  /gene="40"
  /product="gp40"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_40"
    /note=Original Glimmer call @bp 32336 has strength 10.12; Genemark calls start at 32336
    /note=SSC: 32336-32112 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 2.4366E-42 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.652, -3.368377069717189, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617960,95.9459,2.4366E-42 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 32336 Stop:32112 REV
    /note=CP: Good CP
    /note=ORF: not longest possible ORF- rbs shows one that is longer but overlaps with the next gene
    /note=Gap: -1, overlap of 1
    /note=RBS Scores: Z-value= 2.647; Final Score= -3.368
    /note=BLAST-Start: Q1:T1
    /note=BLAST-Function: Hypothetical protein, Prescottella equi
    /note=Starterator: NA
    /note=Function: Hypothetical Protein
    /note=Synteny: NA
    /note=HHPred: inconclusive/unreliable- closest hit was “DUF3197”, but %pob= 72.28%
    /note=CD: none
    /note=TMHMM: none

CDS complement (32336 - 32668)
  /gene="41"
  /product="gp41"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_41"
    /note=Original Glimmer call @bp 32668 has strength 15.57; Genemark calls start at 32668
    /note=SSC: 32668-32336 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 8.64376E-68 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.058, -3.7612584775992985, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617959,95.4545,8.64376E-68 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 32668 Stop: 32336 REV
    /note=CP: Good CP
    /note=ORF: Yes, longest ORF
    /note=Gap: 6
    /note=RBS scores: Z-value=3.056 (better z-scores were smaller genes); Final Score=-3.761
    /note=BLAST-Start: hypothetical protein, Prescottella equi, 92.73%, e-value=0, q1:t1
    /note=Starterator: madraxi, Jflix2, & Shagrat called MA start
    /note=Function: Hypothetical protein
    /note=Synteny: Found in same gene sequence as Jflix2&Shagrat, but not exactly lined up in gene #. 
    /note=HHPred: inconclusive/unreliable; closest hit was “DUF1697” but %prob= 48.12%
    /note=CD: None
    /note=TMHMM: none

CDS complement (32675 - 32917)
  /gene="42"
  /product="gp42"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_42"
    /note=Original Glimmer call @bp 32905 has strength 4.81; Genemark calls start at 32917
    /note=SSC: 32917-32675 CP: no SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_35 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 2.01558E-42 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.91, -3.8666016581442175, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_35 [Rhodococcus phage Jflix2]],,WIF20526,93.75,2.01558E-42 SIF-HHPRED:  SIF-Syn: 
    /note=Start 32905, Stop 32675; LO:No; Gap:12; CP:good, yes; RBS:one binding site with better values and longer gene length, brings gap to 0; 
    /note=Starterator:Does not match start used by other CF phages; BLAST-start: q1:t5. indicates that genes in other phages use a start that lines up with the start that has better RBS values.
    /note=Start changed?: YES, 32917; 
    /note=BLAST Function:hypothetical protein; Synteny:No;
    /note=HHPred:No good results.
    /note=Function:Unknown
    /note=
    /note=START CHANGE: Old Start:32905, New Start:32917; Old Gap:12, New Gap:0; BLAST: q1:t5 in other CF phages indicates that new start matches better than old start; 
    /note=Starterator:Old Madraxi start did not match starts used by other CF phages;
    /note=Overall, this evidence indicates that a start at 32917 should be used

CDS complement (32918 - 33358)
  /gene="43"
  /product="gp43"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_43"
    /note=Original Glimmer call @bp 33358 has strength 13.23; Genemark calls start at 33358
    /note=SSC: 33358-32918 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 3.66523E-84 GAP: 53 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.652, -3.95820260462814, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617958,93.7931,3.66523E-84 SIF-HHPRED: DUF3846 ; Domain of unknown function (DUF3846),,,PF12957.11,80.137,99.5 SIF-Syn: 
    /note=Start 33358; Stop 32918; Gap: 53; CP: good, yes; LO: yes; RBS: other good scores, but chosen start also good and longest;
    /note=BLAST-Start: first and third hit Q1:T1, other hits are shorter;  Starterator: Only 3 members of pham, start called by 2;
    /note=Start changed?: NO
    /note=BLAST-function: hypothetical protein; Synteny: Jflix has gene in similar position;
    /note=HHPRED: All hits unknown function;
    /note=FUNCTION: Unknown

CDS complement (33412 - 33621)
  /gene="44"
  /product="gp44"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_44"
    /note=Original Glimmer call @bp 33621 has strength 10.17; Genemark calls start at 33621
    /note=SSC: 33621-33412 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 5.89569E-38 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.816, -2.9625409806968013, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617957,97.1014,5.89569E-38 SIF-HHPRED:  SIF-Syn: 
    /note=Start 33621; Stop 33412; Overlap: 8; CP: good, cp not fully covered (BAD!); LO: yes; RBS: best score, similar scores shorten length;
    /note=BLAST-Start: first 5 hits Q1:T1; Starterator: Other CF phages have same start called, start present in all members;
    /note=Start changed?: NO
    /note=BLAST-function: hypothetical protein for all hits; Synteny: JFlix and Shagrat (CF) had gene in similar area
    /note=HHPRED: No good hits
    /note=Function: Unknown

CDS complement (33614 - 34072)
  /gene="45"
  /product="gp45"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_45"
    /note=Original Glimmer call @bp 34072 has strength 11.18; Genemark calls start at 34072
    /note=SSC: 34072-33614 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 2.46457E-100 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.477, -3.75071250087134, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33145,98.0392,2.46457E-100 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 34073, Stop: 33613; Overlap 1; CP: Good, yes; LO: No; RBS: best scores!;
    /note=BLAST-Start: q1:t1; Starterator: Matches starts of other similar phages; 
    /note=Start changed?: NO;
    /note=BLAST-Function: Hypothetical Protein (R. equi); Synteny: Yes, Jflix2; 
    /note=HHPred: Data not significant;
    /note=Function: Unknown;

CDS complement (34072 - 34410)
  /gene="46"
  /product="gp46"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_46"
    /note=Original Glimmer call @bp 34410 has strength 12.65; Genemark calls start at 34410
    /note=SSC: 34410-34072 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_39 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 5.90189E-56 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.398, -3.978223840957539, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_39 [Rhodococcus phage Jflix2]],,WIF20530,89.4737,5.90189E-56 SIF-HHPRED:  SIF-Syn: 
    /note=Start 34410; Stop 34072; Gap: 1 CP: good, yes; LO: no; RBS: best score!;
    /note=Blast-Start: First and third hit Q1:T1, second hit Q4:T4; Starterator: Pham only has CF members, all phages call same start;
    /note=Start changed?: NO;
    /note=Blast-function: hypothetical protein for all hits; Synteny: JFlix had gene in similar area;
    /note=HHPRED: No hits
    /note=Function: Unknown

CDS complement (34412 - 34561)
  /gene="47"
  /product="gp47"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_47"
    /note=Original Glimmer call @bp 34561 has strength 13.08; Genemark calls start at 34561
    /note=SSC: 34561-34412 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 97.9592% 9.4285E-24 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.309, -1.9310779259753799, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617953,94.0,9.4285E-24 SIF-HHPRED:  SIF-Syn: 
    /note=Start 34561, Stop 34412; CP:good, does not contain all CP; LO:yes; Gap:10; RBS:best score!; 
    /note=BLAST-Start: one hit, q1:t1; ST: start is only found in Jflix2 and is used;
    /note=Start changed?:NO
    /note=BLAST-function: hypothetical protein from R. equi; Synteny:Jflix2 has same orpham at gen 40;
    /note=HHPRED:No good matches;
    /note=FUNCTION: Unknown

CDS complement (34572 - 34991)
  /gene="48"
  /product="gp48"
  /function="membrane protein"
  /locus tag="Madraxi_48"
    /note=Original Glimmer call @bp 34991 has strength 13.77; Genemark calls start at 34991
    /note=SSC: 34991-34572 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.38499E-86 GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.5052746077145835, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617952,94.2446,1.38499E-86 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 34991, Stop: 34572; REV gene, good CP; LO: yes; Gap: 16; RBS:best score! 
    /note=BLAST:alignment is q1:t1 for the first 2 results, but they worsen with the 3rd, lengths vary as well; Starterator: 100% used start; 
    /note=Start changed?: NO;
    /note=Blast function: hypothetical protein, protein kinase, membrane protein; 
    /note=Synteny: very similar location to Jflix2 but different from REQ1; 
    /note=HHPred:Nothing significant; 
    /note=DeepTMHMM:Significant results, appears to be a transmembrane protein;
    /note=FUNCTION: membrane protein;
    /note=
    /note=MR: Don`t forget to add pieces of evidence to strengthen your point. I agree that it should me a membrane protein, but also note that the zone of overlap with conflicting functions is mostly the transmembrane domain

CDS complement (35008 - 35232)
  /gene="49"
  /product="gp49"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_49"
    /note=Original Glimmer call @bp 35232 has strength 12.42; Genemark calls start at 35232
    /note=SSC: 35232-35008 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_42 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 1.0008E-36 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.703, -3.5505148060375804, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_42 [Rhodococcus phage Jflix2]],,WIF20533,86.4865,1.0008E-36 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 35232, Stop: 35008, CP is good, REV gene, LO: no; RBS:best score!;
    /note=BLAST: q1:t1 for all 4 blast results, all blast results are within 1bp in length; Starterator: confirms start location; 
    /note=Start changed?:NO;
    /note=Blast Function is only hypothetical protein; Synteny: location is similar to Jflix2 but very different from REQ1;
    /note=HHPred offered no viable alternatives;
    /note=FUNCTION: Unknown;

