Pecaan Notes from students for Phage SUE2

CDS 75 - 542
  /gene="1"
  /product="gp1"
  /function="terminase, small subunit"
  /locus tag="Sue2_1"
    /note=Original Glimmer call @bp 75 has strength 9.99; Genemark calls start at 102
    /note=SSC: 75-542 CP: yes SCS: both-gl ST: SS BLAST-Start: [terminase small subunit [Arthrobacter phage VResidence]],,NCBI, q1:s1 99.3548% 2.69545E-93 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -2.583959800616441, yes F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Arthrobacter phage VResidence]],,UYL87606,93.5065,2.69545E-93 SIF-HHPRED: Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97},,,6Z6E_C,53.5484,98.6 SIF-Syn: SIF-Syn: (terminase small subunit, 1st gene; right terminase large subunit)
    /note=Original Glimmer call @bp 75 has strength 9.99; GeneMark calls start at 102
    /note=SSC: (75 to 542) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (aligns with VResidence_1, NCBI, q1:s1, 99%, 3e^-93) Gap: (NA) LO: (no) RBS: (Kibler6, Karlin Medium, 3.067, -2.584, yes) F: (terminase small subunit) SIF-BLAST: (terminase small subunit, NCBI, VResidence_1, UYL87606, 93.5065%, 3e^-93) SIF-HHPred: (terminase small subunit, HHPred, 6Z6E_C, 53.5484%, 98.65% SIF-Syn: (terminase small subunit, right terminase large subunit)

CDS 539 - 2245
  /gene="2"
  /product="gp2"
  /function="terminase, large subunit"
  /locus tag="Sue2_2"
    /note=Original Glimmer call @bp 539 has strength 11.43; Genemark calls start at 539
    /note=SSC: 539-2245 CP: yes SCS: both ST: SS BLAST-Start: [terminase large subunit [Arthrobacter phage VResidence]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.134, -4.455662434380964, no F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Arthrobacter phage VResidence]],,UYL87607,95.4225,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,93.1338,100.0 SIF-Syn: SIF-Syn: (terminase large subunit, VResidence, upstream gene is terminase small unit and downstream gene is portal protein)
    /note=F: (terminase large subunit) SIF-BLAST: (terminase large subunit, NCBI, VResidence_2, UYL87607.1, 92.96%, 0.0) SIF-HHPred: (terminase large subunit, 6Z6D_A, 89.69%, 100)

CDS 2267 - 3634
  /gene="3"
  /product="gp3"
  /function="Portal Protein"
  /locus tag="Sue2_3"
    /note=Original Glimmer call @bp 2267 has strength 11.85; Genemark calls start at 2267
    /note=SSC: 2267-3634 CP: yes SCS: both ST: SS BLAST-Start: [phage portal protein [Pseudarthrobacter siccitolerans] ],,NCBI, q1:s1 100.0% 0.0 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.03, -2.523003374675015, yes F: Portal Protein SIF-BLAST: ,,[phage portal protein [Pseudarthrobacter siccitolerans] ],,WP_050053393,93.6123,0.0 SIF-HHPRED: Portal protein; Bacteriophage, SPP1, Portal Protein, Head completion proteins, Connector Complex, DNA Channel, VIRAL PROTEIN; 2.7A {Bacillus subtilis},,,7Z4W_B,91.8681,100.0 SIF-Syn: SIF-Syn: (Portal Protein, Terminase large subunit and Capsid maturation protease, Adolin)
    /note=The Blast-Start is correct because I blasted the gene from the phagesdb website, and the same phage was the best match. When looking at the RBS based on PECAAN and the ORF the data didn`t match up, but I chose to go with the data from PECAAN because the Z score and Final Score.
    /note=
    /note=SSC: (2267, 3634) CP: (yes) SCS: (glimmer) ST: (SS) Blast-Start: (KeAliii, PECAAN, Q1:S1, 100%, E-Value: 0) Gap: (21bp) LO: (yes) RBS: Kibler7, Karlin Medium, 3.03, -2.523, yes) F: ( Portal Protein) SIF-BLAST: ( Portal Protien, PECAAN, KeAlii, WP_050053393, 93.6%, E-Value:0) SIF-HHPred: (Portal Protien, PECAAN, 7Z4W_B, 85.77%, 100) SIF-Syn: (Portal Protien, Terminase large subunit and Capsid maturation protease, Adolin)

CDS 3657 - 5714
  /gene="4"
  /product="gp4"
  /function="Capsid maturation protease and VIP2-like ADP-ribosyltransferase toxin"
  /locus tag="Sue2_4"
    /note=Original Glimmer call @bp 3657 has strength 11.12; Genemark calls start at 3693
    /note=SSC: 3657-5714 CP: yes SCS: both-gl ST: SS BLAST-Start: [head maturation protease [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 0.0 GAP: 22 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.11, -2.338663114094478, yes F: Capsid maturation protease and VIP2-like ADP-ribosyltransferase toxin SIF-BLAST: ,,[head maturation protease [Arthrobacter phage KeAlii] ],,YP_010678121,90.9489,0.0 SIF-HHPRED: d.166.1.1 (A:265-550) automated matches {Anthrax bacillus (Bacillus anthracis) [TaxId: 1392]} | CLASS: Alpha and beta proteins (a+b), FOLD: ADP-ribosylation, SUPFAM: ADP-ribosylation, FAM: ADP-ribosylating toxins,,,SCOP_d4dv8a1,37.5182,99.8 SIF-Syn: flanked by portal and scaffolding protein; Matched with VResidence
    /note=Function could be Capsid maturation or VIP2-like ...chose both.
    /note=
    /note=SSC: (3657, 5714) CP: (yes) SCS: (both) ST: ( BLAST-Start: Gap: LO: RBS: F: SIF-BLAST: SIF-HHPred: SIF-Syn

CDS 5771 - 6130
  /gene="5"
  /product="gp5"
  /function="hypothetical protein"
  /locus tag="Sue2_5"
    /note=Original Glimmer call @bp 5771 has strength 8.91; Genemark calls start at 5771
    /note=SSC: 5771-6130 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE15_gp05 [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 99.1597% 8.95727E-67 GAP: 56 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.781, -3.103539494358988, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE15_gp05 [Arthrobacter phage KeAlii] ],,YP_010678122,90.7563,8.95727E-67 SIF-HHPRED:  SIF-Syn: SIF-SYN: NKF
    /note=SSC: Start: 5771bp Stop: 6130bp CP: yes SCS: Both ST: SS Blast-Start: KeAlii_G5, NCBI, Q:1 S:1, Coverage: 99%, Evalue: 8.96e-67 Gap: 56bp gap LO: yes RBS Kibler6, Karlin Medium, Zscore: 2.817, Finale Score: -3.104, yes F: NKF SIF-Blast: hypothetical protein, NCBI, KeAlii_G5, YP_010678122, allingment: 90.8%, Evalue: 8,96e-67 SIF-HHpred: NKF   SIF-SYN:NKF

CDS 6247 - 6783
  /gene="6"
  /product="gp6"
  /function="scaffolding protein"
  /locus tag="Sue2_6"
    /note=Original Glimmer call @bp 6247 has strength 21.26; Genemark calls start at 6247
    /note=SSC: 6247-6783 CP: yes SCS: both ST: SS BLAST-Start: [head scaffolding protein [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 4.03416E-79 GAP: 116 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -3.3503726477288405, yes F: scaffolding protein SIF-BLAST: ,,[head scaffolding protein [Arthrobacter phage KeAlii] ],,YP_010678123,80.4348,4.03416E-79 SIF-HHPRED: Scaffold protein; major capsid protein, HK97-like fold, scaffolding protein, procapsid, VIRUS; 3.72A {Staphylococcus phage 80alpha},,,6B0X_b,64.6067,98.9 SIF-Syn: scaffolding protein, flanked by capsid maturation protease and major capsid protein, compared to VResidence
    /note=Original Glimmer call @bp 6247 has strength 21.26
    /note=SSC: (6247, 6783bp) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (KeAlii, NCBI, Q1:S1, 71.74%, 4e-79) (KeAlii_6, PhagesDB, Q1:S1, 71%, 5e-67) Gap: (116bp) LO: (no) RBS: (Kibler6, Karlin Medium, 3.067, -3.350, yes) F: (scaffolding protein) SIF-BLAST: (scaffolding protein, NCBI, KeAlii, YP_010678123.1, 71.74%, 4e-79) (scaffolding protein, PhagesDB, KeAlii_6, 71%, 5e-67) SIF-HHPred: (Probable capsid assembly scaffolding protein, UniProt, Mycobacterium phage D29, O64209, 56.22%, 99.59) SIF-Syn: (scaffolding protein, upstream gene: major capsid protein, downstream gene: NKF, compared to KeAlii)
    /note=
    /note=SSC: (6247, 6783bp) - taken from DNAMAster
    /note=CP: (yes) - GeneMark shows coding potential for the entire selected gene from the start codon that was auto-annotated
    /note=SCS: (both) - DNAMAster called for both Glimmer and GeneMark since there was no note saying otherwise
    /note=ST: (SS) - Starterator placed Sue2_6 in pham 1850 and this gene called for the most annotated start, which was start number 20
    /note=BLAST-Start: (KeAlii, NCBI, Q1:S1, 71%, 4e-79) (KeAlii_6, PhagesDB, Q1:S1, 71%, 5e-67)
    /note=Gap: (116bp) - unusual that there is a gap this long in this case because it is not between a forward and reverse gene - unable to extend the upstream gene (LORF) - no reason to extend gene 6 because there is  coding potential from the current start to the stop codon
    /note=LO: (no) - Not the longest open reading frame for Sue2_6 but no reason to extend the start based on results from blasting and GeneMark - good coding potential
    /note=RBS: (Kibler6, Karlin Medium, 3.067, -3.350, yes) - taken from the RBS frame in DNAMAster
    /note=F: (scaffolding protein) - determined from NCBI and PhagesDB blast - checked with the official function list
    /note=SIF-BLAST: (scaffolding protein, NCBI, KeAlii, YP_010678123.1, 71.74%, 4e-79) (scaffolding protein, PhagesDB, KeAlii_6, 71%, 5e-67) - results from the NCBI and PhagesDB blast
    /note=SIF-HHPred: (Probable capsid assembly scaffolding protein, UniProt, Mycobacterium phage D29, O64209, 56.22%, 99.59) - not sure about te function of this match
    /note=SIF-Syn: (scaffolding protein, upstream gene: major capsid protein, downstream gene: NKF, KeAlii) - Phamorator supports the information recorded but I am not really sure what the function of the downstream gene is because the text is overlapping and I am not sure how to tell if it is for gene 4 or gene 5

CDS 6842 - 7795
  /gene="7"
  /product="gp7"
  /function="major capsid protein"
  /locus tag="Sue2_7"
    /note=Original Glimmer call @bp 6842 has strength 18.02; Genemark calls start at 6842
    /note=SSC: 6842-7795 CP: yes SCS: both ST: SS BLAST-Start: [major head protein [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 0.0 GAP: 58 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.767, -5.160958035523474, no F: major capsid protein SIF-BLAST: ,,[major head protein [Arthrobacter phage KeAlii] ],,YP_010678124,96.2145,0.0 SIF-HHPRED: Major capsid protein; P22 Bacteriophage, VIRUS; 3.3A {Salmonella phage P22},,,5UU5_B,92.429,100.0 SIF-Syn: Synteny:
Reedo from the Phams database shows evidence of a major capsid protein at gene:7, start: 6854. Gene 7 is flanked by a scaffolding protein at gene 6 and a head-to-tail adaptor at gene 8.
    /note=Original Glimmer call @bp 6842 has strength 18.02
    /note=SSC: (Start: 6842bp, Stop: 7795bp), CP: (Yes), SCS: (Both), ST: (SS), Blast Start: (Phage Name: KeAlii, Gene Number: 7, Phage Database: PhagesDB/NCBI, Q/S Value: 1/1, E-Value: e-164, % Identification: 100.00%), Gene length: 954, Gap: (53 (longest reading frame), LO: (Yes), RBS: (Shine Dalgarno Scoring Matrix: Kibler6, Shine Dalgarno Spacing Matrix: Karlin Medium, Z-Value: 1.767, Final-Value: -5.161, Best Choice: Yes), Function: (Major Head Protein), SIF-BLAST: (Function: Major Head Protein, Arthrobacter phage KeAlii, Database: NCBI, Phage Name: KeAlii, Gene Number: 7, Database Accession Number: YP_010678124.1, %Alignment: 100.00%, E-Value: 0.0), SIF-HHPred: (NKF/Function: Major Capsid Protein, Database: PECAAN, Phage Name: Salmonella, Gene Number: 22, Hit: 5UU5_B, %Coverage: 92.429%, Probability: 100, E-Value: 5.1e-27), SIF-Syn:  (Function: Major Capsid Protein , Flanking Genes: Gene 6: Scaffolding protein, Gene 8: Head-to-tail Adaptor , Phages Used: Reedo, Database: Phams )

