Student Annotations from Pecan

CDS 1 - 1506
  /gene="1"
  /product="gp1"
  /function="terminase, large subunit"
  /locus tag="Kukla_1"
    /note=Original Glimmer call @bp 1 has strength 14.17; Genemark calls start at 1
    /note=SSC: 1-1506 CP: yes SCS: both ST: NA BLAST-Start: [terminase large subunit [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 0.0 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.176, -2.1924212546750814, yes F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Arthrobacter phage TripleJ] ],,YP_009884404,99.002,0.0 SIF-HHPRED: Terminase, large subunit; phage defense, pattern-recognition receptor, nlr, stand, atpase, ANTIVIRAL PROTEIN; HET: ATP;{Salmonella enterica},,,8DGC_F,91.8164,100.0 SIF-Syn: SIF-Syn: (terminase large subunit, upstream portal protein)
    /note=Original Glimmer call @bp 1 has strength 14.17
    /note=SSC: (1 to 1506) CP:(yes) SCS: (both) ST: (NA) BLAST-Start: (aligns with TripleJ_1, NCBI, q1:s1, 100%, 0) Gap: (NA) LO: (yes) RBS: (Kibler6, Karlin Medium, 3.173, -2.192, yes) F: (terminase large subunit) SIF-BLAST: (terminase large subunit, NCBI, YP_009884404, 99.002%, 0) SIF-HHPred: (terminase large subunit, HHPred, 8DGCF_F, 91.8164%, 100) SIF-Syn: (terminase large subunit, upstream portal protein)

CDS 1515 - 3053
  /gene="2"
  /product="gp2"
  /function="portal protein"
  /locus tag="Kukla_2"
    /note=Original Glimmer call @bp 1515 has strength 11.44; Genemark calls start at 1515
    /note=SSC: 1515-3053 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 0.0 GAP: 8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.36, -3.9166971242758706, no F: portal protein SIF-BLAST: ,,[portal protein [Arthrobacter phage TripleJ] ],,YP_009884405,98.6328,0.0 SIF-HHPRED: Portal protein B; Complex, VIRAL PROTEIN; 4.0A {Escherichia phage Lambda},,,8K39_a,85.1562,100.0 SIF-Syn: SIF-Syn: (portal protein, TripleJ, upstream gene 1 is terminase and downstream gene 3 is MuF- like minor capsid protein)
    /note=Original Glimmer call @bp 1515 has strength 11.44 SSC: (1515, 3053) CP: (yes) SCS: (both) ST: (NA) Blast-Start: (TripleJ_2, NCBI, Q1:S1, 100%, 0.0) Gap: (8 bp) LO: (NA) RBS: (Kibler 6, Karlin Medium, 2.356, –3.917, yes) F: (portal protein) SIF-BLAST: (portal protein, NCBI, TripleJ_2, YP_009884405.1, 96.29%, 0.0) SIF-HHPred: (portal protein, 8K39_a, 77.11%, 100) SIF-Syn: (portal protein, TripleJ, upstream gene 1 is terminase and downstream gene 3 is MuF- like minor capsid protein)

CDS 3064 - 4104
  /gene="3"
  /product="gp3"
  /function="Hypothetical Protein"
  /locus tag="Kukla_3"
    /note=Original Glimmer call @bp 3064 has strength 9.38; Genemark calls start at 3064
    /note=SSC: 3064-4104 CP: yes SCS: both ST: SS BLAST-Start: [minor head protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -4.387988835334809, no F: Hypothetical Protein SIF-BLAST: ,,[minor head protein [Arthrobacter phage TripleJ] ],,YP_009884406,97.9769,0.0 SIF-HHPRED: Phage_min_cap2 ; Phage minor capsid protein 2,,,PF06152.15,72.2543,99.9 SIF-Syn: Gene 3 matched with TripleJ gene 3. The flanking genes is portal protein and capsid maturation protease.
    /note=Phamorator called gene 3 a Muf-like capsid protein but according to the functional assignment document we use hypothetical protein instead.
    /note=Potential minor capsid protein
    /note=Original Glimmer call @bp 3064 has strength 9.38
    /note=SSC: (3064,4104) CP: (yes) SCS: (glimmer) ST: (SS) Blast-Start: (TripleJ, Pecaan,Q1:S1,  EValue:0) Gap: (10 basepair) LO: (yes) RBS: (Kibler7, Karlin Medium, 2.129, -4.388, yes) F:(Hypothetical Protein)  SIF-BLAST: (Minor head protein, TripleJ, Pecaan, YP_009884406, 97.9769%, Evalue:0) SIF-HHPred: (Minor head protein, HHPred, Q38442, 90.9%, 100) SIF-Syn: (Hypothetical Protein, upstream: portal protein, downstream: capsid maturation, TripleJ_3)

CDS complement (4101 - 4235)
  /gene="4"
  /product="gp4"
  /function="hypothetical protein"
  /locus tag="Kukla_4"
    /note=Original Glimmer call @bp 4235 has strength 2.33
    /note=SSC: 4235-4101 CP: yes SCS: glimmer ST: NI BLAST-Start: [3-oxoacyl-ACP reductase [Arthrobacter phage TripleJ] ],,NCBI, q2:s13 97.7273% 3.61606E-22 GAP: 56 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.534, -4.774753077400917, no F: hypothetical protein SIF-BLAST: ,,[3-oxoacyl-ACP reductase [Arthrobacter phage TripleJ] ],,YP_009884407,76.3636,3.61606E-22 SIF-HHPRED:  SIF-Syn: 
    /note=Potentially delete this gene.  There is a bit of reverse CP and there is a BLAST hit to Arthrobacter sp, but not strong evidence.

CDS 4292 - 5254
  /gene="5"
  /product="gp5"
  /function="capsid maturation protease"
  /locus tag="Kukla_5"
    /note=Original Glimmer call @bp 4292 has strength 12.96; Genemark calls start at 4292
    /note=SSC: 4292-5254 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Brevibacterium sp. p3-SID960] ],,NCBI, q5:s4 97.5% 6.76878E-59 GAP: 56 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.129, -4.387988835334809, no F: capsid maturation protease SIF-BLAST: ,,[hypothetical protein [Brevibacterium sp. p3-SID960] ],,WP_259875241,56.535,6.76878E-59 SIF-HHPRED: Peptidase_S77 ; Prohead core protein serine protease,,,PF03420.17,45.625,99.7 SIF-Syn: SIF-Syn: Capsid Maturation Protein, Flanking gene: MuF-like minor capsid protease, Forward: NKF, TripleJ
    /note=Original Glimmer call @bp 4292 has strength 12.96
    /note=SSC: Start: 4292bp Stop: 5254bp
    /note=CP: Yes
    /note=SCS: Both
    /note=ST: SS
    /note=Blast-Start: BreviBacterium sp. p3-SID960, NCBI, Q:5 S:4, Coverage: 97%, Evalue: 7e-59. 
    /note=Gap: 56bp gap 
    /note=LO: No 
    /note=RBS: Kibbler6, Karlin Medium, Zscore: 2.129, Finale Score: -4.388, no
    /note=F: Capsid Maturation Protease
    /note=SIF-Blast: Hypothetical protein, NCBI, BreviBacterium sp. p3-SID960_GX, WP_259875241, allignment: 42.90%, Evalue: 7e-59
    /note=SIF-HHPred: Serine Protease, Pfam, Bacteriophage T4, PF03420.17, allignment: 74%, probablility: 99.73%. 
    /note=SIF-Syn: Capsid Maturation Protein, Flanking gene: MuF-like minor capsid protease, Forward: NKF, TripleJ

CDS 5268 - 5615
  /gene="6"
  /product="gp6"
  /function="hypothetical protein"
  /locus tag="Kukla_6"
    /note=Original Glimmer call @bp 5268 has strength 15.62; Genemark calls start at 5268
    /note=SSC: 5268-5615 CP: yes SCS: both ST: NI BLAST-Start: [head decoration [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 2.29589E-73 GAP: 13 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.261, -2.2821867859826788, yes F: hypothetical protein SIF-BLAST: ,,[head decoration [Arthrobacter phage TripleJ] ],,YP_009884409,99.1304,2.29589E-73 SIF-HHPRED: Capsid fiber protein; bacteriophage, phi29, prohead, VIRUS; HET: SO4; 1.8A {Bacillus phage phi29},,,6QYY_A,83.4783,99.4 SIF-Syn: NKF
    /note=PHAM 4884 has scaffolding protein and minor capsid. HHPred Capsid fibers; mainly DUF 
    /note=
    /note=Original Glimmer call @bp 5268 has strength 15.62
    /note=SSC: (5268bp, 5615bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (TripleJ, NCBI, Q1:S1, 98.26%, 2e-73) (TripleJ_6, PhagesDB, Q1:S1, 98%, 4e-60) Gap: (13bp) LO: (yes) RBS: (Kibler6, Karlin Medium, 3.259, -2.282, yes) F: (NKF) SIF-BLAST: (head decoration, NCBI, TripleJ, YP_009884409.1, 98.26%, 2e-73) (NKF, PhagesDB, TripleJ_6, 98%, 4e-60) SIF-HHPred: (Uncharacterized conserved protein, Pfam, DUF2190, PF09956.13, 96.07%, 99.81) SIF-Syn: (NKF)

CDS 5627 - 6694
  /gene="7"
  /product="gp7"
  /function="major capsid protein"
  /locus tag="Kukla_7"
    /note=Original Glimmer call @bp 5627 has strength 13.37; Genemark calls start at 5621
    /note=SSC: 5627-6694 CP: yes SCS: both-gl ST: NA BLAST-Start: [major capsid protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s3 100.0% 0.0 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.261, -1.993391246735709, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Arthrobacter phage TripleJ] ],,YP_009884410,99.4398,0.0 SIF-HHPRED: Gp27 major capsid protein; phage G, major capsid protein, decoration protein, capsid, icosahedral, gp26, gp27, VIRUS; 6.1A {Bacillus virus G},,,6WKK_D,79.1549,99.2 SIF-Syn: TripleJ from the phams database shows evidence of Major Head Protein at gene #7 and has the same pham: 147757 at gene #7 from Kuala from PECAAN database. Gene #7 is flanked by gene #6 and gene #8 which both have no known function. Both Kuala and TripleJ share the same pham for gene #6: 4884 and gene #8: 145821.
    /note=Original Glimmer call @bp 5627 has strength 13.37; GeneMark calls start at 5621
    /note=SSC: (Start: 5627, Stop: 6694), CP: (Yes), SCS: (Both), ST: (NA), Blast Start: (Phage Name: TripleJ, Gene Number: 7, Phage Database: NCBI/PhagesDB, Q/S Value: 1/3, E-Value: 0.0, % Identification: 99), Gene Length: (1068),Gap: (12-1=11), LO: (No), RBS: (Shine Dalgarno Scoring Matrix: Kibler6, Shine Dalgarno Spacing Matrix: Karlin Medium, Z-Value: 3.259, Final-Value: -3.236, Best Choice: No), Function: (Major Capsid Protein), SIF-BLAST: (Function: Major Capsid Protein, Database: NCBI/PhagesDB, Phage Name: TripleJ, Gene Number: 7, Database Accession Number: YP_009884410.1, %Alignment: 99.44%, E-Value: 0.0), SIF-HHPred: (/Function: Gp27 Major Capsid Protein, Database: HHPred, Phage Name: Donellivirus Gee, Gene Number: 26/27, Hit: 6WKK_D, %Alignment: 83.57, Probability: 99.18), SIF-Syn: (Function: Major Head Protein, Flanking Genes: Sue2/Kukla: Gene #6: NKF, Gene #8: NKF, Phages Used: TripleJ (from Phams database))

CDS 6781 - 7152
  /gene="8"
  /product="gp8"
  /function="hypothetical protein"
  /locus tag="Kukla_8"
    /note=Original Glimmer call @bp 6781 has strength 11.37; Genemark calls start at 6781
    /note=SSC: 6781-7152 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein HYQ00_gp08 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 8.50627E-70 GAP: 86 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.176, -2.17469248771465, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp08 [Arthrobacter phage TripleJ] ],,YP_009884411,99.187,8.50627E-70 SIF-HHPRED:  SIF-Syn: NKF
    /note=SSC: (6781, 7152) CP: (Yes) SCS: (Both) ST: (NA) BLAST-Start: (TripleJ_8, NCBI, Q1:S1, 100%, 9e-70) Gap: (86 bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 3.176, -2.175, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 7146 - 7574
  /gene="9"
  /product="gp9"
  /function="hypothetical protein"
  /locus tag="Kukla_9"
    /note=Original Glimmer call @bp 7146 has strength 8.69; Genemark calls start at 7146
    /note=SSC: 7146-7574 CP: yes SCS: both ST: SS BLAST-Start: [DUF6093 family protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 1.38138E-89 GAP: -7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.611, -3.95820260462814, yes F: hypothetical protein SIF-BLAST: ,,[DUF6093 family protein [Arthrobacter phage TripleJ] ],,YP_009884412,92.9577,1.38138E-89 SIF-HHPRED: DUF6093 ; Family of unknown function (DUF6093),,,PF19586.3,83.0986,99.9 SIF-Syn: NKF, downstream NKF, upstream minor capsid protein
    /note=Original Glimmer call @bp 7146 has strength 8.69
    /note=SSC: (7146, 7574) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (TripleJ, NCBI, Q1:S1, 100%, 1e-89)  Gap: (6 bp overlap) LO: (yes) RBS: (Kilber 6, Karlin Medium, 2.611, -3.958, yes) F: (NKF) SIF-Blast: (NKF, NCBI, TripleJ, YP_009884412.1, 88.74%, 1e-89) SIF-HHPred: (NKF, HHPred,  3F3B_A, 83, 97.97%) SIF-Syn: ( NKF, downstream NKF, upstream minor capsid protein)

