CDS 147 - 362
  /gene="1"
  /product="gp1"
  /function="hypothetical protein"
  /locus tag="Johnathan_1"
    /note=Original Glimmer call @bp 147 has strength 9.69; Genemark calls start at 147
    /note=SSC: 147-362 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_ARROYO_2 [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 1.06713E-45 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.972, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_ARROYO_2 [Microbacterium phage Arroyo] ],,QDH93419,100.0,1.06713E-45 SIF-HHPRED: DUF3499 ; Protein of unknown function (DUF3499),,,PF12005.11,71.831,67.2 SIF-Syn: No synteny
    /note=Start: 147 
    /note=GI/GM favored: both
    /note=Gap/Overlap : 207
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.97 Final= -2.52, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 67.2% prob

CDS 362 - 685
  /gene="2"
  /product="gp2"
  /function="terminase, small subunit"
  /locus tag="Johnathan_2"
    /note=Original Glimmer call @bp 362 has strength 13.71; Genemark calls start at 362
    /note=SSC: 362-685 CP: yes SCS: both ST: SS BLAST-Start: [terminase small subunit [Microbacterium phage Burritobowl] ],,NCBI, q1:s1 100.0% 2.06056E-67 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.543, -7.739651338564521, no F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Microbacterium phage Burritobowl] ],,QNJ56161,100.0,2.06056E-67 SIF-HHPRED: Terminase_4 ; Phage terminase, small subunit,,,PF05119.15,75.7009,96.5 SIF-Syn: terminase, small subunit, upstream of terminase large subunit in Abigail
    /note=Start: 362
    /note=Gl/GM favored: both
    /note=Gap/Overlap: -1
    /note=Contains all CP: yes
    /note=SD score: Z=0.543, Final=-7.740, not best score but suggested start
    /note=Most annotated: yes
    /note=Most Conserved: yes
    /note=Q1:s1: yes
    /note=SIF-BLASTp: terminase small subunit, GenBank, from Abigail, QNJ56161,100% alignment, eval= 2.06e-67
    /note=SIF-HHPRED : terminase small subunit, Pfam, 75% alignment, 96.5% probability; next hit with small terminase of phage HK97, 6Z6E_B, prob=70.8%

CDS 689 - 2317
  /gene="3"
  /product="gp3"
  /function="terminase, large subunit"
  /locus tag="Johnathan_3"
    /note=Original Glimmer call @bp 689 has strength 10.1; Genemark calls start at 689
    /note=SSC: 689-2317 CP: yes SCS: both ST: NI BLAST-Start: [terminase large subunit [Microbacterium phage CroZenni]],,NCBI, q1:s1 100.0% 0.0 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.972, -2.442961286954254, yes F: terminase, large subunit SIF-BLAST: ,,[terminase large subunit [Microbacterium phage CroZenni]],,QWY79826,99.8155,0.0 SIF-HHPRED: Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97},,,6Z6D_A,90.7749,100.0 SIF-Syn: downstream of terminase small subunit and upstream of portal and MuF-like fusion protein in Abigail and Burritobowl
    /note=Start: 689
    /note=Gl/GM favored: both
    /note=Gap/Overlap: 3, LORF
    /note=Contains all CP: yes
    /note=SD score: Z= 2.972 Final=-2.443, best score
    /note=Most annotated:  no starterator report
    /note=Most Conserved: no starterator report
    /note=Q1:s1: yes
    /note=SIF-BLASTp: terminase large subunit, GenBank, from CroZenni, QWY79826,99.8% alignment, eval= 0
    /note=SIF-HHPRED: terminase large subunit, Enterobacteria phage HK97, 6Z6D_A, 90.8% alignment, 100% probability

CDS 2329 - 4353
  /gene="4"
  /product="gp4"
  /function="portal protein"
  /locus tag="Johnathan_4"
    /note=Original Glimmer call @bp 2329 has strength 8.81; Genemark calls start at 2329
    /note=SSC: 2329-4353 CP: yes SCS: both ST: NI BLAST-Start: [portal and MuF-like fusion protein [Microbacterium phage Albright] ],,NCBI, q1:s1 100.0% 0.0 GAP: 11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.796, -2.8970853586582503, no F: portal protein SIF-BLAST: ,,[portal and MuF-like fusion protein [Microbacterium phage Albright] ],,QTF82179,100.0,0.0 SIF-HHPRED: Phage portal protein, HK97 family; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus},,,6TE9_A,52.6706,100.0 SIF-Syn: downstream of terminase large subunit and upstream of capsid maturation protease in Abigail
    /note=Start: 2329
    /note=Gl/GM favored: both
    /note=Gap/Overlap: 11, LORF
    /note=Contains all CP: yes
    /note=SD score: Z=2.796, Final=-2.897, best score
    /note=Most annotated: no
    /note=Most Conserved: no
    /note=Q1:s1: yes
    /note=SIF-BLASTp: 	portal and MuF-like fusion protein,  Albright,  100% alignment, eval= 0
    /note=SIF-HHPRED: phage portal protein, gene transfer agent, Rhodobacter capsulatus, 6TE9_A, 52.7% alignment, 100% probability

CDS 4353 - 5105
  /gene="5"
  /product="gp5"
  /function="capsid maturation protease"
  /locus tag="Johnathan_5"
    /note=Original Glimmer call @bp 4353 has strength 12.04; Genemark calls start at 4353
    /note=SSC: 4353-5105 CP: yes SCS: both ST: SS BLAST-Start: [capsid maturation protease [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 3.12149E-180 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.972, -2.5052746077145835, yes F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Microbacterium phage Arroyo] ],,QDH93423,100.0,3.12149E-180 SIF-HHPRED: Prohead core protein protease; protease pentamer, phage T4, prohead, HYDROLASE; 1.943A {Enterobacteria phage T4},,,5JBL_A,74.4,98.3 SIF-Syn: capside maturation protease, downstream of portal MuF- like fusion protein, upstream of major capsid protein
    /note=Start: 4353
    /note=Gl/GM favored: both
    /note=Gap/Overlap: -1
    /note=Contains all CP: yes
    /note=SD score: Z=2.972, Final=-2.505, best score
    /note=Most annotated: yes
    /note=Most Conserved: yes
    /note=Q1:s1: yes
    /note=SIF-BLASTp: capsid maturation protease,  Arroyo, 100% alignment, eval= 3.12e-180
    /note=SIF-HHPRED: capsid assembly protease gp21, phage T4, 5JBL_A, 74.4% alignment, 98.3% probability

CDS 5142 - 6323
  /gene="6"
  /product="gp6"
  /function="major capsid protein"
  /locus tag="Johnathan_6"
    /note=Original Glimmer call @bp 5142 has strength 11.63; Genemark calls start at 5142
    /note=SSC: 5142-6323 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Microbacterium phage Abigail]],,NCBI, q1:s1 100.0% 0.0 GAP: 36 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.729, -5.080915947802713, no F: major capsid protein SIF-BLAST: ,,[major capsid protein [Microbacterium phage Abigail]],,QXN73506,100.0,0.0 SIF-HHPRED: Major capsid protein; Virus Procapsid particles, VIRUS; 5.2A {Enterobacteria phage HK97},,,3QPR_D,99.7455,100.0 SIF-Syn: major capsid protein, downstream from capsid maturation protease in Abigail
    /note=Start: 5142
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 36 
    /note=Contains all CP: yes
    /note=Most annotated: yes
    /note=Most conserved: yes 
    /note=SD score: z= 1.729 Final= -5.081, not best score but suggested start
    /note=Q1:s1: yes
    /note=SIF-BLASTp: major capsid protein,  Abigail,100% alignment, eval= 0
    /note=SIF-HHPRED: major capsid protein, phage HK97, 3QPR_D, 99.7% alignment, 100% probability

CDS 6389 - 6730
  /gene="7"
  /product="gp7"
  /function="hypothetical protein"
  /locus tag="Johnathan_7"
    /note=Original Glimmer call @bp 6389 has strength 11.02; Genemark calls start at 6389
    /note=SSC: 6389-6730 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BURRITOBOWL_7 [Microbacterium phage Burritobowl] ],,NCBI, q1:s1 100.0% 8.4912E-72 GAP: 65 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.085, -4.85287563363746, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BURRITOBOWL_7 [Microbacterium phage Burritobowl] ],,QNJ56166,100.0,8.4912E-72 SIF-HHPRED: GH94N_like_1; Glycoside hydrolase family 94 N-terminal-like domain of uncharacterized function.,,,cd11747,29.2035,44.0 SIF-Syn: none
    /note=Start: 6389
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 65
    /note=Contains all CP: yes
    /note=Most annotated: yes
    /note=Most conserved: yes 
    /note=SD score: z= 2.085 Final= -4.853, not best score but suggested start
    /note=Q1:s1: yes
    /note=SIF-BLASTp: no functional hits with eval below e-7
    /note=SIF-HHPRED: top hit had 44% probability (cd11747)