CDS 7875 - 8270
  /gene="8"
  /product="gp8"
  /function="head-to-tail adaptor"
  /locus tag="Sue2_8"
    /note=Original Glimmer call @bp 7875 has strength 11.92; Genemark calls start at 7875
    /note=SSC: 7875-8270 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail adaptor [Arthrobacter phage ObiToo]],,NCBI, q1:s1 100.0% 1.82565E-68 GAP: 79 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.264, -2.0162541296952132, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Arthrobacter phage ObiToo]],,WGH21184,88.5496,1.82565E-68 SIF-HHPRED: a.229.1.1 (A:) Hypothetical protein YqbG {Bacillus subtilis [TaxId: 1423]} | CLASS: All alpha proteins, FOLD: Hypothetical protein YqbG, SUPFAM: Hypothetical protein YqbG, FAM: Hypothetical protein YqbG,,,SCOP_d1xn8a_,83.2061,99.2 SIF-Syn: head-to-tail adaptor, downstream gene ObiToo_7, function: major tail protein, upstream gene ObiToo_9, function: NKF, same Pham as Sue2_9
    /note=SSC: (7875, 8270) CP: (Yes) SCS: (Both) ST: (NI) BLAST-Start: (ObiToo_8, NCBI, Q1:S1, 100%, 2e-68) Gap: (79 bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 3.264, -2.016, yes) F:(head-to-tail adaptor) SIF-BLAST: (head-to-tail adaptor, NCBI, ObiToo_8, WGH21184.1, 83.21%, 2e-68) SIF-HHPred: (head-to-tail adaptor, SCOPe, Hypothetical Protein YqbG, SCOP_d1xn8a, 80.9%, 99.24%) SIF-Syn: (head-to-tail adaptor, downstream gene ObiToo_7, function: major tail protein, upstream gene ObiToo_9, function: NKF, same Pham as Sue2_9)
    /note=
    /note=HHPred alignment call was made based on the presence of the crystal structure of Bacillus protein YqbG, which the SEA-PHAGES database says the protein must have in order to call the head-to-tail adaptor function.

CDS 8280 - 8396
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="Sue2_9"
    /note=Original Glimmer call @bp 8280 has strength 21.2; Genemark calls start at 8280
    /note=SSC: 8280-8396 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein PQE16_gp09 [Arthrobacter phage Reedo] ],,NCBI, q1:s1 97.3684% 3.85718E-11 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.363, -3.8366550365551095, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE16_gp09 [Arthrobacter phage Reedo] ],,YP_010678192,84.2105,3.85718E-11 SIF-HHPRED:  SIF-Syn: NFK, upstream gene is head-to-tail adaptor, downtail stream is head-to-tail stopper, Vresidence
    /note=SSC: (8280, 8396) CP: (yes) SCS: (both) ST:(NA) BLAST-Start: (NFK, no matches with an e-value above 10e-4) Gap: (1bp overlap) LO: (yes) RBS: (Kilber6, Karlin Medium, 2.396, -3.387, yes) F:(NFK) SIF-BLAST: (NFK, no matches with an e-value above 10e-4) SIF-HHPred: (NFK, no matches with a probability above 90%) SIF-Syn: (NFK, upstream gene is head-to-tail adaptor, downtail stream is head-to-tail stopper, Vresidence )

CDS 8396 - 8734
  /gene="10"
  /product="gp10"
  /function="head-to-tail stopper"
  /locus tag="Sue2_10"
    /note=Original Glimmer call @bp 8396 has strength 13.43; Genemark calls start at 8396
    /note=SSC: 8396-8734 CP: yes SCS: both ST: NI BLAST-Start: [head-to-tail stopper [Arthrobacter phage VResidence]],,NCBI, q1:s1 96.4286% 2.07847E-42 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.575, -3.534757715066017, yes F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Arthrobacter phage VResidence]],,UYL87615,76.3158,2.07847E-42 SIF-HHPRED: Stopper protein Rcc01689; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_E,95.5357,99.7 SIF-Syn: head-to-tail stopper, upstream 2 gene is head to tail adaptor, downstream 2 genes is tail terminator, Vresidence
    /note=Original Glimmer call @bp 8396 has strength 13.43
    /note=
    /note=SSC: (8396, 8734) CP: (yes) SCS: (both) ST: (NI) Blast-Start: (no significant BLAST alignments) Gap: (7bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.609, -3.535, yes) F: (NKF) SIF-BLAST: (NKF, no matches with e values below 10e-7) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (head-to-tail stopper, upstream gene is NKF, downstream gene is NKF, Vresidence)

CDS 8727 - 9035
  /gene="11"
  /product="gp11"
  /function="hypothetical protein"
  /locus tag="Sue2_11"
    /note=Original Glimmer call @bp 8727 has strength 8.09; Genemark calls start at 8727
    /note=SSC: 8727-9035 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Arthrobacter sp. EPSL27] ],,NCBI, q1:s1 99.0196% 1.4934E-41 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.81, -5.518457498840032, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Arthrobacter sp. EPSL27] ],,WP_066431362,84.466,1.4934E-41 SIF-HHPRED: DUF5403 ; Family of unknown function (DUF5403),,,PF17395.6,76.4706,96.9 SIF-Syn: SIF-Syn: (Sue2_11 is similar to Wildwest_12 but has a NKF.)
    /note=SSC: (8727/9035) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (Arthrobacter Sp. EPSL_27, NCBI, 1:1, 99%, 2E-41) Gap: (8bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.810, -5.518, Yes) F: (NKF) SIF-BLAST: (NKF, Arhtrobacter Sp. EPSL_27, Pecaan, WP_066431362, 84.47%, 1.49E-41) SIF-HHPred: (NKF, Pecaan, DUF_5403, PF17395.6, 76.47%, 96.9%) SIF-Syn: (Sue2_11 is similar to Wildwest_12 but has a NKF.)

CDS 9043 - 9456
  /gene="12"
  /product="gp12"
  /function="tail terminator"
  /locus tag="Sue2_12"
    /note=Original Glimmer call @bp 9043 has strength 9.29; Genemark calls start at 9043
    /note=SSC: 9043-9456 CP: yes SCS: both ST: SS BLAST-Start: [tail terminator [Arthrobacter phage VResidence]],,NCBI, q1:s1 100.0% 4.41372E-62 GAP: 7 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.128, -4.85287563363746, no F: tail terminator SIF-BLAST: ,,[tail terminator [Arthrobacter phage VResidence]],,UYL87617,88.5714,4.41372E-62 SIF-HHPRED: TAIL-TO-HEAD JOINING PROTEIN GP17; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_G,95.6204,99.4 SIF-Syn: Sif-syn: (Sue2 matches with gene 13 of wildwest, function: tail-terminator)
    /note=SCS:(9043, 9456), CP: (yes), SCS: (both), ST: (SS), Gap: (8), Lo: (No)  RBS: (Kelber 6, Karlin Medium: 2.303,-4.869), F:(tail terminator) SIF-Blast: (Tail Terminator, Wildwest, NCBI, 82%,100%, 4.41e-62) SIF-HHPred: (6tE9_F, Tailterminator, 99.3%,96.3%,5.3e-11), Sif-syn: (Sue2 matches with gene 13 of wildest, function: tail-terminator)

CDS 9472 - 10023
  /gene="13"
  /product="gp13"
  /function="major tail protein"
  /locus tag="Sue2_13"
    /note=Original Glimmer call @bp 9472 has strength 14.51; Genemark calls start at 9472
    /note=SSC: 9472-10023 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Arthrobacter phage VResidence]],,NCBI, q1:s1 98.3607% 9.32312E-108 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.781, -3.3136498407041004, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage VResidence]],,UYL87618,90.6593,9.32312E-108 SIF-HHPRED: YSD1_22 major tail protein; Bacteriophage tail, helical assembly, VIRAL PROTEIN; 3.5A {Bacteriophage sp.},,,6XGR_M,92.3497,98.5 SIF-Syn: Matches gene 14 on Wildwest: upstream tail terminator/downstream tail assembly chaperone
    /note=SSC: (9472, 10023) CP (yes) SCS (both) ST: (SS) BLAST-Start: (major tail protien,16,NCBI, Target From:1 Quary to: 1, 92.3496%,0.000012) Gap: (16) LO: (yes) RBS:(Kibler 6, Karin Medium, 3.264,-2.016,yes) F: (major tail protein) SIF-BLAST: (major tail protein, NCBI,Arthrobacter Phage VResidence, UYL87618, 98.3607%, 9.32312e-108) SIF HHPred: (major tail protien, PDB, N/A,6XGR_M, 92.3497%, 98.5) SIF-Syn: (Matches gene 14 on Wildwest: tail assmebly chaperone, Upstream matches gene 13 on Wildwest: tail terminator, Downstream matches gene 15 on Wildwest : tail assembly chaperone)

CDS 10128 - 10391
  /gene="14"
  /product="gp14"
  /function="tail assembly chaperone"
  /locus tag="Sue2_14"
    /note=Original Glimmer call @bp 10128 has strength 18.11; Genemark calls start at 10128
    /note=SSC: 10128-10391 CP: yes SCS: both ST: NI BLAST-Start: [tail assembly chaperone [Arthrobacter phage VResidence]],,NCBI, q3:s4 97.7011% 1.39961E-36 GAP: 104 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.264, -2.0162541296952132, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage VResidence]],,UYL87619,82.9545,1.39961E-36 SIF-HHPRED:  SIF-Syn: Match with Gene 15 on VResidence
    /note=SSC: (10128, 10391) CP: (Yes) SCS: (Both) ST: (SS) Blast-Start: ( NCBI, hypothetical protein, Target To 106, Target From 36, 91.46%, 6.09e-25) Gap: (106 bp) LO: (Yes) RBS: (Kibler 6, Karlin Medium, 0.486, -7.818) F: (NFK) SIF-BLAST: (hypothetical protein, NCBI, VResidence_14, UYL87619.1, 88% 1e-36), SIF-HHPred: (Phage tail assembly chaperone, HHPred, Phage_TAC_10, 82.7586 % 94.8%), SIF-Syn: (Match with Gene 15 on VResidence)

CDS join(10128..10385,10385..10759)
  /gene="15"
  /product="gp15"
  /function="tail assembly chaperone"
  /locus tag="Sue2_15"
    /note=
    /note=SSC: 10128-10759 CP: yes SCS: neither ST: NI BLAST-Start: [tail assembly chaperone [Arthrobacter phage VResidence]],,NCBI, q3:s4 95.7143% 1.06355E-97 GAP: -264 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.264, -2.0162541296952132, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage VResidence]],,UYL87620,81.4634,1.06355E-97 SIF-HHPRED:  SIF-Syn: 
    /note=Programmed Frame shift gene

CDS 10752 - 13142
  /gene="16"
  /product="gp16"
  /function="tape measure protein"
  /locus tag="Sue2_16"
    /note=Original Glimmer call @bp 10752 has strength 13.35; Genemark calls start at 10785
    /note=SSC: 10752-13142 CP: yes SCS: both-gl ST: SS BLAST-Start: [tape measure protein [Arthrobacter phage MaGuCo]],,NCBI, q1:s1 99.7487% 0.0 GAP: -9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.275, -1.993391246735709, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Arthrobacter phage MaGuCo]],,WGH20307,74.3329,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,12.3116,99.9 SIF-Syn: Match: MaGuCo gene 15 tape measure protein
Flanking: MaGuCo gene 14 tail assembly chaperon; MaGuCo gene 16 minor tail protein
    /note=Original Glimmer call @bp 10752 has strength 13.35; GeneMark calls start at 10785
    /note=SSC: [start: 10752, stop: 13142] CP: [Yes] SCS: [Glimmer only] ST: [SS] BLAST-Start: [Arthrobacter phage MaGuCo, gn: 15, NCBI, Q:1 S:1, coverage: 99.7487%, e-value: 0.0] Gap: [8bp overlap] LO: [NA] RBS: [Kibler 6, Karlin Medium, z-score: 3.314, final score: -1.993, Yes] F: [tape measure protien] SIF-BLAST: [tape measure protien, NCBI, Arthrobacter phage MaGuCo gn: 15, WGH20307, percent alignment: 74.3329%, e-value: 0.0] SIF-HHpred: [tape measure protien, RCSB PDB, 6V8I_BF, alignment: 12.3116%, probability: 99.9%] SIF-Syn: [tape measure protien, gene match: gene 15 tape measure protein, flanking genes: gene 14 tail assembly chaperon; gene 16 minor tail protein, Arthrobacter phage MaGuCo] Tmhmm: [Yes]