CDS 7582 - 7962
  /gene="10"
  /product="gp10"
  /function="minor capsid protein"
  /locus tag="Kukla_10"
    /note=Original Glimmer call @bp 7582 has strength 10.61; Genemark calls start at 7582
    /note=SSC: 7582-7962 CP: yes SCS: both ST: NI BLAST-Start: [tail completion or Neck1 protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 3.0123E-38 GAP: 7 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.012, -5.402512189985548, no F: minor capsid protein SIF-BLAST: ,,[tail completion or Neck1 protein [Arthrobacter phage TripleJ] ],,YP_009884413,70.0787,3.0123E-38 SIF-HHPRED: Minor_capsid_2 ; Minor capsid protein,,,PF11114.12,71.4286,99.5 SIF-Syn: minor capsid protein, upstream gene is NKF, downstream gene is tail terminator, TripleJ
    /note=Some "phage morphogenesis protein" not a function
    /note=Original Glimmer call @bp 7582 has strength 10.61
    /note=
    /note=SSC: (7582, 7962) CP: (yes) SCS: (both) ST: (NI) Blast-Start: (no sigficant BLAST alignments) Gap: (7bp gap) LO: (yes) RBS: (Kibler 6, Karlin Medium, 2.012, -5.403, yes) F: (minor capsid protein) SIF-Blast: (NKF, no matches with e-values below 10e-7) SIF-HHpred: (minor capsid protein, HHpred, Minor_capsid_2, PF11114.12, 99.5) SIF-Syn: (minor capsid protein, upstream gene is NKF, downstream gene is tail terminator, TripleJ)

CDS 7949 - 8389
  /gene="11"
  /product="gp11"
  /function="tail terminator"
  /locus tag="Kukla_11"
    /note=Original Glimmer call @bp 7949 has strength 9.8; Genemark calls start at 7949
    /note=SSC: 7949-8389 CP: yes SCS: both ST: SS BLAST-Start: [tail terminator [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 4.22529E-37 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.213, -4.228094514819432, no F: tail terminator SIF-BLAST: ,,[tail terminator [Arthrobacter phage TripleJ] ],,YP_009884414,66.6667,4.22529E-37 SIF-HHPRED: Tail terminator protein Rcc01690; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_F,98.6301,99.5 SIF-Syn: SIF-Syn: (Kukla_11 is similar to TripleJ_11 with a function of tail terminator, but is flanked by minor capsid protein and major tail protein)
    /note=SSC: (7949/8389) CP: (Yes) SCS: (Both) ST: (SS) Blast-Start: (TripleJ_11, NCBI, 1:1, 100%, 1E-42) Gap: (14bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 2.213, -4.228, Yes) F: (Tail Terminator) SIF-BLAST: (Tail Terminator, Pecaan, TripleJ_11, YP_009884414) SIF-HHPred: (Tail Terminator, Pecaan, Rhodobacter Capsulatus, 6TE9_F, 98.63%, 99.5%) SIF-Syn: (Kukla_11 is similar to TripleJ_11 with a function of tail terminator, but is flanked by minor capsid protein and major tail protein)

CDS 8401 - 8631
  /gene="12"
  /product="gp12"
  /function="hypothetical protein"
  /locus tag="Kukla_12"
    /note=Original Glimmer call @bp 8401 has strength 9.44; Genemark calls start at 8401
    /note=SSC: 8401-8631 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp12 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 4.78907E-31 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.261, -1.993391246735709, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp12 [Arthrobacter phage TripleJ] ],,YP_009884415,83.3333,4.78907E-31 SIF-HHPRED:  SIF-Syn: NFK
    /note=SSC: (8212,8631) CP: (Yes) SCS: (Both) ST: (SS) F: (NFK) RBS: (Kelber 6, Karlin Medium 1.844,-5.070) SIF-BLAST- (NFK) SIF-HHPRED:(NFK) SIF-Syk: (NFK)

CDS 8634 - 9155
  /gene="13"
  /product="gp13"
  /function="major tail protein"
  /locus tag="Kukla_13"
    /note=Original Glimmer call @bp 8634 has strength 11.97; Genemark calls start at 8634
    /note=SSC: 8634-9155 CP: yes SCS: both ST: NI BLAST-Start: [major tail protein [Arthrobacter phage EvePickles]],,NCBI, q1:s1 100.0% 1.40084E-123 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.421, -3.771433305309111, no F: major tail protein SIF-BLAST: ,,[major tail protein [Arthrobacter phage EvePickles]],,UYL88302,100.0,1.40084E-123 SIF-HHPRED: Tail tube protein; Virus, Phage, Lambda, Siphoviridae, Tail, Tube;{Escherichia virus Lambda},,,7T2E_B,98.2659,91.1 SIF-Syn: SIF-Syn: (Matches gene 13 on TripleJ: major tail protein, Upstream matches gene 12 on TripleJ: NKF, Downstream matches gene 15 on TripleJ : tail assembly chaperone)
    /note=SS: (8634,9155) CP: (yes) SCS: (both) ST: (NI) Blast- Start: (Matches Arthrobacter Phage EvePickles,3, NCBI, Target From:1 Query To:173, 1.40084e-123) Gap: (3) LO: (yes) RBS: (Kibler 6 Karlin Medium, 2.421,-3.771, yes) F: (major tail protein) SIF-BLAST: (major tail protein, NCBI, Arthrobacter Phage EvePickles, UYL88302, 100%, 1.40084e-123) SIF-HHPred: (tail tube protein, PDB, Phage Lambda, 7T2E_B, 98.2659%, 91.1)
    /note=SIF-Syn: (Matches gene 13 on TripleJ: major tail protein, Upstream matches gene 12 on TripleJ: NKF, Downstream matches gene 15 on TripleJ : tail assembly chaperone)

CDS 9254 - 9919
  /gene="14"
  /product="gp14"
  /function="tail assembly chaperone"
  /locus tag="Kukla_14"
    /note=Original Glimmer call @bp 9254 has strength 14.92; Genemark calls start at 9254
    /note=SSC: 9254-9919 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Arthrobacter phage Faja] ],,NCBI, q1:s1 100.0% 7.6523E-149 GAP: 98 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -5.426906901365179, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage Faja] ],,YP_010656303,97.7376,7.6523E-149 SIF-HHPRED: Phage_TAC_5 ; Phage XkdN-like tail assembly chaperone protein, TAC,,,PF08890.15,52.0362,92.2 SIF-Syn: Matches gene 15 on Triple J, tail assembly chaperone
    /note=SSC: (9254, 9919) CP: (Yes) SCS: (Glimmer Only) ST: (NI) Blast-Start: (Matches Arthobacterphage Faja, NCBI, Target From: 1 Target To: 221, 100%, 7.6523e-149) Gap: (99) LO: (Yes) RBS: (Kibler 6, Karlin Medium, 2.129, -5.427, no) F: (tail assembly chaperone) SIF-BLAST: (tail assembly chaperone, NCBI, VResidence, YP_010656303, 97.7376%, 7.6523e-149), SIF-HHPred: (tail assembly chaperone,  HHPred, Phage_TAC_5, PF08890.15, 52.0362%, 92.2), SIF-Syn: (Matches gene 15 on Triple J, tail assembly chaperone)

CDS join(9254..9637,9637..10227)
  /gene="15"
  /product="gp15"
  /function="tail assembly chaperone"
  /locus tag="Kukla_15"
    /note=
    /note=SSC: 9254-10227 CP: yes SCS: neither ST: SS BLAST-Start: [tail assembly chaperone [Arthrobacter phage Faja] ],,NCBI, q1:s1 100.0% 7.62307E-165 GAP: -666 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -5.426906901365179, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Arthrobacter phage Faja] ],,YP_010656302,81.1728,7.62307E-165 SIF-HHPRED:  SIF-Syn: 

CDS 10473 - 14528
  /gene="16"
  /product="gp16"
  /function="tape measure protein"
  /locus tag="Kukla_16"
    /note=Original Glimmer call @bp 10473 has strength 10.75; Genemark calls start at 10491
    /note=SSC: 10473-14528 CP: yes SCS: both-gl ST: NA BLAST-Start: [tape measure protein [Arthrobacter phage EvePickles]],,NCBI, q1:s1 99.852% 0.0 GAP: 244 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.953, -4.698398734893535, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Arthrobacter phage EvePickles]],,UYL88306,81.5083,0.0 SIF-HHPRED: Tape measure protein; Neck, Portal, T5, VIRUS, VIRAL PROTEIN; 3.2A {Escherichia phage DT57C},,,8HQO_x,56.0326,96.1 SIF-Syn: flanked with tail assembly chaperone and minor tail protein
    /note=Original Glimmer call @bp 10473 has strength 10.75; GeneMark calls start at 10491
    /note=SSC: (10473 to 14528) CP: (yes) SCS: (both) ST: (NA) BLAST-Start: (aligns with EvePickles_19, NCBI, s1:q1, 99.852%, 0) Gap: (81 bp) LO: (no) RBS: (Kibler6, Karlin Medium, 1.948, -4.698, yes) F: (tape measure protein) SIF-BLAST: (tape measure protein, NCBI, UYL88306, 81.5083%, 0) SIF-HHPred: (NKF) SIF-Syn: (tape measure protein, downstream tail assembly chaperone, upstream minor tail protein)

CDS 14545 - 15453
  /gene="17"
  /product="gp17"
  /function="minor tail protein"
  /locus tag="Kukla_17"
    /note=Original Glimmer call @bp 14545 has strength 6.76; Genemark calls start at 14545
    /note=SSC: 14545-15453 CP: yes SCS: both ST: NA BLAST-Start: [minor tail protein [Arthrobacter phage Faja] ],,NCBI, q1:s1 100.0% 0.0 GAP: 16 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.098, -2.2763497933341483, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage Faja] ],,YP_010656306,98.3444,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_C,94.0397,100.0 SIF-Syn: SIF-Syn: (minor tail protein, Faja, upstream gene 18 is tape measure protein and downstream gene 19 is minor tail protein)
    /note=Original Glimmer call @bp 14545 has strength 6.76 SSC: (14545, 15453) CP: (yes) SCS: (both) ST: (NA) Blast-Start: (Faja_20, NCBI, Q1:S1, 100%, 0.0) Gap: (16 bp) LO: (no) RBS: (Kibler 6, Karlin Medium, 3.095, -2.276, yes) F: (minor tail protein) SIF-BLAST: (minor tail protein, NCBI, Faja_20, YP_010656306.1, 94.04%, 0.0) SIF-HHPred: (distal tail protein, 2X8K_c, 96.83%, 99.97) SIF-Syn: (minor tail protein, Faja, upstream gene 18 is tape measure protein and downstream gene 19 is minor tail protein)

CDS 15456 - 16433
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="Kukla_18"
    /note=Original Glimmer call @bp 15456 has strength 9.13; Genemark calls start at 15456
    /note=SSC: 15456-16433 CP: yes SCS: both ST: SS BLAST-Start: [virion structural protein [Arthrobacter phage Faja] ],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.711, -5.21028209587241, no F: minor tail protein SIF-BLAST: ,,[virion structural protein [Arthrobacter phage Faja] ],,YP_010656307,98.7692,0.0 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,46.7692,98.9 SIF-Syn: (Minor tail protein, upstream: minor tail protein, downstream: minor tail protein, TripleJ_27)
    /note=Both Pecaan and NCBI Blast results were the exact same, so I just went with Pecaan. The DNA Master RBS results were better than Pecaan as the Final score was the less negative one and the Z score was closer to 2. The Syf-Syn was difficult because they color (pham groups) didn`t line up and I had to look but the flanking genes were the same. 
    /note=
    /note=Original Glimmer call @bp 15456 has strength 9.13
    /note=SSC: (15456, 16433)  CP: (Yes) SCS: (glimmer) ST:(SS)  Blast-Sart: (Faja, Pecaan, Q1:S1, 100, EValue-0) Gap: (2) LO: (no) RBS:(Kibler7, Karlin Medium, 1.755, -5.081, yes) F:(Minor tail protein) SIF-BLAST:(Minor tIL PROTEIN, Pecaan, Faja, YP_010656307, 98.7692, EValue-0) SIF-HHPred:(Receptor Binding Protein, Pecaan, 4L9B_A, 30.79%, 98.9) SIF-Syn: (Minor tail protein, upstream:minor tail protein, downstream: minortail protein, TripleJ_27)

CDS 16456 - 16689
  /gene="19"
  /product="gp19"
  /function="hypothetical protein"
  /locus tag="Kukla_19"
    /note=Original Glimmer call @bp 16456 has strength 11.73; Genemark calls start at 16456
    /note=SSC: 16456-16689 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein [Arthrobacter sp. B3I4] ],,NCBI, q1:s1 98.7013% 2.44286E-23 GAP: 22 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.771, -3.0301037898918786, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Arthrobacter sp. B3I4] ],,WP_307035721,76.6234,2.44286E-23 SIF-HHPRED:  SIF-Syn: 

CDS 16686 - 17423
  /gene="20"
  /product="gp20"
  /function="minor tail protein"
  /locus tag="Kukla_20"
    /note=Original Glimmer call @bp 16686 has strength 7.18; Genemark calls start at 16686
    /note=SSC: 16686-17423 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Arthrobacter phage EvePickles]],,NCBI, q4:s1 98.7755% 4.30802E-74 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.233, -4.4583299492266635, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage EvePickles]],,UYL88310,71.7742,4.30802E-74 SIF-HHPRED:  SIF-Syn: SIF-SYN: Minor Tail Protein, Flanking Gene: NKF, Endolysin, Bacteriophage: EvePickles
    /note=Original Glimmer call @bp 16686 has strength 7.18
    /note=SSC: Start: 16686bp Stop: 17423bp 
    /note=Cp: Yes 
    /note=SCS: Both 
    /note=ST: NI
    /note=Blast-Start: EvePickles_G23, NCBI, Q: 4 S:1, Coverage: 98% 
    /note=Evalue: 4e-74
    /note=Gap: 4bp overload 
    /note=LO: Yes 
    /note=RBS: Kibbler6, Karlin Medium, Zscore: 2.233, Finale Score: -4.458, no
    /note=F: Minor tail Protein 
    /note=SIF-Blast: Minor Tail Protein, NCBI, EvePickles_G23, UYL88310.1, allignment: 58.46%, Evalue: 4e-74
    /note=SIF-HHPred: NKF 
    /note=SIF-SYN: Minor Tail Protein, Flanking Gene: NKF, Endolysin, Bacteriophage EvePickles