CDS 6765 - 7325
  /gene="8"
  /product="gp8"
  /function="head-to-tail adaptor"
  /locus tag="Johnathan_8"
    /note=Original Glimmer call @bp 6765 has strength 12.56; Genemark calls start at 6765
    /note=SSC: 6765-7325 CP: yes SCS: both ST: NI BLAST-Start: [head-to-tail adaptor [Microbacterium phage Abigail]],,NCBI, q1:s1 100.0% 1.00641E-128 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.061, -2.604595770381943, yes F: head-to-tail adaptor SIF-BLAST: ,,[head-to-tail adaptor [Microbacterium phage Abigail]],,QXN73508,100.0,1.00641E-128 SIF-HHPRED: 15 PROTEIN; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_C,96.7742,99.4 SIF-Syn: head-to-tail adaptor, upstream of head-to-tail stopper in Abigail
    /note=Start: 6765 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 34
    /note=Contains all CP: yes
    /note=Most annotated: no
    /note=Most conserved: no (inconclusive) 
    /note=SD score: z= 3.061 Final= -2.065, best score
    /note=Q1:s1: yes
    /note=SIF-BLASTp: head-to-tail adaptor, Abigail ,100% alignment, eval= 1.0e-128
    /note=SIF-HHPRED: gp15, Bacillus phage SPP1 , 5A21_C, 96.7% alignment, 99.4% probability

CDS 7325 - 7654
  /gene="9"
  /product="gp9"
  /function="head-to-tail stopper"
  /locus tag="Johnathan_9"
    /note=Original Glimmer call @bp 7325 has strength 12.15; Genemark calls start at 7325
    /note=SSC: 7325-7654 CP: yes SCS: both ST: SS BLAST-Start: [head-to-tail stopper [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 4.1396E-74 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.972, -2.523003374675015, yes F: head-to-tail stopper SIF-BLAST: ,,[head-to-tail stopper [Microbacterium phage Arroyo] ],,QDH93427,100.0,4.1396E-74 SIF-HHPRED: HEAD COMPLETION PROTEIN GP16; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_E,97.2477,99.7 SIF-Syn: 
    /note=Start 7325
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -1
    /note=Contains all CP: yes
    /note=Most annotated: yes
    /note=Most conserved: yes
    /note=SD score: z= 3.061 Final= -2.065
    /note=SIF-BLASTp: head-to-tail stopper, NCBI, Abigail 9, QDH93427, 100% alignment, e-value = 4.14e-74 
    /note=SIF-HHPRED: head completion protein, gp16, BACILLUS PHAGE SPP1, 5A21_E, 97.2% alignment, 99.7% probability

CDS 7654 - 7911
  /gene="10"
  /product="gp10"
  /function="hypothetical protein"
  /locus tag="Johnathan_10"
    /note=Original Glimmer call @bp 7654 has strength 10.57; Genemark calls start at 7642
    /note=SSC: 7654-7911 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_BURRITOBOWL_10 [Microbacterium phage Burritobowl] ],,NCBI, q1:s1 100.0% 1.69511E-53 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.852, -4.819059260305101, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BURRITOBOWL_10 [Microbacterium phage Burritobowl] ],,QNJ56169,100.0,1.69511E-53 SIF-HHPRED: DUF5403 ; Family of unknown function (DUF5403),,,PF17395.5,78.8235,93.6 SIF-Syn: No synteny
    /note=Start: 7654
    /note=GI/GM favored: Glimmer only 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.8 Final= -4.8, best score 
    /note=Q1:s1: yes
    /note=SIF-BLASTp: no functional hit below e^-7
    /note=SIF-HHPRED:no matches above 90% probability

CDS 7911 - 8306
  /gene="11"
  /product="gp11"
  /function="tail terminator"
  /locus tag="Johnathan_11"
    /note=Original Glimmer call @bp 7911 has strength 9.69; Genemark calls start at 7911
    /note=SSC: 7911-8306 CP: yes SCS: both ST: SS BLAST-Start: [tail terminator [Microbacterium phage Burritobowl] ],,NCBI, q1:s1 100.0% 3.4275E-87 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.721, -2.9754816289569264, no F: tail terminator SIF-BLAST: ,,[tail terminator [Microbacterium phage Burritobowl] ],,QNJ56170,100.0,3.4275E-87 SIF-HHPRED: TAIL-TO-HEAD JOINING PROTEIN GP17; VIRAL PROTEIN, VIRAL INFECTION, TAILED BACTERIOPHAGE, SIPHOVIRIDAE, SPP1, VIRAL ASSEMBLY, HEAD-TO-TAIL INTERFACE, DNA GATEKEEPER, ALLOSTERIC MECHANISM; 7.2A {BACILLUS PHAGE SPP1},,,5A21_G,95.4198,99.4 SIF-Syn: tail terminator, upstream of major tail protein in burritobowl
    /note=Start: 7911
    /note=GI/GM favored: both
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes
    /note=Most conserved: yes 
    /note=SD score: z= 2.7 Final= -2.9, final score was best, gap for other was too large
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: tail terminator, Genbank, Burritobowl 11, QNJ56170, 100% alignment, evalue= 2.43e-87
    /note=SIF-HHPRED: tail-to-head joining protein, BACILLUS PHAGE SPP1,5A21_G, 95.4% alignment, 99.4% probability

CDS 8320 - 9117
  /gene="12"
  /product="gp12"
  /function="major tail protein"
  /locus tag="Johnathan_12"
    /note=Original Glimmer call @bp 8320 has strength 11.4; Genemark calls start at 8320
    /note=SSC: 8320-9117 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Microbacterium phage Avocadoman] ],,NCBI, q1:s1 100.0% 0.0 GAP: 13 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.203, -2.0162541296952132, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Avocadoman] ],,QOP64841,100.0,0.0 SIF-HHPRED: YSD1_22 major tail protein; Bacteriophage tail, helical assembly, VIRAL PROTEIN; 3.5A {Bacteriophage sp.},,,6XGR_M,70.566,98.1 SIF-Syn: major tail protein, downstream of tail terminator
    /note=Start: 8320
    /note=GI/GM favored: both
    /note=Gap/Overlap : 13 
    /note=Contains all CP: yes 
    /note=Most annotated: yes
    /note=Most conserved: yes
    /note=SD score: z= 3.2 Final= -2.0, best score
    /note=Q1:s1: yes
    /note=SIF-BLASTp: major tail protein, genbank, Avocadoman 12, QOP64841, 100% alignment, evalue= 0 
    /note=SIF-HHPRED: major tail protein, PDB, bacteriophage, 6XGR_M, 70.5% alignment, 98.1% probability

CDS 9243 - 9551
  /gene="13"
  /product="gp13"
  /function="tail assembly chaperone"
  /locus tag="Johnathan_13"
    /note=Original Glimmer call @bp 9243 has strength 11.43; Genemark calls start at 9243
    /note=SSC: 9243-9551 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 1.443E-67 GAP: 125 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.908, -4.700704706091107, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Arroyo] ],,QDH93431,100.0,1.443E-67 SIF-HHPRED: GP24_25 ; Mycobacteriophage tail assembly protein,,,PF17388.5,84.3137,97.8 SIF-Syn: tail assembly chaperone, downstream of major tail protein in Burritobowl.
    /note=Start: 9243 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 125 gap
    /note=Contains all CP: yes 
    /note=Most annotated: y
    /note=Most conserved: y
    /note=SD score: z= 1.908 Final= -4.701, not best score
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: tail assembly chaperone, genbank, Arroyo, QDH93431, 100% alignment, e-value=1.4e-67 
    /note=SIF-HHPRED: tail assembly protein, pfam,  PF17388.5, 84.3% alignment, 97.8% probability
    /note=Frameshift: Occurs at 9251 in the genome: Frameshift -1

CDS 9593 - 9934
  /gene="14"
  /product="gp14"
  /function="tail assembly chaperone"
  /locus tag="Johnathan_14"
    /note=Original Glimmer call @bp 9593 has strength 6.42; Genemark calls start at 9593
    /note=SSC: 9593-9934 CP: yes SCS: both ST: NA BLAST-Start: [tail assembly chaperone [Microbacterium phage Arroyo] ],,NCBI, q1:s118 100.0% 1.86535E-75 GAP: 41 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.295, -6.353805630002573, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Arroyo] ],,QDH93432,49.1304,1.86535E-75 SIF-HHPRED: Phage_Gp15 ; Bacteriophage Gp15 protein,,,PF06854.14,30.9735,95.8 SIF-Syn: yes, part of tail assembly chaperone in Burritobowl, upstream of tapemeasure gene
    /note=Start: 9243 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 125 gap
    /note=Contains all CP: yes 
    /note=Most annotated: y 
    /note=Most conserved: y
    /note=SD score: z= 1.908 Final= -4.701, not best score
    /note=Q1:s1: yes
    /note=SIF-BLASTp: tail assembly chaperone, Genbank, Arroyo, Gene accession: QDH93432, Alignment:
    /note=49.1%, e-value: 1.8e-75
    /note=SIF-HHPRED: phage protein gp15, PFam, Hit: PF06854.14, Alignment: 31%,
    /note=Probability: 95.8%
    /note=Frameshift: Occurs at 9517 in the genome: Frameshift -1