CDS 13142 - 14602
  /gene="17"
  /product="gp17"
  /function="minor tail protein"
  /locus tag="Sue2_17"
    /note=Original Glimmer call @bp 13142 has strength 14.9; Genemark calls start at 13142
    /note=SSC: 13142-14602 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Wildwest]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.954, -3.2535385006449706, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Wildwest]],,WNO26037,87.4227,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_C,93.8272,99.9 SIF-Syn: 
    /note=Original Glimmer call @bp 13142 has strength 14.90
    /note=SSC: (13142 to 14602) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (aligns with Wildwest_18, NCBI, q1: s1, 100%, 0) Gap: (0 bp) LO: (yes) RBS: (Kibler 7, Broad, 3.017, -2.836, yes) F: (minor tail protein) SIF-BLAST: (minor tail protein, NCBI, Wildwest_18, WNO26036, 87.4227, 0) SIF-HHPred: (minor tail protein, HHPred, 2X8K_C, 93.8272%, 99.9%) SIF-Syn: (minor tail protein, left tape measure protein, right minor tail protein)

CDS 14593 - 15807
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="Sue2_18"
    /note=Original Glimmer call @bp 14593 has strength 11.48; Genemark calls start at 14593
    /note=SSC: 14593-15807 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Wildwest]],,NCBI, q1:s1 100.0% 0.0 GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.128, -4.97781437024576, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Wildwest]],,WNO26038,92.3267,0.0 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_A,99.0099,99.7 SIF-Syn: SIF-Syn: (minor tail protein, Wildwest, upstream gene 18 is minor tail protein and downstream gene 20 is minor tail protein)
    /note=F: (minor tail protein) SIF-BLAST: (minor tail protein, NCBI, Wildwest_19, WNO26038.1, 83.17%, 0.0) SIF-HHPred: (tail protein, 3D37_A, 84.51%, 99.65)

CDS 15808 - 16815
  /gene="19"
  /product="gp19"
  /function="minor tail protein"
  /locus tag="Sue2_19"
    /note=Original Glimmer call @bp 15808 has strength 13.92; Genemark calls start at 15808
    /note=SSC: 15808-16815 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Wildwest]],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.52, -3.649482460397077, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Wildwest]],,WNO26039,91.3174,0.0 SIF-HHPRED:  SIF-Syn: 
    /note=In order to make the best decision the blast information I checked the NCBI website and based on the EValue the NCBI website was a better match then Pecaan. The HHPred database was a better option for the annotations because of the probability being higher and the EValue being lower. The HHPred website is also updated more often than Pecaan.
    /note=
    /note=Original Glimmer call @bp 15808 has strength 13.92 
    /note=SSC:(15808,16815)  CP: (yes) SCS: (glimmer) ST: SS Blast-Start( Wildwest, NCBI, Q1:S1, EValue-0) Gap:( 0bp) LO: (No) RBS: (Kibler 7, Karlin Medium, 2.52, -3.649, yes) F: (minor tail protien) SIF-BLAST: (long tail fiber protein, HHPred, Enterobacterio phage, 37, Q9G0B5, 43%, EValue-0.0028) SIF-SYN: (minor tail protein, minor tail protien and minor tail protein, Adolin)

CDS 16812 - 17894
  /gene="20"
  /product="gp20"
  /function="minor tail protein"
  /locus tag="Sue2_20"
    /note=Original Glimmer call @bp 16812 has strength 17.38; Genemark calls start at 16812
    /note=SSC: 16812-17894 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Arthrobacter phage Wildwest]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.03, -2.5052746077145835, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Wildwest]],,WNO26040,91.1111,0.0 SIF-HHPRED: Receptor Binding Protein; beta sandwich domain, phage receptor binding protein, Lactococcus lactis pellicle cell wall polyphosphosaccharide, VIRAL PROTEIN; 1.75A {Lactococcus phage 1358},,,4L9B_A,47.5,99.0 SIF-Syn: Follows minor tail protein; like Wildwest
    /note=Original Glimmer call @bp 16812 has strength 17.38
    /note=GENE 20 PhagesDB
    /note=FUNCTION: minor tail protein
    /note=SSC: (16812, 17894)
    /note=CP: yes
    /note=SCS: (Glimmer)
    /note=ST: (SS)
    /note=BLAST-Start: (Wildwest, 21, PhagesDB, Q1:S1, 91.1%, 99.03%)
    /note=Gap: (-4)
    /note=LO: No
    /note=RBS: Kibler 6, Karlin Medium, 3.03, -2.505, yes)
    /note=F: (minor tail protein)
    /note=SIF-BLAST: (minor tail protein, NCBI, Wildwest, WNO26040, Q1:S1, 91.1%,0)
    /note=SIF-HHPred: (receptor binding protein, HHPres, 4L9B_4, 91.1%, 99.03%)
    /note=SIF-Syn: (minor tail protein, upstream: minor tail protein, downstream: minor tail protein, Wildwest_21)

CDS 17971 - 18432
  /gene="21"
  /product="gp21"
  /function="hypothetical protein"
  /locus tag="Sue2_21"
    /note=Original Glimmer call @bp 17971 has strength 9.17; Genemark calls start at 17971
    /note=SSC: 17971-18432 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 1.37361E-62 GAP: 76 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.767, -5.733054803473993, no F: hypothetical protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage KeAlii] ],,YP_010678138,82.3529,1.37361E-62 SIF-HHPRED:  SIF-Syn: SIF-Syn: NKF
    /note=Original Glimmer call @bp 17971 has strength 9.17
    /note=SSC: Start: 17971bp Stop: 18432bp
    /note=CP: Yes
    /note=SCS: Both
    /note=ST: SS
    /note=Blast-Start: KeAlli, NCBI, Q:1 S:1, Coverage: 100% Evalue: 1E-62. 
    /note=Gap: 76bp gap 
    /note=LO: Yes
    /note=RBS: Kibbler6, Karlin medium, Zscore: 1.767, Finale Score: -5.733, no 
    /note=F: NKF
    /note=SIF Blast: Membrane Protein, NCBI, KeAlli, YP_010678138.1, 
    /note=Alignment: 68.39%, Evalue: 1E-62
    /note=SIF-HHPred: NKF
    /note=SIF-Syn: NKF

CDS 18425 - 18823
  /gene="22"
  /product="gp22"
  /function="hypothetical protein"
  /locus tag="Sue2_22"
    /note=Original Glimmer call @bp 18425 has strength 13.73; Genemark calls start at 18425
    /note=SSC: 18425-18823 CP: yes SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 1.22475E-69 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.531, -3.627004739933808, yes F: hypothetical protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage KeAlii] ],,YP_010678139,90.1515,1.22475E-69 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 18425 has strength 13.73
    /note=SSC: (18425bp, 18823bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (KeAlii, NCBI, Q1:S1, 78.03%, 1e-69) (KeAlii_22, PhagesDB, Q1:S1, 78%, 3e-55) Gap: (8bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.564, -3.627, yes) F: (NKF) SIF-BLAST: (membrane protein, NCBI, KeAlii, YP_010678139.1, 78.03%, 1e-69) (unknown, PhagesDB, KeAlii_22, 78%, 3e-55) SIF-HHPred: (probable spanin, UniProt, Escherichia phage P2, P51770, 30%, 98.25) SIF-Syn: (NKF)
    /note=
    /note=SSC: (18425bp, 18823bp) - found on DNAMAster
    /note=CP: (yes) - not consistent throughout the entire gene so I am a little unsure, but there is coding potential throughout most of the gene
    /note=SCS: (both) - DNAMAster calls for both Glimmer and GeneMark and it does not show that it is calling for GeneMark specifically
    /note=ST: (NI) - Sue2_22 was found under "Genes that do not have the "Most Annotated" start"
    /note=BLAST-Start: (KeAlii, NCBI, Q1:S1, 78.03%, 1e-69) (KeAlii_22, PhagesDB, Q1:S1, 78%, 3e-55)
    /note=Gap: (8bp overlap) - this makes sense for this gene because it is less than 50bp and it is not between a forward and a reverse gene
    /note=LO: (yes)
    /note=RBS: (Kibler6, Karlin Medium, 2.564, -3.627, yes) - the RBS scores given on DNAMAster show that this is the best start and LORF
    /note=F: (NKF) - I am not sure about the function of this gene because there is not really any good proof that it has a known function based off of comparison to the genes that it matched with
    /note=SIF-BLAST: (membrane protein, NCBI, KeAlii, YP_010678139.1, 78.03%, 1e-69) (unknown, PhagesDB, KeAlii_22, 78%, 3e-55) - These are the blast results that led me to conclude that the function of gene 22 is unknown
    /note=SIF-HHPred: (probable spanin, UniProt, Escherichia phage P2, P51770, 30%, 98.25) - HHPred matches with a phage that is different from NCBI and PhagesDB but the %alignment is very low compared to the other results. The results from the other databases were overall better so I do not think we can determine a function from HHPred either - the function for this phage gene also is not included in the official function list
    /note=SIF-Syn: (NKF) - The function of the gene that it was compared with and has synteny with is not clear on Phamerator - the immediate flanking genes are also not categorized to have a specific function

CDS 18846 - 19097
  /gene="23"
  /product="gp23"
  /function="hypothetical protein"
  /locus tag="Sue2_23"
    /note=Original Glimmer call @bp 18846 has strength 17.61; Genemark calls start at 18846
    /note=SSC: 18846-19097 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp23 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 8.36502E-40 GAP: 22 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.167, -3.0637723674875006, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp23 [Arthrobacter phage DrSierra] ],,YP_010678348,91.5663,8.36502E-40 SIF-HHPRED:  SIF-Syn: Synteny: DrSierra from the Phams database shows evidence of no known function at Gene 23: Start: 18674. Gene 23 is flanked by no known function at Gene 22 and Deoxynucleoside Monophosphate Kinase at Gene 24.
    /note=Original Glimmer call @bp 18846 has strength 17.61
    /note=SSC: (Start: 18846bp, Stop: 19097bp), CP: (Yes), SCS: (Both), ST: (SS), Blast Start: (Phage Name: DrSierra, Gene Number: 23, Phage Database: PhagesDB/NCBI, Q/S Value: 1/1, E-Value: 9e-40, % Identification: 84.34%), Gene Length: 252bp, Gap: (22 bp), LO: (Yes), RBS: (Shine Dalgarno Scoring Matrix: Kibler6, Shine Dalgarno Spacing Matrix: Karlin Medium, Z-Value: 3.167, Final-Value: -3.064, Best Choice: Yes), Function: (No Known Function), SIF-BLAST: (No Known Function, Database: NCBI, Phage Name: DrSierra, Gene Number: 23, Database Accession Number: YP_010678348, %Alignment: 91.57, E-Value: 8.37e-40), SIF-HHPred: No Known Function, SIF-Syn:  (No Known Function, Flanking Genes: Gene 22: NKF, Gene 24: deoxynucleoside monophosphate kinase, Phages Used: DrSierra)

CDS 19097 - 19291
  /gene="24"
  /product="gp24"
  /function="membrane protein"
  /locus tag="Sue2_24"
    /note=Original Glimmer call @bp 19097 has strength 9.05; Genemark calls start at 19097
    /note=SSC: 19097-19291 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Crewmate] ],,NCBI, q1:s1 100.0% 2.44501E-33 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.871, -5.004720841432911, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Crewmate] ],,YP_010678276,96.875,2.44501E-33 SIF-HHPRED:  SIF-Syn: NKF
    /note=SSC: (19097, 19291) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (Crewmate_25, NCBI, Q1:S1, 100%, 2e-33) Gap: (1 bp overlap) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.871, -5.005, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 19348 - 20793
  /gene="25"
  /product="gp25"
  /function="Endolysin"
  /locus tag="Sue2_25"
    /note=Original Glimmer call @bp 19348 has strength 12.89; Genemark calls start at 19348
    /note=SSC: 19348-20793 CP: yes SCS: both ST: NI BLAST-Start: [endolysin [Arthrobacter phage Wildwest]],,NCBI, q1:s1 100.0% 0.0 GAP: 56 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.264, -2.033982896655645, yes F: Endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Wildwest]],,WNO26073,86.6667,0.0 SIF-HHPRED: d.118.1.1 (A:174-344) Peptidoglycan-recognition protein-LE {Fruit fly (Drosophila melanogaster) [TaxId: 7227]},,,d2cb3a1,29.5218,99.8 SIF-Syn: endolysin, upstream gene is NFK, dmatches VREsidence; no holin
    /note=Original Glimmer call @bp 19348 has strength 12.89
    /note=SSC: (19348, 20793) CP: (yes) SCS: (both) ST: (NI) Blast-Start: (Wildwest, NCBI, Q1:S1, 100%, 0.0) Gap: (57 bp) LO: (yes) RBS: (Kilber 6, Karlin Medium, 3.264, -2.034, yes) F: (Endolysin) SIF-BLAST: (Endolysin, NCBI, Wildwest, YP_010678141.1, 78.60%, 0.0) SIF-HHPred: (Peptidoglycan Recognizing Protein, HHpred, hypothetical protein, 3D2Y_A, 70.8%, 99.59) SIF-Syn: (Deoxynucleoside monophosphate kinase, upstream gene is NFK, downstream gene is NFK)