CDS complement (35238 - 35432)
  /gene="50"
  /product="gp50"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_50"
    /note=Original Glimmer call @bp 35432 has strength 9.3; Genemark calls start at 35432
    /note=SSC: 35432-35238 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 5.86194E-35 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.878, -4.9859951363913995, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617950,98.4375,5.86194E-35 SIF-HHPRED:  SIF-Syn: 
    /note=Start 35432, Stop 35238; CP:good, yes; LO:yes; Overlap:4; RBS:only one score, good values; 
    /note=BLAST-Start: 3 hits, R. equi bacteria and phages, all have q1:t1; ST: start is found in Jflix2 and REQ1 and is used in both;
    /note=Start change?: NO
    /note=BLAST-function: hypothetical protein; Synteny:same orpham in Jflix2 at 44 and REQ1 at 14; 
    /note=HHPRED:No good matches;
    /note=FUNCTION: Unknown

CDS complement (35429 - 35596)
  /gene="51"
  /product="gp51"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_51"
    /note=Original Glimmer call @bp 35596 has strength 9.82; Genemark calls start at 35596
    /note=SSC: 35596-35429 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_45 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 4.16318E-28 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.222, -2.4634880269616195, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_45 [Rhodococcus phage Jflix2]],,WIF20536,96.3636,4.16318E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Start 35596, Stop 35429; CP: good, yes; LO: no, but longest caused overlap; Gap: 5; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS complement (35602 - 35883)
  /gene="52"
  /product="gp52"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_52"
    /note=Original Glimmer call @bp 35883 has strength 14.89; Genemark calls start at 35883
    /note=SSC: 35883-35602 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 1.22005E-54 GAP: 89 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33152,94.6237,1.22005E-54 SIF-HHPRED:  SIF-Syn: 
    /note=Start 35883, Stop 35602; CP: good, yes; LO: yes; Gap: 89; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS complement (35973 - 37040)
  /gene="53"
  /product="gp53"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_53"
    /note=Original Glimmer call @bp 37049 has strength 14.52; Genemark calls start at 37040
    /note=SSC: 37040-35973 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_48 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 0.0 GAP: 34 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.916, -5.196364068324326, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_48 [Rhodococcus phage Jflix2]],,WIF20539,100.0,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start 37040, original 3` end was 37049, changed because it is called more often in Starterator and returns better scores, Stop 35973; CP: good, yes; LO: no, but longer orfs return worse scores; Gap: 34, original gap was 25; RBS: best score; BLAST-start: Q4:T1; Starterator: called 50% of the time when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: plasmid-like protein found in myobacterium phage genomes, unknown function; HHPred: both hits have unknown domain
    /note=FUNCTION: hypothetical protein

CDS complement (37075 - 37404)
  /gene="54"
  /product="gp54"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_54"
    /note=Original Glimmer call @bp 37404 has strength 10.1; Genemark calls start at 37404
    /note=SSC: 37404-37075 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.63838E-53 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.249, -4.289050940760858, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617947,81.5789,1.63838E-53 SIF-HHPRED:  SIF-Syn: 
    /note=Start 37404, Stop 37075; CP: good, yes; LO: no, but has best scores and least overlap - look into lengthening if gene 56 is deleted; Gap: 25; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS complement (37419 - 37613)
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_55"
    /note=Original Glimmer call @bp 37613 has strength 16.37; Genemark calls start at 37613
    /note=SSC: 37613-37419 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein RoPhREQ1_gp21 [Rhodococcus phage REQ1] ],,NCBI, q1:s1 100.0% 9.33966E-39 GAP: 539 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.757, -3.4367891292046218, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein RoPhREQ1_gp21 [Rhodococcus phage REQ1] ],,YP_005087273,100.0,9.33966E-39 SIF-HHPRED:  SIF-Syn: 
    /note=Start 37613, Stop 37419; CP: good, yes; LO: no, longer orfs yield worse scores; Gap: 539; RBS: best score; BLAST-start: Q1:T1; Starterator: called 75% of the time when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: uncharacterized protein
    /note=FUNCTION: hypothetical protein

CDS 38153 - 39541
  /gene="56"
  /product="gp56"
  /function="serine integrase"
  /locus tag="Madraxi_56"
    /note=Original Glimmer call @bp 38282 has strength 13.15; Genemark calls start at 38153
    /note=SSC: 38153-39541 CP: yes SCS: both-gm ST: NI BLAST-Start: [recombinase family protein [Prescottella equi]],,NCBI, q1:s1 100.0% 0.0 GAP: 539 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.698, -7.392277536015967, no F: serine integrase SIF-BLAST: ,,[recombinase family protein [Prescottella equi]],,MBM4617945,96.3203,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=Start 38153, changed from 38282 because it did not contain all of the coding potential, Stop 39541; CP: good, yes; LO: no, but no cp added; Gap: 2; RBS: best score; BLAST-start: Q1:T27; Starterator: difficult to identify for changed start;
    /note=BLAST-function: serine integrase; Synteny: no; Conserved domain: serine recombinase; HHPred: serine integrase, integrase/serine recombinase
    /note=FUNCTION: serine integrase

CDS complement (38105 - 38281)
  /gene="57"
  /product="gp57"
  /function="(delete)"
  /locus tag="Madraxi_57"
    /note=Original Glimmer call @bp 38281 has strength 3.87
    /note=SSC: 38281-38105 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: 1324 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.518, -6.02875577836303, no F: (delete) SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start 38281, Stop 38105; Gap: -128; CP: none; BLAST-start: no calls;  DeepTMHMM: signal domain and outside membrane
    /note=FUNCTION: We recommend this gene for deletion due to no BLAST matches, no coding potential, massive overlap, and only Glimmer called for it.
    /note=
    /note=MR: I cannot see the coding potential but it seems like it should be deleted if there is none

CDS complement (39606 - 40160)
  /gene="58"
  /product="gp58"
  /function="immunity repressor"
  /locus tag="Madraxi_58"
    /note=Original Glimmer call @bp 40160 has strength 8.38; Genemark calls start at 40160
    /note=SSC: 40160-39606 CP: yes SCS: both ST: SS BLAST-Start: [immunity repressor [Rhodococcus phage Jflix2]],,NCBI, q4:s1 98.3696% 8.73051E-77 GAP: 436 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.764, -3.2123487306667524, yes F: immunity repressor SIF-BLAST: ,,[immunity repressor [Rhodococcus phage Jflix2]],,WIF20543,80.1136,8.73051E-77 SIF-HHPRED:  SIF-Syn: 
    /note=Start 40160, Stop 39606; CP: good, yes; LO: yes; Gap: 436 (investigate possible gene in this gap); RBS: best score; BLAST-start: Q4:T1; Starterator: called when present;
    /note=BLAST-function: immunity repressor; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: helix-turn-helix domain; HHPred: transcription regulator
    /note=FUNCTION: immunity repressor due to gene 58 being an integrase and HHpred confirmed a helix-turn-helix domain

CDS 40597 - 40941
  /gene="59"
  /product="gp59"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_59"
    /note=Original Glimmer call @bp 40597 has strength 10.94; Genemark calls start at 40597
    /note=SSC: 40597-40941 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 9.96713E-52 GAP: 436 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.381, -3.9531326986493704, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570325,85.8407,9.96713E-52 SIF-HHPRED:  SIF-Syn: 
    /note=Start 40597, Stop 40941; CP: good, yes; LO: yes; Gap: 436 (investigate possible gene in this gap); RBS: best score; BLAST-start: Q1:T1; Starterator: orpham;
    /note=BLAST-function: hypothetical protein; Synteny: orpham in similar place in Jflix2; Conserved domain: none; HHPred: TERS_BPTS, probable terminase
    /note=FUNCTION: hypothetical protein

CDS 41063 - 41515
  /gene="60"
  /product="gp60"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_60"
    /note=Original Glimmer call @bp 41063 has strength 11.65; Genemark calls start at 41063
    /note=SSC: 41063-41515 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 98.6667% 9.16608E-90 GAP: 121 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.298, -2.0162541296952132, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570324,88.6667,9.16608E-90 SIF-HHPRED:  SIF-Syn: 
    /note=Start 41063, Stop 41515; CP: good, yes; LO: yes; Gap: 121; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS 41518 - 41772
  /gene="61"
  /product="gp61"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_61"
    /note=Original Glimmer call @bp 41518 has strength 5.96; Genemark calls start at 41518
    /note=SSC: 41518-41772 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_56 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 3.71556E-42 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.102, -4.454678451133587, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_56 [Rhodococcus phage Jflix2]],,WIF20547,92.5926,3.71556E-42 SIF-HHPRED:  SIF-Syn: 
    /note=Start 41518, Stop 41772; CP: good, yes; LO: no, but no cp added; Gap: 2; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS 41853 - 42227
  /gene="62"
  /product="gp62"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_62"
    /note=Original Glimmer call @bp 41853 has strength 14.08; Genemark calls start at 41853
    /note=SSC: 41853-42227 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 3.08855E-40 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.91, -2.7653702713535186, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570322,70.2479,3.08855E-40 SIF-HHPRED:  SIF-Syn: 
    /note=Start 41853, Stop 42227; CP: good, yes; LO: yes; Gap: 80; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: no hits
    /note=FUNCTION: hypothetical protein