CDS complement (9958 - 10173)
  /gene="15"
  /product="gp15"
  /function="hypothetical protein"
  /locus tag="Johnathan_15"
    /note=Original Glimmer call @bp 10173 has strength 3.61; Genemark calls start at 10173
    /note=SSC: 10173-9958 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AVOCADOMAN_15 [Microbacterium phage Avocadoman]],,NCBI, q1:s1 100.0% 5.00905E-43 GAP: 215 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.47, -3.588526034455651, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AVOCADOMAN_15 [Microbacterium phage Avocadoman]],,QOP64844,100.0,5.00905E-43 SIF-HHPRED: d.230.4.1 (B:33-84) D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain {Clostridium sticklandii [TaxId: 1511]},,,d1xrsb2,53.5211,57.9 SIF-Syn: No synteny
    /note=Start: 10173 (rev)
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 215 
    /note=Contains all CP: no
    /note=Most annotated: yes 
    /note=Most conserved: no 
    /note=SD score: z= 2.47 Final= -3.59, best 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e^-7
    /note=SIF-HHPRED: no functional fits with a probability above 90%

CDS 10389 - 13148
  /gene="16"
  /product="gp16"
  /function="tape measure protein"
  /locus tag="Johnathan_16"
    /note=Original Glimmer call @bp 10389 has strength 11.49; Genemark calls start at 10389
    /note=SSC: 10389-13148 CP: no SCS: both ST: SS BLAST-Start: [tape measure protein [Microbacterium phage Avocadoman] ],,NCBI, q1:s1 100.0% 0.0 GAP: 215 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.13, -4.229395370396053, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage Avocadoman] ],,QOP64845,100.0,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,59.7388,98.5 SIF-Syn: tape measure, upstream of minor tail protein in Albright
    /note=Start: 10389 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 215 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.13 Final= -4.23, final score was best 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: tape measure protein, genbank, Avocadoman, QOP64845, 100% alignment, evalue=0
    /note=SIF-HHPRED: tape measure protein, PDB, Staphylococcus virus 80alpha, 6VAI_ AF, 59.7% alignment, 98.5% probability

CDS 13145 - 13999
  /gene="17"
  /product="gp17"
  /function="minor tail protein"
  /locus tag="Johnathan_17"
    /note=Original Glimmer call @bp 13145 has strength 9.5; Genemark calls start at 13145
    /note=SSC: 13145-13999 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.428, -4.5049749909507835, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Arroyo] ],,QDH93435,99.6479,0.0 SIF-HHPRED: Distal Tail Protein, gp58; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BD,97.5352,100.0 SIF-Syn: minor tail protein, upstream from minor tail protein and downstream from tape measure protein in Burritobowl.
    /note=Start: 13145
    /note=GI/GM favored: both
    /note=Gap/Overlap : -4 
    /note=Contains all CP: yes 
    /note=Most annotated: no 
    /note=Most conserved: y 
    /note=SD score: z= 2.4  Final= -4.5, best scores
    /note=Q1:s1: yes
    /note=SIF-BLASTp: minor tail protein, genbank, Arroyo, QDH93435, 99.6% alignment, evalue = 0 
    /note=SIF-HHPRED: distal tail protein,  S aureus virus, 6VAI_BD, 97.5% alignment, 100% probability

CDS 13999 - 15969
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="Johnathan_18"
    /note=Original Glimmer call @bp 13999 has strength 8.32; Genemark calls start at 13999
    /note=SSC: 13999-15969 CP: yes SCS: both ST: NI BLAST-Start: [minor tail protein [Microbacterium phage Avocadoman]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.918, -4.820269098574683, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Avocadoman]],,QOP64847,96.4992,0.0 SIF-HHPRED: Tail-Associated Lysin, gp59; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_CE,54.7256,99.8 SIF-Syn: minor tail protein, downstream from minor tail protein in Abigail.
    /note=Start: 13999
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -1 , LORF
    /note=Contains all CP: yes 
    /note=Most annotated: no 
    /note=Most conserved: no
    /note=SD score: z= 1.9 Final= -4.8, not best, but others have too big of gaps
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: minor tail protein, genbank, Avocadoman, QOP64847, 96.5% alignment, evalue=0 
    /note=SIF-HHPRED: tail associated lysin, Staphylococcus virus 80alpha, 6V8I_CE, 54% alignment, 99.8% probability

CDS 15962 - 16135
  /gene="19"
  /product="gp19"
  /function="hypothetical protein"
  /locus tag="Johnathan_19"
    /note=Original Glimmer call @bp 15962 has strength 1.52
    /note=SSC: 15962-16135 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein QDW44_gp19 [Microbacterium phage BubbaBear] ],,NCBI, q1:s1 100.0% 1.28183E-21 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.507, -3.430952136556091, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein QDW44_gp19 [Microbacterium phage BubbaBear] ],,YP_010753861,82.7586,1.28183E-21 SIF-HHPRED: Alpha-aminoadipate carrier protein lysW; ATP-dependent amine/thiol ligase family, ATP-dependent amine/thiol ligase, LysW, Enzyme-Carrier protein complex, LIGASE; HET: SO4, ADP, GLU; 1.8A {Sulfolobus tokodaii},,,3VPB_E,59.6491,94.8 SIF-Syn: No synteny
    /note=Start: 15962 
    /note=GI/GM favored: Glimmer only 
    /note=Gap/Overlap : -8 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.5 Final= -3.4, best score
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e-7 
    /note=SIF-HHPRED: Mu-like prophage, 	PF10122.12, 66.6% alignment, 91.8% probability

CDS 16135 - 17223
  /gene="20"
  /product="gp20"
  /function="minor tail protein"
  /locus tag="Johnathan_20"
    /note=Original Glimmer call @bp 16135 has strength 11.19; Genemark calls start at 16135
    /note=SSC: 16135-17223 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Abigail]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.972, -2.5052746077145835, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Abigail]],,QXN73520,98.0663,0.0 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,42.8177,99.7 SIF-Syn: minor tail protein, upstream of minor tail protein
    /note=Start: 16135
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.9 Final= -2.5, best for both 
    /note=Q1:s1: yes
    /note=SIF-BLASTp: minor tail protein, genbank, Abigail, QSN73520, 98.1% alignment, evalue= 0 
    /note=SIF-HHPRED: receptor binding protein, Lactococcus phage 1358, 4L9B_A, 92.48% alignment, probability 99.7%

CDS 17233 - 18036
  /gene="21"
  /product="gp21"
  /function="minor tail protein"
  /locus tag="Johnathan_21"
    /note=Original Glimmer call @bp 17233 has strength 8.78; Genemark calls start at 17233
    /note=SSC: 17233-18036 CP: no SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Doobus]],,NCBI, q1:s1 100.0% 0.0 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.213, -2.0111200136961407, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Doobus]],,QZE10241,99.6255,0.0 SIF-HHPRED: DUF859 ; Siphovirus protein of unknown function (DUF859),,,PF05895.15,47.5655,99.4 SIF-Syn: minor tail protein, downstream of minor tail protein and upstream of endolysin in Abigail.
    /note=Start: 17233
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 9 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 3.2 Final= -2.0, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: minor tail protein, genbank, Doobus, QZE10241, 99.6% alignment, evalue= 0 
    /note=SIF-HHPRED: Siphovirus protein of unknown function , PF05895.15, 47% alignment, 99.4% probability; other hits above 90% are with eukaryotes

CDS 18048 - 18797
  /gene="22"
  /product="gp22"
  /function="endolysin"
  /locus tag="Johnathan_22"
    /note=Original Glimmer call @bp 18048 has strength 9.88; Genemark calls start at 18048
    /note=SSC: 18048-18797 CP: yes SCS: both ST: NI BLAST-Start: [endolysin [Microbacterium phage Avocadoman]],,NCBI, q1:s1 100.0% 0.0 GAP: 11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.213, -1.993391246735709, yes F: endolysin SIF-BLAST: ,,[endolysin [Microbacterium phage Avocadoman]],,QOP64851,99.5984,0.0 SIF-HHPRED: D-alanyl-D-alanine carboxypeptidase; Vancomycin resistance, peptidase, metallopeptidase family M15, HYDROLASE; HET: MSE, GOL, PG4; 1.65A {Enterococcus faecalis V583},,,5ZHF_B,51.4056,99.6 SIF-Syn: downstream of minor tail and upstream of holin in Abigail
    /note=Start: 18048 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 11 
    /note=Contains all CP: yes
    /note=Most annotated: no 
    /note=Most conserved: yes 
    /note=SD score: z= 3.2 Final= -1.9, best score
    /note=Q1:s1: yes
    /note=SIF-BLASTp: endolysin, genbank, Avocadoman, QOP64851, 99.6% alignment, evalue = 0 
    /note=SIF-HHPRED: D-alanyl-D-alanine carboxypeptidase, Enterococcus faecalis V583, 5ZHF_B, 51.4% alignment, 99.6% probability