CDS 20911 - 21525
  /gene="26"
  /product="gp26"
  /function="deoxynucleoside monophosphate kinase"
  /locus tag="Sue2_26"
    /note=Original Glimmer call @bp 20911 has strength 17.46; Genemark calls start at 20941
    /note=SSC: 20911-21525 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein [Pseudarthrobacter siccitolerans] ],,NCBI, q1:s1 100.0% 8.03691E-127 GAP: 117 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.264, -1.953940808934884, yes F: deoxynucleoside monophosphate kinase SIF-BLAST: ,,[hypothetical protein [Pseudarthrobacter siccitolerans] ],,WP_050053373,93.5961,8.03691E-127 SIF-HHPRED: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE; TRANSFERASE, PHOSPHOTRANSFERASE; HET: DGP, OCS; 2.0A {Enterobacteria phage T4} SCOP: c.37.1.1,,,1DEK_A,93.1373,99.8 SIF-Syn: deoxynucleoside monophosphate kinase, upstream gene is NKF, downstream gene is NKF, Phives
    /note=SSC: (20911, 21525) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (no significant BLAST alignments) Gap: (118bp gap) LO: (no) RBS: (Kibler6, Karlin Medium, 3.264, -1.954, yes) F: (NKF) SIF-Blast: (NKF, no matches with e-values below 10e-7) SIF-HHPred: (Deoxynucleoside monophosphate kinase, HHpred, Tequatrovirus T4, 1DEK_A, 93.1373%, 99.8%) SIF-Syn: (deoxynucleoside monophosphate kinase, upstream gene is NKF, downstream gene is NKF, Phives)

CDS 21609 - 22199
  /gene="27"
  /product="gp27"
  /function="hypothetical protein"
  /locus tag="Sue2_27"
    /note=Original Glimmer call @bp 21609 has strength 8.53; Genemark calls start at 21609
    /note=SSC: 21609-22199 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE15_gp26 [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 97.9592% 1.86718E-88 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.792, -5.679831809821832, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE15_gp26 [Arthrobacter phage KeAlii] ],,YP_010678143,81.6327,1.86718E-88 SIF-HHPRED:  SIF-Syn: SIF-Syn: (Sue2_27 is similar to Wildwest_26 but has a NFK.)
    /note=SSC: (21609/22199) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (KeAlii_26, NCBI, 1:1, 97%, 2E-88) Gap: (None) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.792, -5.680, Yes) F: (NKF) SIF-BLAST: (NKF, Pecaan, KeAlii_26, YP_010678143, 81.63%, 1.87E-88) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (Sue2_27 is similar to Wildwest_26 but has a NKF.)

CDS 22367 - 23227
  /gene="28"
  /product="gp28"
  /function="exonuclease"
  /locus tag="Sue2_28"
    /note=Original Glimmer call @bp 22397 has strength 15.98; Genemark calls start at 22502
    /note=SSC: 22367-23227 CP: yes SCS: both-cs ST: NI BLAST-Start: [exonuclease [Arthrobacter phage KeAlii] ],,NCBI, q11:s1 96.1538% 0.0 GAP: 167 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.84, -4.990886107097708, no F: exonuclease SIF-BLAST: ,,[exonuclease [Arthrobacter phage KeAlii] ],,YP_010678144,94.9091,0.0 SIF-HHPRED: Mitochondrial genome maintenance exonuclease 1; human MGME1, DNA complex, DNA exonuclease, DNA BINDING PROTEIN; 2.702A {Homo sapiens},,,5ZYT_C,81.4685,99.8 SIF-Syn: Sif-syn: (sue2 28 matches with gene 27 of wildest, function: exonuclease)
    /note=SSC: (22367,23227) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (KeAlii_-, NCBI, 1:11, 99%,1e-161) Gap:(168bp) LO (Yes) RBS (Kibler6, Karlin Medium 1.84, -4.991,True) F: (exonuclease) SIF-BLAST: (RECB-exonuclease, KeAii, NCBI WNQ26046, 95.9%, 1.5e-180) SIF-HHPred: (Mitochondrial genome maintenance exonuclease 1) Sif-syn: (sue2 28 matches with gene 27 of wildest, function: exonuclease)
    /note=No starterator; went with LORF and to cover the CP.

CDS 23242 - 23610
  /gene="29"
  /product="gp29"
  /function="nucleoside deoxyribosyltransferase"
  /locus tag="Sue2_29"
    /note=Original Glimmer call @bp 23242 has strength 8.62; Genemark calls start at 23242
    /note=SSC: 23242-23610 CP: no SCS: both ST: SS BLAST-Start: [DUF4406 domain-containing protein [Pseudarthrobacter siccitolerans] ],,NCBI, q1:s1 99.1803% 1.04162E-58 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.995, -6.691756296460556, no F: nucleoside deoxyribosyltransferase SIF-BLAST: ,,[DUF4406 domain-containing protein [Pseudarthrobacter siccitolerans] ],,WP_083435243,83.6066,1.04162E-58 SIF-HHPRED: c.23.14.2 (A:1-118) Hypothetical protein PA1492 {Pseudomonas aeruginosa [TaxId: 287]} | CLASS: Alpha and beta proteins (a/b), FOLD: Flavodoxin-like, SUPFAM: N-(deoxy)ribosyltransferase-like, FAM: Hypothetical protein PA1492,,,SCOP_d1t1ja1,90.1639,99.7 SIF-Syn: Matches gene 28 on Wildwest: nucleoside deoxyribosyltransferase, Upstream matches gene 29 on Wildwest: LAGLIDADG endonuclease, Downstream matches gene 27 on Wildwest : RecB-like exonuclease/helicase
    /note=very small CP not covered; scores and SS chosen.
    /note=SSC: (23242,23610) CP:(yes) SCS:(both) ST: (N/A) BLAST-Start: (nuceloside deoxyribosyltransferase, 15, NCBI, Target From: 2 Quary To: 1, 2e-15) Gap:(15) LO:(no) RBS:(Kibler 6 Karlin Medium, 0.995,-6.692, no) F: (nuceloside deoxyribosyltransferase) SIF-BLAST: (domain-containing protien, NCBI, Berrie, WP_083435243,99.1803,1.04162e-58) SIF-HHPred: (hypothetical protein, SCOPe,Pseudomonas aeruginosa, SCOP_d1t1ja1, 90.1639%, 99.7) SIF-Syn: (Matches gene 28 on Wildwest: nucleoside deoxyribosyltransferase, Upstream matches gene 29 on Wildwest: LAGLIDADG endonuclease, Downstream matches gene 27 on Wildwest : RecB-like exonuclease/helicase)

CDS 23607 - 24014
  /gene="30"
  /product="gp30"
  /function="LAGLIDADG endonuclease"
  /locus tag="Sue2_30"
    /note=Original Glimmer call @bp 23607 has strength 10.21; Genemark calls start at 23607
    /note=SSC: 23607-24014 CP: yes SCS: both ST: SS BLAST-Start: [LAGLIDADG endonuclease [Arthrobacter phage VResidence]],,NCBI, q3:s2 98.5185% 1.00216E-79 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.933, -2.707694805492614, yes F: LAGLIDADG endonuclease SIF-BLAST: ,,[LAGLIDADG endonuclease [Arthrobacter phage VResidence]],,UYL87634,92.5373,1.00216E-79 SIF-HHPRED: I-CREI; ENDONUCLEASE, GROUP I MOBILE INTRON, INTRON HOMING, CHLOROPLAST DNA, LAGLIDADG MOTIF; 3.0A {Chlamydomonas reinhardtii} SCOP: d.95.2.1,,,1AF5_A,76.2963,99.4 SIF-Syn: Matches gene 29 on VResidence, laglidadg endonuclease
    /note=SSC: (23607, 24014) CP: (No) SCS: (Glimmer) ST: (NI) BLAST-Start: (NCBI, Arthrobacter phage VResidence, Target From: 0, Target To: 134), 98.52% coverage, 9.72728e-80) Gap: (-3/0) LO: (No) RBS: (Kibler 6, Karlin Medium, 11, 2.933, -2.708, yes) F: (NKF), SIF-BLAST:  (Arthrobacter phage, NCBI, VResidence, UYL87634, 92.5373% alignment, 1.00216e-79) SIF-HHPred: (laglidadg endonuclease, HHPred, SCOP_d2vboa_, 75.2593% alignment, 99.6) SIF-Syn: (Matches gene 29 on VResidence, laglidadg endonuclease)

CDS 24135 - 24851
  /gene="31"
  /product="gp31"
  /function="recombination directionality factor"
  /locus tag="Sue2_31"
    /note=Original Glimmer call @bp 24135 has strength 18.73; Genemark calls start at 24135
    /note=SSC: 24135-24851 CP: yes SCS: both ST: SS BLAST-Start: [recombination directionality factor [Arthrobacter phage VResidence]],,NCBI, q1:s1 100.0% 6.82353E-146 GAP: 120 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.933, -3.5527928455068705, yes F: recombination directionality factor SIF-BLAST: ,,[recombination directionality factor [Arthrobacter phage VResidence]],,UYL87635,92.437,6.82353E-146 SIF-HHPRED: Gp3-like ; Recombination directionality factor-like,,,PF18897.4,87.8151,100.0 SIF-Syn: SIF-Syn: (Upstream gene is the recombination directionality factor, downstream gene is tape measure protein.)
    /note=SSC: (24135,24851) CP: (yes) SCS: (Glimmer Only) ST: (SS) Blast Start: (KeAlii_30, NCBI, Q1:S1, 100% coverage, e-value is 2e153) Gap: (120bp) LO: (yes) RBS: (Kibler6, Karlin Medium, z score: 2.933, final score: -3.553, yes) F: (recombination directionality factor) SIF: (Supporting (information for function) SIF-HHPred:	(Recombination directionality factor, PDB, hit number: PF18897.4, percent alignment 87.8151%, 100% probability.)

CDS 24851 - 24967
  /gene="32"
  /product="gp32"
  /function="hypothetical protein"
  /locus tag="Sue2_32"
    /note=Original Glimmer call @bp 24851 has strength 10.23; Genemark calls start at 24851
    /note=SSC: 24851-24967 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE19_gp31 [Arthrobacter phage Tweety19] ],,NCBI, q1:s1 100.0% 1.47052E-4 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.303, -4.1022174314215265, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE19_gp31 [Arthrobacter phage Tweety19] ],,YP_010678422,71.0526,1.47052E-4 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 24851 has strength 10.23
    /note=SSC: [start: 24851, stop: 24967] CP: [Yes] SCS: [Both] ST: [SS] BLAST-Start: [Arthrobacter phage Tweety19, gn: 31, NCBI, Q:1 S:1, coverage: 100%, e-value: 2e-04] Gap: [1bp overlap] LO: [NA] RBS: [Kibler6, Karlin Medium, z-score: 2.335, final score: -4.102, Yes] F: [hypothetical protien] SIF-BLAST: [hypothetical protien, NCBI, Athrobacter phage Tweety19, gn: 31, YP_010678422, percent alignment: 71%, e-value: 0.0] SIF-HHPred: [NKF, no matches with a probabilitly over 90%] SIF-Syn: [NKF, flanking genes: 848 (162); 132100 (57), Arthrobacter phage Tweety19]
    /note=
    /note=CP but no strong BNLAST hits

CDS 25042 - 25371
  /gene="33"
  /product="gp33"
  /function="hypothetical protein"
  /locus tag="Sue2_33"
    /note=Original Glimmer call @bp 25042 has strength 11.84; Genemark calls start at 25042
    /note=SSC: 25042-25371 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE15_gp32 [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 3.25543E-52 GAP: 74 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.03, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE15_gp32 [Arthrobacter phage KeAlii] ],,YP_010678149,81.6514,3.25543E-52 SIF-HHPRED:  SIF-Syn: 
    /note=Original Glimmer call @bp 25042 has strength 11.84
    /note=SSC: (25042 to 25371) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (aligns with KeAlii_32, phagedb, q1:s1, 100%, 2e^-41) Gap: (74 bp) LO: (yes) RBS: (Kibler6, Karlin Medium, 3.067, -2.443, yes) F: (hypothetical protein) SIF-BLAST: (hypothetical protein, NCBI, KeAlii_32, YP_010678149, 81.6514%, 0) SIF-HHPred: (hypothetical protein, HHPred, 8P66_B, 33.0275%, 87.7) SIF-Syn: (hypothetical protein, downstream NKF, upstream NrdH-like glutaredoxin)