CDS 42224 - 42604
  /gene="63"
  /product="gp63"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_63"
    /note=Original Glimmer call @bp 42224 has strength 10.47; Genemark calls start at 42224
    /note=SSC: 42224-42604 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q2:s4 99.2064% 4.8509E-73 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.774, -5.141468244704366, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33162,93.75,4.8509E-73 SIF-HHPRED:  SIF-Syn: 
    /note=Start 42224, Stop 42604; CP: good, yes; LO: no, but no cp added; Gap: -2; RBS: best score; BLAST-start: Q1:T1; Starterator: called when present;
    /note=BLAST-function: hypothetical protein; Synteny: yes, member of pham in similar place in Jflix2; Conserved domain: none; HHPred: unknown saccharide family
    /note=FUNCTION: hypothetical protein

CDS 42601 - 43107
  /gene="64"
  /product="gp64"
  /function="WhiB family transcription factor"
  /locus tag="Madraxi_64"
    /note=Original Glimmer call @bp 42601 has strength 8.57; Genemark calls start at 42601
    /note=SSC: 42601-43107 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 94.6429% 1.4409E-69 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.308, -4.104100924355445, no F: WhiB family transcription factor SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570320,76.5432,1.4409E-69 SIF-HHPRED: Transcriptional regulator WhiB; RNA polymerase, Transcription factor, Iron cluster, TRANSCRIPTION-TRANSFERASE-DNA complex;{Streptomyces venezuelae},,,8DY7_H,52.9762,99.7 SIF-Syn: 
    /note=Start: 42601; Stop: 43107; Overlap: -3; CP: Yes, start includes all CP; LO: Yes; RBS: Yes;
    /note=BLAST-start: Q1:T1, some hits shorten the gene in the alignment; Starterator: Same start in Jflix2, and draft of REQ1 has the same start; BLAST-function: WhiB transcription factor; Conserved Domain: WhiB-transcription factor in actinobacteria; Synteny: similar location in REQ1/Jflix -WhiB family transcription factor; HHPred:Whib (has a high probability hit to something of unknown origin) and things of insignificant probability. FUNCTION: Whib family transcription factor

CDS 43104 - 43436
  /gene="65"
  /product="gp65"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_65"
    /note=Original Glimmer call @bp 43104 has strength 16.45; Genemark calls start at 43104
    /note=SSC: 43104-43436 CP: yes SCS: both ST: NI BLAST-Start: [Cas4 exonuclease [Rhodococcus phage Jflix2]],,NCBI, q4:s2 97.2727% 3.8817E-64 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.968, -2.7254235724530456, yes F: Hypothetical Protein SIF-BLAST: ,,[Cas4 exonuclease [Rhodococcus phage Jflix2]],,WIF20551,96.2963,3.8817E-64 SIF-HHPRED:  SIF-Syn: 
    /note=Start:43104; Stop:43436; Gap:-3 (overlap); CP: Good enough, Leaves out a bit of CP, likely not significant based on RBS; LO: No; RBS: Longer starts have worse scores (also there’s already overlap); BLAST-start: 3rd hit Q1:T1, 2 hits Q4:T2; ST: Start not seen in the other CF phages included; Synteny: In Jflix2, does not have the same start; BLAST-function: hypothetical protein; HHPred: No Significant hits(high prob, but too low e-value); FUNCTION(checked on approved list): Hypothetical protein - no exonuclease domains; has weak non-sig HHPred hit to nuclease domain

CDS 43549 - 44451
  /gene="66"
  /product="gp66"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_66"
    /note=Original Glimmer call @bp 43549 has strength 11.0; Genemark calls start at 43567
    /note=SSC: 43549-44451 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein RoPhREQ1_gp32 [Rhodococcus phage REQ1] ],,NCBI, q44:s1 85.0% 6.91838E-118 GAP: 112 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.998, -3.109529858048176, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein RoPhREQ1_gp32 [Rhodococcus phage REQ1] ],,YP_005087284,77.9923,6.91838E-118 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 43549; Stop: 44451; Gap: 112; CP: coding potential does not include start; LO: No; RBS: starts #5 and 8 have better scores and would shorten gene; BLAST-start: All starts Q44:1; Startrator: called in JFlix2, Start 1; BLAST-function: hypothetical protein; Synteny: shows up similar in JFlix2 and REQ1; HHPred: no significant  hits; FUNCTION: hypothetical protein

CDS 44448 - 44702
  /gene="67"
  /product="gp67"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_67"
    /note=Original Glimmer call @bp 44448 has strength 15.82; Genemark calls start at 44448
    /note=SSC: 44448-44702 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_63 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 98.8095% 1.37601E-45 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.523003374675015, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_63 [Rhodococcus phage Jflix2]],,WIF20554,93.9759,1.37601E-45 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 44448; Stop: 44702; Gap:-3 (overlap); CP: Good, includes start; LO: Yes; RBS: Best scores; BLAST-start: Q1:T1, one hit shortens it a bit; Startrator: same start present in Jflix; BLAST-function: Hypothetical Protein; Synteny: Seen in Jflix2 with a different start; Conserved Domain: Protein of unknown function (DUF3310); HHPred: No significant hits (high prob, too low e); FUNCTION(checked on approved list): Hypothetical Protei

CDS 44803 - 45510
  /gene="68"
  /product="gp68"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_68"
    /note=Original Glimmer call @bp 44803 has strength 10.85; Genemark calls start at 44803
    /note=SSC: 44803-45510 CP: yes SCS: both ST: SS BLAST-Start: [DUF3310 domain-containing protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.45839E-116 GAP: 100 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.816, -2.9625409806968013, no F: Hypothetical Protein SIF-BLAST: ,,[DUF3310 domain-containing protein [Prescottella equi] ],,MBM4617934,78.9256,1.45839E-116 SIF-HHPRED: DUF3310 ; Protein of unknwon function (DUF3310),,,PF11753.12,25.1064,99.5 SIF-Syn: 
    /note=Start: 44803; Stop: 45510; Gap - 100; CP: good, CP includes the start; LO: Yes; RBS: best score, others would shorten gene/have worse scores; BLAST-start: Q1:T1 in three/five hits; BLAST-Function: hypothetical protein, domain-containing protein, and nucleotide kinase; Starterator: called with REQ1, Start ; Synteny: Seen in REQ1 with a different start; HHPred: no significant hits; FUNCTION: hypothetical protein

CDS 45503 - 45730
  /gene="69"
  /product="gp69"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_69"
    /note=Original Glimmer call @bp 45503 has strength 16.18; Genemark calls start at 45503
    /note=SSC: 45503-45730 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.5399E-21 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.249, -4.210365747859001, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570314,72.0,1.5399E-21 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 45503; Stop: 45730; Gap: -7 Overlap; CP: includes all the start;  LO: Yes; RBS: Best one, any other ones would shorten gene significantly and have lower scores; BLAST-start: Q1:T1 and Q4:T2, only two hits; BLAST-function: Hypothetical Protein; Starterator: Jflix2 has an earlier start, but it is the only other one in the pham
    /note=BLAST-function: Hypothetical Protein; Synteny: Seen in Jflix2, but earlier, is gene 66; HHPred: No significant hits; FUNCTION: Hypothetical Protein

CDS 45727 - 45975
  /gene="70"
  /product="gp70"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_70"
    /note=Original Glimmer call @bp 45727 has strength 14.49; Genemark calls start at 45727
    /note=SSC: 45727-45975 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_66 [Rhodococcus phage Jflix2]],,NCBI, q3:s7 97.561% 7.5285E-9 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.153, -4.490107201936413, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_66 [Rhodococcus phage Jflix2]],,WIF20556,56.7901,7.5285E-9 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 45727; Stop: 45975; Overlap: -4; CP: includes start, good coding potential; LO: Yes; RBS:Best score, any other would shorten the gene significantly; BLAST-start: Mostly Q1:T1, hits do not align with our selected start; Starterator: Called in JFlix2 and REQ1; BLAST-function: hypothetical protein; Synteny: Seen in JFlix2 near similar area and seen earlier in REQ1; HHPred: no sig hits; FUNCTION(checked on approved list): hypothetical protein

CDS 45972 - 46295
  /gene="71"
  /product="gp71"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_71"
    /note=Original Glimmer call @bp 45972 has strength 12.19; Genemark calls start at 45972
    /note=SSC: 45972-46295 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_67 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 4.482E-51 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.477, -5.763084442243425, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_67 [Rhodococcus phage Jflix2]],,WIF20557,86.9159,4.482E-51 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 45972; Stop: 46295; Gap: -3 Overlap; CP: Good, start included; LO: Yes; RBS: Best RBS, others would shorten gene significantly; BLAST-start: Q1:T1; Startrator: Has most common start, Jflix being the only other with this pham; BLAST-function: Hypothetical protein; Synteny: Seen in Jflix2 but earlier on as gene 68; HHPred: No sig hits; FUNCTION(checked on approved list): Hypothetical Protein

CDS 46285 - 46524
  /gene="72"
  /product="gp72"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_72"
    /note=Original Glimmer call @bp 46285 has strength 7.3; Genemark calls start at 46285
    /note=SSC: 46285-46524 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_68 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 1.87897E-34 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.477, -3.7329837339109084, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_68 [Rhodococcus phage Jflix2]],,WIF20558,83.5443,1.87897E-34 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 46285; Stop: 46524; Gap: 9; CP: good CP, includes the start; LO: Yes; RBS: best score, others were worse/shortened gene; BLAST-start: Q1:T1 in both hits; BLAST-function: hypothetical protein; Startrator: does not have most annotated start, oher CF phages call the same start; Synteny: gene number 69 in Jflix2 and 70 in Shagrat; Conserved Domains: PD-(D/E)XK nuclease superfamily. Members of this family belong to the PD-(D/E)XK nuclease superfamily.; HHPred: No Sig Hits; FUNCTION(checked on approved list): Hypothetical Protein