CDS 17420 - 18367
  /gene="21"
  /product="gp21"
  /function="endolysin"
  /locus tag="Kukla_21"
    /note=Original Glimmer call @bp 17420 has strength 14.07; Genemark calls start at 17420
    /note=SSC: 17420-18367 CP: yes SCS: both ST: NI BLAST-Start: [endolysin [Arthrobacter phage Gorpy] ],,NCBI, q2:s3 99.6825% 1.80227E-175 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.36, -3.898968357315439, no F: endolysin SIF-BLAST: ,,[endolysin [Arthrobacter phage Gorpy] ],,UVF60989,84.7619,1.80227E-175 SIF-HHPRED: Peptidase M23; membrane protein, enzyme, TRANSPORT PROTEIN; HET: ADP;{Vibrio cholerae},,,8TZL_E,36.1905,99.1 SIF-Syn: flanked by minor tail proteins
    /note=Most likely the endolysin; HHPred evidence for peptidase
    /note=
    /note=Original Glimmer call @bp 17420 has strength 14.07
    /note=SSC: (17420bp, 18367bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (Gorpy, NCBI, Q2:S3, 79.05%, 2e-175) (Isolde_27, PhagesDB, Q2:S3, 79%, 1e-144) Gap: (4bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.356, -3.899, yes) F: (NKF) SIF-BLAST: (endolysin, NCBI, Gorpy, UVF60989.1, 79.05%, 2e-175) (lysin A, PhagesDB, Isolde_27, 79%, 1e-144) SIF-HHPred: (membrane protein, RCSB PDB, Vibrio cholerae, 8TZL_E, 25.92%, 99.11) SIF-Syn: (NKF)

CDS 18379 - 18687
  /gene="22"
  /product="gp22"
  /function="holin"
  /locus tag="Kukla_22"
    /note=Original Glimmer call @bp 18379 has strength 8.49; Genemark calls start at 18379
    /note=SSC: 18379-18687 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein PP640_gp25 [Arthrobacter phage Faja] ],,NCBI, q1:s1 100.0% 2.72795E-46 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.166, -2.1958114445137396, yes F: holin SIF-BLAST: ,,[hypothetical protein PP640_gp25 [Arthrobacter phage Faja] ],,YP_010656311,86.2745,2.72795E-46 SIF-HHPRED:  SIF-Syn: upstream is potential endolysin, downstream is minor tail protein
    /note=Pham is conserved; hints of holin; upstream is potential lysin; HHpred is weak but the TMHMM predicts 2 transmembrane 
    /note=
    /note=SSC: (Start: 18379, Stop: 18687), CP: (Yes), SCS: (Both), ST: (SS), Blast Start: (Phage Name: EvePickles, Gene Number: 25, Phage Database: PhagesDB, Q/S Value: 1/1, E-Value: 2e-41, % Identification: 82), Gene Length: (309), Gap: (12-1=11), LO: (No), RBS: (Shine Dalgarno Scoring Matrix: Kibler6, Shine Dalgarno Spacing Matrix: Karlin Medium, Z-Value: 3.163, Final-Value: -2.196, Best Choice: No), Function: (No Known Function), SIF-BLAST: (No Known Function/Hypothetical Protein, Database: NCBI, Phage Name: EvePickles, Gene Number: 25, Database Accession Number: UYL88312.1, %Alignment: 82.35, E-Value: 2e-36), SIF-HHPred: (Function: Signal Peptidase Complex Subunit, Database: HHPred, Phage Name: N/A, Gene Number: N/A, Hit: 7P2Q_D, %Alignment: 32.98, Probability: 33.7), SIF-Syn: (No Known Function)

CDS 18700 - 19824
  /gene="23"
  /product="gp23"
  /function="minor tail protein"
  /locus tag="Kukla_23"
    /note=Original Glimmer call @bp 18700 has strength 11.75; Genemark calls start at 18700
    /note=SSC: 18700-19824 CP: yes SCS: both ST: NA BLAST-Start: [minor tail protein [Arthrobacter phage EvePickles]],,NCBI, q1:s1 100.0% 0.0 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.098, -2.2763497933341483, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Arthrobacter phage EvePickles]],,UYL88313,92.246,0.0 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,93.5829,99.6 SIF-Syn: Aligns with TripleJ_26, flanking upstream gene 24, function: NKF but same Pham, flanking downstream gene 27, function: minor tail protein
    /note=SSC: (18700, 19824) CP: (Yes) SCS: (Both) ST: (NA) BLAST-Start: (EvePickles_26, NCBI, Q1:S1, 100%, 0.0) Gap: (12 bp) LO: (Yes) RBS: (KIbler6, Karlin Medium, 3.098, -2.276, yes) F: (minor tail protein) SIF-BLAST: (minor tail protein, NCBI, EvePickles_26, UYL88313.1, 92.2%, 0.0) SIF-HHPred: (minor tail protein, PDB, hypothetical protein, 3D37_A, 89.5%, 99.6%) SIF-Syn: (Aligns with TripleJ_26, flanking upstream gene 24, function: NKF but same Pham, flanking downstream gene 27, function: minor tail protein)

CDS 19824 - 20756
  /gene="24"
  /product="gp24"
  /function="minor tail protein"
  /locus tag="Kukla_24"
    /note=Original Glimmer call @bp 19824 has strength 14.22; Genemark calls start at 19824
    /note=SSC: 19824-20756 CP: yes SCS: both ST: SS BLAST-Start: [tail protein [Arthrobacter phage Faja] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -3.5707972674952195, yes F: minor tail protein SIF-BLAST: ,,[tail protein [Arthrobacter phage Faja] ],,YP_010656313,96.129,0.0 SIF-HHPRED: Putative tail fiber protein; Complex, VIRAL PROTEIN; 3.8A {Ralstonia phage GP4},,,8JOV_4,39.3548,96.7 SIF-Syn: minor tail protein, downstream gene minor tail protein, upstream gene minor tail protein
    /note=Original Glimmer call @bp 19824 has strength 14.22
    /note=SSC: (19824, 20756) CP: (yes) SCS: (both) ST:(SS) BLAST-Start: (Faja, NCBI. Q1:S1, 100%, 0.0) Gap: (no gap) LO: (yes) RBS: (Kilber 6, Karlin Medium, 2.516, -3.571, yes) F:(minor tail protein) SIF-Blast: (minor tail protein, NCBI, Faja, YP_010656313.1, 90.32, 0.0) SIF-HHPred: (tail fiber protein, HHPred, Ralstonia, 8JOV_4, .232, 96.71) SIF-Syn: (minor tail protein, downstream gene minor tail protein, upstream gene minor tail protein)

CDS 20756 - 21115
  /gene="25"
  /product="gp25"
  /function="hypothetical protein"
  /locus tag="Kukla_25"
    /note=Original Glimmer call @bp 20756 has strength 9.16; Genemark calls start at 20756
    /note=SSC: 20756-21115 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_EVEPICKLES_28 [Arthrobacter phage EvePickles]],,NCBI, q1:s1 100.0% 2.27019E-60 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.363, -3.8932062518944837, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_EVEPICKLES_28 [Arthrobacter phage EvePickles]],,UYL88315,86.5546,2.27019E-60 SIF-HHPRED:  SIF-Syn: NKF, left gene is a minor tail protein, right gene is NKF, TripleJ
    /note=Original Glimmer call @bp 20756 has strength 9.16
    /note=
    /note=SSC: (20756, 21115) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (no significant BLAST alignments) Gap: (1bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.363, -3.893, 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, left gene is a minor tail protein, right gene is NKF, TripleJ)

CDS 21124 - 21849
  /gene="26"
  /product="gp26"
  /function="hypothetical protein"
  /locus tag="Kukla_26"
    /note=Original Glimmer call @bp 21124 has strength 10.91; Genemark calls start at 21124
    /note=SSC: 21124-21849 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_EVEPICKLES_29 [Arthrobacter phage EvePickles]],,NCBI, q1:s1 100.0% 2.973E-160 GAP: 8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.129, -4.4057176022952405, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_EVEPICKLES_29 [Arthrobacter phage EvePickles]],,UYL88316,96.2656,2.973E-160 SIF-HHPRED:  SIF-Syn: SIF-Syn: (Kukla_26 is similar to TripleJ_29 but has NKF)
    /note=SSC: (21124/21849) CP: (Yes) SCS: (Both) ST: (SS) Blast-Start: (EvePickles_29, NCBI, 1:1, 100%, 3E-160) Gap: (0bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.416, -7.440, No) F: (NKF) SIF-BLAST: (NKF, Pecaan, EvePickles_29, UYL88316, 96.27%, 2.97E-160) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (Kukla_26 is similar to TripleJ_29 but has NKF)

CDS 21859 - 22236
  /gene="27"
  /product="gp27"
  /function="hypothetical protein"
  /locus tag="Kukla_27"
    /note=Original Glimmer call @bp 21859 has strength 7.05; Genemark calls start at 21859
    /note=SSC: 21859-22236 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp30 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 1.75314E-43 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -4.325675514574479, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp30 [Arthrobacter phage TripleJ] ],,YP_009884433,78.7402,1.75314E-43 SIF-HHPRED:  SIF-Syn: (NKF)
    /note=Gene 28_ Kukla
    /note=
    /note=SSC: (21856,22236) CP: (yes) SCS: (Both) ST: (SS) F: (NKF) RBS: (Kelber 6, Karlin Medium 2.129,-4.326) SIF-Blast: (NKF) SIF-HHPred: (NKF) SIF-Syk: (NKF)

CDS 22239 - 23315
  /gene="28"
  /product="gp28"
  /function="hydrolase"
  /locus tag="Kukla_28"
    /note=Original Glimmer call @bp 22239 has strength 13.33; Genemark calls start at 22239
    /note=SSC: 22239-23315 CP: yes SCS: both ST: NI BLAST-Start: [SGNH/GDSL hydrolase family protein [Arthrobacter sp. PvP023] ],,NCBI, q1:s1 100.0% 1.4633E-179 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.263, -4.184392147131822, yes F: hydrolase SIF-BLAST: ,,[SGNH/GDSL hydrolase family protein [Arthrobacter sp. PvP023] ],,WP_209742770,81.0585,1.4633E-179 SIF-HHPRED: c.23.10.0 (A:) automated matches {Parabacteroides merdae [TaxId: 411477]} | CLASS: Alpha and beta proteins (a/b), FOLD: Flavodoxin-like, SUPFAM: SGNH hydrolase, FAM: automated matches,,,SCOP_d4q9aa_,54.7486,99.8 SIF-Syn: SIF-Syn: (Matches no gene on TripleJ, Upstream matches gene 28 on TripleJ: NKF, Downstream matches no gene on TripleJ )
    /note=best evidence- HHPred lysophospholipase L1-like esterase [Arthrobacter sp. PvP023].
    /note=ACCESSION   MBP1135119
    /note=Use hydrolase as general classification 
    /note=
    /note=SS: (22239, 23315) CP: (no) SCS: (both) ST: (N/A) Blast-Start: (Matches Arthrobacter sp. PvP023, 3, NCBI, Target From: 1 Query To: 358, 1.4633e-179) Gap: (3) LO: (yes) RBS: (Kibler 6 Karlin Medium, 2.258, -4.184, yes) F: (hydrolase) SIF-BLAST: (hydrolase, NCBI, Arthrobacter sp. PvP023, WP_209742770, 81.0585%, 1.4633e-179) SIF-HHPred: (Alpha and beta proteins, SCOPe, N/A, SCOP_d4q9aa_, 54.7486%, 99.8) SIF-Syn: ( Matches no gene on TripleJ, Upstream matches gene 28 on TripleJ: NKF, Downstream matches no gene on TripleJ )

CDS complement (23319 - 24104)
  /gene="29"
  /product="gp29"
  /function="hydrolase"
  /locus tag="Kukla_29"
    /note=Original Glimmer call @bp 24104 has strength 10.34; Genemark calls start at 24104
    /note=SSC: 24104-23319 CP: yes SCS: both ST: NI BLAST-Start: [SGNH/GDSL hydrolase family protein [Mycetocola zhadangensis]],,NCBI, q7:s10 91.954% 7.06357E-35 GAP: 51 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.435, -3.741100290036245, no F: hydrolase SIF-BLAST: ,,[SGNH/GDSL hydrolase family protein [Mycetocola zhadangensis]],,RLQ82677,47.4453,7.06357E-35 SIF-HHPRED: c.23.10.0 (A:) automated matches {Pseudoalteromonas sp. [TaxId: 336179]} | CLASS: Alpha and beta proteins (a/b), FOLD: Flavodoxin-like, SUPFAM: SGNH hydrolase, FAM: automated matches,,,SCOP_d3hp4a_,72.0307,99.9 SIF-Syn: flanked with another potential hydrolase
    /note=Evidence for esterase in several clusters; chose to go with broader group
    /note=
    /note=SSC: (24104, 23319) CP: (Yes) SCS: (Glimmer Only) ST: (NI) Blast-Start: (Matches SGNH/GDSL hydrolase family protein, NCBI, Target From: 10 Target To: 258, 91.954%, 7.06357e-35) Gap: (789) LO: (Yes) RBS: (Kibler 6, Karlin Medium, 2.435, -3.741, no ) F: (NKF) SIF-BLAST: (NKF, NCBI, SGNH/GDSL, RLQ82677, 47,4453% , 7.06357e-35), SIF-HHPred: (hydrolase, HHPred, SGNH, SCOP_d3hp4a_, 72.0307%, 99.9), SIF-Syn: (NKF)

CDS complement (24156 - 25310)
  /gene="30"
  /product="gp30"
  /function="acetyltransferase"
  /locus tag="Kukla_30"
    /note=Original Glimmer call @bp 25310 has strength 6.45; Genemark calls start at 25310
    /note=SSC: 25310-24156 CP: yes SCS: both ST: NA BLAST-Start: [acyltransferase [Rhodococcus ruber] ],,NCBI, q24:s27 92.7083% 2.55556E-125 GAP: 134 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.641, -6.4589402468268435, no F: acetyltransferase SIF-BLAST: ,,[acyltransferase [Rhodococcus ruber] ],,WP_269602736,65.8854,2.55556E-125 SIF-HHPRED: OpgC_C ; OpgC protein,,,PF10129.13,89.5833,100.0 SIF-Syn: SIF-Syn: flanked by hydrolases and HTH DNA binding
    /note=PF01757 This family includes a range of acyltransferase enzymes. This domain is found in a wide range of acyltransferase enzymes, including, mainly, bacterial proteins which catalyse the transfer of acyl groups, other than amino-acyl, from one compound to another, such as Glucans biosynthesis protein C (OPGC) 
    /note=
    /note=
    /note=SSC: (25310,24156) CP: (yes) SCS: (Glimmer only) Starterator: (NA) Blast Start:(Hum25_Draft_27, NCBI, Q1:S1, 92% coverage, e-value is 5e26) Gap: (125 bp) LO: (no) RBS: (Kibler6, Karlin Medium, z score: 1.641, final score: -6.186, yes) F: (No known function) SIF: (NKF) SIF-HHPred: (NKF)