CDS 18803 - 19285
  /gene="23"
  /product="gp23"
  /function="holin"
  /locus tag="Johnathan_23"
    /note=Original Glimmer call @bp 18803 has strength 10.26; Genemark calls start at 18803
    /note=SSC: 18803-19285 CP: yes SCS: both ST: SS BLAST-Start: [holin [Microbacterium phage Abigail]],,NCBI, q1:s4 100.0% 1.42638E-108 GAP: 5 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.546, -3.4892599424135016, yes F: holin SIF-BLAST: ,,[holin [Microbacterium phage Abigail]],,QXN73523,98.1595,1.42638E-108 SIF-HHPRED: DUF6163 ; Family of unknown function (DUF6163),,,PF19660.2,84.375,80.8 SIF-Syn: holin, downstream of endolysin in Abigail
    /note=Start: 18803 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 5 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.546 Final= -3.489, best scores 
    /note=Q1:s1: yes
    /note=SIF-BLASTp: holin, genbank, Abigail, QXN73523, 98.2% alignment, evalue =1.4 e-108 
    /note=SIF-HHPRED: no functional hit with a probability above 90%
    /note=4 TMHs

CDS 19296 - 19637
  /gene="24"
  /product="gp24"
  /function="membrane protein"
  /locus tag="Johnathan_24"
    /note=Original Glimmer call @bp 19296 has strength 9.49; Genemark calls start at 19296
    /note=SSC: 19296-19637 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BUBBABEAR_24 [Microbacterium phage BubbaBear] ],,NCBI, q1:s1 100.0% 5.03954E-70 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.972, -2.523003374675015, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_BUBBABEAR_24 [Microbacterium phage BubbaBear] ],,QCG77285,100.0,5.03954E-70 SIF-HHPRED: PspB ; Phage shock protein B,,,PF06667.15,53.9823,96.2 SIF-Syn: No synteny
    /note=Start: 19296
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 10 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.972  Final= -2.523 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: membrane protein, Abigail, eval= 5e-70, 100% identity 
    /note=SIF-HHPRED: DNA stabilization protein; tail needle, viral genome-ejection, Enterobacteria phage HK620, 	5BU5_D, 51% alignment, 93% probability
    /note=MEMBRANE PROTEIN: one TMH domain and one membrane domain predicted by Topcons (ran at website) and SOSUI indicates that it is a membrane protein

CDS 19641 - 19868
  /gene="25"
  /product="gp25"
  /function="membrane protein"
  /locus tag="Johnathan_25"
    /note=Original Glimmer call @bp 19641 has strength 10.39; Genemark calls start at 19641
    /note=SSC: 19641-19868 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Doobus]],,NCBI, q1:s1 100.0% 4.06581E-45 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.529, -3.911270251972219, no F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Doobus]],,QZE10245,100.0,4.06581E-45 SIF-HHPRED: Halogen_Hydrol ; 5-bromo-4-chloroindolyl phosphate hydrolysis protein,,,PF10112.12,54.6667,74.9 SIF-Syn: no synteny
    /note=Start: 19641 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 3 
    /note=Contains all CP: yes
    /note=Most annotated: yes 
    /note=Most conserved: yes
    /note=SD score: z= 2.53 Final= -2.9, not the best score but has the smallest gap 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: membrane protein, Doobus, QZE10245, 100% alignment, evalue= 4.1e -45 
    /note=SIF-HHPRED: no functional hit with a probability above 90%
    /note=2 TMHs based on TmHmm

CDS 20110 - 20766
  /gene="26"
  /product="gp26"
  /function="hypothetical protein"
  /locus tag="Johnathan_26"
    /note=Original Glimmer call @bp 20110 has strength 14.98; Genemark calls start at 20110
    /note=SSC: 20110-20766 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AVOCADOMAN_26 [Microbacterium phage Avocadoman]],,NCBI, q1:s1 100.0% 1.10614E-154 GAP: 241 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.118, -2.13349812375341, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AVOCADOMAN_26 [Microbacterium phage Avocadoman]],,QOP64855,99.5413,1.10614E-154 SIF-HHPRED: DUF1599 ; Nucleotide modification associated domain 1,,,PF07659.14,14.2202,84.0 SIF-Syn: none
    /note=Start: 20110 
    /note=GI/GM favored: both
    /note=Gap/Overlap : 241 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 3.12 Final= -2.13, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: Nucleotide modification associated domain 1, siphoviridae sps., eval=1.3e-14, 60.8% align
    /note=SIF-HHPRED: no functional hits above a probability of 90%, top hit 84%

CDS 20763 - 20909
  /gene="27"
  /product="gp27"
  /function="hypothetical protein"
  /locus tag="Johnathan_27"
    /note=Original Glimmer call @bp 20763 has strength 8.53; Genemark calls start at 20763
    /note=SSC: 20763-20909 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LYNLEN_28 [Microbacterium phage Lynlen] ],,NCBI, q1:s1 100.0% 1.02671E-26 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.507, -6.458895366205956, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYNLEN_28 [Microbacterium phage Lynlen] ],,QJD53437,100.0,1.02671E-26 SIF-HHPRED: g.41.5.1 (A:) automated matches {Mycobacterium ulcerans [TaxId: 362242]},,,d2m4ya_,62.5,90.6 SIF-Syn: No synteny
    /note=Start: 20763 
    /note=GI/GM favored: yes 
    /note=Gap/Overlap : -4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.50 Final= -6.45, not best scores (best overlap) 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e-7 
    /note=SIF-HHPRED:  no functional hits above 90% probability

CDS 20974 - 21852
  /gene="28"
  /product="gp28"
  /function="Cas4 exonuclease"
  /locus tag="Johnathan_28"
    /note=Original Glimmer call @bp 20974 has strength 10.98; Genemark calls start at 20974
    /note=SSC: 20974-21852 CP: yes SCS: both ST: NI BLAST-Start: [Cas4 family exonuclease [Microbacterium phage Doobus]],,NCBI, q1:s1 100.0% 0.0 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.584, -3.618090370183562, yes F: Cas4 exonuclease SIF-BLAST: ,,[Cas4 family exonuclease [Microbacterium phage Doobus]],,QZE10248,100.0,0.0 SIF-HHPRED: Cas4_I-A_I-B_I-C_I-D_II-B; CRISPR/Cas system-associated protein Cas4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA.,,,cd09637,80.137,98.7 SIF-Syn: No synteny
    /note=Start: 20974 
    /note=GI/GM favored: yes
    /note=Gap/Overlap : 64 
    /note=Contains all CP: yes 
    /note=Most annotated: yes
    /note=Most conserved: no 
    /note=SD score: z= 2.58 Final= -3.62, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: Cas4 family exonuclease, genbank, Doobus, QZE10248, 100% alignment, evalue = 0 
    /note=SIF-HHPRED: PDDEXK_1 ; PD-(D/E)XK nuclease superfamily, PF12705.10, 67% alignment, 98.4% probability AND CRISPR-associated exonuclease, Cas4 family, Pyrobaculum calidifontis, 4R5Q_A, 65% alignment, 98.1% probability (only aligning with exonuclease domain and not the helicase domain of RecB)

CDS 21852 - 22016
  /gene="29"
  /product="gp29"
  /function="hypothetical protein"
  /locus tag="Johnathan_29"
    /note=Original Glimmer call @bp 21852 has strength 9.13; Genemark calls start at 21852
    /note=SSC: 21852-22016 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_SANSAFET_30 [Microbacterium phage SansAfet] ],,NCBI, q1:s1 100.0% 7.93278E-29 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.727, -5.166207523958222, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_SANSAFET_30 [Microbacterium phage SansAfet] ],,QFP94286,100.0,7.93278E-29 SIF-HHPRED: CC-Hex*-L24D; coiled coil, tetramer, synthetic, antiparallel, cc-hex, DE NOVO PROTEIN; HET: SO4; 1.2A {N/A},,,PF19744.2,46.2963,55.8 SIF-Syn: No synteny
    /note=Start: 21852 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.727 Final= -5.166, not the best score, but best overlap/gap
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 55.8%