CDS 46508 - 47317
  /gene="73"
  /product="gp73"
  /function="Cas4 exonuclease"
  /locus tag="Madraxi_73"
    /note=Original Glimmer call @bp 46508 has strength 10.58; Genemark calls start at 46508
    /note=SSC: 46508-47317 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 99.6283% 0.0 GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.529, -5.795782549058414, no F: Cas4 exonuclease SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570311,99.2565,0.0 SIF-HHPRED: Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA.,,,cd09637,73.9777,99.7 SIF-Syn: 
    /note=Start: 46508; Stop: 47317; Gap: 15; CP: Good, included by start; LO: Yes; RBS: Best start, some have better scores but would shorten gene significantly; BLAST-start: Mostly Q1:T1; Startrator: Same start called in Jflix2 , detected in Req1 with the same start; BLAST-function: hypothetical protein some called as exonuclease; Synteny: Found in REQ1 as gene 39 & JFlix2 as gene 70; HHPred : Hitting Cas4 exonuclease, good probability and e-value; FUNCTION(checked on approved list): Cas4 Exonuclease; has hit to and to the PD-(D/E)XK nuclease superfamily

CDS 47301 - 47459
  /gene="74"
  /product="gp74"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_74"
    /note=Original Glimmer call @bp 47301 has strength 15.07; Genemark calls start at 47301
    /note=SSC: 47301-47459 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_70 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 1.27192E-27 GAP: -17 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.153, -4.411422009034556, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_70 [Rhodococcus phage Jflix2]],,WIF20560,98.0769,1.27192E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 47301; Stop: 47459; Gap: -17; CP: good CP, includes start; LO: No; RBS: best score; BLAST-start:Q1:T1; Starterator: Called with JFLix2; BLAST-function: hypothetical protein; Synteny: Found in similar area in JFlix as Gene 71; HHPred: No Sig Hits; FUNCTION(checked on approved list): hypothetical protein

CDS 47623 - 48270
  /gene="75"
  /product="gp75"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_75"
    /note=Original Glimmer call @bp 47623 has strength 12.77; Genemark calls start at 47623
    /note=SSC: 47623-48270 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.30696E-90 GAP: 163 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.411, -3.951037378843707, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570310,76.1468,1.30696E-90 SIF-HHPRED: Single-strand binding protein; Single-strand binding protein, DNA BINDING PROTEIN; HET: MSE; 1.8A {Deinococcus radiodurans} SCOP: b.40.4.3,,,1SE8_A,80.0,95.4 SIF-Syn: 
    /note=Start: 47623; Stop: 48270; Gap: 163; CP: Good, start includes it; LO: Yes; RBS: Best RBS; BLAST-start: First 2; Q1:T1; Startrator: Same start called in Jflix, same start present in REQ1 draft; BLAST-function: Mostly; Hypothetical Protein and 1 SSB protein; Synteny: Seen in as gene 72 in  Jflix2 and REQ1 gene 42; HHPred: No Sig hits, bad e-values; FUNCTION(checked on approved list): Hypothetical Protein
    /note=HHPred hits are not strong enough choose SSB protein as was done in Jflix2.

CDS 48349 - 48705
  /gene="76"
  /product="gp76"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_76"
    /note=Original Glimmer call @bp 48349 has strength 14.9; Genemark calls start at 48349
    /note=SSC: 48349-48705 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_72 [Rhodococcus phage Jflix2]],,NCBI, q4:s5 83.0508% 1.98056E-39 GAP: 78 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.8, -3.1375990994182024, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_72 [Rhodococcus phage Jflix2]],,WIF20562,77.6699,1.98056E-39 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember#: 3 (Jflix2 and REQ1). cpQuality: Good (covers all cp). longestORF: Yes. bestORF: Yes. gap/overlap: 78n gap
    /note=> RBS: best start. BLAST Start: Q4:T5. Starterator: call this one of "Most Annotated" start, found in start 1 along with Jflix2 and REQ1. BLAST Function: hypothetical protein 
    /note=> Phamerator: No Listed Function. Synteny: Matches Jflix2 with previous 4-5 previous and next ORFs, present but unaligned in REQ1, not present in Shagrat
    /note=> CDomain: None. TMDomain: None. HHPred:No Good Hits (No DeepTMHMM hits) 
    /note=> Keep start, Not enough info to call function

CDS 48705 - 48926
  /gene="77"
  /product="gp77"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_77"
    /note=Original Glimmer call @bp 48705 has strength 4.14
    /note=SSC: 48705-48926 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_73 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 98.6301% 5.76062E-35 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.015, -4.778071418780228, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_73 [Rhodococcus phage Jflix2]],,WIF20563,87.5,5.76062E-35 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember#: 3 (Jflix2 and REQ1). cpQuality: Okay (covers all cp but not much cp overall). longestORF: Yes. bestORF: Yes (could start 1 later but would miss poor cp)
    /note=> gap/overlap: 1n overlap. RBS: Not best start, but very close (we should keep bc other option will shorten length). BLAST Start: Q1:T1. Starterator: call this one of "Most Annotated" start, found in start 2 along with Jflix2 and REQ1
    /note=> BLAST Function: hypothetical protein. Phamerator: No Listed Function. Synteny: Matches Jflix2 with previous 4-5 previous and next ORFs
    /note=> CDomain: None. TMDomain: None. HHPred: No Good Hits (No DeepTMHMM hits)
    /note=> keep start, not enough info for function

CDS 48893 - 49078
  /gene="78"
  /product="gp78"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_78"
    /note=Original Glimmer call @bp 48893 has strength 9.22; Genemark calls start at 48893
    /note=SSC: 48893-49078 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 98.3607% 6.16193E-35 GAP: -34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.92, -4.897971560974249, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570309,96.7742,6.16193E-35 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember#: 2 (Jflix2). cpQuality: Okay (covers all cp but not much cp overall). longestORF: Yes. bestORF: Yes. gap/overlap: 32n overlap
    /note=> RBS: Not best, but close (other strat will not cover all cp so should not change). BLAST Start: Q1:T1
    /note=> Starterator: call this one of "Most Annotated" start, found in start 1 along with Jflix2 and REQ1. Start kept
    /note=> BLAST Function: hypothetical protein. Phamerator: No Listed Function. Synteny: Matches Jflix2 with previous 4-5 previous and next ORFs
    /note=> CDomain: None. TMDomain: None. HHPred: No Good Hits (No DeepTMHMM hits)
    /note=> start kept, not enough info for function

CDS 49078 - 49353
  /gene="79"
  /product="gp79"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_79"
    /note=Original Glimmer call @bp 49078 has strength 10.91; Genemark calls start at 49078
    /note=SSC: 49078-49353 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 98.9011% 3.79227E-37 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.249, -4.210365747859001, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570308,86.3636,3.79227E-37 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember#: 93 (All CF phages, Singleton ‘Sleepyhead’, DP, CT, A8, J). cpQuality: Good. longestORF: No (would cause more overlap if starts earlier). bestORF: Yes. gap/overlap: 1n overlap
    /note=> RBS: best start. BLAST Start: Q1:T1. Starterator: call this one of "Most Annotated" start, found in start 4 along with Jflix2. Start kept
    /note=> BLAST Function: hypothetical protein. Phamerator: No Listed Function. Synteny: Matches Jflix2 with previous 4-5 previous and next ORFs
    /note=> CDomain: None. TMDomain: None. HHPred: No Good Hits (No DeepTMHMM hits)
    /note=> keep start, not enough info

CDS 49350 - 49697
  /gene="80"
  /product="gp80"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_80"
    /note=Original Glimmer call @bp 49350 has strength 10.95; Genemark calls start at 49350
    /note=SSC: 49350-49697 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q4:s3 97.3913% 4.68014E-65 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.925, -5.3524728754355015, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570307,90.3509,4.68014E-65 SIF-HHPRED: DUF6197 ; Family of unknown function (DUF6197),,,PF19698.3,97.3913,99.8 SIF-Syn: 
    /note=> phamMember#: 93 (same pham as gene 80). cpQuality: Good (covers all cp). longestORF: No (starting earlier would cause more overlap). bestORF: Not best score. gap/overlap: 4n overlap
    /note=> RBS: other good RBS, but chosen still good. BLAST Start: Q4:T3. starterator: does not have the "Most Annotated" start, found 6 out of 52 members in pham. But called 100% of the time when present. Start kept (could come back to look more in depth)
    /note=> BLAST Function: hypothetical function. Phamerator: No Listed Function. Synteny: Appears in 2 or 3’s in all four CF Phages
    /note=> CDomain: None. TMDomain: None. HHPred: No Good Hits (No DeepTMHMM hits)
    /note=> keep start, not enough info for function