CDS complement (25445 - 26038)
  /gene="31"
  /product="gp31"
  /function="hypothetical protein"
  /locus tag="Kukla_31"
    /note=Original Glimmer call @bp 26038 has strength 8.17; Genemark calls start at 25966
    /note=SSC: 26038-25445 CP: yes SCS: both-gl ST: NA BLAST-Start: [hypothetical protein [Arthrobacter sp. ES3-54] ],,NCBI, q12:s3 94.4162% 2.27642E-69 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.013, -2.5359491958734357, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Arthrobacter sp. ES3-54] ],,WP_277526559,73.0159,2.27642E-69 SIF-HHPRED:  SIF-Syn: Unknown
    /note=Original Glimmer call @bp 26038 has strength 8.17; GeneMark calls start at 25966
    /note=SSC: [start: 26038, stop: 25445] CP: [Yes] SCS: [Glimmer] ST: [NA] BLAST-Start: [Arthrobacter sp. ES3-54, gn: ?, NCBI, Q:3 S:12, coverage: 94.4%, e-value: 2.27642e-69] Gap: [4bp overlap] LO: [Yes] RBS: [Kibler6, Karlin Medium, z-score: 3.010, final value: -2.536, Yes] F: [NKF] SIF-BLAST: [hypothetical protein, NCBI, Arthrobacter sp. ES3-54, accession number: WP_277526559, percent alignment: 73.0159, e-value: 2.27642e-69] SIF-HHPred: [NKF, no matches with a probability over 90%] SIF-Syn: [NKF, No phage gene to compare to as the matching gene is from an Arthrobacter genome] Tmhmm: [3 predicted]

CDS complement (26035 - 26271)
  /gene="32"
  /product="gp32"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Kukla_32"
    /note=Original Glimmer call @bp 26271 has strength 9.17; Genemark calls start at 26271
    /note=SSC: 26271-26035 CP: yes SCS: both ST: SS BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage Shoya] ],,NCBI, q1:s1 98.7179% 7.98936E-36 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.543, -3.5316035464369326, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage Shoya] ],,YP_010649649,85.1852,7.98936E-36 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_d6hn7b1,73.0769,99.0 SIF-Syn: 
    /note=Original Glimmer call @bp 26271 has strength 9.17
    /note=SSC: (26271 to 26035) (reverse) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (aligns with Shoya_29, NCBI, s1:q1, 98.7179%, 7.98936e^-34) Gap: (2 bp) LO: (yes) RBS: (Kibler6, Karlin Medium, -3.532, 2.538, yes) F: (helix-turn-helix DNA binding domain protein) SIF-BLAST: (helix-turn-helix DNA binding domain protein, NCBI, YP_010649649, 85.1852%, 7.98936e^-34) SIF-HHPred: (helix-turn-helix DNA binding domain protein, HHPred, SCOP_d6hn7b1, 73.0769%, 99%) SIF-Syn: (helix-turn-helix DNA binding domain protein, downstream NKF, upstream NKF)

CDS complement (26274 - 26417)
  /gene="33"
  /product="gp33"
  /function="hypothetical protein"
  /locus tag="Kukla_33"
    /note=Original Glimmer call @bp 26417 has strength 10.1; Genemark calls start at 26417
    /note=SSC: 26417-26274 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PP640_gp36 [Arthrobacter phage Faja] ],,NCBI, q1:s1 100.0% 6.72525E-23 GAP: 50 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.702, -5.309117108752867, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PP640_gp36 [Arthrobacter phage Faja] ],,YP_010656322,100.0,6.72525E-23 SIF-HHPRED:  SIF-Syn: SIF-Syn: (NKF, TripleJ, gene 34 matches gene 35, flanking genes are NKF)
    /note=Original Glimmer call @bp 26417 has strength 10.10 SSC: (26417, 26274) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (Faja_36, NCBI, Q1:S1, 100%, 7e-23) Gap: (4 bp) LO: (NA) RBS: (Kibler 6, Karlin Medium, 1.697, -5.309, yes) F: (NKF) SIF-BLAST: (NKF, NCBI, Faja_39, YP_010656322.1, 95.74%, 7e-23) SIF-HHPred: (NKF) SIF-Syn: (NKF, TripleJ, gene 34 matches gene 35, flanking genes are NKF)

CDS 26468 - 26929
  /gene="34"
  /product="gp34"
  /function="hypothetical protein"
  /locus tag="Kukla_34"
    /note=Original Glimmer call @bp 26573 has strength 5.48; Genemark calls start at 26486
    /note=SSC: 26468-26929 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein PP358_gp32 [Arthrobacter phage Shoya] ],,NCBI, q36:s1 77.1242% 2.5941E-74 GAP: 50 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.065, -4.460666092178802, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PP358_gp32 [Arthrobacter phage Shoya] ],,YP_010649652,94.9153,2.5941E-74 SIF-HHPRED:  SIF-Syn: NKF, no matches with a probability above 90%) SIF-Syn: (NKF, upstream NKF, downstream NKF
    /note=Changes start to cover. the CP.  strange forward among the reverse.
    /note=
    /note=SSC: (26573, 26929) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (Shoya, NCBI, Q1:S1, 82%, 1e-06) Gap: (155 bp) LO: (NO) RBS: (Kilber6, Karlin Medium, 1.29, -6.754, yes) F: (NKF) SIF-Blast: (NKF, NCBI, Shoya, YP_010649651.1, 60.98%, 1e-06) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (NKF, upstream NKF, downstream NKF)

CDS complement (27116 - 28255)
  /gene="35"
  /product="gp35"
  /function="tyrosine integrase"
  /locus tag="Kukla_35"
    /note=Original Glimmer call @bp 28255 has strength 10.73; Genemark calls start at 28255
    /note=SSC: 28255-27116 CP: yes SCS: both ST: SS BLAST-Start: [integrase [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 99.7361% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.722, -3.0713502170045657, yes F: tyrosine integrase SIF-BLAST: ,,[integrase [Arthrobacter phage TripleJ] ],,YP_009884440,99.2064,0.0 SIF-HHPRED: Int protein; transposase protein-DNA complex, tyrosine recombinase, Y-transposase, Tn916-like conjugative transposon, antibiotic resistance transfer, RECOMBINATION; 2.5A {Enterococcus faecalis},,,6EMY_B,76.2533,100.0 SIF-Syn: SIF-Syn: Tyrosine Integrase, Flanking genes: NKF, Helix-turn Helix DNA Binding Protein, Bacteriophage: TripleJ
    /note=Original Glimmer call @bp 28255 has strength 10.73
    /note=SSC: Start: 28255 Stop: 27116 
    /note=CP: yes 
    /note=SCS: Both 
    /note=ST: NI
    /note=Blast-Start: TripleJ_G37, NCBI, Q:1 S:1, Coverage: 99%, Evalue: 0
    /note=Gap: 1bp overload
    /note=LO: yes 
    /note=RBS: kibler6, Karlin Medium, Zscore: 2.722, Finale Score: -3.071, yes 
    /note=F:Tyrosine Integrase 
    /note=SIF-Blast: Integrase, NCBI, TripleJ_G37, YP_009884440.1, Allignment: 97.62%, Evlaue:0
    /note=SIF-HHPred: (INT Protein, PBD, Enterococcus faecalis, 6EMY_B, allignment: 91.48%, Probablility 100%), (Integrase, PBD, Lambdavirus lambda, 1Z1B_B, allignment: 91.57%, Probablility: 100%)
    /note=SIF-Syn: Tyrosine Integrase, Flanking genes: NKF, Helix-turn Helix DNA Binding Protein, Bacteriophage: TripleJ

CDS complement (28255 - 28491)
  /gene="36"
  /product="gp36"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Kukla_36"
    /note=Original Glimmer call @bp 28491 has strength 6.96; Genemark calls start at 28491
    /note=SSC: 28491-28255 CP: yes SCS: both ST: NI BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 2.04932E-49 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.924, -3.9507328541789084, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage TripleJ] ],,YP_009884441,100.0,2.04932E-49 SIF-HHPRED: DUF3263 ; Protein of unknown function (DUF3263),,,PF11662.12,89.7436,99.9 SIF-Syn: helix-turn-helix DNA binding domain protein, flanking genes: upstream: metallopeptidase, downstream: tyrosine integrase, compared to TripleJ genome
    /note=Original Glimmer call @bp 28491 has strength 6.96
    /note=SSC: (28491bp, 28255bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (TripleJ, NCBI, Q1:S1, 98.72%, 2e-49) (TripleJ_38, PhagesDB, Q1:S1, 98%, 7e-39) Gap: (8bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.92, -3.951, yes) F: (helix-turn-helix DNA binding domain protein) SIF-BLAST: (helix-turn-helix DNA binding domain protein, PhagesDB, TripleJ_38, 98%, 7e-39) (helix-turn-helix DNA binding domain protein, NCBI, TripleJ, YP_009884441.1, 98.72%, 2e-49) SIF-HHPred: (Protein of unknown function, Pfam, DUF3263, PF11662.12, 89.74%, 99.9) SIF-Syn: (helix-turn-helix DNA binding domain protein, flanking genes: upstream: metallopeptidase, downstream: tyrosine integrase, compared to TripleJ genome)

CDS complement (28484 - 28870)
  /gene="37"
  /product="gp37"
  /function="metalloprotease"
  /locus tag="Kukla_37"
    /note=Original Glimmer call @bp 28669 has strength 10.05; Genemark calls start at 28885
    /note=SSC: 28870-28484 CP: yes SCS: both-cs ST: NA BLAST-Start: [metallo-protease [Arthrobacter phage TripleJ] ],,NCBI, q1:s6 100.0% 3.74846E-88 GAP: 65 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.193, -4.541779190262089, no F: metalloprotease SIF-BLAST: ,,[metallo-protease [Arthrobacter phage TripleJ] ],,YP_009884442,95.4887,3.74846E-88 SIF-HHPRED: IrrE protein; Deinococcus, Radiotolerance, Gene regulation, Metallopeptidase, IrrE; HET: MSE; 2.6A {Deinococcus deserti},,,3DTE_A,89.0625,99.8 SIF-Syn: SIF-Syn: Matches gene on TripleJ, Upstream matches gene 38 on TripleJ: helix-turn-helix DNA binding domain protein, Downstream matches no gene on TripleJ )
    /note=SS: (28669, 28484) & SCS: (glimmer only) CP: (yes) ST: (NA) Blast-Start: (Matches Arthrobacter Phage TripleJ, 65, NCBI, Query From: 1 Subject To: 6, 3.74846e-88) SIF-BLAST: (metallopeptidase, NCBI, Arthrobacter phage TripleJ, YP_009884442, 100%,3.25827e-34) Gap: (65 LO: (no) RBS: (Kibler 6 Karlin Medium, 2.193, -4.542, yes) F: (metalloprotease) & SIF-HHPred: (metallopeptidase, 65PDB, TripleJ , 3DTE_A, 89.0625%, 99.8  SIF-Syn: Matches gene 39 on TripleJ: metallopeptidase, Upstream matches gene 38 on TripleJ: helix-turn-helix DNA binding domain protein, Downstream matches gene 40 on TripleJ: helix-turn-helix DNA binding domain protein)

CDS complement (28936 - 29307)
  /gene="38"
  /product="gp38"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Kukla_38"
    /note=Original Glimmer call @bp 29307 has strength 9.28; Genemark calls start at 29307
    /note=SSC: 29307-28936 CP: yes SCS: both ST: SS BLAST-Start: [transcriptional repressor [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 6.1603E-82 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.785, -3.080676611399484, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[transcriptional repressor [Arthrobacter phage TripleJ] ],,YP_009884443,99.187,6.1603E-82 SIF-HHPRED: Nucleoid-associated protein EspR; ALL HELICAL, HELIX-TURN-HELIX MOTIF, TRANSACTIONAL REGULATOR, DNA BINDING, TRANSCRIPTION; 3.3A {Mycobacterium tuberculosis},,,4NDW_B,89.4309,98.4 SIF-Syn: Aligns with TripleJ_40, downstream gene 39, function: helix-turn-helix DNA binding domain, upstream gene 41, function: helix-turn-helix DNA binding domain
    /note=Potential repressor
    /note=
    /note=SSC: (29307, 28936) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (TripleJ_40, NCBI, Q1:S1, 100%, 6e-82) Gap: (12 bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 2.785, -3.081, yes) F: (helix-turn-helix DNA binding domain) SIF-BLAST: (helix-turn-helix DNA binding domain, NCBI, TripleJ_40, YP_009884443, 99.2%, 6e-82) SIF-HHPred: (helix-turn-helix DNA binding domain, PDB, hypothetical protein, 4NDW_B, 70.6%, 99.38%) SIF-Syn: (Aligns with TripleJ_40, downstream gene 39, function: helix-turn-helix DNA binding domain, upstream gene 41, function: helix-turn-helix DNA binding domain)

CDS complement (29320 - 29802)
  /gene="39"
  /product="gp39"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Kukla_39"
    /note=Original Glimmer call @bp 29583 has strength 7.96; Genemark calls start at 29802
    /note=SSC: 29802-29320 CP: yes SCS: both-gm ST: NA BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 3.19881E-98 GAP: 242 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.032, -4.610716907820384, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage TripleJ] ],,YP_009884444,97.5,3.19881E-98 SIF-HHPRED: a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]},,,d2r1jl1,41.875,98.1 SIF-Syn: helix-turn-helix DNA binding domain, upstream gene helix-turn-helix DNA binding, downstream gene helix-turn-helix DNA binding domain
    /note=Went with GeneMark to fill the gap and cover the CP.
    /note=Potential repressor based on HHPREd
    /note=
    /note=Original Glimmer call @bp 29583 has strength 7.96; GeneMark calls start at 29802
    /note=SSC: (29320, 29583) CP: (yes) SCS: (both) ST: (NA) BLAST-Start: (TripleJ, NCBI, Q3:S76, 97%, 4e-42) Gap: (13 bp) LO: (no) RBS: (Kilber6, Karlin Medium, 2.945, -2.681, yes) F: (helix turn helix DNA binding domain protein) SIF-Blast: (helix-turn-helix DNA binding domain protein, NCBI, TripleJ, YP_009884444.1, 95.29%, 4e-42) SIF-HHPred: (NKF, no matches with a probabilty above 90%) SIF-Syn: (helix-turn-helix DNA binding domain, upstream gene helix-turn-helix DNA binding, downstream gene helix-turn-helix DNA binding domain)