CDS 22013 - 22396
  /gene="30"
  /product="gp30"
  /function="hypothetical protein"
  /locus tag="Johnathan_30"
    /note=Original Glimmer call @bp 22013 has strength 7.14; Genemark calls start at 22013
    /note=SSC: 22013-22396 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_ARROYO_31 [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 6.73282E-88 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.276, -4.060971128237648, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_ARROYO_31 [Microbacterium phage Arroyo] ],,QDH93448,100.0,6.73282E-88 SIF-HHPRED: c.52.1.35 (A:) stNUC {Salmonella phage SETP3 [TaxId: 424944]},,,d4qboa1,42.5197,69.7 SIF-Syn: No synteny
    /note=Start: 22013 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -4
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.276 Final= -4.061, second best score, best overlap 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e-7 
    /note=SIF-HHPRED: no functional hits above 90%, top hit 69.7%

CDS 22510 - 23046
  /gene="31"
  /product="gp31"
  /function="MazG-like nucleotide pyrophosphohydrolase"
  /locus tag="Johnathan_31"
    /note=Original Glimmer call @bp 22510 has strength 7.39; Genemark calls start at 22510
    /note=SSC: 22510-23046 CP: yes SCS: both ST: SS BLAST-Start: [MazG-like nucleotide pyrophosphohydrolase [Microbacterium phage Abigail]],,NCBI, q1:s1 100.0% 5.50977E-130 GAP: 113 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.69, -3.869197702737806, yes F: MazG-like nucleotide pyrophosphohydrolase SIF-BLAST: ,,[MazG-like nucleotide pyrophosphohydrolase [Microbacterium phage Abigail]],,QXN73531,100.0,5.50977E-130 SIF-HHPRED: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE; HYDROLASE, DIMERIC DUTPASE; HET: SO4, GOL; 1.7A {DEINOCOCCUS RADIODURANS},,,2YF4_D,74.1573,100.0 SIF-Syn: mazg-like nucleotide pyrophosphohydrolase, upstream of thymidylate kinase in Abigail.
    /note=Start: 22510 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 113 (there is an option for a start with a -4 gap but it is not present in most members of the pham and not most annotated based on starterator)
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.69 Final= -3.869, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: mazg-like nucleotide pyrophosphohydrolase, genbank, Abigail, QXN73531, 100% alignment, 5.51e-130
    /note=SIF-HHPRED: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE, Deinococcus radiodurans, 2YF4_D, 74.16% alignment, 100% probability

CDS 23043 - 23552
  /gene="32"
  /product="gp32"
  /function="thymidylate kinase"
  /locus tag="Johnathan_32"
    /note=Original Glimmer call @bp 23043 has strength 9.43; Genemark calls start at 23043
    /note=SSC: 23043-23552 CP: yes SCS: both ST: SS BLAST-Start: [thymidylate kinase [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 2.25892E-118 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.626, -4.083954423845364, yes F: thymidylate kinase SIF-BLAST: ,,[thymidylate kinase [Microbacterium phage Arroyo] ],,QDH93450,99.4083,2.25892E-118 SIF-HHPRED: Thymidylate kinase; Structural Genomics, PSI-Biology, Midwest Center for Structural Genomics, MCSG, Mtb Proteins Conferring Susceptibility to Known Mtb; HET: MSE, MES, PG4; 1.55A {Staphylococcus aureus} SCOP: c.37.1.0,,,4MQB_B,97.0414,99.6 SIF-Syn: thymidylate kinase, downstream from mazg-like nucleotide pyrophosphohydrolase and upstream from recombination directionality factor in Burritobowl.
    /note=Start: 23043
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.63 Final= -4.08, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: thymidylate kinase,  Arroyo, QDH93450, 99.41% alignment, e-value = 2.26e-118 
    /note=SIF-HHPRED: thymidylate kinase, Staph aureus, 4MQB_B, 97% alignment, 99.6% probability

CDS 23568 - 24317
  /gene="33"
  /product="gp33"
  /function="recombination directionality factor"
  /locus tag="Johnathan_33"
    /note=Original Glimmer call @bp 23568 has strength 11.71; Genemark calls start at 23568
    /note=SSC: 23568-24317 CP: yes SCS: both ST: SS BLAST-Start: [recombination directionality factor [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 9.1556E-179 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.085, -5.426906901365179, yes F: recombination directionality factor SIF-BLAST: ,,[recombination directionality factor [Microbacterium phage Arroyo] ],,QDH93451,100.0,9.1556E-179 SIF-HHPRED: Gp3-like ; Recombination directionality factor-like,,,PF18897.3,83.9357,100.0 SIF-Syn: recombination directionality factor, downstream of thymidylate kinase in Burritobowl.
    /note=Start: 23568 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 15, LORF
    /note=Contains all CP: yes 
    /note=Most annotated: no, does not have most annotated start
    /note=Most conserved: y for EB
    /note=SD score: z= 2.09 Final= -5.43, best z-score and best gap
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: recombination directionality factor, Genbank, Arroyo, QDH93451, 100% alignment, e value= 9.16 e-179 
    /note=SIF-HHPRED: recombination directionality factor, Pfam,  PF18897.3, 83.9% alignment, 100% probability

CDS complement (24478 - 24747)
  /gene="34"
  /product="gp34"
  /function="hypothetical protein"
  /locus tag="Johnathan_34"
    /note=Original Glimmer call @bp 24747 has strength 10.79; Genemark calls start at 24747
    /note=SSC: 24747-24478 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AVOCADOMAN_34 [Microbacterium phage Avocadoman] ],,NCBI, q1:s1 100.0% 8.48252E-55 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.422, -5.7955239634706, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AVOCADOMAN_34 [Microbacterium phage Avocadoman] ],,QOP64863,98.8764,8.48252E-55 SIF-HHPRED: RNR_inhib ; Ribonucleotide reductase inhibitor,,,PF08591.13,19.1011,77.2 SIF-Syn: none
    /note=Start: 24747 
    /note=GI/GM favored: yes 
    /note=Gap/Overlap : 73, LORF
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.422 Final= -5.796, not the best, but best gap 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: No functional hit below e-7 
    /note=SIF-HHPRED: No functional hit with a probability above 90%, top hit 77.2%

CDS 24821 - 25051
  /gene="35"
  /product="gp35"
  /function="thioredoxin"
  /locus tag="Johnathan_35"
    /note=Original Glimmer call @bp 24821 has strength 17.74; Genemark calls start at 24821
    /note=SSC: 24821-25051 CP: yes SCS: both ST: SS BLAST-Start: [thioredoxin [Microbacterium phage Avocadoman] ],,NCBI, q1:s1 100.0% 1.38736E-46 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.092, -5.410872673788094, yes F: thioredoxin SIF-BLAST: ,,[thioredoxin [Microbacterium phage Avocadoman] ],,QOP64864,100.0,1.38736E-46 SIF-HHPRED: THIOREDOXIN; OXIDOREDUCTASE, GLUTAREDOXIN, TRX, GRX; 1.18A {BACILLUS CEREUS} SCOP: c.47.1.0,,,3ZIT_A,93.4211,99.2 SIF-Syn: thioredoxin, upstream of holliday junction resolvase in Burritobowl
    /note=Start: 24821 
    /note=GI/GM favored: yes 
    /note=Gap/Overlap : 73 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.092 Final= -5.419, best score
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: thioredoxin, Genbank, Doobus, QOP64864, 100% alignment, evalue = 1.4e-146 
    /note=SIF-HHPRED: thioredoxin, Pfam, BACILLUS CEREUS, 3ZIT_A, 93.42% alignment, 99.2% probability

CDS 25051 - 25377
  /gene="36"
  /product="gp36"
  /function="Holliday junction resolvase"
  /locus tag="Johnathan_36"
    /note=Original Glimmer call @bp 25051 has strength 10.6; Genemark calls start at 25051
    /note=SSC: 25051-25377 CP: yes SCS: both ST: NI BLAST-Start: [holliday junction resolvase [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 1.89643E-68 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.345, -3.914968956777623, yes F: Holliday junction resolvase SIF-BLAST: ,,[holliday junction resolvase [Microbacterium phage Arroyo] ],,QDH93454,99.0741,1.89643E-68 SIF-HHPRED: HOLLIDAY-JUNCTION RESOLVASE; HYDROLASE, ENZYME, HOMOLOGOUS RECOMBINATION, HOLLIDAY JUNCTION RESOLVING ENZYME, NUCLEASE, ARCHAEA, THERMOPHILE; HET: EDO, SO4; 1.8A {SULFOLOBUS SOLFATARICUS} SCOP: c.52.1.18,,,1OB8_B,88.8889,99.4 SIF-Syn: Holliday junction resolvase, downstream of thioredoxin in Burritobowl
    /note=Start: 25051 
    /note=GI/GM favored: yes 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: no starterator report
    /note=Most conserved: no starterator report
    /note=SD score: z= 2.34 Final= -3.91, best score
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: holliday junction resolvase, Genbank, Arroyo, QDH93454, 99.07% alignment, e-value = 1.9e-68 
    /note=SIF-HHPRED: holliday junction resolvase, SULFOLOBUS SOLFATARICUS, 10B8_B, 88.89% alignment, 99.4% probability AND HJR homolog, Bacillus subtilis, 4QBN_B, 93% alignment, 97% probability