CDS 49694 - 49978
  /gene="81"
  /product="gp81"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_81"
    /note=Original Glimmer call @bp 49694 has strength 14.04; Genemark calls start at 49694
    /note=SSC: 49694-49978 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_77 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 98.9362% 3.40661E-35 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.603, -3.759198113603886, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_77 [Rhodococcus phage Jflix2]],,WIF20567,85.2273,3.40661E-35 SIF-HHPRED: DUF6197 ; Family of unknown function (DUF6197),,,PF19698.3,97.8723,99.8 SIF-Syn: 
    /note=> phamMember#: 3 (Jflix2 and REQ1). cpQuality: Good. longestORF: No (starting earlier would cause more overlap). bestORF: Yes. gap/overlap: 4n overlap. RBS: best start  
    /note=> BLAST Start: Q1:T1. starterator: does not have the "Most Annotated" start, found in 2 out of 52 members in pham. But called 100% of the time when present. Start kept. BLAST Function: hypothetical function 
    /note=> Phamerator: No Listed Function (same as 81). Synteny: Appears in 1’s or 2’s or 3’s in all four CF Phages (same as 81)
    /note=> CDomain: None (same as 81). TMDomain: None (same as 81). HHPred: No Good Hits (No DeepTMHMM hits)
    /note=> keep start, not enough info for function

CDS 49975 - 50181
  /gene="82"
  /product="gp82"
  /function="membrane protein"
  /locus tag="Madraxi_82"
    /note=Original Glimmer call @bp 49975 has strength 16.11; Genemark calls start at 49975
    /note=SSC: 49975-50181 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_78 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 3.03389E-11 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.051, -4.702334767722353, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_78 [Rhodococcus phage Jflix2]],,WIF20568,62.8571,3.03389E-11 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember#: 3 (Jflix2 and REQ1). cpQuality: Good (covers most cp). longestORF: No (starting earlier would cause more overlap). bestORF: Yes. gap/overlap: 4n overlap
    /note=> RBS: Best start. BLAST Start: Q1:T1. starterator: does not have the "Most Annotated" start, found in 1 of 3 pham, 100% called when present. Start kept
    /note=> BLAST Function: hypothetical protein. Phamerator: No listed function
    /note=> Synteny: Same left adjacent Gene as Jflix2, appears in Shagrat as well. CDomain: None. TMDomain: None. HHPred: No Good Hits (Two transmembrane regions found within protein via DeepTMHMM)
    /note=> keep start, most likely transmembrane protein

CDS 50174 - 50401
  /gene="83"
  /product="gp83"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_83"
    /note=Original Glimmer call @bp 50174 has strength 14.12; Genemark calls start at 50174
    /note=SSC: 50174-50401 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 97.3333% 1.29011E-40 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.064, -2.5052746077145835, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4570304,93.3333,1.29011E-40 SIF-HHPRED:  SIF-Syn: 
    /note=>phamMember#: 2 (Shagrat). cpQuality: Good (covers most cp). longestORF: No (starting earlier would cause more overlap). bestORF: Yes. gap/overlap: 8n overlap
    /note=> RBS: best start . BLAST Start: Q1:T1. starterator: does not have the "Most Annotated" start, found in 1 of 3 pham, 100% called when present 
    /note=> Start kept. BLAST Function: hypothetical protein. Phamerator: No listed function. Synteny: good, matches with surrounding genes pretty well. Minor shuffling
    /note=>No conserved domains. No TM domains. HHPred: No Good Hits (No DeepTMHMM hits). no info to call function

CDS 50398 - 50958
  /gene="84"
  /product="gp84"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_84"
    /note=Original Glimmer call @bp 50398 has strength 14.8; Genemark calls start at 50398
    /note=SSC: 50398-50958 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 4.25302E-102 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.844, -2.90473872338446, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33178,86.8852,4.25302E-102 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember# 2 (REQ1) cpQuality: Good (covers most cp). longestORF: No (starting earlier would cause more overlap). bestORF: Yes. gap/overlap: 4n overlap
    /note=> RBS: best score. BLAST start: Q:1T:1. Starterator:  does not have the "Most Annotated" start, found in 1 of 2 pham member, called 100% when present. Start kept
    /note=> BLAST Function: hypothetical protein. No function listed in Phamerator. Synteny: seems to be shuffled into place near genes with good synteny. Only match is in Shagrat
    /note=> No conserved domains. no transmembrane domains. HHPred:No Good Hits (No DeepTMHMM hits). No info to call function

CDS 50958 - 51173
  /gene="85"
  /product="gp85"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_85"
    /note=Original Glimmer call @bp 50958 has strength 11.32; Genemark calls start at 50958
    /note=SSC: 50958-51173 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s15 90.1408% 1.75721E-27 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.199, -4.6033671133628555, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33179,64.9485,1.75721E-27 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember#: 2 (Jflix2). cpQuality: Good (covers most cp). longestORF: No (starting earlier would cause more overlap). bestORF: Yes. gap/overlap: 1n overlap
    /note=> RBS: other options but still good start. BLAST start: Q:20T:34. Starterator: no annotations, found in 2 of 2 pham member, called 50% when present. Start kept
    /note=> BLAST Function: hypothetical protein. No listed phamerator function. Synteny: decent, nearby genes are similar in Jflix2
    /note=> no conserved domains. no transmembrane domains. HHPred: No Good Hits (No DeepTMHMM hits). no info to call function

CDS 51170 - 51472
  /gene="86"
  /product="gp86"
  /function="toxin in toxin/antitoxin system, BrnT-like"
  /locus tag="Madraxi_86"
    /note=Original Glimmer call @bp 51230 has strength 8.85; Genemark calls start at 51170
    /note=SSC: 51170-51472 CP: yes SCS: both-gm ST: SS BLAST-Start: [DUF4258 domain-containing protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 1.21853E-63 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.91, -3.4175091270247986, yes F: toxin in toxin/antitoxin system, BrnT-like SIF-BLAST: ,,[DUF4258 domain-containing protein [Prescottella equi] ],,MBM4617919,97.0,1.21853E-63 SIF-HHPRED: DUF4258 ; Domain of unknown function (DUF4258),,,PF14076.10,63.0,99.3 SIF-Syn: 
    /note=> phamMember#: 3 (Jflix2 and REQ1). cpQuality: Okay (covers most cp). longestORF: No (unnecessary to start earlier). bestORF: No (could start later and still cover all good cp). gap/overlap: 56n gap
    /note=> RBS: Not the best score, but close. Start kept. BLAST start: Q1:T21. Starterator: have the "Most Annotated" start but do not call it, found in 2 of 2 pham member, called 50% when present 
    /note=> BLAST Function: domain containing protein. Phamerator function: BrnT-like protein in Jflix2. Synteny: decent matches with surrounding genes in Jflix2
    /note=> No conserved domains. No transmembrane domains. HHPred: a few hits to “BrnT toxin”, but E value is low (No DeepTMHMM hits).  Most likely a BrnT toxin because the HHpred hit matches Jflix2
    /note=
    /note=Changed to longest ORF based on Starterator and BLAST T1:Q1

CDS 51482 - 52018
  /gene="87"
  /product="gp87"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_87"
    /note=Original Glimmer call @bp 51482 has strength 12.73; Genemark calls start at 51482
    /note=SSC: 51482-52018 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q2:s4 99.4382% 6.71906E-113 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.286, -4.150999100097377, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617918,95.0276,6.71906E-113 SIF-HHPRED:  SIF-Syn: 
    /note=> phamMember#: 3 (Jflix2 and REQ1). cpQuality: Good (covers all cp). longestORF: Yes. bestORF: Yes. gap/overlap: 9n gap
    /note=> RBS: Not best score but close. Start kept. BLAST Start: Q2:T4. Starterator: calls this "Most Annotated" start, found in 3 of 3 of pham, called 100% when present 
    /note=> BLAST Function: hypothetical protein. No phamerator function. Synteny: matches well with surrounding genes
    /note=> No conserved domains. No transmembrane domains. HHPred: No good hits (No DeepTMHMM hits). No info to call function

CDS 51996 - 52262
  /gene="88"
  /product="gp88"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_88"
    /note=Original Glimmer call @bp 51996 has strength 5.43; Genemark calls start at 51996
    /note=SSC: 51996-52262 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 4.52998E-56 GAP: -23 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.079, -4.565177092733586, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617917,97.7273,4.52998E-56 SIF-HHPRED: DUF6083 ; Family of unknown function (DUF6083),,,PF19561.3,81.8182,99.7 SIF-Syn: 
    /note=Start: 51996; Stop: 52262
    /note=Pham: 27286 members: 3
    /note=CP: Not very good (2 spikes, not consistent coverage), but covers all available
    /note=LP ORF: Yes, longest possible
    /note=Gap: -23 (overlap)
    /note=RBS: 2nd best score, but much larger gene than the best score.
    /note=BLAST-Start: Q1:T1
    /note=Starterator: Jflix2, Madraxi called
    /note=BLAST-Funtion: Hypothetical protein; Rhodococcus Equi
    /note=Phamerator Function: NA
    /note=Synteny: found in Jflix2 but different #
    /note=Conserved Domain/TMHMM: NA
    /note=HHPred: DUF6083 ; Family of unknown function, High probability and good E value
    /note=FUNCTION: Hypothetical protein

CDS 52269 - 52397
  /gene="89"
  /product="gp89"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_89"
    /note=Original Glimmer call @bp 52269 has strength 13.23; Genemark calls start at 52269
    /note=SSC: 52269-52397 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_JFLIX2_87 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 4.12745E-17 GAP: 6 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.794070146961553, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_87 [Rhodococcus phage Jflix2]],,WIF20577,92.8571,4.12745E-17 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 52269; Stop: 52397
    /note=Pham: 16531 members: 3
    /note=CP: Covers all CP
    /note=LP ORF: Yes, longest possible
    /note=Gap: 6
    /note=RBS: Best Score!
    /note=BLAST-Start: Q1:T1
    /note=BLAST-Funtion: Hypothetical protein; Rhodococcus Equi Jflix2
    /note=Starterator: NA
    /note=Phamerator Function: Found in Jflix2 and REQ1, started in 3/3
    /note=Synteny: found in Jflix2 but different #
    /note=Conserved Domain/TMHMM: NA
    /note=HHPred: inconclusive, E value too low
    /note=FUNCTION: Hypothetical protein