CDS 30045 - 30314
  /gene="40"
  /product="gp40"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Kukla_40"
    /note=Original Glimmer call @bp 30045 has strength 5.69; Genemark calls start at 30045
    /note=SSC: 30045-30314 CP: no SCS: both ST: SS BLAST-Start: [helix-turn-helix transcriptional regulator [Arthrobacter sp. B3I4] ],,NCBI, q1:s1 95.5056% 7.39632E-52 GAP: 242 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.233, -4.759359944890645, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix transcriptional regulator [Arthrobacter sp. B3I4] ],,WP_307035832,93.2584,7.39632E-52 SIF-HHPRED: a.35.1.2 (C:) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} | CLASS: All alpha proteins, FOLD: lambda repressor-like DNA-binding domains, SUPFAM: lambda repressor-like DNA-binding domains, FAM: Phage repressors,,,SCOP_d3jxbc_,71.9101,98.6 SIF-Syn: helix-turn-helix DNA binding domain, left gene is helix-turn-helix DNA binding domain protein, right gene is NKF
    /note=Small amount of CP not covered.
    /note=Original Glimmer call @bp 30045 has strength 5.69
    /note=
    /note=SSC: (30045, 30314) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (no significant BLAST alignments) Gap: (463bp gap) LO: (no) RBS: (Kibler6, Karlin Medium, 2.233, -4.759, yes) F: (helix-turn-helix DNA binding domain protein) SIF-Blast: (NKF, no matches with e values below 10e-7) SIF-HHpred: (helix-turn-helix DNA binding domain, HHpred, Salmonella bacteriophage, SCOP_d3jxbc_, 71.91, 98.6) SIF-Syn: (helix-turn-helix DNA binding domain, left gene is helix-turn-helix DNA binding domain protein, right gene is NKF)

CDS 30345 - 30515
  /gene="41"
  /product="gp41"
  /function="hypothetical protein"
  /locus tag="Kukla_41"
    /note=Original Glimmer call @bp 30345 has strength 10.54; Genemark calls start at 30345
    /note=SSC: 30345-30515 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp43 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 2.85225E-29 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.952, -4.762070819318045, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp43 [Arthrobacter phage TripleJ] ],,YP_009884446,100.0,2.85225E-29 SIF-HHPRED:  SIF-Syn: SIF-Syn: (Kukla_42 is similar to TripleJ_43, but has a NKF)
    /note=SSC: (30345/30515) CP: (Yes) SCS: (Both) ST: (SS) Blast-Start: (TripleJ_43, NCBI, 1:1, 100%, 3E-29) Gap: (4bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.952, -4.762, Yes) F: (NKF) SIF-BLAST: (NKF, Pecaan, TripleJ_43, YP_009884446, 100%, 2.85E-29) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (Kukla_42 is similar to TripleJ_43, but has a NKF)

CDS 30512 - 31033
  /gene="42"
  /product="gp42"
  /function="hydrolase"
  /locus tag="Kukla_42"
    /note=Original Glimmer call @bp 30512 has strength 7.38; Genemark calls start at 30512
    /note=SSC: 30512-31033 CP: yes SCS: both ST: SS BLAST-Start: [hydrolase [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 2.23161E-107 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.737, -3.1210096757316057, no F: hydrolase SIF-BLAST: ,,[hydrolase [Arthrobacter phage TripleJ] ],,YP_009884447,95.3757,2.23161E-107 SIF-HHPRED: HAD_SAK_2 ; HAD domain in Swiss Army Knife RNA repair proteins,,,PF18143.5,89.0173,99.9 SIF-Syn: Sif-syn: (Kukla 44 matches with TripleJ 44 almost perfectly, Function:hydrolase)
    /note=HHPred to various types of hydrolases
    /note=
    /note=SSC: (30512,31033) CP: (yes) SCS: (Both) ST: (SS) RBS: (kelber 6, Karlin Medium 2.737, -3.121) F: (hydrolase) SIF-Blast: (NCBI, QFG09588.1, hydrolase, TripleJ, 89.6%, 95.4%, 2.23e-107) SIF-HHPred: (PF18143.5, RNA repair proteins, 99.9%, 89%, 2.4e-22) SIF-PhagesDB: (TripleJ, Hydrolase, 173 matches with 173, 2e-99) Sif-syn: (Kukla 44 matches with TripleJ 44 almost perfectly, Function:hydrolase)

CDS 31030 - 31185
  /gene="43"
  /product="gp43"
  /function="hypothetical protein"
  /locus tag="Kukla_43"
    /note=Original Glimmer call @bp 31030 has strength 9.41; Genemark calls start at 31030
    /note=SSC: 31030-31185 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_JINKIES_60 [Arthrobacter phage Jinkies]],,NCBI, q1:s1 98.0392% 1.79471E-8 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.124, -4.416294366073912, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_JINKIES_60 [Arthrobacter phage Jinkies]],,QPK40191,64.1509,1.79471E-8 SIF-HHPRED: KaiA; KaiA, Circadian Clock Protein; 2.03A {Synechococcus elongatus PCC 7942} SCOP: a.186.1.1, l.1.1.1, c.23.1.5,,,1R8J_A,96.0784,63.5 SIF-Syn: (NKF)
    /note=SS: (31030, 31185) CP: (yes) SCS: (both) ST: (SS) Blast- Start: (NKF) Gap: (overlap of 3)  
    /note=LO: (no) RBS: (Kibler 6 Karlin Medium, 2.124, -4.416, yes)  F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 31182 - 31457
  /gene="44"
  /product="gp44"
  /function="hypothetical protein"
  /locus tag="Kukla_44"
    /note=Original Glimmer call @bp 31182 has strength 7.67; Genemark calls start at 31182
    /note=SSC: 31182-31457 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp46 [Arthrobacter phage TripleJ] ],,NCBI, q3:s10 96.7033% 1.35502E-49 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.942, -4.862260131515226, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp46 [Arthrobacter phage TripleJ] ],,YP_009884449,83.6735,1.35502E-49 SIF-HHPRED: a.4.5.70 (A:6-96) Hypothetical protein GOS_3836187 {Environmental samples [TaxId: 33858]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: Marine metagenome family WH1,,,SCOP_d2od5a1,81.3187,95.7 SIF-Syn: Matches gene 46 on Triple J, hypothetical protein
    /note=SSC: (31182, 31457) CP: (Yes) SCS: (Glimmer Only) ST: (NI) Blast-Start: (Matches PBI_TRIPLEJ_46, hypothetical protein, NCBI, Target From: 10 Target To: 97, 96.7033%, 1.35502e-49 ) Gap: (-3) LO: (No) RBS: (Kibler 6, Karlin Medium, 1.094, -6.594, no) F: (NKF) SIF-BLAST: (NKF, NCBI, PBI_TRIPLEJ_46, YP_009884449, 78.5714%, 1.35502e-49), SIF-HHPred: (hypothetical protein, HHPred, GOS_3836187, 	SCOP_d2od5a1, 81.3187%, 95.7), SIF-Syn: (Matches gene 46 on Triple J, hypothetical protein)

CDS 31444 - 31653
  /gene="45"
  /product="gp45"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Kukla_45"
    /note=Original Glimmer call @bp 31507 has strength 10.77; Genemark calls start at 31444
    /note=SSC: 31444-31653 CP: no SCS: both-gm ST: NA BLAST-Start: [helix-turn-helix DNA binding domain protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 2.52404E-38 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.459, -3.769471247018311, no F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[helix-turn-helix DNA binding domain protein [Arthrobacter phage TripleJ] ],,YP_009884450,98.5075,2.52404E-38 SIF-HHPRED: Recombination Directionality Factor RdfS; Excisionase, Recombination Directionality Factor, winged helix-turn-helix, superhelix, DNA BINDING PROTEIN; HET: GOL; 2.45A {Mesorhizobium japonicum R7A},,,8DGL_A,81.1594,98.3 SIF-Syn: SIF-Syn: (flanking genes NKF)
    /note=Moved start to overlap to cover CP.
    /note=
    /note=SSC: (31507,31653) CP: (yes) SCS: (Glimmer only) ST: (NI) Blast Start: (TripleJ_47, NCBI, Q1:S1, 100% coverage, e-value is 7e27) Gap: (49 bp) LO: (no) RBS: (Kibler6, Karlin Medium, z score: 2.849, final score: -3.769) F: (helix-turn-helix DNA binding protein) SIF: (helix-turn-helix DNA binding protein, NCBI, TripleJ_47, accession number:YP_009884450.1, 100% alignment, e value: 7e27) SIF-HHPred: (DNA binding protein, PDB, hit number: SCOP_d6hn6b1, percent alignment 93.75%, 98.8% probability.)

CDS 31650 - 31868
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="Kukla_46"
    /note=Original Glimmer call @bp 31650 has strength 0.86; Genemark calls start at 31650
    /note=SSC: 31650-31868 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp48 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 4.92182E-42 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.867, -2.7653702713535186, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp48 [Arthrobacter phage TripleJ] ],,YP_009884451,100.0,4.92182E-42 SIF-HHPRED: HTH_58 ; Helix-turn-helix domain,,,PF19575.3,44.4444,98.2 SIF-Syn: NKF 
matching gene: 48
flanking genes: gene 47 helix-turn-helix DNA binding domain protein; gene 49 NKF
    /note=Small amount of CP not covered.  Better scores/acceptable overlap
    /note=some hits to HTH; not consistent or strong
    /note=
    /note=Original Glimmer call @bp 31650 has strength 0.86
    /note=SSC: [start: 31650, stop: 31868] CP: [Yes] SCS: [Both] ST: [Yes] BLAST-Start: [Arthrobacter phage TripleJ, gn: 48, NCBI, Q:1 S:1, coverage: 100%, e-value: 4.9e-42] Gap: [4bp overlap] LO: [No] RBS; [Kibler 6, Karlin Medium, z-score: 2.863, final score: -2.765, Yes] F:[NKF] SIF-BLAST: [hypothetical protein, NIH, Arthrobacter phage TripleJ, gn: 48, YP_009884451, percent alignment: 100%, e-value: 4.9e-42] SIF-HHpred: [NKF, InterPro, PF11242.12, percent alignment: 41.6667%, probablitity: 98.5] SIF-Syn: [NKF, matching gene: 48, flanking genes: gene 47 helix-turn-helix DNA binding domain protein; gene 49 NKF] Tmhmm: [No]

CDS 31993 - 32358
  /gene="47"
  /product="gp47"
  /function="hypothetical protein"
  /locus tag="Kukla_47"
    /note=Original Glimmer call @bp 31993 has strength 12.93; Genemark calls start at 31993
    /note=SSC: 31993-32358 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein HYQ00_gp49 [Arthrobacter phage TripleJ] ],,NCBI, q1:s40 100.0% 1.40945E-81 GAP: 124 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.155, -2.2186743274732437, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp49 [Arthrobacter phage TripleJ] ],,YP_009884452,75.625,1.40945E-81 SIF-HHPRED:  SIF-Syn: 
    /note=Original Glimmer call @bp 31993 has strength 12.93
    /note=SSC: (31993 to 32358) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (aligns with TripleJ_49, NCBI, q1:s40, 100, 1.40945e^-81) Gap: (124 bp) LO: (no) RBS: (KIbler6, Karlin Medium, 3.152, -2.219, yes)  F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF, upstream NKF, downstream NKF)

CDS 32355 - 32483
  /gene="48"
  /product="gp48"
  /function="hypothetical protein"
  /locus tag="Kukla_48"
    /note=Original Glimmer call @bp 32355 has strength 14.49; Genemark calls start at 32355
    /note=SSC: 32355-32483 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp51 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 6.50344E-18 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.254, -4.413617268040186, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp51 [Arthrobacter phage TripleJ] ],,YP_009884454,97.619,6.50344E-18 SIF-HHPRED:  SIF-Syn: SIF-Syn: (NKF, Triple J, gene 50 matches gene 51, flanking genes are NKF)
    /note=Original Glimmer call @bp 32355 has strength 14.49 SSC: (32355, 32483) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (TripleJ_51, NCBI, Q1:S1, 100%, 7e-18) Gap: (4 bp overlap) LO: (NA) RBS: (Kibler 6, Karlin Medium, 2.249, -4,414, yes) F: (NKF) SIF-BLAST: (NKF, NCBI, TripleJ_51, YP_009884454.1, 95.24%, 7e-18) SIF-HHPred: (NKF) SIF-Syn: (NKF, Triple J, gene 50 matches gene 51, flanking genes are NKF)

CDS 32486 - 32668
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="Kukla_49"
    /note=Original Glimmer call @bp 32486 has strength 7.4; Genemark calls start at 32486
    /note=SSC: 32486-32668 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp52 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 98.3333% 2.88825E-33 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.878, -4.857784300446364, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp52 [Arthrobacter phage TripleJ] ],,YP_009884455,96.6667,2.88825E-33 SIF-HHPRED: Prok-RING_2 ; Prokaryotic RING finger family 2,,,PF14445.10,36.6667,56.9 SIF-Syn: NKF
    /note=Original Glimmer call @bp 32486 has strength 7.40
    /note=SSC: (32486,32668) CP: (no) SCS: (both-GL) ST:(SS) Blast-Start: TripleJ, 52, Pecaan, Q1:S1, 98.33%, E-value- 2.88825E-33) Gap: (2 basepair) LO: (yes) RBS: (Kibler7, Karlin Medium, 1.878, -4.858, yes) F:(NKF) SIF-BLAST:(Hypothetical Protein, TripleJ_52, Pecaan, YP_009884455,96.6667%,Evalue-2.88825E-33) SIF-HHPred: (Prok-RING_2, Pecaan, PF14445.10, 41.07%, 56.5) Syf-Syn: (NKF)

CDS 32665 - 32838
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="Kukla_50"
    /note=Original Glimmer call @bp 32665 has strength 10.22; Genemark calls start at 32665
    /note=SSC: 32665-32838 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp53 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 1.23199E-28 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.155, -3.0637723674875006, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp53 [Arthrobacter phage TripleJ] ],,YP_009884456,91.2281,1.23199E-28 SIF-HHPRED:  SIF-Syn: 
    /note=Original Glimmer call @bp 32486 has strength 7.40
    /note=SSC: (32665, 32838) CP: (yes) SCS: (both) ST:(SS) Blast-Start: (TripleJ_53, NCBI, Q1:S1, 100%, E-value- 1.23199e-28) Gap: (overlaps 2 bp) LO: (No) RBS: (Kibler6, Karlin Medium, 3.155, -3.064, yes) F:(NKF) SIF-BLAST:(NKF, TripleJ_52, NCBI, YP_009884456, 91.2281%, 1.23199e-28) SIF-HHPred: (NKF) Syf-Syn: (NKF, upstream exonuclease, downstream NKF)