CDS 25407 - 25700
  /gene="37"
  /product="gp37"
  /function="hypothetical protein"
  /locus tag="Johnathan_37"
    /note=Original Glimmer call @bp 25407 has strength 16.35; Genemark calls start at 25407
    /note=SSC: 25407-25700 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AVOCADOMAN_37 [Microbacterium phage Avocadoman]],,NCBI, q1:s1 100.0% 4.15917E-61 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.564, -5.511537306530897, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AVOCADOMAN_37 [Microbacterium phage Avocadoman]],,QOP64866,100.0,4.15917E-61 SIF-HHPRED: Septum site-determining protein MinC; MinC, Bacillus subtilis, FtsZ inhibitor, CELL CYCLE; NMR {Bacillus subtilis},,,2M4I_A,39.1753,71.9 SIF-Syn: No synteny
    /note=Start: 25407
    /note=GI/GM favored: both  
    /note=Gap/Overlap : 29, LORF
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.564  Final= -5.512, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e-7 
    /note=SIF-HHPRED: no function hits above 90% probability, top hit 71.9%

CDS 25786 - 26055
  /gene="38"
  /product="gp38"
  /function="hypothetical protein"
  /locus tag="Johnathan_38"
    /note=Original Glimmer call @bp 25786 has strength 11.15; Genemark calls start at 25786
    /note=SSC: 25786-26055 CP: yes SCS: both ST: NA BLAST-Start: [hypothetical protein SEA_BABYYODA_40 [Microbacterium phage BabyYoda]],,NCBI, q1:s1 100.0% 2.49684E-43 GAP: 85 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.203, -2.0162541296952132, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BABYYODA_40 [Microbacterium phage BabyYoda]],,QTF81974,86.8132,2.49684E-43 SIF-HHPRED: Phage_P2_GpE ; Phage P2 GpE,,,PF06528.15,26.9663,33.3 SIF-Syn: No synteny
    /note=Start: 25786 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 85, smallest gap
    /note=Contains all CP: yes 
    /note=Most annotated: no report 
    /note=Most conserved: no report  
    /note=SD score: z= 3.203 Final= -2.016, best scores
    /note=Q1:s1: y
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 33.1%

CDS 26055 - 26240
  /gene="39"
  /product="gp39"
  /function="hypothetical protein"
  /locus tag="Johnathan_39"
    /note=Original Glimmer call @bp 26055 has strength 13.75; Genemark calls start at 26055
    /note=SSC: 26055-26240 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BURRITOBOWL_40 [Microbacterium phage Burritobowl] ],,NCBI, q1:s1 100.0% 3.88743E-32 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.07, -4.436903688233993, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BURRITOBOWL_40 [Microbacterium phage Burritobowl] ],,QNJ56198,100.0,3.88743E-32 SIF-HHPRED: Regulation of nuclear pre-mRNA domain-containing protein 1B; Structural Genomics Consortium, SGC, TRANSCRIPTION; 2.2A {Homo sapiens},,,4FLA_D,72.1311,74.4 SIF-Syn: none
    /note=Start: 26055
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.07 Final= -4.437, best scores 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no function hit below e -7 
    /note=SIF-HHPRED: no functional hit above probability 90%, top hit 74.4%

CDS 26360 - 28864
  /gene="40"
  /product="gp40"
  /function="DNA primase/helicase"
  /locus tag="Johnathan_40"
    /note=Original Glimmer call @bp 26360 has strength 10.93; Genemark calls start at 26360
    /note=SSC: 26360-28864 CP: yes SCS: both ST: SS BLAST-Start: [DNA primase/helicase [Microbacterium phage Albright]],,NCBI, q1:s1 100.0% 0.0 GAP: 119 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.727, -3.7907710954237626, no F: DNA primase/helicase SIF-BLAST: ,,[DNA primase/helicase [Microbacterium phage Albright]],,QTF82214,99.7602,0.0 SIF-HHPRED: Primase; primase, helicase, ssDNA-binding protein, TRANSFERASE; HET: SO4; 2.406A {Nitratiruptor phage NrS-1},,,6K9C_A,32.1343,100.0 SIF-Syn: DNA primase, upstream of DNA polymerase I in Avocadoman
    /note=Start: 26360
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 119, LORF
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.73 Final= -3.791, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: DNA primase/helicase, Genbank, Albright, QTF82214, 99.76% alignment, e-value = 0 
    /note=SIF-HHPRED: DNA primase,  Ecoli phage T7, 1NUI_A, 35% alignment, 99.6% probability  (appears to have both primase and helicase domains with several hits)

CDS 28861 - 30735
  /gene="41"
  /product="gp41"
  /function="DNA polymerase I"
  /locus tag="Johnathan_41"
    /note=Original Glimmer call @bp 28861 has strength 11.05; Genemark calls start at 28861
    /note=SSC: 28861-30735 CP: yes SCS: both ST: SS BLAST-Start: [DNA polymerase I [Microbacterium phage Albright]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.972, -2.523003374675015, yes F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Microbacterium phage Albright]],,QTF82215,99.359,0.0 SIF-HHPRED: DNA polymerase I; mycobacteria, DNA polymerase, Flap endonuclease, TRANSFERASE; 2.713A {Mycolicibacterium smegmatis},,,6VDE_B,95.3526,100.0 SIF-Syn: DNA Polymerase I, downstream of DNA primase in Avocadoman
    /note=Start: 28861
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.972 Final= -2.523, best scores 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: DNA Polymerase I, Genbank, Albright, QTF82215, 99.36% alignment, e-value = 0 
    /note=SIF-HHPRED: DNA Polymerase I, M smeg, 6VDE_B, 95% alignment, 100% probability

CDS 30735 - 30935
  /gene="42"
  /product="gp42"
  /function="hypothetical protein"
  /locus tag="Johnathan_42"
    /note=Original Glimmer call @bp 30735 has strength 5.13; Genemark calls start at 30735
    /note=SSC: 30735-30935 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BUBBABEAR_42 [Microbacterium phage BubbaBear] ],,NCBI, q1:s1 100.0% 1.63048E-41 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.333, -4.707395188728813, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BUBBABEAR_42 [Microbacterium phage BubbaBear] ],,QCG77303,100.0,1.63048E-41 SIF-HHPRED: Zn-ribbon_RPC11; C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III. The C-terminal zinc ribbon domain (C-ribbon) of subunit C11 (Zn-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage.,,,cd10509,59.0909,90.8 SIF-Syn: No synteny
    /note=Start: 30735 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.333 Final= -4.707, best scores 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e -7 
    /note=SIF-HHPRED: no bacterial functional hits above 90% probability (zinc ribbon domain)

CDS 30932 - 31234
  /gene="43"
  /product="gp43"
  /function="hypothetical protein"
  /locus tag="Johnathan_43"
    /note=Original Glimmer call @bp 30932 has strength 9.63; Genemark calls start at 30932
    /note=SSC: 30932-31234 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ANNALIE_45 [Microbacterium phage AnnaLie] ],,NCBI, q1:s1 100.0% 5.44401E-66 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.972, -2.583959800616441, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANNALIE_45 [Microbacterium phage AnnaLie] ],,QOC59494,100.0,5.44401E-66 SIF-HHPRED: DUF4164 ; Domain of unknown function (DUF4164),,,PF13747.9,39.0,45.3 SIF-Syn: No synteny
    /note=Start: 30932
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.972 Final= -2.584, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hits below e -7 
    /note=SIF-HHPRED: no functional hits above 90%, top hit 45.3%

CDS 31234 - 31953
  /gene="44"
  /product="gp44"
  /function="DNA binding protein"
  /locus tag="Johnathan_44"
    /note=Original Glimmer call @bp 31234 has strength 12.22; Genemark calls start at 31234
    /note=SSC: 31234-31953 CP: yes SCS: both ST: SS BLAST-Start: [DNA binding protein [Microbacterium phage Lynlen]],,NCBI, q1:s1 100.0% 7.84943E-168 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.232, -4.364952153961186, no F: DNA binding protein SIF-BLAST: ,,[DNA binding protein [Microbacterium phage Lynlen]],,QJD53455,99.5816,7.84943E-168 SIF-HHPRED: RNA polymerase sigma factor RpoS; Transcription-activator, DNA/RNA, SigmaS, beta`, TRANSCRIPTION, Transferase-DNA complex; 3.26A {Escherichia coli},,,6OMF_F,97.908,99.9 SIF-Syn: No synteny
    /note=Start: 31234 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.23  Final= -4.37, not best scores, but best overlap 
    /note=Q1:s1: yes
    /note=SIF-BLASTp: DNA binding protein, Genbank, Lynlen, QJD53455, 99.58% alignment, e-value= 7.85e-168 
    /note=SIF-HHPRED: RNA polymerase sigma factor RpoS, Escherichia coli, 6OMF_F, 97.91% alignment, 99.9% probability AND SigA, Mtb, 6FBV_F, 99% alignment, 99.9% probability