CDS 52399 - 52818
  /gene="90"
  /product="gp90"
  /function="membrane protein"
  /locus tag="Madraxi_90"
    /note=Original Glimmer call @bp 52399 has strength 15.61; Genemark calls start at 52399
    /note=SSC: 52399-52818 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 1.22292E-78 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.721, -3.2232696953924083, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,MBM4617916,86.6667,1.22292E-78 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 52399; Stop: 52818
    /note=Pham: 23772  members: 3
    /note=CP: Really good CP, full and even coverage
    /note=LP ORF: Yes, longest possible 
    /note=Gap: 1
    /note=RBS: Best Score!
    /note=BLAST-Start: Q1:T1
    /note=BLAST-Funtion: Hypothetical protein: Rhodococcus Equi
    /note=Starterator: Start found and started in Jflix2. (also found in one other, but not started)
    /note=Phamerator Function: NA
    /note=Synteny: found in Jflix2 but different #
    /note=HHPred: inconclusive, E value too low
    /note=TMHMM: 3 matches for TMD

CDS 52811 - 53170
  /gene="91"
  /product="gp91"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_91"
    /note=Original Glimmer call @bp 52826 has strength 9.42; Genemark calls start at 52811
    /note=SSC: 52811-53170 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_89 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 90.7563% 5.98873E-27 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.731, -3.791591111008034, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_89 [Rhodococcus phage Jflix2]],,WIF20579,66.3717,5.98873E-27 SIF-HHPRED: DUF6197 ; Family of unknown function (DUF6197),,,PF19698.3,87.395,99.8 SIF-Syn: 
    /note=Start: 52826 *New: 52811; Stop: 53170
    /note=Pham: 142581 members:52
    /note=Support: GeneMark calls at 52811, Glimmer at 52826
    /note=CP: Good CP, covers all
    /note=LP ORF: not longest possible *New: longest possible
    /note=Gap: 7 *New: Overlap -8
    /note=RBS: not best score, *New: Best Score!
    /note=BLAST-Start: Q3:T6
    /note=BLAST-Funtion: Hypothetical protein, Rhodococcus phage Jflix2
    /note=Starterator: not called by Madraxi, Jflix2 and Shagrat. Only called by 1/52 with start, changing will allow better start call. 
    /note=Phamerator Function: NA
    /note=Synteny: NA
    /note=Conserved Domain/TMHMM: NA
    /note=HHPred: DUF6197 ; Family of unknown function. High probability and good E value
    /note=FUNCTION: Hypothetical protein
    /note=
    /note=START CHANGE: initial: 52826; final: 52811; Reasoning: Still covers CP, minimal overlap (-8), RBS scores get better, BLAST-Start changes Gap from 7 to -8, and Starterator only called original start 1/52 times, not good enough evidence to stay.

CDS 53163 - 53606
  /gene="92"
  /product="gp92"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_92"
    /note=Original Glimmer call @bp 53163 has strength 14.2; Genemark calls start at 53163
    /note=SSC: 53163-53606 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s42 97.9592% 4.33406E-54 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.062, -4.538672476131182, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617915,55.2381,4.33406E-54 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 53163; Stop: 53606
    /note=Pham: 22528 members: 2
    /note=Support: Glimmer and GeneMark both caught
    /note=CP: does not cover all CP, but if we move back there is a large overlap 
    /note=LP ORF:  not longest possible ORF- rbs shows 2 that are longer but overlaps with the next gene
    /note=Gap: -8  (overlap)
    /note=RBS:  not best score, best score longer having a big overlap
    /note=BLAST-Start: Q1:T42 for the best BLAST match (bacteria), but the other two matches (phages) started further into the genes (Q38:T48 and Q16:T19 respectively) 
    /note=BLAST-Funtion: Hypothetical protein; 2xRhodococcus phage and 1 Rhodococcus equi.  
    /note=Starterator: found in REQ1 but not called (found in 1 of 2 genes in pham)
    /note=Phamerator Function: NA
    /note=Synteny: Has a similar sequence in an earlier REQ1 section
    /note=Conserved Domain/TMHMM: NA
    /note=HHPred: inconclusive, E value too high
    /note=FUNCTION: Hypothetical protein

CDS 53676 - 54011
  /gene="93"
  /product="gp93"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_93"
    /note=Original Glimmer call @bp 53676 has strength 10.73; Genemark calls start at 53676
    /note=SSC: 53676-54011 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 2.1023E-47 GAP: 69 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.064, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4617914,80.531,2.1023E-47 SIF-HHPRED: DNA_pack_N ; Probable DNA packing protein, N-terminus,,,PF02500.19,64.8649,99.1 SIF-Syn: 
    /note=Start: 53676; Stop: 54011
    /note=Pham: 138666  members: 4
    /note=CP: covers all coding potential
    /note=LP ORF: longest possible!
    /note=Gap: 69
    /note=RBS: Best Score!
    /note=BLAST-Start: Q1:T1
    /note=BLAST-Funtion: Hypothetical protein, found in 2 Rhodococcus phages (including Jflix2) and one Rhodococcus equi bacteria. 
    /note=Starterator: found in ¾ genes in pham, called 100% of the time. 
    /note=Phamerator Function: NA
    /note=Synteny: nothing concrete, is close to 94795 like in Jflix2 and close to 22528 like in REQ1. 
    /note=Conserved Domain/TMHMM: NA
    /note=HHPred: DNA_pack_N ; Probable DNA packing protein, high possibility and good e value. ONLY VALID FOR tectiviridae (function list), cannot call 
    /note=FUNCTION: Hypothetical protein

CDS 54008 - 54199
  /gene="94"
  /product="gp94"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_94"
    /note=Original Glimmer call @bp 54020 has strength 4.9; Genemark calls start at 54020
    /note=SSC: 54008-54199 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_JFLIX2_93 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 98.4127% 2.39111E-35 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.477, -3.75071250087134, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_93 [Rhodococcus phage Jflix2]],,WIF20583,98.3871,2.39111E-35 SIF-HHPRED:  SIF-Syn: 
    /note=CP: Good CP
    /note=LP ORF: yes
    /note=Gap: 8
    /note=RBS: best final score, second to best z-value
    /note=BLAST-Start: q:1t:5
    /note=BLAST-Funtion: Hypothetical protein SEA_JFLIX2_93; Rhodococcus equi
    /note=Starterator: Doesn’t call
    /note=Phamerator Function: NA
    /note=Synteny: same gene on Jflix #93
    /note=HHPred: N/A (low %identity)
    /note=FUNCTION: Hypothetical Protein

CDS 54209 - 56455
  /gene="95"
  /product="gp95"
  /function="DNA primase/polymerase/helicase"
  /locus tag="Madraxi_95"
    /note=Original Glimmer call @bp 54209 has strength 12.23; Genemark calls start at 54209
    /note=SSC: 54209-56455 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JFLIX2_94 [Rhodococcus phage Jflix2]],,NCBI, q1:s1 99.5989% 0.0 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.309, -2.0111200136961407, yes F: DNA primase/polymerase/helicase SIF-BLAST: ,,[hypothetical protein SEA_JFLIX2_94 [Rhodococcus phage Jflix2]],,WIF20584,88.8446,0.0 SIF-HHPRED: Regulatory protein repA; replicative DNA helicase structural changes, REPLICATION; HET: SO4; 1.95A {Escherichia coli} SCOP: c.37.1.11,,,1NLF_C,29.5455,99.7 SIF-Syn: 
    /note=Start: 54209; Stop: 56455
    /note=Pham: 18413  members: 3
    /note=CP: good CP
    /note=LP ORF: yes
    /note=Gap: 9
    /note=RBS: best score; others shortened gene too much
    /note=BLAST-Start: q1:t1
    /note=BLAST-Function: DNA Primase/polymerase (82.15)
    /note=Starterator: calls most annotated start
    /note=Phamerator Function: Primase/polymerase
    /note=Synteny: same as gene 94 on Jflix2
    /note=Conserved Domain/TMHMM: NA
    /note=HHPred: DNA Helicase (99.74), DNA primase/helicase (99.53)
    /note=FUNCTION: DNA primase/polymease/helicase (yes, all three according to function list...) NEEDS TO BE CHECKED
    /note=RDJ: Yes, has all 3 domains in the sense that it has a the bifunctional primase/polymerase domain AND it has a helicase domain.