CDS 32835 - 33680
  /gene="51"
  /product="gp51"
  /function="exonuclease"
  /locus tag="Kukla_51"
    /note=Original Glimmer call @bp 32835 has strength 15.5; Genemark calls start at 32835
    /note=SSC: 32835-33680 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Arthrobacter sp. Soil763] ],,NCBI, q3:s5 99.2883% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.019, -2.583959800616441, yes F: exonuclease SIF-BLAST: ,,[hypothetical protein [Arthrobacter sp. Soil763] ],,WP_056738121,94.6996,0.0 SIF-HHPRED: Mitochondrial genome maintenance exonuclease 1; human MGME1, DNA complex, DNA exonuclease, DNA BINDING PROTEIN; 2.702A {Homo sapiens},,,5ZYT_C,88.6121,99.9 SIF-Syn: SIF-Syn: Exonuclease, Flanking genes: NKF, Jinkies
    /note=Original Glimmer call @bp 32835 has strength 15.50
    /note=SSC: Start: 32835 Stop: 33680
    /note=CP: yes 
    /note=SCS: Both
    /note=ST: NI
    /note=Blast-Start: (Arthrobacter sp. Soil763, NCBI, Q:3 S:5, Coverage: 99%, Evalue: 0), (Jinkies_G39, PhagesDB, Q:1 S:1, Evalue: 1e-60)
    /note=Gap:4bp overload 
    /note=Lo: no 
    /note=RBS: kibler6, Karlin Medium, Zscore: 3.019, Final Score: -2.584, Yes 
    /note=F: Exonuclease 
    /note=SIF-Blast: (Hypothetical protein, NCBI, Arthrobacter sp. Soil76, 	WP_056738121, allignment: 91.4%, Evalue: 0.0), (Exonuclease, PhagesDB, Jinkies_G39, allignment: 46%, Evlaue: 1e-60)
    /note=SIF-HHPred: Exonuclease, PBD, Homo Sapiens, 5ZYT_C, allignment: 57.06%, probability: 99.88%
    /note=SIF-Syn: Exonuclease, Flanking genes: NKF, Bacteriophage: Jinkies

CDS 33677 - 34645
  /gene="52"
  /product="gp52"
  /function="RecT-like DNA pairing protein"
  /locus tag="Kukla_52"
    /note=Original Glimmer call @bp 33677 has strength 13.11; Genemark calls start at 33677
    /note=SSC: 33677-34645 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein [Arthrobacter sp. Soil763] ],,NCBI, q1:s1 98.1366% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.119, -4.408951082954879, no F: RecT-like DNA pairing protein SIF-BLAST: ,,[hypothetical protein [Arthrobacter sp. Soil763] ],,WP_056738120,92.8125,0.0 SIF-HHPRED: Recombination protein bet; Annealase, Synaptase, SSAP, Single-strand annealing protein, DNA annealing intermediate, Recombinase, Two-component recombinase, Viral, DNA-binding, RECOMBINATION-DNA complex; 3.3A {Escherichia virus Lambda},,,7UJL_A,41.9255,99.8 SIF-Syn: RecT-like DNA pairing protein, Flanking genes: upstream: exonuclease, downstream: ssDNA binding protein, compared using TripleJ
    /note=Original Glimmer call @bp 33677 has strength 13.11
    /note=SSC: (33677bp, 34645bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (Jinkies_41, PhagesDB, Q1:S1, 55%, 
    /note=6e-85) (Soil763, NCBI, Q1:S1, 90.82%, 0.0) Gap: (4bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.115, -4.409, yes) F: (RecT-like ssDNA binding protein) SIF-BLAST: (RecT-like ssDNA binding protein, Jinkies_41, PhagesDB, 55%, 6e-85) (Hypothetical protein, Soil763, NCBI, WP_056738120.1, 90.82%, 0.0) SIF-HHPred: (Recombination protein, UniProt, Lambda, P03698, 78.5, 99.94) SIF-Syn: (RecT-like DNA pairing protein, Flanking genes: upstream: exonuclease, downstream: ssDNA binding protein, compared using TripleJ)

CDS 34645 - 34866
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="Kukla_53"
    /note=Original Glimmer call @bp 34645 has strength 3.18; Genemark calls start at 34645
    /note=SSC: 34645-34866 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Arthrobacter sp. StoSoilB22] ],,NCBI, q1:s1 75.3425% 9.10943E-14 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.536, -4.116640962647576, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Arthrobacter sp. StoSoilB22] ],,WP_223941873,63.4921,9.10943E-14 SIF-HHPRED:  SIF-Syn: SIF-Syn: (Kukla_54 is an orpham so there is no SIF-Syn)
    /note=SSC: (34645/34866) CP: (Yes) SCS: (Both) ST: (NA) Blast-Start: (StoSoilB22, StoSoilB22_22, NCBI, 1:1, 75%, 9E-14) Gap: (2bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.342, -6.053, No) F: (NKF) SIF-BLAST: (NKF, StoSoilB22_22, WP_223941873, 64.49%, 9.1E-14) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (Kukla_54 is an orpham so there is no SIF-Syn)

CDS 34866 - 35303
  /gene="54"
  /product="gp54"
  /function="SSB protein"
  /locus tag="Kukla_54"
    /note=Original Glimmer call @bp 34866 has strength 9.36; Genemark calls start at 34866
    /note=SSC: 34866-35303 CP: yes SCS: both ST: SS BLAST-Start: [single strand DNA binding protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 84.8276% 3.3915E-79 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -3.649482460397077, yes F: SSB protein SIF-BLAST: ,,[single strand DNA binding protein [Arthrobacter phage TripleJ] ],,YP_009884459,80.1325,3.3915E-79 SIF-HHPRED: Single-stranded DNA-binding protein; DNA binding, quaternary structure, plasticity, inhibitor development, DNA BINDING PROTEIN; HET: FMT; 1.92A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)},,,7F5Y_B,80.6897,100.0 SIF-Syn: Aligns with TripleJ_56, flanking downstream TripleJ_57, function: NrdH-like glutaredoxin, flanking upstream TripleJ_53, function: NKF but has same Pham
    /note=SSC: (34866, 35303) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (TripleJ_56, NCBI, Q1:S1, 84%, 4e-79) Gap: (1 bp overlap) LO: (Yes) RBS: (Kibler6, Karlin Medium, 2.516, -3.649, yes) F: (SSB Protein) SIF-BLAST: (SSB Protein, NCBI, TripleJ_56, YP_009884459, 80.1%, 4e-79) SIF-HHPred: (SSB Protein, PDB, hypothetical protein, 7F5Y_B, 71.1%, 99.95%) SIF-Syn: (Aligns with TripleJ_56, flanking downstream TripleJ_57, function: NrdH-like glutaredoxin, flanking upstream TripleJ_53, function: NKF but has same Pham)

CDS 35378 - 35701
  /gene="55"
  /product="gp55"
  /function="NrdH-like glutaredoxin"
  /locus tag="Kukla_55"
    /note=Original Glimmer call @bp 35378 has strength 12.5; Genemark calls start at 35378
    /note=SSC: 35378-35701 CP: yes SCS: both ST: SS BLAST-Start: [NrdH-like glutaredoxin [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 2.85933E-70 GAP: 74 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.924, -2.707694805492614, yes F: NrdH-like glutaredoxin SIF-BLAST: ,,[NrdH-like glutaredoxin [Arthrobacter phage TripleJ] ],,YP_009884460,99.0654,2.85933E-70 SIF-HHPRED: Circadian clock protein KaiB; Transcription Regulator, foldswitch; HET: ADP; 1.8A {Thermosynechococcus elongatus} SCOP: c.47.1.15,,,5JWO_B,86.9159,99.3 SIF-Syn: nrdH-like gltearodxin, downstream gene SSdna binding protein, NKF upstream gene
    /note=Original Glimmer call @bp 35378 has strength 12.50
    /note=SSC: (35378, 35701) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (TripleJ, NCBI, Q1:S1, 100%, 3e-70) Gap: (75 bp) LO: (no) RBS: (Kilber6, Karlin Medium, 2.924, -2.708, yes) F: (nrdH-like glutearodxin) SIF-Blast: (nrdH-like-glutearodxin, NCBI, TripleJ, YP_009994460.1, 96.26%, 3e-70) SIF-HHPred: (circadian clock protein, HHPred, 5JWO_B, .91%, 2.1E-10) SIF-Syn: (nrdH-like gltearodxin, downstream gene SSdna binding protein, NKF upstream gene)

CDS 35698 - 35829
  /gene="56"
  /product="gp56"
  /function="hypothetical protein"
  /locus tag="Kukla_56"
    /note=Original Glimmer call @bp 35698 has strength 9.84
    /note=SSC: 35698-35829 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein HYQ00_gp58 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 5.28357E-11 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.018, -4.702334767722353, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp58 [Arthrobacter phage TripleJ] ],,YP_009884461,79.0698,5.28357E-11 SIF-HHPRED: g.41.1.1 (A:139-173) Methionyl-tRNA synthetase (MetRS), Zn-domain {Pyrococcus abyssi [TaxId: 29292]} | CLASS: Small proteins, FOLD: Rubredoxin-like, SUPFAM: Methionyl-tRNA synthetase (MetRS), Zn-domain, FAM: Methionyl-tRNA synthetase (MetRS), Zn-domain,,,SCOP_d1rqga3,44.186,92.4 SIF-Syn: NKF, left gene is NrdH-like glutaredoxin, right gene is helix-turn-helix DNA binding domain protein
    /note=Original Glimmer call @bp 35698 has strength 9.84 ** not called by GeneMark
    /note=
    /note=SSC: (35698, 35829) CP: (no) SCS: (Glimmer only) ST: (NI) Blast-Start: (no significant BLAST alignments) Gap: (4bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 2.018, -4.702, yes) F: (NKF) SIF-Blast: (NKF, no matches with e values above 10e-7) SIF-HHpred: (Methionyl-tRNA synthetase, HHpred, Pyrococcus abyssi, SCOP_d1rqga3, 44.19, 92.4) SIF-Syn: (NKF, left gene is NrdH-like glutaredoxin, right gene is helix-turn-helix DNA binding domain protein)

CDS 35826 - 36047
  /gene="57"
  /product="gp57"
  /function="DNA binding protein"
  /locus tag="Kukla_57"
    /note=Original Glimmer call @bp 35826 has strength 6.24; Genemark calls start at 35808
    /note=SSC: 35826-36047 CP: no SCS: both-gl ST: SS BLAST-Start: [DNA binding protein [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 98.6301% 1.76685E-32 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.991, -4.970213310205538, no F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Arthrobacter phage TripleJ] ],,YP_009884462,81.3333,1.76685E-32 SIF-HHPRED: Gene 1 protein; gp1, octamer, DNA-binding, VIRAL PROTEIN; 1.502A {Shigella phage Sf6},,,4DYQ_A,64.3836,95.7 SIF-Syn: SIF-Syn: (Kukla_58 is similar to TripleJ_59 with a function of helix-turn-helix DNA binding domain protein, but is flanked by NrdH-like glutaredoxin and methyltransferase)
    /note=SSC: (35826/36047) CP: (Yes) SCS: (Both) ST: (SS) Blast-Start: (TripleJ_59, NCBI, 1:1, 98%, 2E-32) Gap: (11bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 2.201, -4.236, No) F: (DNA Binding Protein) SIF-BLAST: (DNA Binding Protein, Pecaan, TripleJ_59, YP_009884462, 81.33%, 1.77E-32) SIF-HHPred: (DNA Binding Protein, HHPred, Shigella_6, 4DYQ_A, 48%, 95.74%) SIF-Syn: (Kukla_58 is similar to TripleJ_59 with a function of helix-turn-helix DNA binding domain protein, but is flanked by NrdH-like glutaredoxin and methyltransferase)

CDS 36053 - 36976
  /gene="58"
  /product="gp58"
  /function="helix-turn-helix DNA binding domain"
  /locus tag="Kukla_58"
    /note=Original Glimmer call @bp 36053 has strength 10.19; Genemark calls start at 36053
    /note=SSC: 36053-36976 CP: yes SCS: both ST: NA BLAST-Start: [MULTISPECIES: helix-turn-helix domain containing protein [unclassified Ornithinimicrobium]],,NCBI, q2:s51 97.0684% 5.95453E-70 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.516, -4.4158953075094765, yes F: helix-turn-helix DNA binding domain SIF-BLAST: ,,[MULTISPECIES: helix-turn-helix domain containing protein [unclassified Ornithinimicrobium]],,WP_131104050,51.2748,5.95453E-70 SIF-HHPRED: Putative uncharacterized protein; DNA BINDING PROTEIN; NMR {Hyperthermus butylicus},,,2LVS_A,38.7622,97.7 SIF-Syn: Flanking genes also HTH DNA binding
    /note=SCS: (36053,36976) CP: (Yes) SCS: Both) ST: (SS) RBS: (Kleber 6,Karlin Medium 2.516, -4.416) SIF-Blast: (NKF) SIF-HHPred: (NKF) SIF-Syk: (NKF)

CDS 36973 - 37515
  /gene="59"
  /product="gp59"
  /function="hypothetical protein"
  /locus tag="Kukla_59"
    /note=Original Glimmer call @bp 36973 has strength 5.76; Genemark calls start at 36973
    /note=SSC: 36973-37515 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein PP353_gp60 [Arthrobacter phage Kumotta] ],,NCBI, q1:s1 94.4444% 6.16154E-80 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.711, -5.351280609534597, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PP353_gp60 [Arthrobacter phage Kumotta] ],,YP_010649467,80.3468,6.16154E-80 SIF-HHPRED:  SIF-Syn: SIF-Syn: (NKF)
    /note=SS: (36973, 37515) CP: (yes) SCS: (both) ST: (SS) Blast-Start: (Matches Arthrobacter Phage Kumotta, 3, NCBI, Target From: 1 Query To: 170, 6.16154e-80) Gap: (overlap of 3) RBS: (Kibler 6 Karlin Medium, 1.711, -5.351, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 37872 - 38264
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="Kukla_60"
    /note=Original Glimmer call @bp 37872 has strength 6.34; Genemark calls start at 37773
    /note=SSC: 37872-38264 CP: yes SCS: both-gl ST: NI BLAST-Start: [replication initiation protein [Arthrobacter phage TripleJ] ],,NCBI, q3:s7 97.6923% 9.39352E-88 GAP: 356 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.155, -2.156361006712914, yes F: hypothetical protein SIF-BLAST: ,,[replication initiation protein [Arthrobacter phage TripleJ] ],,YP_009884465,94.0299,9.39352E-88 SIF-HHPRED:  SIF-Syn: 
    /note=Keep Glimmer instead of filling the gap. CP and scores.
    /note=Tried adding a gene to fill gap; some CP but no evidence of potential protein coding gene.
    /note=
    /note=SSC: (37872, 38264) CP: (Yes) SCS: (Glimmer Only) ST: (NI) Blast-Start: (Matches PBI_TRIPLEJ_62, hypothetical protein, NCBI, Target From: 7 Target To: 133, 94.0299%, 9.39352e-88) Gap: (357) LO: (Yes) RBS: (Kibler 6, Karlin Medium, 3.155, -2.156, yes) F: (NKF) SIF-BLAST: (NKF, NCBI, PBI_TRIPLEJ_62, YP_009884465	, 97.6923%, 9.39352e-88), SIF-HHPred: (N-terminal phage replisome organiser, HHPred, PF09681.14%, 62.3077%, 98.6), SIF-Syn: (Matches gene 62 on Triple J, NKF)

CDS 38458 - 38868
  /gene="61"
  /product="gp61"
  /function="hypothetical protein"
  /locus tag="Kukla_61"
    /note=Original Glimmer call @bp 38458 has strength 4.08
    /note=SSC: 38458-38868 CP: yes SCS: glimmer ST: NI BLAST-Start: [hypothetical protein HYQ00_gp63 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 3.06687E-80 GAP: 193 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.867, -2.9063687850157054, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp63 [Arthrobacter phage TripleJ] ],,YP_009884466,95.5882,3.06687E-80 SIF-HHPRED:  SIF-Syn: 
    /note=SSC: (38859,38431) CP: (yes) SCS: (Glimmer only) ST: (NA) Blast Start: (Raqqa_draft81, NCBI, Q1:S1, … coverage, e-value is 8e80) Gap: (193bp) LO: (no) RBS: (Kibler6, Karlin Medium, z score: 2.867, final score: -2.906) F: (no known function) SIF: (NKF, NCBI, Raqqa_draft81, % alignment, e value: 8e80) SIF-HHPRed: (NKF, PDB, hit number: PF19938.3, percent alignment 19.1176, 81.2% probability.)