CDS 25374 - 25640
  /gene="34"
  /product="gp34"
  /function="NrdH-like glutaredoxin"
  /locus tag="Sue2_34"
    /note=Original Glimmer call @bp 25374 has strength 15.71; Genemark calls start at 25374
    /note=SSC: 25374-25640 CP: yes SCS: both ST: NA BLAST-Start: [NrdH-like glutaredoxin [Arthrobacter phage Cassia]],,NCBI, q1:s1 100.0% 3.60613E-48 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.876, -3.4175091270247986, yes F: NrdH-like glutaredoxin SIF-BLAST: ,,[NrdH-like glutaredoxin [Arthrobacter phage Cassia]],,WGH21107,89.7727,3.60613E-48 SIF-HHPRED: GLUTAREDOXIN-LIKE PROTEIN NRDH; ELECTRON TRANSPORT, NRDH, THIOREDOXIN, GLUTAREDOXIN, REDOX PROTEIN; 1.7A {ESCHERICHIA COLI} SCOP: c.47.1.1,,,1H75_A,85.2273,99.5 SIF-Syn: SIF-Syn: (NrdH-like glutaredoxin, Cassia, upstream gene 32 is NKF and downstream gene 35 is NKF)
    /note=Original Glimmer call @bp 25374 has strength 15.71 SSC: (25374, 25640) CP: (yes) SCS: (both) ST: (NA) Blast-Start: (Cassia_34, NCBI, Q1:S1, 100%, 4e-48) Gap: (2 bp) LO: (NA) RBS: (Kibler 6, Karlin Medium, 2.912, -3.418, yes) F: (NrdH-like glutaredoxin) SIF-BLAST: (NrdH-like glutaredoxin, NCBI, Cassia_34, WGH21107.1, 85.23%, 4e-48) SIF-HHPred: (glutaredoxin-like protein NrdH, 1H75_A, 92.59%, 99.5) SIF-Syn: (NrdH-like glutaredoxin, Cassia, upstream gene 32 is NKF and downstream gene 35 is NKF)

CDS 25637 - 26242
  /gene="35"
  /product="gp35"
  /function="metallophosphoesterase"
  /locus tag="Sue2_35"
    /note=Original Glimmer call @bp 25637 has strength 13.09; Genemark calls start at 25637
    /note=SSC: 25637-26242 CP: yes SCS: both ST: SS BLAST-Start: [phosphoesterase [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 98.5075% 3.48895E-113 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.933, -3.5527928455068705, yes F: metallophosphoesterase SIF-BLAST: ,,[phosphoesterase [Arthrobacter phage KeAlii] ],,YP_010678152,85.5721,3.48895E-113 SIF-HHPRED: Vacuolar protein sorting-associated protein 29; complex, cellular trafficking, endosomal sorting, HYDROLASE; 1.5A {Homo sapiens} SCOP: d.159.1.7, l.1.1.1,,,5GTU_A,82.5871,99.5 SIF-Syn: Sue2 gene 35 matches with KeAlii gene 35 with the function being Metallophospoesterase. The two flanking genes are Nrdl-like glutaredoxin and holiday junction resolvase)
    /note=Original Glimmer call @bp 25637 has strength 13.09
    /note=SSC: (25637,26242) CP: (yes) SCS: (glimmer) ST: (SS) Blast-Start: (KeAlii, Pecaan, Q1:, S1, 98%, Evalue-3.48895E-113) Gap:( 4 bp overlap) LO: (no) RBS: (Kibler7, Karlin Medium, 2.896,-3.138, yes) F:( DNA Primase/Helicase) SIF-BLAST: Metallophosphoesterase, Pecaan, KeAlii, YP_010678152.1, 78.61%, EValue: 4e-113) SIF-HHPred: (Hydrolase, Pecaan, 5GTU_A, 82.59%, 99.5) SIF Syn: (Metallophospoesterase,Nrdl-like glutaredoxin, holiday junction resolvase)

CDS 26239 - 26682
  /gene="36"
  /product="gp36"
  /function="Holliday junction resolvase"
  /locus tag="Sue2_36"
    /note=Original Glimmer call @bp 26239 has strength 10.3; Genemark calls start at 26239
    /note=SSC: 26239-26682 CP: yes SCS: both ST: SS BLAST-Start: [holliday junction resolvase [Arthrobacter phage Iter] ],,NCBI, q1:s1 100.0% 4.57207E-75 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.531, -3.627004739933808, yes F: Holliday junction resolvase SIF-BLAST: ,,[holliday junction resolvase [Arthrobacter phage Iter] ],,URQ05025,87.7551,4.57207E-75 SIF-HHPRED: Holliday junction resolvase; archeal holliday junction resolvase helicase DNA binding enzyme phage 15-6 thermus thermophilus, RECOMBINATION; HET: SO4, MSE; 2.5A {Thermus thermophilus phage 15-6},,,7BGS_A,76.8708,99.5 SIF-Syn: (holliday junction resolvase, upstream: metallophosphoesterase, downstream: no known function, Wildwest_35)

CDS complement (26719 - 26877)
  /gene="37"
  /product="gp37"
  /function="hypothetical protein"
  /locus tag="Sue2_37"
    /note=Original Glimmer call @bp 26877 has strength 4.99; Genemark calls start at 26877
    /note=SSC: 26877-26719 CP: no SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_KEALII_68 [Arthrobacter phage KeAlii]],,NCBI, q4:s3 90.3846% 9.52067E-7 GAP: 145 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.933, -3.1725816037952645, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_KEALII_68 [Arthrobacter phage KeAlii]],,WEM34621,53.0303,9.52067E-7 SIF-HHPRED:  SIF-Syn: SIF-Syn:NKF
    /note=Has coding potential but no strong BLAST hits. 
    /note=Small amount of CP not covered.  Scores and gaps are better with SS.
    /note=
    /note=Original Glimmer call @bp 26877 has strength 4.99
    /note=SSC: Start: 26877bp Stop: 26719bp
    /note=CP: yes 
    /note=SCS: Both 
    /note=ST: NI
    /note=Blast-Start: KeAlli_68, NCBI, Q:4 S:3, Coverage: 90%, Evalue: 1E-6.
    /note=Gap:145bp
    /note=LO:no
    /note=RBS: Kibler6, Karlin Medium, Zvalue:2.970, Final Score:-3.173, yes.
    /note=F:NKF
    /note=SIF-Blast: NKF
    /note=SIF-HHpred: NKF
    /note=SIF-Syn:NKF

CDS 27023 - 29533
  /gene="38"
  /product="gp38"
  /function="DNA primase/helicase"
  /locus tag="Sue2_38"
    /note=Original Glimmer call @bp 27023 has strength 12.84; Genemark calls start at 27023
    /note=SSC: 27023-29533 CP: yes SCS: both ST: NI BLAST-Start: [DNA primase/helicase [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 0.0 GAP: 145 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.363, -3.9166971242758706, no F: DNA primase/helicase SIF-BLAST: ,,[DNA primase/helicase [Arthrobacter phage KeAlii] ],,YP_010678154,93.6527,0.0 SIF-HHPRED: Putative primase C962R; polymerase, primase, PrimPol, Helicase, DNA BINDING PROTEIN; HET: ANP;{African swine fever virus BA71V},,,8IQI_C,55.3828,100.0 SIF-Syn: DNA primase/helicase, upstream: DNA polymerase 1, downstream: holliday junction resolvase, compared to KeAlii
    /note=Original Glimmer call @bp 27023 has strength 12.84
    /note=SSC: (27023bp, 29533bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (KeAlii, NCBI, Q1:S1, 89.84%, 0.0) (KeAlii_37, PhagesDB, Q1:S1, 90%, 0.0) Gap: (145bp) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.395, -3.917, no) F: (DNA primase/helicase) SIF-BLAST: (DNA primase/helicase, NCBI, KeAlii, YP_010678154.1, 89.84%, 0.0) (DNA primase/helicase, PhagesDB, KeAlii_37, 90%, 0.0) SIF-HHPred: (DNA primase, UniProt, Enterobacteria phage P4, P10277, 91.89%, 100) SIF-Syn: (DNA primase/helicase, upstream: DNA polymerase 1, downstream: holliday junction resolvase, compared to KeAlii)
    /note=
    /note=SSC: (27023bp, 29533bp)
    /note=CP: (yes)
    /note=SCS: (both)
    /note=ST: (NI) - found under "Genes that do not have the "Most Annotated" start"
    /note=BLAST-Start: (KeAlii, NCBI, Q1:S1, 89.84%, 0.0) (KeAlii_37, PhagesDB, Q1:S1, 90%, 0.0)
    /note=Gap: (145bp)
    /note=LO: (yes)
    /note=RBS: (Kibler6, Karlin Medium, 2.395, -3.917, no) - The last row on the RBS table is the best on scores
    /note=F: (DNA primase/helicase) - based on the comparison gene functions - they all match this function
    /note=SIF-BLAST: (DNA primase/helicase, NCBI, KeAlii, YP_010678154.1, 89.84%, 0.0) (DNA primase/helicase, PhagesDB, KeAlii_37, 90%, 0.0)
    /note=SIF-HHPred: (DNA primase, UniProt, Enterobacteria phage P4, P10277, 91.89%, 100)
    /note=SIF-Syn: (DNA primase/helicase, upstream: DNA polymerase 1, downstream: holliday junction resolvase, phage: KeAlii)

CDS 29548 - 29760
  /gene="39"
  /product="gp39"
  /function="hypothetical protein"
  /locus tag="Sue2_39"
    /note=Original Glimmer call @bp 29548 has strength 17.92; Genemark calls start at 29548
    /note=SSC: 29548-29760 CP: yes SCS: both ST: SS BLAST-Start:  GAP: 14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.153, -4.801936092881806, no F: hypothetical protein SIF-BLAST:  SIF-HHPRED: b.34.20.1 (A:7-71) Uncharacterized protein YorP {Bacillus subtilis [TaxId: 1423]} | CLASS: All beta proteins, FOLD: SH3-like barrel, SUPFAM: YorP-like, FAM: YorP-like,,,SCOP_d2heqa1,92.8571,95.7 SIF-Syn: 
    /note=ORpham with no BLAST hits but coding potential and HHPRED hit. 
    /note=Original Glimmer call @bp 29548 has strength 17.92
    /note=SSC: (Start: 29548bp, Stop: 29760bp), CP: (Yes), SCS: (Both), ST: (SS), Blast Start: (Phage Name: Maureen, Gene Number: 40, Phage Database: PhagesDB, Q/S Value: 2/73, E-Value: 0.94, % Identification: 51%), Gene Length: 212, Gap: (14 bp), LO: (Yes), RBS: (Shine Dalgarno Scoring Matrix: Kibler6, Shine Dalgarno Spacing Matrix: Karlin Medium, Z-Value: 2.153, Final-Value: -4.802, Best Choice: Yes), Function: (No Known Function), SIF-BLAST: (No Known Function, Database: Conserved Domain Database/PhagesDB, Phage Name: Maureen, Gene Number: 40, Database: PECAAN Accession Number: TIGR01394, %Alignment: 3.703, E-Value: 0.00132), SIF-HHPred: (No Known Function/Uncharacterized Protein, Database: SCOPe, Phage Name: Bacillus Subtilis, Hit: SCOP_d2heqa1, %Coverage: 92.86, Probability: 95.7), SIF-Syn: (, Flanking Genes:, Phages Used: )

CDS 29761 - 29871
  /gene="40"
  /product="gp40"
  /function="hypothetical protein"
  /locus tag="Sue2_40"
    /note=Genemark calls start at 29761
    /note=SSC: 29761-29871 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_VRESIDENCE_39 [Arthrobacter phage VResidence]],,NCBI, q1:s1 100.0% 2.33369E-16 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.199, -3.190747670785515, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_VRESIDENCE_39 [Arthrobacter phage VResidence]],,UYL87643,100.0,2.33369E-16 SIF-HHPRED:  SIF-Syn: NKF
    /note=Has coding potential
    /note=
    /note=SCS: (29761, 29871) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (VResidence_39, NCBI, Q1:S1, 97.22%, 2e-16) Gap: (0 bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 3.199, -3.191, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 29872 - 30054
  /gene="41"
  /product="gp41"
  /function="hypothetical protein"
  /locus tag="Sue2_41"
    /note=Original Glimmer call @bp 29872 has strength 10.73; Genemark calls start at 29872
    /note=SSC: 29872-30054 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Pseudarthrobacter siccitolerans] ],,NCBI, q1:s1 80.0% 5.34209E-25 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.031, -6.698691601206935, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Pseudarthrobacter siccitolerans] ],,WP_161799516,92.1569,5.34209E-25 SIF-HHPRED:  SIF-Syn: DNA polymerase I, upstream and downstream gene NFK
    /note=SSC: (29872, 30054) CP: (yes) SCS: (both) ST:(NI) BLAST-Start: (hypothetical protein, NCBI, Q1:S1, 80%, 6e-25) Gap: (1 bp) LO: (no) RBS: (Kilber6, Karlin Medium, 1.031, -6.699, yes) F:(DNA Polymerase I) SIF-Blast: (hypothetical protein, NCBI, WP_161799516.1, 95.83%, 6e-25) SIF-HHPred: (NFK) SIF-Syn: (DNA polymerase I, upstream and downstream gene NFK)