CDS 56457 - 56693
  /gene="96"
  /product="gp96"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_96"
    /note=Original Glimmer call @bp 56457 has strength 9.18; Genemark calls start at 56457
    /note=SSC: 56457-56693 CP: yes SCS: both ST: NA BLAST-Start:  GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.91, -2.827683592113848, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start: 56457; Stop: 56693
    /note=Pham:  139007 members:1
    /note=CP: Good CP
    /note=LP ORF:yes
    /note=Gap:1
    /note=RBS: best score
    /note=BLAST-Start: q:2t:58
    /note=BLAST-Funtion: BLUF domain-containing protein (LOW %identity)
    /note=Starterator: N/A
    /note=Phamerator Function: N/A
    /note=Synteny: N/A
    /note=HHPred: (Low % identity)
    /note=FUNCTION: Hypothetical protein

CDS 56697 - 57317
  /gene="97"
  /product="gp97"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_97"
    /note=Genemark calls start at 56697
    /note=SSC: 56697-57317 CP: yes SCS: genemark ST: NA BLAST-Start: [hypothetical protein [Rhodococcus erythropolis] ],,NCBI, q1:s1 84.9515% 3.44995E-33 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.592, -3.78206099656339, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Rhodococcus erythropolis] ],,WP_095971563,47.0339,3.44995E-33 SIF-HHPRED: Phage_rep_org_N ; N-terminal phage replisome organiser (Phage_rep_org_N),,,PF09681.14,38.835,98.4 SIF-Syn: 
    /note=Start: 56697
    /note=Stop: 57317
    /note=Pham:  138889 members: 1
    /note=Support: N/A
    /note=CP: Good CP
    /note=LP ORF: N/A
    /note=Gap: 3
    /note=RBS: N/A
    /note=BLAST-Start: q:1t:1
    /note=BLAST-Funtion: Hypothetical protein; very low %identity
    /note=Starterator: N/A
    /note=Phamerator Function: N/A
    /note=Synteny: N/A
    /note=Conserved Domain/TMHMM: N/A
    /note=HHPred: Replisome; 98.38% 1.3x10^-5
    /note=FUNCTION: Replisome (not on official function list)

CDS 57314 - 57625
  /gene="98"
  /product="gp98"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_98"
    /note=Original Glimmer call @bp 57314 has strength 12.41; Genemark calls start at 57314
    /note=SSC: 57314-57625 CP: yes SCS: both ST: SS BLAST-Start:  GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.298, -2.0949393225970705, yes F: Hypothetical Protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start: 57314; Stop: 57625
    /note=Pham: 139141 members: 1
    /note=CP: good CP
    /note=LP ORF: yes
    /note=Gap: -3
    /note=RBS: best score
    /note=BLAST-Start: q8:t144
    /note=Starterator: N/A
    /note=BLAST-Funtion: family transcriptional regulator, but has poor e-value, not good evidence. 
    /note=Phamerator Function: N/A
    /note=Synteny: N/A
    /note=Conserved Domain/TMHMM: N/A
    /note=HHPred: inconclusive, probability too low
    /note=FUNCTION: Hypothetical protein

CDS 57728 - 58162
  /gene="99"
  /product="gp99"
  /function="endonuclease VII"
  /locus tag="Madraxi_99"
    /note=Original Glimmer call @bp 57728 has strength 8.72; Genemark calls start at 57728
    /note=SSC: 57728-58162 CP: yes SCS: both ST: SS BLAST-Start: [endonuclease VII [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 1.58355E-81 GAP: 102 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.034, -4.65945827897842, yes F: endonuclease VII SIF-BLAST: ,,[endonuclease VII [Rhodococcus phage Jflix2]],,WIF20587,84.4156,1.58355E-81 SIF-HHPRED: Restriction endonuclease Hpy99I; ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, HPY99I, PSEUDOPALINDROME, HYDROLASE-DNA COMPLEX; HET: 1PE; 1.5A {Helicobacter pylori},,,3GOX_B,87.5,99.7 SIF-Syn: 
    /note=Start: 57728; Stop: 58162
    /note=Pham: 142147 members: 956
    /note=CP: good CP
    /note=LP ORF: yes
    /note=Gap: 2
    /note=RBS: best score bc others significantly shortened gene
    /note=BLAST-Start: q:1t:1
    /note=Starterator: N/A
    /note=BLAST-Funtion: Endonuclease VII; Rhosococcus phage JFLIX2
    /note=Phamerator Function: Endocluease VII
    /note=Synteny: same as gene 101 on Shagrat and gene 97 on Jflix2
    /note=Conserved Domain/TMHMM: CD says endonuclease, TMHMM N/A
    /note=HHPred: Endonuclease, probability=99.7
    /note=FUNCTION: Endonuclease, endonuclease VII
    /note=
    /note=MR: good call

CDS 58159 - 58470
  /gene="100"
  /product="gp100"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_100"
    /note=Original Glimmer call @bp 58159 has strength 13.66; Genemark calls start at 58159
    /note=SSC: 58159-58470 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi]],,NCBI, q1:s1 100.0% 6.37241E-60 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.512, -3.9486724901834958, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi]],,NKS33192,96.1165,6.37241E-60 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 58159 Stop: 58470 FOR
    /note=CP: good CP
    /note=LP ORF: yes
    /note=Gap: -3 (overlap)
    /note=RBS: best score, others shortened the gene
    /note=BLAST-Start: q1:t1
    /note=Starterator: called MA start with Jflix2
    /note=BLAST-Funtion: Hypothetical protein; Prescotella equi
    /note=Phamerator Function: N/A
    /note=Synteny: Same gene found on JFlix2 as #92
    /note=CD: none
    /note=TMHMM: 1 tmr called
    /note=HHPred: inconclusive, probability too low
    /note=
    /note=MR: good call

CDS 58653 - 59276
  /gene="101"
  /product="gp101"
  /function="serine hydrolase"
  /locus tag="Madraxi_101"
    /note=Original Glimmer call @bp 58653 has strength 11.61; Genemark calls start at 58653
    /note=SSC: 58653-59276 CP: yes SCS: both ST: SS BLAST-Start: [cutinase family protein [Prescottella equi] ],,NCBI, q1:s7 100.0% 1.31667E-144 GAP: 182 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.897, -5.711975353186392, no F: serine hydrolase SIF-BLAST: ,,[cutinase family protein [Prescottella equi] ],,MBM4616424,95.7747,1.31667E-144 SIF-HHPRED: Cutinase-like enzyme; cutinase-like enzyme, biodegradable plastic degrading enzyme, alpha/beta hydrolase fold, hydrolase; HET: CAD; 1.7A {Pseudozyma antarctica},,,7CW1_B,77.2947,99.9 SIF-Syn: 
    /note=Start: 58653.Stop: 59276; Gap:182; Good CP; LO: no; RBS: not best score and not best length; Blast: only second result was q1:t1 and 1st result was q1:t7; Starterator: does not have most annotated start but current start is called 100% of time when present (only present in Madraxi and Jflix2); START: no change
    /note=Blast function: most common is cutinase family protein but serine hydrolase is also present; Synteny: Jflix gene is in similar location but is serine hydrolase; HHPRED: Cutinase like enzyme is highly favored and common but serine hydrolase shows very good promise; Approved Func: meets criteria for serine hydrolase; FUNCTION: Serine Hydrolase
    /note=
    /note=MR: Cutinase is nonexistent in the approved function list, definitely a serine hydrolase

CDS 59347 - 60069
  /gene="102"
  /product="gp102"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Madraxi_102"
    /note=Original Glimmer call @bp 59347 has strength 9.94; Genemark calls start at 59347
    /note=SSC: 59347-60069 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 95.0% 1.2954E-136 GAP: 70 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.662, -3.812150084159046, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4616423,91.342,1.2954E-136 SIF-HHPRED: a.6.1.5 (B:1-69) automated matches {Escherichia phage [TaxId: 10710]} | CLASS: All alpha proteins, FOLD: Putative DNA-binding domain, SUPFAM: Putative DNA-binding domain, FAM: Terminase gpNU1 subunit domain,,,SCOP_d6hn7b1,25.4167,97.7 SIF-Syn: 
    /note=Start 59347, Stop 60069; Gap:71; CP:Good, does not cover all CP; LO:Yes; RBS: Best score!;
    /note=BLAST: R.equi bacteria and phages, first two matches are q1:t1, matches after first two vary; Starterator:Shares start with Jflix2; Start changed?: NO;
    /note=BLAST-function:one hypothetical protein and one helix-turn-helix DNA binding domain protein; Syteny: Yes; HHPred: Secondary structure shows multiple alpha helices (roughly 5) separated my spacers of roughly 5 amino acids; Official Function List: Criteria Need to find 2-3 alpha helices in the seqence separated by small spacer regions of 3-4 amino acid, this hasn`t been found for this gene;  Function: helix-turn-helix DNA binding domain.

CDS 60318 - 60668
  /gene="103"
  /product="gp103"
  /function="DNA binding protein"
  /locus tag="Madraxi_103"
    /note=Original Glimmer call @bp 60318 has strength 3.82
    /note=SSC: 60318-60668 CP: yes SCS: glimmer ST: SS BLAST-Start: [DNA binding protein [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 7.53813E-66 GAP: 248 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.477, -3.75071250087134, yes F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Rhodococcus phage Jflix2]],,WIF20591,97.4138,7.53813E-66 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,62.069,98.2 SIF-Syn: 
    /note=Start 60318, Stop 60668; Gap: 249; CP: does cover, low CP; RBS: Best scores; BLAST: best match q19:t19; Starterator: start 22 called 100% with Jflix2; Start Changed?: No;
    /note=BLAST Function: DNA binding protein, 92% identity with Jflix2; Synteny: Yes, Jflix2; HHPred: No significant hits; Official Function List: No notes; Function: Likely DNA binding protein;
    /note=Has HTH but with separated by 5 aa; has possible HNH but not any nuclease hits; I believe Debbie made chose DNA binding protein over HTH domain protein on Jflix2 last year
    /note=
    /note=MR: I`m getting a ton of HNH endonuclease and general endonuclease hits, and checked the sequence for the HNH over 30 aas as the function list dictates (this gene contains it). I don`t remember exactly what debbie said but maybe check notes