CDS 38865 - 39524
  /gene="62"
  /product="gp62"
  /function="nuclease"
  /locus tag="Kukla_62"
    /note=Original Glimmer call @bp 38865 has strength 7.45; Genemark calls start at 38865
    /note=SSC: 38865-39524 CP: yes SCS: both ST: NI BLAST-Start: [endonuclease [Arthrobacter phage Isolde] ],,NCBI, q3:s6 84.0183% 1.37703E-98 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.098, -2.417348306996335, yes F: nuclease SIF-BLAST: ,,[endonuclease [Arthrobacter phage Isolde] ],,YP_010656170,83.5979,1.37703E-98 SIF-HHPRED: MmcB-like ; DNA repair protein MmcB-like,,,PF06319.16,70.7763,99.8 SIF-Syn: Right arm is mainly NKF
    /note=PF06319 This family includes Caulobacter MmcB (CCNA_03580), which is involved in DNA repair. It has been proposed to be an endonuclease that creates the substrate for translesion synthesis [1].
    /note=Went with nuclease since there is not function for endonuclease and the specific nucleases on the list are not supported. 
    /note=
    /note=SSC: (38865, 39524) CP: (Yes) SCS: (Glimmer Only) ST: (NI) Blast-Start: (Matches Arthrobacter phage Isolde, endonuclease, NCBI, Target From: 6 Target To: 189, 85.0183%, 1.37703e-98) Gap: (6) LO: (no) RBS: (Kibler 6, Karlin Medium, 2.271, -5.633, yes) F: (NKF) SIF-BLAST: (endonuclease, NCBI, Arthrobacter phage Isolde, YP_010656170, 983.5979%, 1.37703e-98), SIF-HHPred: (DNA repair protein MmcB-like, HHPred, PF06319.16, 70.7763%, 99.8), SIF-Syn: (NKF)

CDS 39521 - 39844
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="Kukla_63"
    /note=Original Glimmer call @bp 39521 has strength 3.33; Genemark calls start at 39521
    /note=SSC: 39521-39844 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HYQ00_gp64 [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 90.6542% 1.22803E-58 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.77, -5.166207523958222, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp64 [Arthrobacter phage TripleJ] ],,YP_009884467,92.8571,1.22803E-58 SIF-HHPRED:  SIF-Syn: NKF, no matches with a probability above 90%) SIF-Syn: (NKF, Upstream NKF, downstream NKF
    /note=SSC: (39521, 39844) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (TripleJ, NCBI, Q1:S1, 90%, 1e-58) Gap: (4bp overlap) LO: (yes) RBS: (kilber 6, karlin medium, 1.77, -5.166, yes) F: (NKF) SIF-Blast: (NKF, NCBI, TripleJ, YP_009884467.1, 92.85%, 90.8163) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (NKF, Upstream NKF, downstream NKF)

CDS 39872 - 40009
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="Kukla_64"
    /note=Original Glimmer call @bp 39872 has strength 5.09; Genemark calls start at 39872
    /note=SSC: 39872-40009 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CASSIA_39 [Arthrobacter phage Cassia]],,NCBI, q1:s1 88.8889% 1.45553E-15 GAP: 27 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.57, -4.443838065747148, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CASSIA_39 [Arthrobacter phage Cassia]],,WGH21112,92.5,1.45553E-15 SIF-HHPRED:  SIF-Syn: NKF
    /note=SSC: (39872, 40009) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (Cassia_39, NCBI, Q1:S1, 88%, 2e-15) Gap: (27 bp) LO: (No) RBS: (Kibler6, Karlin Medium, 2.57, -4.44, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 40006 - 40383
  /gene="65"
  /product="gp65"
  /function="RusA-like resolvase"
  /locus tag="Kukla_65"
    /note=Original Glimmer call @bp 40006 has strength 6.64; Genemark calls start at 40006
    /note=SSC: 40006-40383 CP: yes SCS: both ST: NI BLAST-Start: [RusA-like Holliday junction resolvase [Arthrobacter phage TripleJ] ],,NCBI, q1:s1 100.0% 5.15645E-81 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.019, -2.583959800616441, yes F: RusA-like resolvase SIF-BLAST: ,,[RusA-like Holliday junction resolvase [Arthrobacter phage TripleJ] ],,YP_009884468,97.6,5.15645E-81 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,53.6,99.7 SIF-Syn: RusA-like resolvase, flanking genes: upstream: NKF; downstream: NKF, compared to TripleJ
    /note=Original Glimmer call @bp 40006 has strength 6.64
    /note=SSC: (40006bp, 40383bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (TripleJ_65, PhagesDB, Q1:S1, 96%, 3e-65) (TripleJ, NCBI, Q1:S1, 96%, 5e-81) Gap: (2bp overlap) LO: (yes) RBS: (Kibler6, Karlin Medium, 3.016, -2.584, yes) F: (RusA-like resolvase) SIF-BLAST: (RusA-like resolvase, PhagesDB, TripleJ_65, 96%, 3e-65) (RusA-like Holliday junction resolvase, NCBI, TripleJ, YP_009884468.1, 96%, 5e-81) SIF-HHPred: (Holliday junction resolvase, RCSB PDB, 7BGS_A, 53.6%, 99.7) SIF-Syn: (RusA-like resolvase, flanking genes: upstream: NKF; downstream: NKF, compared to TripleJ)

CDS 40486 - 40704
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="Kukla_66"
    /note=Original Glimmer call @bp 40486 has strength 5.86
    /note=SSC: 40486-40704 CP: yes SCS: glimmer ST: NA BLAST-Start: [hypothetical protein HYQ00_gp67 [Arthrobacter phage TripleJ] ],,NCBI, q14:s5 81.9444% 1.90098E-19 GAP: 102 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.155, -2.156361006712914, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp67 [Arthrobacter phage TripleJ] ],,YP_009884470,90.4762,1.90098E-19 SIF-HHPRED:  SIF-Syn: SIF-Syn: (NKF, TripleJ, gene 70 matches gene 74, flanking genes are NKF)
    /note=​​Original Glimmer call @bp 40486 has strength 5.86 ** not called by GeneMark SSC: (40486, 40704) CP: (yes) SCS: (Glimmer) ST: (NA) Blast-Start: (TripleJ_67, NCBI, Q14:S5, 81%, 2e-19) Gap: (101 bp) LO: (no) RBS: (Kibler 6, Karlin Medium, 3.152, -2.156, yes) F: (NKF) SIF-BLAST: (NKF, NCBI, TripleJ_67, YP_009884470.1, 94.92%, 2e-19) SIF-HHPred: (NKF) SIF-Syn: (NKF, TripleJ, gene 70 matches gene 74, flanking genes are NKF)

CDS 40701 - 40955
  /gene="67"
  /product="gp67"
  /function="hypothetical protein"
  /locus tag="Kukla_67"
    /note=Original Glimmer call @bp 40701 has strength 7.12; Genemark calls start at 40701
    /note=SSC: 40701-40955 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ZUCKER_54 [Arthrobacter phage Zucker]],,NCBI, q1:s1 100.0% 6.81707E-51 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.505, -5.13636943114082, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ZUCKER_54 [Arthrobacter phage Zucker]],,UUG70013,97.619,6.81707E-51 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 40701 has strength 7.12
    /note=SSC: (40701,40955) CP: (Yes) SCS:(both) ST: (SS) Blast-Start: (SEA_ZUCKER_54, Pecaan, Q1:S1, 100%, E-value: 6.81707E-51) Gap: (3) LO: (Yes) RBS: (Kibler7, Karlin Medium, 2.529, -4.138, yes) F:(NKF) SIF-BLAST: Hypothetical Protein, Pecaan, SEA_ZUCKER_54, UUG70013, 97.619%, E-value: 6.81707E-51) SIF-HHPred: (NKF, Pecaan, PF11305.12, 63.8%, 85.9) Sif-Syn: (NKF)

CDS 40952 - 41098
  /gene="68"
  /product="gp68"
  /function="hypothetical protein"
  /locus tag="Kukla_68"
    /note=Original Glimmer call @bp 40952 has strength 7.41
    /note=SSC: 40952-41098 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein QEO99_gp51 [Arthrobacter phage Bauer] ],,NCBI, q1:s1 100.0% 2.01911E-24 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.611, -3.368377069717189, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QEO99_gp51 [Arthrobacter phage Bauer] ],,YP_010761344,95.8333,2.01911E-24 SIF-HHPRED:  SIF-Syn: Match: Bauer gene 51 NKF
Flanking: Bauer gene 50 NKF; Bauer gene 52 NKF
    /note=Original Glimmer call @bp 40952 has strength 7.41 ** not called by GeneMark
    /note=
    /note=SCC: [start: 40952, stop: 41098] CP: [Yes] SCS: [Glimmer Only] ST: [SS] BLAST-Start: [Arthrobacter phage Bauer, gn: 51, NCBI, Q:1 S:1, coverage: 100%, e-value: 2.01911e-24] Gap: [4bp overlap] LO: [NA] RBS: [Kibler6, Karlin Medium, z-score: 3.016, final score: -2.584, Yes] F: [NKF] SIF-BLAST: [hypothetical protien, NCBI, Arthrobacter phage Bauer, gn: 51, YP_010761344, percent alignment: 95.83%, e-value: 2.01911e-24] SIF-HHPred: [NKF, no matches over 90% probability] SYF-Syn: [NKF, matching gene: gene 51 NKF, flanking genes: gene 50 NFK; gene 52 NKF, Arthrobacter phage Bauer]

CDS 41095 - 41700
  /gene="69"
  /product="gp69"
  /function="hypothetical protein"
  /locus tag="Kukla_69"
    /note=Original Glimmer call @bp 41095 has strength 7.27; Genemark calls start at 41095
    /note=SSC: 41095-41700 CP: no SCS: both ST: NA BLAST-Start: [hypothetical protein PP637_gp42 [Arthrobacter phage Persistence] ],,NCBI, q118:s47 41.2935% 2.47577E-28 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.583, -5.542591178556752, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PP637_gp42 [Arthrobacter phage Persistence] ],,YP_010656043,46.9231,2.47577E-28 SIF-HHPRED:  SIF-Syn: SIF-Syn: NKF
    /note=Original Glimmer call @bp 41095 has strength 7.27
    /note=SSC: Start: 41095bp Stop: 41700bp 
    /note=CP: Yes A small amount uncovered LORF
    /note=SCS: Both 
    /note=ST: NI
    /note=Blast-Start: Persitence_G42, NCBI, Q:118, S:47, coverage: 41%, Evalue: 3e-28.
    /note=Gap: 4bp overload
    /note=LO: Yes 
    /note=RBS: Kibbler6, Karlin Medium, Zscore: 1.583, Final Score: -5.543, No
    /note=F: NKF 
    /note=SIF-Blast: Hypothetical Protein, NCBI, Persistence_G42, YP_010656043, allignment: 65.06%, Evalue: 3e-28
    /note=SIF-HHPred: NKF 
    /note=SIF-Syn: NKF

CDS 41712 - 41888
  /gene="70"
  /product="gp70"
  /function="hypothetical protein"
  /locus tag="Kukla_70"
    /note=Original Glimmer call @bp 41712 has strength 3.02; Genemark calls start at 41712
    /note=SSC: 41712-41888 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein QEO99_gp54 [Arthrobacter phage Bauer] ],,NCBI, q1:s6 100.0% 5.52119E-29 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.093, -6.580199818159162, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QEO99_gp54 [Arthrobacter phage Bauer] ],,YP_010761347,88.8889,5.52119E-29 SIF-HHPRED:  SIF-Syn: NKF
    /note=Original Glimmer call @bp 41712 has strength 3.02
    /note=SSC: (41712bp, 41888bp) CP: (yes) SCS: (both) ST: (NI) BLAST-Start: (Bauer_54, PhagesDB, Q1:S6, 96%, 5e-25) (Bauer, NCBI, Q1:S1, 96.55%, 6e-29) Gap: (11bp) LO: (no) RBS: (Kibler6, Karlin Medium, 1.093, -6.580, no) F: (NKF) SIF-BLAST: (NKF, PhagesDB, Bauer_54, 96%, 5e-25) (hypothetical protein, Bauer, NCBI, YP_010761347.1, 96.55%, 6e-29) SIF-HHPred: (no significant matches with a probability above 90%) SIF-Syn: (NKF)