CDS 30222 - 32132
  /gene="42"
  /product="gp42"
  /function="DNA polymerase"
  /locus tag="Sue2_42"
    /note=Original Glimmer call @bp 30222 has strength 14.45; Genemark calls start at 30222
    /note=SSC: 30222-32132 CP: yes SCS: both ST: NI BLAST-Start: [DNA polymerase I [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 0.0 GAP: 167 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.188, -2.4634880269616195, yes F: DNA polymerase SIF-BLAST: ,,[DNA polymerase I [Arthrobacter phage KeAlii] ],,YP_010678157,95.5975,0.0 SIF-HHPRED: Apicoplast DNA polymerase; DNA polymerase, exonulease, apicoplast, Plasmodium falciparum, REPLICATION, TRANSFERASE; HET: PEG, EDO; 2.5A {Plasmodium falciparum (isolate 3D7)},,,7SXQ_B,97.0126,100.0 SIF-Syn: DNA polymerase I, upstream gene is NKF, downstream gene is NKF, KeAlii
    /note=Original Glimmer call @bp 30222 has strength 14.45
    /note=
    /note=SSC: (30222, 32132) CP: (yes) SCS: (both) ST: (NI) Blast-Start: (KeAlii_40, NCBI, Q1:S1, 91%, 0.0) Gap: (168bp overlap) LO: (no) RBS: (Kibler6, Karlin Medium, 3.225, -2.463, yes) F: (DNA polymerase) SIF-Blast: (DNA polymerase, NCBI, KeAlii_40, YP_010678157.1, 91%, 0.0) SIF-HHPred: (DNA polymerase, HHpred, Plasmodium falciparum 3D7, 7SXQ_B, 97.01%, 100%) SIF-Syn: (DNA polymerase I, upstream gene is NKF, downstream gene is NKF, KeAlii)

CDS 32129 - 32431
  /gene="43"
  /product="gp43"
  /function="DNA ligase"
  /locus tag="Sue2_43"
    /note=Original Glimmer call @bp 32129 has strength 13.01; Genemark calls start at 32129
    /note=SSC: 32129-32431 CP: yes SCS: both ST: SS BLAST-Start: [DNA ligase [Arthrobacter phage Amyev] ],,NCBI, q1:s1 97.0% 1.98556E-56 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.861, -5.024743752121617, yes F: DNA ligase SIF-BLAST: ,,[DNA ligase [Arthrobacter phage Amyev] ],,YP_010677745,91.0891,1.98556E-56 SIF-HHPRED: d.142.2.2 (A:) Adenylation domain of NAD+-dependent DNA ligase {Enterococcus faecalis [TaxId: 1351]} | CLASS: Alpha and beta proteins (a+b), FOLD: ATP-grasp, SUPFAM: DNA ligase/mRNA capping enzyme, catalytic domain, FAM: Adenylation domain of NAD+-dependent DNA ligase,,,SCOP_d3ba9a_,64.0,99.3 SIF-Syn: SIF-Syn: (Sue2_43 is similar to Wildwest_41 with a function of DNA ligase, but is flanked by DNA polymerase I and DNA binding protein.)
    /note=SSC: (32129/32431) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (Amyev_43, NCBI, 1:1, 97%, 2E-56) Gap: (8bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.8961, -5.025, Yes) F: (DNA Ligase) SIF-BLAST: (DNA Ligase, NCBI, Amyev_43, YP_010677745.1, 97%, 2E-56) SIF-HHPred: (DNA Ligase, Pecaan, Enterococcus Faecalis, SCOP_d3ba9a_, 64%, 99.3%) SIF-Syn: (Sue2_43 is similar to Wildwest_41 with a function of DNA ligase, but is flanked by DNA polymerase I and DNA binding protein.)

CDS 32428 - 32745
  /gene="44"
  /product="gp44"
  /function="hypothetical protein"
  /locus tag="Sue2_44"
    /note=Original Glimmer call @bp 32428 has strength 8.02; Genemark calls start at 32428
    /note=SSC: 32428-32745 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JANEEMI_46 [Arthrobacter phage Janeemi]],,NCBI, q1:s1 97.1429% 8.0102E-41 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.767, -5.080915947802713, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JANEEMI_46 [Arthrobacter phage Janeemi]],,UVK63566,77.451,8.0102E-41 SIF-HHPRED:  SIF-Syn: 
    /note=SSC: (32428,32745) CP: (Yes) SCS: (both) ST: (SS) Gap (-4) LO: (No, recalls a overlap of -184) RBS: (Kilber6, Karlin Medium 0.892, -7.049) F: (NKF) Blast-Start: (NFK) SIF-HHPred: (NFK) PhagesDB Blast: (NFK) Sif Syn: (NFK)

CDS 32968 - 33750
  /gene="45"
  /product="gp45"
  /function="DNA binding protein"
  /locus tag="Sue2_45"
    /note=Original Glimmer call @bp 32968 has strength 17.58; Genemark calls start at 32968
    /note=SSC: 32968-33750 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 100.0% 2.94225E-112 GAP: 222 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.933, -2.996490344739583, yes F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Arthrobacter phage KeAlii] ],,YP_010678159,83.0116,2.94225E-112 SIF-HHPRED: RNA polymerase sigma factor RpoS; Transcription-activator, DNA/RNA, SigmaS, beta`, TRANSCRIPTION, Transferase-DNA complex; 3.26A {Escherichia coli},,,6OMF_F,96.9231,100.0 SIF-Syn: (Matches gene 43 on Wildwest: DNA binding protein, Upstream matches gene 45 on Wildwest: helix-turn-helix DNA binding domain protein, Downstream matches gene 42 on Wildwest : DNA ligase)
    /note=SS: (32968, 33750) CP: (yes) SCS: (both) ST: ( NI ) Blast- Start: (Matches Arthrobacter Phage KeAlii, 223, NCBI, Target From: 1 Quary To: 260, 2.94225e-112) Gap: (223) LO: (yes) RBS: (Kibler 6 Karlin Medium, 2.933, -2.996, yes) F: ( DNA binding protein) SIF-BLAST: (DNA binding protein, NCBI, KeAlii, YP_010678159, 100%, 83.0116%, 2.94225e-112) SIF-HHPred: (RNA polymerase sigma factor RpoS, Escherichia coli, 6OMF_F, 96.9231, 100) SIF-Syn: (Matches gene 43 on Wildwest: DNA binding protein, Upstream matches gene 45 on Wildwest: helix-turn-helix DNA binding domain protein, Downstream matches gene 42 on Wildwest : DNA ligase)

CDS 33801 - 34094
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="Sue2_46"
    /note=Original Glimmer call @bp 33801 has strength 14.86; Genemark calls start at 33801
    /note=SSC: 33801-34094 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_VRESIDENCE_45 [Arthrobacter phage VResidence]],,NCBI, q1:s1 93.8144% 3.10359E-39 GAP: 50 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.933, -2.996490344739583, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_VRESIDENCE_45 [Arthrobacter phage VResidence]],,UYL87649,80.0,3.10359E-39 SIF-HHPRED:  SIF-Syn: Matches gene 44 on VResidence, DNA binding protein
    /note=SSC: (33801, 34094) CP: (Yes) SCS: (Both) ST (NI) BLAST-Start: (Marches Arthrobacter Phage VResidence, 45, NCBI, Target From: 1 Target To: 92, 93.8144 % coverage, 3.10359e-39 ), Gap: (51), LO: (Yes) RBS: (Kibler 6, Karlin Medium, 13, 2.933, -2.996, yes) F: (holin) SIF-BLAST (holin, NCBI, VResidence, 	UYL87649, 80%, 3.10359e-39) SID-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (Matches gene 44 on VResidence, DNA binding protein)

CDS 34213 - 34812
  /gene="47"
  /product="gp47"
  /function="SprT-like protease"
  /locus tag="Sue2_47"
    /note=Original Glimmer call @bp 34213 has strength 14.71; Genemark calls start at 34213
    /note=SSC: 34213-34812 CP: no SCS: both ST: SS BLAST-Start: [SprT-like protease [Arthrobacter phage Cassia]],,NCBI, q1:s1 99.4975% 1.46108E-125 GAP: 118 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -2.5052746077145835, yes F: SprT-like protease SIF-BLAST: ,,[SprT-like protease [Arthrobacter phage Cassia]],,WGH21119,93.4343,1.46108E-125 SIF-HHPRED: SprT-like ; SprT-like family,,,PF10263.13,50.2513,99.1 SIF-Syn: SIF-Syn: (Upstream gene is serine integrase, downstream is SprT-like protease)
    /note=Original Glimmer call @bp 34213 has strength 14.71. SSC.: (34213, 34812) CP: (yes) SCS: (Glimmer Only) ST: (SS) Blast Start: (Cassia_46, NCBI, Q1:1, 99% coverage, e value is 1e112.) Gap: (49bp) LO: (yes) RBS: (Kibler 6, Karlin Medium, 2 score:0.498, finale score: -7.810, yes) F: (SprT-like protease) SIF: (SPrT-like protease, NCBI, Cassia_46, accession number: WGH2119.1, alignment 99%, e value: 1112) SIF-HHPred: (SPrT-like domain containin protein, PDB, hit number:
    /note=GMDW_A, percent alignment 50.75%, 99.6 probability)
    /note=
    /note=A small amount of cp not covered; scores are much better. SS

CDS 34930 - 35172
  /gene="48"
  /product="gp48"
  /function="hypothetical protein"
  /locus tag="Sue2_48"
    /note=Original Glimmer call @bp 34930 has strength 20.57; Genemark calls start at 34930
    /note=SSC: 34930-35172 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE19_gp60 [Arthrobacter phage Tweety19] ],,NCBI, q1:s1 100.0% 4.70495E-40 GAP: 117 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.876, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE19_gp60 [Arthrobacter phage Tweety19] ],,YP_010678439,90.0,4.70495E-40 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 34930 has strength 20.57
    /note=SSC: [start: 34930, stop: 35172] CP: [Yes] SCS: [Both] ST: [SS] BLAST-Start: [Arthrobacter phage Tweety19, gn: 49, NCBI, Q:1 S:1, coverage: 100%, e-value: 4.5e-40] Gap: [117bp gap] LO: [Yes] RBS: [Kibler6, Karlin Medium, z-score: 2.912, final score: -2.845, Yes] F: [hypothetical protien] SIF-BLAST: [hypothetical protien, NCBI, Tweety19, gn: 49, YP_010678439, percent alignment: 90%, 4.5e-40] SIF-HHPred: [NKF, no matches with a probability over 90%] SIF-Syn: [Note that the phamerator doesn`t line up well between the target gene and Tweety19 gn: 49, NKF, upstream: NKF 12485 (2); NKF 2921 (41), Arthrobacter phage Tweety19]