CDS 60697 - 60858
  /gene="104"
  /product="gp104"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_104"
    /note=Original Glimmer call @bp 60697 has strength 13.05; Genemark calls start at 60697
    /note=SSC: 60697-60858 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 86.7924% 5.82956E-8 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.498, -3.769471247018311, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,WP_286462195,26.6667,5.82956E-8 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 60697,Stop:60858; Gap: 28; Good CP; LO: no; RBS: slightly better than longer ones but shortens the length plus best CP; 
    /note=Blast: lots of results with q1:t1; Starterator: most annotated start; START: no change
    /note=Blast function: hypothetical protein; Synteny: location similar to Jflix2; HHPRED: no good results; FUNCTION: unknown
    /note=
    /note=MR: Checked, good call

CDS 61181 - 61597
  /gene="105"
  /product="gp105"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_105"
    /note=Genemark calls start at 61181
    /note=SSC: 61181-61597 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q37:s40 73.913% 1.58927E-27 GAP: 322 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.521, -5.749944389475372, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4616420,49.4565,1.58927E-27 SIF-HHPRED:  SIF-Syn: 
    /note=Start 61181, Stop 61597; Overlap: 451; CP: Good, high CP; LO: No; RBS: 2nd longest ORF, longest ORF has no CP at start; 
    /note=BLAST: 3 hits, poor matches, 1st hit q72:t5; Starterator: not in most annotated start, start called 100% of time; Start Changed?: No;
    /note=BLAST Function: hypothetical protein (Prescottella equi); Synteny: yes, with Jflix2; HHPred: No significant hits; Function: Unknown
    /note=
    /note=MR: checked, good call

CDS complement (60810 - 61631)
  /gene="106"
  /product="gp106"
  /function="delete"
  /locus tag="Madraxi_106"
    /note=Original Glimmer call @bp 61631 has strength 6.36
    /note=SSC: 61631-60810 CP: yes SCS: glimmer ST: NA BLAST-Start: [LOW QUALITY PROTEIN: mucin-2-like [Lagopus muta]],,NCBI, q19:s578 71.7949% 6.31693E-8 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.476, -5.904919908336359, no F: delete SIF-BLAST: ,,[LOW QUALITY PROTEIN: mucin-2-like [Lagopus muta]],,XP_048788626,2.97575,6.31693E-8 SIF-HHPRED:  SIF-Syn: 
    /note=Start 61631, Stop 60810; Overlap;451; CP: Poor CP, start covers CP; LO:No; RBS:Many starts with better scores and longer gene lengths; 
    /note=BLAST-start:One match, very poor numbers, q45:t141; Starterator: No data; Start changed?: NO
    /note=Blast-function: Synteny:No; HHPred:No significant data; Function:It is likely best to delete this gene as it has major overlap with another gene and BLAST hits are insignificant.
    /note=
    /note=MR: checked, i would agree with deletion
    /note=HS: Support!

CDS complement (61621 - 61740)
  /gene="107"
  /product="gp107"
  /function="delete"
  /locus tag="Madraxi_107"
    /note=Original Glimmer call @bp 61740 has strength 4.13
    /note=SSC: 61740-61621 CP: no SCS: glimmer ST: NI BLAST-Start:  GAP: -17 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.083, -4.635604911695725, no F: delete SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start:61740, Stop:61621; CP: No CP; LO:Yes; RBS:Best option; BLAST-start:q4:t12; Starterator: no data; Start changed?:No.
    /note=BLAST-function:One hit for a binding protein but E-Value of 0.4 and low % identity, not significant match; Synteny:No; HHPred:No significant hits;
    /note=Function:Unknown, may be best to delete this gene due to its very poor alignment and weak e-value with BLAST
    /note=
    /note=MR: with no cp and bad blast matches I would agree with deletion

CDS complement (61724 - 62326)
  /gene="108"
  /product="gp108"
  /function="glycosylase"
  /locus tag="Madraxi_108"
    /note=Genemark calls start at 62326
    /note=SSC: 62326-61724 CP: yes SCS: genemark ST: SS BLAST-Start: [glycosyltransferase [Rhodococcus phage Jflix2]],,NCBI, q1:s1 100.0% 1.8678E-134 GAP: 88 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.799, -2.996985748252251, yes F: glycosylase SIF-BLAST: ,,[glycosyltransferase [Rhodococcus phage Jflix2]],,WIF20594,99.0,1.8678E-134 SIF-HHPRED: N-glycosylase/DNA lyase; ogg, helix-hairpin-helix, glycosylase, 8-oxoguanine, 8-oxoG, SsOGG, DNA damage, DNA repair, Glycosidase, Hydrolase, Lyase, Multifunctional enzyme, Nuclease; HET: SO4, GOL; 1.9A {Sulfolobus solfataricus},,,3FHG_A,38.0,97.0 SIF-Syn: 
    /note=CP is variable but strong at places throughout this ORF; No CP in other reading frames. Starterator shows this gene does not have MA start, but this start is shared with Jflix2. HHPred hit to glycosylase domain; Jflix2 and Shagrat BLAST hits were called similar, but a little hard to explain: glycosyltransferase (Jflix2) and DNA??? glycolsylase (Shagrat)
    /note=
    /note=MR: Not sure what happened for the Jflix and shagrat calls but glycosyltransferase seems to be the best accepted call

CDS complement (62415 - 62702)
  /gene="109"
  /product="gp109"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_109"
    /note=Original Glimmer call @bp 62702 has strength 2.38; Genemark calls start at 62702
    /note=SSC: 62702-62415 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q8:s6 92.6316% 4.33732E-28 GAP: 29 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.998, -2.644643059745525, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4616418,74.2268,4.33732E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Start: 62702 Stop: 62415; Gap: 29; CP: good; LO: no, RBS: best RBS values across the board and second longest ORF; 
    /note=Blast-start: first result was q26:t24 and second was q6:t3 (only 2 results); Starterator: has the most annotated start; START: no change
    /note=Blast Function: hypothetical protein; Synteny: very similar location to Jflix2 and Shagrat, Jflix2 has function glycosyltransferase; HHPRED: no good results; DeepTMHMM:Domain match; FUNCTION: Possibly glycosyltransferase based on Jflix2
    /note=
    /note=MR: Jflix does not have it as a glycosyltransferase, it is a hypothetical protein there too, I would keep it as is

CDS complement (62732 - 63145)
  /gene="110"
  /product="gp110"
  /function="Hypothetical Protein"
  /locus tag="Madraxi_110"
    /note=Original Glimmer call @bp 63073 has strength 7.88; Genemark calls start at 63145
    /note=SSC: 63145-62732 CP: no SCS: both-gm ST: SS BLAST-Start: [hypothetical protein [Prescottella equi] ],,NCBI, q1:s1 100.0% 2.95677E-88 GAP: 175 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.309, -2.0720764396375664, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein [Prescottella equi] ],,MBM4616417,96.3504,2.95677E-88 SIF-HHPRED:  SIF-Syn: 
    /note=ORIGINAL CALLED START: Start: 63073 Stop: 62732, Gap: 249; CP: Good, start does not cover all CP; LO: No; RBS: 4th longest ORF, longest ORF has much higher score that covers CP; Starterator: Madraxi only matches start in unrelated phage, Jflix 2 has called start that indicates a longer start; BLAST-Start: Top hit is Q1:T25, this indicates a longer start that matches the exact number of new proposed start from RBS; Start Changed?: YES
    /note=
    /note=START CHANGED: New Start 63145; Gap: 177; CP Good, start completely covers; LO: Yes; RBS; Best scores; Starterator: Shares start with cluster phage; BLAST-function: Hypothetical protein (all hits); Synteny: Same gene in Jflix present in same area; HHPRED: No significant hits; DeepTMHMM: No significant data; FUNCTION: Unknown
    /note=
    /note=MR: Checked, good call

CDS complement (63321 - 63449)
  /gene="111"
  /product="gp111"
  /function="delete"
  /locus tag="Madraxi_111"
    /note=Original Glimmer call @bp 63434 has strength 1.01
    /note=SSC: 63449-63321 CP: no SCS: glimmer-cs ST: NI BLAST-Start:  GAP: 318 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.535, -3.901790486536644, no F: delete SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start:63434, Stop:63321; Gap:247; CP:Good, covers all CP; LO:No, 7th longest; RBS:Ok values, other starts with better values and longer ORFs; BLAST-start:no hits; Starterator: No data; Start changed?:Yes 
    /note=NO; Blast-function:No results;Synteny:No; HHPred:No significant data; Function:Unknown
    /note=
    /note=START Change; Old Start:63434, New Start: 63449; Old gap:334, New Gap:319.  New start lengthens gene and lessens gap slightly and has better scores than current start.
    /note=
    /note=MR: Agree with the start change but also with deletion

CDS 63768 - 63950
  /gene="112"
  /product="gp112"
  /function="delete"
  /locus tag="Madraxi_112"
    /note=Original Glimmer call @bp 63768 has strength 0.73
    /note=SSC: 63768-63950 CP: yes SCS: glimmer ST: NA BLAST-Start:  GAP: 318 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 0.848, -7.157372476012939, no F: delete SIF-BLAST:  SIF-HHPRED:  SIF-Syn: 
    /note=Start: 63768 Stop: 63950; Gap: 333; CP: does not cover the entirety of ORF but is present; LO: yes; RBS: very poor scores comparatively to other possible ORFs; Starterator: no other pham members; START: i recommend either deleting the ORF or moving the ORF start to a shorter length even though it would drastically decrease the length (maybe Start: 63915)
    /note=Blast function: hypothetical protein; Synteny: no other pham members; HHPRED: no good results; FUNCTION: Unknown, it`s likely best to delete this gene.
    /note=
    /note=MR: Definitely delete