CDS 41885 - 42343
  /gene="71"
  /product="gp71"
  /function="hypothetical protein"
  /locus tag="Kukla_71"
    /note=Original Glimmer call @bp 41885 has strength 7.79; Genemark calls start at 41885
    /note=SSC: 41885-42343 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein PP634_gp60 [Arthrobacter phage Richie] ],,NCBI, q6:s1 92.1053% 2.30269E-84 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.08, -2.394841452453112, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PP634_gp60 [Arthrobacter phage Richie] ],,YP_010655781,90.0,2.30269E-84 SIF-HHPRED: DUF4326 ; Domain of unknown function (DUF4326),,,PF14216.10,86.8421,99.9 SIF-Syn: 
    /note=SSC: (41885,42343) CP: (yes) SCS: (both) ST: (NA) BLAST-Start: (NKF) Gap: (-4) LO: (no) RBS: (Kilber6, Karlin Medium (3.08,-2.395) F: (NKF) SIF-Blast: (NKF, probability 83%) SIF-HHPred: (NKF, no matches with a probability above 99%%) SIF-Syn: (NKF)

CDS 42333 - 42464
  /gene="72"
  /product="gp72"
  /function="hypothetical protein"
  /locus tag="Kukla_72"
    /note=Original Glimmer call @bp 42333 has strength 10.97; Genemark calls start at 42333
    /note=SSC: 42333-42464 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QEO99_gp56 [Arthrobacter phage Bauer] ],,NCBI, q1:s1 100.0% 1.63495E-21 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.867, -2.827683592113848, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QEO99_gp56 [Arthrobacter phage Bauer] ],,YP_010761349,97.6744,1.63495E-21 SIF-HHPRED: Nitr_red_assoc ; Conserved nitrate reductase-associated protein (Nitr_red_assoc),,,PF09655.14,39.5349,90.8 SIF-Syn: NKF
    /note=SSC: (42333, 42464) CP: (Yes) SCS: (Both) ST: (SS) BLAST-Start: (Bauer_56, NCBI, Q1:S1, 100%, 2e-21) Gap: (11 bp overlap) LO: (No) RBS: (Kibler6, Karlin Medium, 2.867, -2.828, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 42461 - 42661
  /gene="73"
  /product="gp73"
  /function="hypothetical protein"
  /locus tag="Kukla_73"
    /note=Original Glimmer call @bp 42461 has strength 8.05; Genemark calls start at 42461
    /note=SSC: 42461-42661 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein QEO78_gp39 [Arthrobacter phage Popper] ],,NCBI, q1:s1 100.0% 2.58858E-29 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.945, -2.6814417326944517, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QEO78_gp39 [Arthrobacter phage Popper] ],,YP_010761162,90.9091,2.58858E-29 SIF-HHPRED:  SIF-Syn: NKF, downstream gene NKF, upstream gene NKF
    /note=Original Glimmer call @bp 42461 has strength 8.05
    /note=SSC: (42461, 42661) CP: (yes) SCS: (both) ST: (SS) BLAST-Start: (Popper, NCBI, Q1:S1, 100%, 3e-29) Gap: 4 bp overlap) LO: (no) RBS: (Kilber6, Karlin Medium, 2.945, -2.681, yes) F: (NKF) SIF-Blast: (NKF, Popper, NCBI, YP_010761162.1, 80.30%, 3e-29) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (NKF, downstream gene NKF, upstream gene NKF)

CDS 42658 - 42945
  /gene="74"
  /product="gp74"
  /function="hypothetical protein"
  /locus tag="Kukla_74"
    /note=Original Glimmer call @bp 42658 has strength 6.55; Genemark calls start at 42658
    /note=SSC: 42658-42945 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein PP358_gp50 [Arthrobacter phage Shoya] ],,NCBI, q1:s1 100.0% 1.15764E-57 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.408, -3.7369320822071384, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PP358_gp50 [Arthrobacter phage Shoya] ],,YP_010649670,94.7368,1.15764E-57 SIF-HHPRED:  SIF-Syn: 
    /note=SSC: (42658,42945) CP: (yes) SCS: (both) ST: (NA) BLAST-Start: (NKF) Gap: (-4) LO: (no) RBS: (Kilber6, Karlin Medium (2.408,-3.737) F: (NKF) SIF-Blast: (NKF, probability 90%) SIF-HHPred: (NKF, no matches with a probability above 80%) SIF-Syn: (NKF)

CDS 42973 - 43185
  /gene="75"
  /product="gp75"
  /function="hypothetical protein"
  /locus tag="Kukla_75"
    /note=Original Glimmer call @bp 43057 has strength 4.59
    /note=SSC: 42973-43185 CP: yes SCS: glimmer-cs ST: NA BLAST-Start: [hypothetical protein SEA_RADFAD_71 [Arthrobacter phage RadFad]],,NCBI, q34:s112 52.8571% 0.0333482 GAP: 27 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.048, -6.753979878801637, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RADFAD_71 [Arthrobacter phage RadFad]],,UYL86627,15.0602,0.0333482 SIF-HHPRED:  SIF-Syn: 
    /note=Change to LORF to fill the gap and cover CP
    /note=
    /note=SSC: (43057/43185) CP: (Yes) SCS: (Glimmer Only) ST: (NA) Blast-Start: (No significant BLAST alignments) Gap: (19bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 1.048, -6.754, No) 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: (Kukla_76 is not similar to any genes on TripleJ)

CDS 43182 - 43334
  /gene="76"
  /product="gp76"
  /function="hypothetical protein"
  /locus tag="Kukla_76"
    /note=Original Glimmer call @bp 43167 has strength 3.98
    /note=SSC: 43182-43334 CP: yes SCS: glimmer-cs ST: NA BLAST-Start: [hypothetical protein SEA_RADFAD_52 [Arthrobacter phage RadFad]],,NCBI, q8:s1 84.0% 3.48595E-13 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.155, -4.333505036359522, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_RADFAD_52 [Arthrobacter phage RadFad]],,UYL86656,77.7778,3.48595E-13 SIF-HHPRED:  SIF-Syn: 
    /note=CHanged to -4 overlap and 
    /note=SCS: (43125,43334) CP: (Yes) SCS: (Both) ST: (NO) RBS: (Kleber 6, Karlin Medium 1.639, -5.714) SIF-Blast: (NKF) SIF-HHPred: (NKF) SIF-Syk: (NKF)

CDS 43351 - 43500
  /gene="77"
  /product="gp77"
  /function="hypothetical protein"
  /locus tag="Kukla_77"
    /note=Original Glimmer call @bp 43351 has strength 8.4; Genemark calls start at 43351
    /note=SSC: 43351-43500 CP: yes SCS: both ST: NA BLAST-Start:  GAP: 16 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.019, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST:  SIF-HHPRED:  SIF-Syn: SIF-Syn: (NKF, No identifiable corresponding gene to TripleJ)
    /note=SSC: (43351, 43500) CP: (yes) SCS: (both) ST: (NA) Blast-Start: (MrSmee_Draft_71, Phagesdb, Q1:S1, 34%, 0.25) Gap: (16 bp) LO: (NA) RBS: (Kibler 6, Karlin Medium, 3.016, -2.505, yes) F: (NKF) SIF-BLAST: (NKF, Phagesdb, MrSmee_Draft_71, 56%, 0.25) SIF-HHPred: (NKF) SIF-Syn: (NKF, No identifiable corresponding gene to TripleJ)

CDS 43497 - 43784
  /gene="78"
  /product="gp78"
  /function="hypothetical protein"
  /locus tag="Kukla_78"
    /note=Original Glimmer call @bp 43497 has strength 5.25; Genemark calls start at 43497
    /note=SSC: 43497-43784 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein [Micrococcaceae bacterium]],,NCBI, q1:s3 64.2105% 7.94929E-6 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.468, -3.750998330397795, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Micrococcaceae bacterium]],,HBV11425,35.8696,7.94929E-6 SIF-HHPRED:  SIF-Syn: 
    /note=SSC: (43497,43784) CP: (yes) SCS: (Glimmer Only) ST: (NA) Blast Start: (GlobiWarming_88, NCBI, Q1:S1, 64% coverage, e-value is 8e06) Gap: (-4bp) LO: (no) RBS: (Kibler6, Karlin Medium, z score: 2.468, final score: -3.751) F: (NKF) SIF: (NKF, NCBI, GCM10010525_01460, accession number: GAA2941050.1, 40.98% alignment, e value: 8e06.) SIF-HHPred: (NKF, PDB, hit number: PF10842.12, percent alignment 31.5789, 79.6 probability.)

CDS 43753 - 43965
  /gene="79"
  /product="gp79"
  /function="hypothetical protein"
  /locus tag="Kukla_79"
    /note=Original Glimmer call @bp 43753 has strength 4.52
    /note=SSC: 43753-43965 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein HYQ00_gp79 [Arthrobacter phage TripleJ] ],,NCBI, q15:s4 72.8571% 3.10628E-26 GAP: -32 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.691, -3.7902323473438546, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp79 [Arthrobacter phage TripleJ] ],,YP_009884482,87.5,3.10628E-26 SIF-HHPRED:  SIF-Syn: SIF-Syn: (Kukla_80 is similar to TripleJ_79 but has a NKF)
    /note=No CP in the other reading frame; overlap is the only available start
    /note=SSC: (43753/43965) CP: (Yes) SCS: (Glimmer Only) ST: (SS) Blast-Start: (TripleJ_79, NCBI, 15:4, 72%, 3E-26) Gap: (32bp) LO: (Yes) RBS: (Kibler6, Karlin Medium, 2.399, -4.107, No) F: (NKF) SIF-BLAST: (NKF, Pecaan, TripleJ_79, YP_009884482, 87.5%, 3.11E-26) SIF-HHPred: (NKF, no matches with a probability above 90%) SIF-Syn: (Kukla_80 is similar to TripleJ_79 but has a NKF)

CDS 44062 - 44535
  /gene="80"
  /product="gp80"
  /function="hypothetical protein"
  /locus tag="Kukla_80"
    /note=Original Glimmer call @bp 44062 has strength 7.61; Genemark calls start at 44062
    /note=SSC: 44062-44535 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein BWQ92_22815 [Arthrobacter sp. QXT-31]],,NCBI, q8:s7 94.2675% 4.14964E-21 GAP: 96 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.525, -3.5676719685030167, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein BWQ92_22815 [Arthrobacter sp. QXT-31]],,APX04186,49.6774,4.14964E-21 SIF-HHPRED:  SIF-Syn: NKF
    /note=Gap is LORF
    /note=
    /note=SCS: (44062,44535) CP: (Yes) SCS: (both) ST: (SS) RBS: (Kelber 6, Karlin Medium, 2.525, -3.568) SIF-Blast: (NKF) SIF-HHPred: (NKF) SIF-Syk: (NKF)

CDS 44547 - 45155
  /gene="81"
  /product="gp81"
  /function="hypothetical protein"
  /locus tag="Kukla_81"
    /note=Original Glimmer call @bp 44547 has strength 8.44; Genemark calls start at 44676
    /note=SSC: 44547-45155 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein HYQ00_gp81 [Arthrobacter phage TripleJ] ],,NCBI, q5:s19 98.0198% 1.3566E-121 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -4.466674028236667, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HYQ00_gp81 [Arthrobacter phage TripleJ] ],,YP_009884484,85.1852,1.3566E-121 SIF-HHPRED:  SIF-Syn: SIF-Syn: (NKF)
    /note=SS: (44547, 45155) CP: (yes) SCS: (glimmer) ST: (NI) Blast-Start: (Matches Arthrobacter Phage TripleJ, 12, NCBI, Target From: 19 Query To: 201, 1.3566e-121) Gap: (12) RBS: (Kibler 6 Karlin Medium, 2.124, -4.467, yes) F: (NKF) SIF-BLAST: (NKF) SIF-HHPred: (NKF) SIF-Syn: (NKF)

CDS 45201 - 45845
  /gene="82"
  /product="gp82"
  /function="hypothetical protein"
  /locus tag="Kukla_82"
    /note=Original Glimmer call @bp 45201 has strength 8.48; Genemark calls start at 45252
    /note=SSC: 45201-45845 CP: yes SCS: both-gl ST: NA BLAST-Start: [hypothetical protein [Pseudarthrobacter polychromogenes]],,NCBI, q1:s1 92.0561% 3.11683E-105 GAP: 45 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.701, -3.196631460098011, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein [Pseudarthrobacter polychromogenes]],,WP_188808646,74.2081,3.11683E-105 SIF-HHPRED:  SIF-Syn: NKF
    /note=SSC: (45201,  45845) CP: (Yes) SCS: (Glimmer Only) ST: (NI) Blast-Start: (Matches Pseudarthrobacter polychromogenes, hypothetical protein, NCBI, Target From: 1 Target To: 197, 74.2081%, 3.11683e-105) Gap: (46) LO: (Yes) RBS: (Kibler 6, Karlin Medium, 2.701, -3.197, yes) F: (NKF) SIF-BLAST: (NKF, NCBI,  Pseudarthrobacter polychromogenes, 	WP_188808646, 92.0561%, 3.11683e-105), SIF-HHPred:(YjdM_Zn_Ribbon ; PhnA Zinc-Ribbon, HHPred, PF08274.16, 18.6916%, 96.9), SIF-Syn: (NKF)

CDS 46357 - 46695
  /gene="83"
  /product="gp83"
  /function="hypothetical protein"
  /locus tag="Kukla_83"
    /note=Original Glimmer call @bp 46399 has strength 9.46; Genemark calls start at 46399
    /note=SSC: 46357-46695 CP: yes SCS: both-cs ST: NA BLAST-Start: [DUF6527 family protein [Pseudarthrobacter sp. NIBRBAC000502771] ],,NCBI, q24:s2 70.5357% 2.51183E-21 GAP: 511 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.922, -5.11571101996485, no F: hypothetical protein SIF-BLAST: ,,[DUF6527 family protein [Pseudarthrobacter sp. NIBRBAC000502771] ],,WP_141158271,54.5455,2.51183E-21 SIF-HHPRED:  SIF-Syn: SIF-Syn: (No known function)
    /note=Moved to LORF to cover the CP; scores are not as high.
    /note=
    /note=SSC: (46399,46695) CP: (yes) SCS: (Glimmer only) ST: (NA) Blast Start: (Qui_215, NCBI, Q1:S1, 80% coverage, e-value is 2e55) Gap: (553 bp) LO: (no) RBS: (Kibler6, Karlin Medium, z score: 2.867, final score: -2.765) F: (NKF) SIF: (NKF, NCBI, Pseudarthrobacter sp. NIBRBAC000502771, accession number: WP_141158271.1, 80% alignment, e value: 1e21.) SIF-HHPred: (NKF, PDB, hit number: PF20137.3, percent alignment 59.1837, 99.8% probability.)