CDS 35287 - 35445
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="Sue2_49"
    /note=Original Glimmer call @bp 35287 has strength 18.72; Genemark calls start at 35287
    /note=SSC: 35287-35445 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE13_gp45 [Arthrobacter phage Elezi] ],,NCBI, q1:s1 100.0% 1.63868E-24 GAP: 114 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE13_gp45 [Arthrobacter phage Elezi] ],,YP_010678023,98.0769,1.63868E-24 SIF-HHPRED:  SIF-Syn: 
    /note=Original Glimmer call @bp 35287 has strength 18.72
    /note=SSC: (35287 to 35445) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (aligns with Elezi_45, NCBI, q1:s1, 100, 1.57056e^-24) Gap: (114 bp) LO: (no) RBS: (Kibler6, Karlin Medium, 3.067, -2.523, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 35531 - 36343
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="Sue2_50"
    /note=Original Glimmer call @bp 35531 has strength 14.78; Genemark calls start at 35531
    /note=SSC: 35531-36343 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE17_gp54 [Arthrobacter phage Crewmate] ],,NCBI, q2:s3 99.6296% 9.61366E-133 GAP: 85 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.767, -5.160958035523474, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE17_gp54 [Arthrobacter phage Crewmate] ],,YP_010678305,85.6089,9.61366E-133 SIF-HHPRED:  SIF-Syn: SIF-HHPred: (NKF) SIF-Syn: (NKF, ObiToo, upstream gene 52 is Spr-T-like protease and downstream gene 54 is serine integrase)
    /note=Original Glimmer call @bp 35531 has strength 14.78
    /note=SSC: (35531 to 36343) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (aligns with Crewmate_54, NCBI, q2:s3, 99.6296, 9.2399e^-133) Gap: (85 bp) LO: (yes) RBS: (KIbler6, Karlin Medium, 2.912, -3.418, yes) F: SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF, downstream SprT-like Protease, upstream Serine Integrase)
    /note=
    /note=Original Glimmer call @bp 35531 has strength 14.78 SSC: (35531, 36343) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (ObiToo_53, NCBI, Q3:S4) Gap: (85 bp) LO: (yes) RBS: (Kibler 6, Karlin Medium, 1.795, -5.161, yes) F: (NKF) SIF-BLAST: (NKF, NCBI, ObiToo_53, WGH21229.1, 77.32%, 4e-130) SIF-HHPred: (NKF) SIF-Syn: (NKF, ObiToo, upstream gene 52 is Spr-T-like protease and downstream gene 54 is serine integrase)

CDS 36740 - 37063
  /gene="51"
  /product="gp51"
  /function="hypothetical protein"
  /locus tag="Sue2_51"
    /note=Original Glimmer call @bp 36740 has strength 12.81; Genemark calls start at 36740
    /note=SSC: 36740-37063 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ADOLIN_54 [Arthrobacter phage Adolin]],,NCBI, q1:s1 99.0654% 1.75338E-19 GAP: 396 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ADOLIN_54 [Arthrobacter phage Adolin]],,QHB36636,71.1538,1.75338E-19 SIF-HHPRED:  SIF-Syn: 
    /note=Genemark coding potential begins at 36750.
    /note=
    /note=I checked DNA Master for the RBS scores and Pecaan was better due to having a lower Z score and lower final score.
    /note=Original Glimmer call @bp 36740 has strength 12.81
    /note=SSC: (36740,37063) CP: (yes) SCS: (glimmer) ST: (NI) Blast-Start: (Adolin, 54, Pecaan, Q1:S1, 99%, EValue: 1.68 E-19) Gap: (397 bp overlap) LO: (Yes) RBS: (Kibler7, Karlin Medium, 3.03, -2.505, yes) F: (NKF) SIF-BLAST: (Hypothetical Protein, Pecaan, Adolin, 54, QHB36636, 71.15%, EValue-1.68E-19) SIF-HHPred: (Not called) SIF-Syn: (RNA binding protein, upstream: serine integrase and downstream: RNA binding protein, Adolin_54)

CDS 37060 - 37284
  /gene="52"
  /product="gp52"
  /function="RNA binding protein"
  /locus tag="Sue2_52"
    /note=Original Glimmer call @bp 37060 has strength 20.19; Genemark calls start at 37060
    /note=SSC: 37060-37284 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp50 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 100.0% 2.48216E-36 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -2.583959800616441, yes F: RNA binding protein SIF-BLAST: ,,[hypothetical protein PQE18_gp50 [Arthrobacter phage DrSierra] ],,YP_010678375,91.8919,2.48216E-36 SIF-HHPRED: Ssr3341 protein; HFQ, SM, RNA-BINDING PROTEIN, SRNA, TRANSLATIONAL REGULATION, RNA BINDING PROTEIN; 1.3A {Synechocystis sp. PCC 6803},,,3HFO_A,79.7297,97.0 SIF-Syn: NKF genes; right arm
    /note=RNA Binding Protein; matches pham.
    /note=HHPred hit to RNA binding protein. BLAST hits -hypothetical protein/RNA binding
    /note=Matches Vresidence in location.

CDS 37281 - 38084
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="Sue2_53"
    /note=Original Glimmer call @bp 37281 has strength 14.62; Genemark calls start at 37281
    /note=SSC: 37281-38084 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE17_gp58 [Arthrobacter phage Crewmate] ],,NCBI, q67:s4 46.0674% 2.19528E-19 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.013, -3.3861813518867647, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE17_gp58 [Arthrobacter phage Crewmate] ],,YP_010678309,60.0,2.19528E-19 SIF-HHPRED:  SIF-Syn: SIF-Syn: NKF
    /note=Original Glimmer call @bp 37281 has strength 14.62
    /note=SSC: Start:37281bp Stop: 38084bp
    /note=CP:yes 
    /note=SCS: Both 
    /note=ST: NA
    /note=Blast-Start: (Crewmate_58, NCBI, Q:67 S:4, Coverage: 46%, Evalue: 2E-19)
    /note=Gap: 4bp overload
    /note=LO: Yes
    /note=RBS: Kibler6, Karlin Medium, Zscore: 3.013, Final Score: --3.386, no. 
    /note=F: Hypothetical Protein
    /note=SIF-Blast: NKF, NCBI, Crewmat_58, YP_010678309, Alignment: 45.86%, Evalue: 2E-19
    /note=SIF-HHPred: NKF
    /note=SIF-Syn: NKF

CDS 38086 - 38286
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="Sue2_54"
    /note=Original Glimmer call @bp 38086 has strength 12.21; Genemark calls start at 38086
    /note=SSC: 38086-38286 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE15_gp54 [Arthrobacter phage KeAlii] ],,NCBI, q1:s1 98.4848% 1.62E-21 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -3.095100142625534, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE15_gp54 [Arthrobacter phage KeAlii] ],,YP_010678171,78.2609,1.62E-21 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 38086 has strength 12.21
    /note=SSC: (38086bp, 38286bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (KeAlii, NCBI, Q1:S1, 71.01%, 2e-21) (KeAlii_54, PhagesDB, Q1:S1, 71%, 2e-18) Gap: (1bp) LO: (no) RBS: (Kibler6, Karlin Medium, 3.067, -3.096, yes) F: (NKF) SIF-BLAST: (hypothetical protein, NCBI, KeAlii, YP_010678171.1, 71.01%, 2e-21) (unknown, PhagesDB, KeAlii_54, 71%, 2e-18) SIF-HHPred: (NKF) SIF-Syn: (NKF)
    /note=
    /note=SSC: (38086bp, 38286bp)
    /note=CP: (yes)
    /note=SCS: (both)
    /note=ST: (NI)
    /note=BLAST-Start: (KeAlii, NCBI, Q1:S1, 71.01%, 2e-21) (KeAlii_54, PhagesDB, Q1:S1, 71%, 2e-18)
    /note=Gap: (1bp) - this is an overlap of less than 10bp so it should be alright
    /note=LO: (no) - could be extended to the left but does not make sense because then it would overlap with the downstream gene by more than 50bp
    /note=RBS: (Kibler6, Karlin Medium, 3.067, -3.096, yes)
    /note=F: (NKF) - could not be determined from the comparisons to the KeAlii genes but it may be a protein
    /note=SIF-BLAST: (hypothetical protein, NCBI, KeAlii, YP_010678171.1, 71.01%, 2e-21) (unknown, PhagesDB, KeAlii_54, 71%, 2e-18)
    /note=SIF-HHPred: (NKF) - no results with a probability over 90%
    /note=SIF-Syn: (NKF) - Phamerator shows that there are no genes in KeAlii that align and are in the same Pham as Sue2_22 - not sure what the green shading means

CDS 38279 - 38485
  /gene="55"
  /product="gp55"
  /function="hypothetical protein"
  /locus tag="Sue2_55"
    /note=Original Glimmer call @bp 38279 has strength 7.51; Genemark calls start at 38279
    /note=SSC: 38279-38485 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Pseudarthrobacter siccitolerans] ],,NCBI, q1:s1 100.0% 1.83143E-20 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.304, -4.099420699635851, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Pseudarthrobacter siccitolerans] ],,WP_050053405,73.5294,1.83143E-20 SIF-HHPRED:  SIF-Syn: Reedo from the Phams database shows evidence of no known function at Gene 55: Start: 36416. Gene 55 is flanked by no known function at Gene 54 and no known function at Gene 54.
    /note=Original Glimmer call @bp 38279 has strength 7.51
    /note=SSC: (Start: 38279bp, Stop: 38485), CP: (Yes), SCS: (Both), ST: (SS), Blast Start: (Phage Name: Reedo, Gene Number: 56, Phage Database: NCBI/PhageDB, Q/S Value: 16/17, E-Value: 1e-21, % Identification: 79.25), Gene Length: (216), Gap: (Overlap: 6), LO: (No), RBS: (Shine Dalgarno Scoring Matrix: Kibler6, Shine Dalgarno Spacing Matrix: Karlin Medium, Z-Value: 2.304, Final-Value: -4.099, Best Choice: No), Function: (No Known Function), SIF-BLAST: (No Known Function, Database: PhagesDB/NCBI, Phage Name: Reedo, Gene Number: 56, Database Accession Number: WP_050053405, %Alignment: 73.53, E-Value: 1.76e-20), SIF-HHPred: (No Known Function: , Database: PECAAN, Phage Name: DUF4404, Hit: PF14357.10, %Alignment: 72.06, Probability: 46.7), SIF-Syn:  (No Known Function, Flanking Genes: No Known Function, Phages Used: Reedo)

CDS 38482 - 38739
  /gene="56"
  /product="gp56"
  /function="hypothetical protein"
  /locus tag="Sue2_56"
    /note=Original Glimmer call @bp 38482 has strength 12.85; Genemark calls start at 38482
    /note=SSC: 38482-38739 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Pseudarthrobacter siccitolerans] ],,NCBI, q12:s12 84.7059% 0.0030102 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.646, -3.385117140878946, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Pseudarthrobacter siccitolerans] ],,WP_050053740,49.3976,0.0030102 SIF-HHPRED:  SIF-Syn: 
    /note=SSC: (38482, 38739) CP: (Yes) SCS: (Both) ST: (NA) BLAST-Start: (no significant BLAST alignment) Gap: (4 bp overlap) LO: (Yes) RBS: (Kibler6, Karlin Medium, 2.4646, -3.385, yes) F:(NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)
    /note=NKF, no phage to compare Sue2_56; orpham

CDS 38864 - 39223
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="Sue2_57"
    /note=Original Glimmer call @bp 38864 has strength 16.63; Genemark calls start at 38864
    /note=SSC: 38864-39223 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQD80_gp58 [Arthrobacter phage Lizalica] ],,NCBI, q66:s2 45.3782% 7.95331E-26 GAP: 124 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.03, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQD80_gp58 [Arthrobacter phage Lizalica] ],,YP_010677623,92.7273,7.95331E-26 SIF-HHPRED:  SIF-Syn: NKF, upstream gene NKF, downstream gene NKF
    /note=Original Glimmer call @bp 38864 has strength 16.63
    /note=SSC: (38864, 39223) CP: (yes) SCS: (both) ST: (NA) Blast-Start: (Lizalica, NCBI, 66:2, 45%, 8e-26) Gap: (125bp) LO: (yes) RBS: Kilber 6, Karlin Medium, 3.03, -2.505, yes) SIF-Blast: (NKF, NCBI, Lizalica, YP_010677623.1, 87.04%, 8e-26) SIF-HHPred: NKF, no matches with a probability above 90%) SIF-Syn: (NKF, upstream gene NKF, downstream gene NKF)

CDS 39309 - 39548
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="Sue2_58"
    /note=Original Glimmer call @bp 39309 has strength 18.4; Genemark calls start at 39309
    /note=SSC: 39309-39548 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_PUREGLOBE5_117 [Arthrobacter phage Pureglobe5]],,NCBI, q8:s5 89.8734% 3.44673E-15 GAP: 85 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_PUREGLOBE5_117 [Arthrobacter phage Pureglobe5]],,UYL87480,51.6129,3.44673E-15 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 39309 has strength 18.40
    /note=
    /note=SSC: (39309, 39548) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (no significant BLAST alignments) Gap: (86bp gap) LO: (no) RBS: (Kibler6, Karlin Medium, 3.03, -2.505, yes) F: (NKF) SIF-Blast: (NKF, no matches with e-values below 10e-7) SIF-HHpred: (NKF, no matches with a probability above 90%) SIF-Syn: (NKF)