CDS complement (31950 - 32129)
  /gene="45"
  /product="gp45"
  /function="hypothetical protein"
  /locus tag="Johnathan_45"
    /note=Original Glimmer call @bp 32129 has strength 8.87; Genemark calls start at 32129
    /note=SSC: 32129-31950 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DICKRICHARDS_45 [Microbacterium phage DickRichards] ],,NCBI, q1:s1 100.0% 1.81216E-32 GAP: 63 bp gap LO: no RBS: Kibler 6, Karlin Medium, 0.627, -8.072528763081499, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DICKRICHARDS_45 [Microbacterium phage DickRichards] ],,QOP66362,100.0,1.81216E-32 SIF-HHPRED: Cell density-dependent motility repressor; HOCl, HOCl-specific transcription factor, LysR-type transcription regulator, Hypochlorous acid, hypochlorite, DNA BINDING PROTEIN; 3.3A {Salmonella typhimurium},,,5YDW_A,93.2203,84.1 SIF-Syn: No synteny
    /note=Start: 32129 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 63 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= .627 Final= -8.07, not best score, but ATG start
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit  below e -7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 84%

CDS complement (32193 - 32375)
  /gene="46"
  /product="gp46"
  /function="hypothetical protein"
  /locus tag="Johnathan_46"
    /note=Original Glimmer call @bp 32375 has strength 8.45; Genemark calls start at 32375
    /note=SSC: 32375-32193 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AVGARDIAN_48 [Microbacterium phage AvGardian]],,NCBI, q1:s1 100.0% 1.16829E-30 GAP: 111 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.669, -6.258460324876293, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AVGARDIAN_48 [Microbacterium phage AvGardian]],,QJD49863,93.3333,1.16829E-30 SIF-HHPRED: DUF2642 ; Protein of unknown function (DUF2642),,,PF10842.11,80.0,85.6 SIF-Syn: no synteny
    /note=Start: 32375 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 111
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.67 Final= -6.26, not best, most common start codon (ATG) 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e -7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 85.6%

CDS 32487 - 32645
  /gene="47"
  /product="gp47"
  /function="hypothetical protein"
  /locus tag="Johnathan_47"
    /note=Original Glimmer call @bp 32487 has strength 7.56; Genemark calls start at 32487
    /note=SSC: 32487-32645 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BUBBABEAR_47 [Microbacterium phage BubbaBear] ],,NCBI, q1:s1 100.0% 6.38933E-30 GAP: 111 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.754, -5.679831809821832, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BUBBABEAR_47 [Microbacterium phage BubbaBear] ],,QCG77308,100.0,6.38933E-30 SIF-HHPRED: DNA-directed RNA polymerase subunit P; Transcription, DNA-directed RNA polymerase; HET: ZN; 3.5A {Thermococcus kodakarensis},,,4QIW_P,73.0769,94.5 SIF-Syn: no synteny
    /note=Start: 32487 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: 111
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z=  1.75 Final= -5.680, not best, most common codon (ATG) 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: SprT-like protease, Celaena, 90% coverage, eval= 6e-12
    /note=SIF-HHPRED: DNA-directed RNA polymerase, Thermococcus kodakarensis, 4QIW_P, 73.08% alignment, 94.5% probability
    /note=No evidence of SprT-like protease from hhpred data.

CDS 32645 - 33046
  /gene="48"
  /product="gp48"
  /function="ParB-like nuclease domain"
  /locus tag="Johnathan_48"
    /note=Original Glimmer call @bp 32645 has strength 15.25; Genemark calls start at 32645
    /note=SSC: 32645-33046 CP: yes SCS: both ST: SS BLAST-Start: [ParB-like nuclease domain protein [Microbacterium phage Abigail]],,NCBI, q1:s1 100.0% 5.71008E-92 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.725, -3.0478325568523097, yes F: ParB-like nuclease domain SIF-BLAST: ,,[ParB-like nuclease domain protein [Microbacterium phage Abigail]],,QXN73548,100.0,5.71008E-92 SIF-HHPRED: Stage 0 sporulation protein J; ParB, Chromosome segregation, Chromosome organization, DNA BINDING PROTEIN; HET: CDP, MSE; 1.81A {Bacillus subtilis (strain 168)} SCOP: a.4.14.0, d.268.1.0,,,6SDK_A,92.4812,99.1 SIF-Syn: No synteny
    /note=Start: 32645 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.72 Final= -3.05, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: parB-like nuclease domain protein, Genbank, Abigail, QXN73548, 100% alignment, evalue= 5.71e-92
    /note=SIF-HHPRED: ParB DNA binding Protein, Bacillus subtilis, 6SDK_A, 92.48% alignment, 99.1% 
    /note=probability
    /note=conserved domains- several ParB-like nuclease domains

CDS 33043 - 33477
  /gene="49"
  /product="gp49"
  /function="hypothetical protein"
  /locus tag="Johnathan_49"
    /note=Original Glimmer call @bp 33043 has strength 6.59; Genemark calls start at 33043
    /note=SSC: 33043-33477 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LYNLEN_51 [Microbacterium phage Lynlen]],,NCBI, q1:s1 100.0% 3.57541E-101 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.413, -4.280611589027404, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYNLEN_51 [Microbacterium phage Lynlen]],,QJD53460,99.3056,3.57541E-101 SIF-HHPRED: Uncharacterized protein AcrF1; anti-CRISPR protein, Csy complex, Type I-F CRISPR/Cas system, IMMUNE SYSTEM-RNA complex;{Pseudomonas aeruginosa (strain UCBPP-PA14)},,,5XLO_M,16.6667,78.2 SIF-Syn: No synteny
    /note=Start: 33043 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.41 Final= -4.28, not best score, but best overlap 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 78.2%

CDS 33482 - 33970
  /gene="50"
  /product="gp50"
  /function="hypothetical protein"
  /locus tag="Johnathan_50"
    /note=Original Glimmer call @bp 33482 has strength 12.06; Genemark calls start at 33482
    /note=SSC: 33482-33970 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_KIERAN_47 [Microbacterium phage Kieran]],,NCBI, q1:s17 99.3827% 3.32202E-93 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.584, -5.916882820574897, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein PBI_KIERAN_47 [Microbacterium phage Kieran]],,AVR57208,83.1461,3.32202E-93 SIF-HHPRED: Smg4_UPF3 ; Smg-4/UPF3 family,,,PF03467.18,69.1358,76.2 SIF-Syn: No synteny
    /note=Start: 33482 
    /note=GI/GM favored: both 
    /note=Gap/Overlap : 4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes
    /note=SD score: z=1.58 Final= -5.92, not best but best gap
    /note=Q1:s1: no 
    /note=SIF-BLASTp: no functional hit below e -7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 76.2%

CDS 34035 - 34433
  /gene="51"
  /product="gp51"
  /function="HNH endonuclease"
  /locus tag="Johnathan_51"
    /note=Original Glimmer call @bp 34035 has strength 3.45; Genemark calls start at 34152
    /note=SSC: 34035-34433 CP: yes SCS: both-gl ST: SS BLAST-Start: [HNH endonuclease [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 2.81788E-94 GAP: 64 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.822, -5.711975353186392, no F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Microbacterium phage Arroyo] ],,QDH93468,100.0,2.81788E-94 SIF-HHPRED: HNH endonuclease domain protein; CRISPR-Cas, Cas9, HNH, RuvC, RNA-guided DNA endonuclease, cytoplasmic, Hydrolase; HET: SPD; 2.201A {Actinomyces naeslundii},,,4OGE_A,48.4848,98.3 SIF-Syn: No synteny
    /note=Start: 34035 
    /note=GI/GM favored: Glimmer
    /note=Gap/Overlap : 64, smallest gap
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.82 Final= -5.7, not best score but best gap
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: HNH endonuclease, Genbank, Arroyo, QDH93468, 100% alignment, e value = 2.82e -94
    /note=SIF-HHPRED: HNH endonuclease, Actinomyces naeslundii, 4OGE_A, 98.3% alignment, 48.48% probability
    /note=conserved domain hits with HNH endonuclease

CDS 34592 - 34909
  /gene="52"
  /product="gp52"
  /function="hypothetical protein"
  /locus tag="Johnathan_52"
    /note=Original Glimmer call @bp 34592 has strength 13.86; Genemark calls start at 34592
    /note=SSC: 34592-34909 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ABIGAIL_52 [Microbacterium phage Abigail]],,NCBI, q1:s1 100.0% 3.04664E-67 GAP: 158 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.99, -4.608137800073271, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ABIGAIL_52 [Microbacterium phage Abigail]],,QXN73552,96.1905,3.04664E-67 SIF-HHPRED: d.348.1.1 (A:1-58) Uncharacterized protein SO3888 {Shewanella oneidensis [TaxId: 70863]},,,d2k49a2,45.7143,71.2 SIF-Syn: No synteny
    /note=Start: 34592 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: 158 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.99 Final= -4.61, not best score, but most annotated and conserved 
    /note=Q1:s1: y
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 71.2%