CDS 39553 - 39768
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="Sue2_59"
    /note=Original Glimmer call @bp 39553 has strength 19.37; Genemark calls start at 39553
    /note=SSC: 39553-39768 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JOHNDOE_59 [Arthrobacter phage JohnDoe]],,NCBI, q6:s56 91.5493% 1.10458E-23 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.547, -3.8026703187234707, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JOHNDOE_59 [Arthrobacter phage JohnDoe]],,WGH20772,43.8017,1.10458E-23 SIF-HHPRED: YorP ; YorP protein,,,PF09629.13,88.7324,95.7 SIF-Syn: SIF-Syn: (Sue2_59 has no matching with Wildwest at all and Sue2_59 has NKF.)
    /note=SSC: (39553/39768) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (JohnDoe_59, NCBI, 6:56, 91%, 1E-23) Gap: (None) LO: (Yes) RBS: (Kibler6, Karlin Medium, 2.547, -3.803, Yes) F: (NKF) SIF-BLAST: (NKF, Pecaan, JohnDoe_59, WGH20772, 91.55%, 1E-23) SIF-HHPred: (NKF, Pecaan, YorP, PF09629.14, 83.10%, 97.7%) SIF-Syn: (Sue2_59 has no matching with Wildwest at all and Sue2_59 has NKF.)
    /note=
    /note=HHPREd- YorP? NKF

CDS 39873 - 40190
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="Sue2_60"
    /note=Original Glimmer call @bp 39873 has strength 13.98; Genemark calls start at 39873
    /note=SSC: 39873-40190 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_VRESIDENCE_62 [Arthrobacter phage VResidence]],,NCBI, q4:s3 97.1429% 6.89868E-59 GAP: 104 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.264, -2.033982896655645, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_VRESIDENCE_62 [Arthrobacter phage VResidence]],,UYL87666,90.3846,6.89868E-59 SIF-HHPRED:  SIF-Syn: 
    /note=SSC: (39837,40190) CP: (Yes) SCS: (both) ST: (SS) Gap: (104) LO: (Yes) RBS: (Kibler6, Karlin Medium 3.264,-2.034) Blast-Start: (NFK) F: (NFK) SIF BLAST: (NFK) SIF-HHPred: (NKF) Sif Syn (NFK)

CDS 40180 - 40542
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="Sue2_61"
    /note=Original Glimmer call @bp 40180 has strength 13.97; Genemark calls start at 40180
    /note=SSC: 40180-40542 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_WILDWEST_59 [Arthrobacter phage Wildwest]],,NCBI, q1:s1 99.1667% 6.14152E-72 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.03, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_WILDWEST_59 [Arthrobacter phage Wildwest]],,WNO26078,94.958,6.14152E-72 SIF-HHPRED:  SIF-Syn: (Matches gene 59 on Wildwest: NKF, Upstream matches gene 60 on Wildwest: NKF, Downstream matches no genes on Wildwest)
    /note=SS: (40180, 40542) CP: (yes) SCS: (both)ST: Pham: (NI) Blast-Start: (Matches Arthrobacter Phage WildWest, overlap of 10, NCBI, Target From:1 Query To: 119, 5.89233e-72) Gap: (overlap by 10) LO: (yes) RBS: (Kibler 6 Karlin Medium, 3.067, -2.505, yes) F: (NKF) SIF-BLAST: (hypothetical protein, NCBI, WildWest, WNO26078, 94.958%, 5.89233e-72) SIF-HHPred: (NFK, no matches with a probability above 90%) SIF-Syn: (Matches gene 59 on Wildwest: NKF, Upstream matches gene 60 on Wildwest: NKF, Downstream matches no genes on Wildwest)

CDS 40539 - 40817
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="Sue2_62"
    /note=Original Glimmer call @bp 40539 has strength 12.23; Genemark calls start at 40539
    /note=SSC: 40539-40817 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ADOLIN_66 [Arthrobacter phage Adolin]],,NCBI, q1:s1 100.0% 1.09116E-47 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.118, -4.99877661786583, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ADOLIN_66 [Arthrobacter phage Adolin]],,QHB36648,91.3043,1.09116E-47 SIF-HHPRED:  SIF-Syn: Matches to gene 66 on Adolin, NKF
    /note=SSC: (40539, 40817) CP: (Yes) SCS: (Glimmer only) ST: (NI) BLAST-Start: (Matches Arthrobacter Phage Adolin, 66, NCBI, Target From: 1 Target To: 92, 100 % coverage, 1.04689e-47) Gap: (-3), LO: (No) RBS: (Kibler 6, Karlin Medium, 14, 2.118, -4.999, yes) F: (NKF) SIF-BLAST: (NKF, NCBI, Adolin, QHB36648, 91.3043 %, 1.04689e-47) SIF-HHPred:(NKF, no matches with a probability above 90%) SIF-Syn: (Matches to gene 66 on Adolin, NKF)

CDS 40808 - 40984
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="Sue2_63"
    /note=Original Glimmer call @bp 40808 has strength 18.88; Genemark calls start at 40808
    /note=SSC: 40808-40984 CP: no SCS: both ST: SS BLAST-Start: [membrane protein [Arthrobacter phage Powerpuff] ],,NCBI, q1:s1 98.2759% 3.19025E-21 GAP: -10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.199, -2.4406251440021154, yes F: hypothetical protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage Powerpuff] ],,QGZ17364,84.4828,3.19025E-21 SIF-HHPRED:  SIF-Syn: SIF-Syn: (NKF, matched powerpuff gene 66 pham 139818)
    /note=Original Glimmer call @bp 40808 has strength 18.88. SSC: (40808,40984) CP: (yes) SCS: (Glimmer only) ST: (NI)  Blast Start: (Wildwest_61, NCBI, 98% coverage, e value: 3e21) Gap: (-10 bp) LO: (yes) RBS: ( Kibler6, Karlin Medium, z score:3.199, final score: -2.441, yes) Function: (membrane protein) SIF: (membrane proetin, NCBI, Powerpuff_66, accession number: QGZ17364.1, 98% alignment, e value: 3e21) SIF- HHPred: (Membrane protein, PDB, hit number: 7FO2_D, percent alignment 66.67%, 95.55 probability).
    /note=
    /note=Small amount of cp not covered .LORF

CDS 40974 - 41147
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="Sue2_64"
    /note=Original Glimmer call @bp 40974 has strength 9.69; Genemark calls start at 40974
    /note=SSC: 40974-41147 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PQE18_gp63 [Arthrobacter phage DrSierra] ],,NCBI, q1:s1 92.9825% 4.60318E-11 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.03, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PQE18_gp63 [Arthrobacter phage DrSierra] ],,YP_010678388,68.5185,4.60318E-11 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 40974 has strength 9.69
    /note=SSC: [start: 40974, stop: 41147] CP: [Yes] SCS: [Both] ST:[SS] BLAST-Start: [Arthrobacter phage DrSierra, gn: 63, NCBI, Q:1 S:1, coverage: 92.9%, e-value: 4.41e-11] Gap: [11bp overlap] LO: [No] RBS: [Kibler6, Karlin Medium, z-score: 3.067, final score: -2.505, Yes] F: [hypothetical protien] SIF-BLAST: [hypothetical protien, NCBI, Arthrobacter phage DrSierra, gn: 63, YP_010678388, coverage: 92.9%, e-value: 4.41e-11] SIF-HHPred: [NFK, no matches with over 90% probability] SIF-Syn: [NKF, flanking genes: NKF 139818 (51); NKF 142616 (47), Arthrobacter phage DrSierra]

CDS 41140 - 41283
  /gene="65"
  /product="gp65"
  /function="hypothetical protein"
  /locus tag="Sue2_65"
    /note=Original Glimmer call @bp 41140 has strength 7.12; Genemark calls start at 41140
    /note=SSC: 41140-41283 CP: yes SCS: both ST: NI BLAST-Start: [membrane protein [Arthrobacter phage VResidence]],,NCBI, q1:s1 95.7447% 2.20824E-10 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.298, -3.9716456141594323, yes F: hypothetical protein SIF-BLAST: ,,[membrane protein [Arthrobacter phage VResidence]],,UYL87672,82.2222,2.20824E-10 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 41140 has strength 7.12
    /note=SSC: (41140bp, 41283bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (VResidence, NCBI, Q1:S1, 71.11%, 2e-10) (VResidence_68, PhagesDB, Q1:S1, 71%, 2e-10) Gap: (8bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.330, -3.972, yes) F: (NKF) SIF-BLAST: (membrane protein, NCBI, VResidence, UYL87672.1, 71.11%, 2e-10) (NKF, PhagesDB, VResidence_68, 71%, 2e-10) SIF-HHPred: (Cysteine and tyrosine-rich protein 1, Pfam, CYYR1, PF10873.12, 22.45%, 92.73) SIF-Syn: (NKF)
    /note=
    /note=*very unsure about the function and synteny because NCBI matches with a membrane protein, HHPred matches with a protein first and a membrane protein second, but PhagesDB matches with the same gene as NCBI but has an unknown function

CDS 41273 - 41494
  /gene="66"
  /product="gp66"
  /function="HNH endonuclease"
  /locus tag="Sue2_66"
    /note=Original Glimmer call @bp 41273 has strength 3.56; Genemark calls start at 41273
    /note=SSC: 41273-41494 CP: yes SCS: both ST: NI BLAST-Start: [endonuclease VII [Arthrobacter phage KeAlii] ],,NCBI, q9:s4 73.9726% 1.01143E-17 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.331, -4.043284403711498, yes F: HNH endonuclease SIF-BLAST: ,,[endonuclease VII [Arthrobacter phage KeAlii] ],,YP_010678182,57.7465,1.01143E-17 SIF-HHPRED: Restriction endonuclease Hpy99I; ENDONUCLEASE-DNA COMPLEX, RESTRICTION ENZYME, HPY99I, PSEUDOPALINDROME, HYDROLASE-DNA COMPLEX; HET: 1PE; 1.5A {Helicobacter pylori},,,3GOX_B,94.5205,94.0 SIF-Syn: HNH endonuclease, matches KeAlii_65, flanked by same pham 142616 and HNH endonuclease
    /note=Original Glimmer call @bp 41273 has strength 3.56
    /note=SSC: (41273bp, 41494bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (KeAlii, NCBI, Q9:S4, 72.22%, 1e-17) (KeAlii_65, PhagesDB, Q9:S4, 70%, 5e-19) Gap: (10bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.364, -4.043, yes) F: (HNH endonuclease) SIF-BLAST: (endonuclease VII, KeAlii, NCBI, YP_010678182.1, 72.22%, 1e-17) (NKF, KeAlii_65, PhagesDB, 70%, 5e-19) SIF-HHPred: (Restriction endonuclease, RCSB PDB, Helicobacter pylori J99, 3GOX_A, 28.5%, 96.35) SIF-Syn: (HNH endonuclease, matches KeAlii_65, flanked by same pham 142616 and HNH endonuclease)
    /note=
    /note=*unsure about function - may be endonuclease VII or HNH endonuclease

tRNA 41617 - 41690
  /gene="67"
  /product="tRNA-Trp(cca)"
  /locus tag="SUE2_67"
    /note=tRNA-Trp(cca)
Trim TGC
Score 58.5
Both Aragorn and tRNAScan agree

CDS 41870 - 42175
  /gene="68"
  /product="gp68"
  /function="HNH endonuclease"
  /locus tag="Sue2_68"
    /note=Original Glimmer call @bp 41870 has strength 3.3
    /note=SSC: 41870-42175 CP: yes SCS: glimmer ST: NI BLAST-Start: [HNH endonuclease [Arthrobacter phage Emotion]],,NCBI, q1:s1 98.0198% 4.69696E-47 GAP: 375 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.11, -2.356391881054909, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Arthrobacter phage Emotion]],,WGH21422,73.2759,4.69696E-47 SIF-HHPRED: HNH endonuclease; Thermophilic bacteriophage, HNH Endonuclease, DNA nicking, HYDROLASE; 1.52A {Geobacillus virus E2},,,5H0M_A,63.3663,96.7 SIF-Syn: HNH endonuclease, flanking gene: HNH endonuclease, compared to Wildwest_65
    /note=Original Glimmer call @bp 41870 has strength 3.30 ** not called by GeneMark
    /note=SSC: (41870bp, 42175bp) CP: (no) SCS: (Glimmer) ST: (page not available anymore) BLAST-Start: (Emotion, NCBI, Q1:S1, 77.78%, 5e-47) (Nitro_70, PhagesDB, Q1:S1, 84%, 1e-47) Gap: (??) LO: (no) RBS: (Kibler6, Karlin Medium, 3.147, -2.356, yes) F: (HNH endonuclease) SIF-BLAST: (HNH endonuclease, NCBI, Emotion, WGH21422.1, 77.78%, 5e-47) (HNH endonuclease, PhagesDB, Nitro_70, 84%, 1e-47) SIF-HHPred: (HNH endonuclease, Thermophilic bacteriophage, 50%, 97.92) SIF-Syn: (HNH endonuclease, flanking gene: HNH endonuclease, compared to Wildwest_65)
    /note=
    /note=*coding potential not present from the start to the stop
    /note=** complete overlap with reverse gene - which do we delete??