CDS 34906 - 35064
  /gene="53"
  /product="gp53"
  /function="hypothetical protein"
  /locus tag="Johnathan_53"
    /note=Original Glimmer call @bp 34906 has strength 11.8; Genemark calls start at 34906
    /note=SSC: 34906-35064 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_LYNLEN_55 [Microbacterium phage Lynlen]],,NCBI, q1:s1 100.0% 5.14919E-27 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.918, -4.759312672633257, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_LYNLEN_55 [Microbacterium phage Lynlen]],,QJD53464,98.0769,5.14919E-27 SIF-HHPRED: CP12 polypeptide; Calvin Cycle, Regulation, PHOTOSYNTHESIS; HET: NAD; 1.32A {Thermosynechococcus elongatus (strain BP-1)},,,6GG7_D,84.6154,84.2 SIF-Syn: No synteny
    /note=Start: 34906 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.92 Final= -4.76, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e -7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 84.2%

CDS 35117 - 35617
  /gene="54"
  /product="gp54"
  /function="hypothetical protein"
  /locus tag="Johnathan_54"
    /note=Original Glimmer call @bp 35117 has strength 13.95; Genemark calls start at 35117
    /note=SSC: 35117-35617 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_CROZENNI_55 [Microbacterium phage CroZenni]],,NCBI, q1:s1 100.0% 2.72115E-114 GAP: 52 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.704, -5.274463563926485, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_CROZENNI_55 [Microbacterium phage CroZenni]],,QWY79877,99.3976,2.72115E-114 SIF-HHPRED: Arc_C ; Arc C-lobe,,,PF18162.4,30.1205,73.8 SIF-Syn: No synteny
    /note=Start: 35117 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: 52 
    /note=Contains all CP: yes 
    /note=Most annotated: does not have most annotated
    /note=Most conserved: no 
    /note=SD score: z= 1.7 Final= -5.27, not best score, but covers all coding potential
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90%, top hit 73.8%

CDS 35681 - 35989
  /gene="55"
  /product="gp55"
  /function="hypothetical protein"
  /locus tag="Johnathan_55"
    /note=Original Glimmer call @bp 35681 has strength 6.53; Genemark calls start at 35681
    /note=SSC: 35681-35989 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DOOBUS_54 [Microbacterium phage Doobus]],,NCBI, q1:s1 100.0% 1.03803E-67 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.789, -4.954064444624791, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DOOBUS_54 [Microbacterium phage Doobus]],,QZE10274,99.0196,1.03803E-67 SIF-HHPRED: DUF2188 ; Uncharacterized protein conserved in bacteria (DUF2188),,,PF09954.12,30.3922,82.3 SIF-Syn: No synteny
    /note=Start: 35681 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: 63 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.79  Final= -4.95 best and only score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above a probability of 90%, top hit 82.3%

CDS 35979 - 36551
  /gene="56"
  /product="gp56"
  /function="dihydrofolate reductase"
  /locus tag="Johnathan_56"
    /note=Original Glimmer call @bp 35979 has strength 10.97; Genemark calls start at 35979
    /note=SSC: 35979-36551 CP: yes SCS: both ST: SS BLAST-Start: [dihydrofolate reductase [Microbacterium phage Albright]],,NCBI, q1:s1 98.4211% 9.2952E-131 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.085, -4.325675514574479, yes F: dihydrofolate reductase SIF-BLAST: ,,[dihydrofolate reductase [Microbacterium phage Albright]],,QTF82229,97.9058,9.2952E-131 SIF-HHPRED: Dihydrofolate reductase; OXIDOREDUCTASE; HET: NAP, 5DR; 1.9A {Bacillus anthracis} SCOP: l.1.1.1, c.71.1.0,,,3S9U_A,98.4211,99.9 SIF-Syn: No synteny
    /note=Start: 35979
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -11
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.08 Final= -4.33, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: dihydrofolate reductase, Genbank, Albright, QTF82229, 97.9% alignment, e value 9.30e-131
    /note=SIF-HHPRED: dihydrofolate reductase, Bacillus anthracis, 3S9U_A, 98.4% alignment, 99.9% probability

CDS 36548 - 37075
  /gene="57"
  /product="gp57"
  /function="hypothetical protein"
  /locus tag="Johnathan_57"
    /note=Original Glimmer call @bp 36548 has strength 11.92; Genemark calls start at 36548
    /note=SSC: 36548-37075 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DOOBUS_56 [Microbacterium phage Doobus]],,NCBI, q1:s1 100.0% 5.31577E-98 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.972, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DOOBUS_56 [Microbacterium phage Doobus]],,QZE10276,88.3721,5.31577E-98 SIF-HHPRED: Ndx1; Nudix protein, diadenosine polyphosphate, Ap6A, Thermus thermophilus HB8, hydrolase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics; HET: SO4, GOL; 1.7A {Thermus thermophilus} SCOP: d.113.1.1,,,1VCD_B,26.8571,70.8 SIF-Syn: No synteny
    /note=Start: 36548
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -4 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.972 Final= -2.443, best scores
    /note=Q1:s1: y
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 70.8%

CDS 37075 - 37473
  /gene="58"
  /product="gp58"
  /function="hypothetical protein"
  /locus tag="Johnathan_58"
    /note=Original Glimmer call @bp 37075 has strength 4.69; Genemark calls start at 37075
    /note=SSC: 37075-37473 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BUBBABEAR_58 [Microbacterium phage BubbaBear] ],,NCBI, q1:s1 100.0% 1.71458E-91 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.546, -5.531579584701049, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BUBBABEAR_58 [Microbacterium phage BubbaBear] ],,QCG77319,100.0,1.71458E-91 SIF-HHPRED: HK97 Family Phage Portal Protein; Phage, HK97 family, Portal, Corynebacterium, diphtheriae, PSI, MCSG, Structural Genomics, Protein Structure Initiative, Midwest Center for; HET: MSE, SO4, PO4, GOL; 2.9A {Corynebacterium diphtheriae},,,3KDR_C,56.0606,85.1 SIF-Syn: No synteny
    /note=Start: 37075 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.55 Final= -5.53 final was best, but not z score (best overlap) 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e -7 
    /note=SIF-HHPRED: no functional hit above 90%, top hit 85%

CDS 37470 - 38381
  /gene="59"
  /product="gp59"
  /function="thymidylate synthase"
  /locus tag="Johnathan_59"
    /note=Original Glimmer call @bp 37470 has strength 9.98; Genemark calls start at 37470
    /note=SSC: 37470-38381 CP: yes SCS: both ST: NI BLAST-Start: [thymidylate synthase [Microbacterium phage Arroyo]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.729, -5.432024807810012, no F: thymidylate synthase SIF-BLAST: ,,[thymidylate synthase [Microbacterium phage Arroyo]],,QDH93476,98.6799,0.0 SIF-HHPRED: Thymidylate synthase; SSGCID, Thymidylate synthase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, TRANSFERASE; HET: EDO, CIT; 1.65A {Burkholderia thailandensis} SCOP: d.117.1.0,,,3V8H_B,99.3399,100.0 SIF-Syn: no synteny
    /note=Start: 37470 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -4 
    /note=Contains all CP: yes 
    /note=Most annotated: does not have 
    /note=Most conserved: no 
    /note=SD score: z= 1.73 Final= -5.43, not best score, but best overlap
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: thymidylate synthase, Genbank, Arroyo, QD893476, 98.68% alignment, evalue = 0 
    /note=SIF-HHPRED: thymidylate synthase, PDB, Arroyo, 3V8H_B, 99.33% alignment, 100% probability

CDS 38397 - 38621
  /gene="60"
  /product="gp60"
  /function="hypothetical protein"
  /locus tag="Johnathan_60"
    /note=Original Glimmer call @bp 38397 has strength 14.89; Genemark calls start at 38397
    /note=SSC: 38397-38621 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BURRITOBOWL_62 [Microbacterium phage Burritobowl]],,NCBI, q1:s1 100.0% 4.01744E-44 GAP: 15 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.711, -3.904011946530602, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BURRITOBOWL_62 [Microbacterium phage Burritobowl]],,QNJ56220,100.0,4.01744E-44 SIF-HHPRED: FliG_N ; FliG N-terminal domain,,,PF14842.9,44.5946,77.9 SIF-Syn: no synteny
    /note=Start: 38397 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: 15, LORF
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.71 Final= -3.90, best score
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e -7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 78%

CDS 38621 - 38815
  /gene="61"
  /product="gp61"
  /function="membrane protein"
  /locus tag="Johnathan_61"
    /note=Original Glimmer call @bp 38621 has strength 9.97; Genemark calls start at 38621
    /note=SSC: 38621-38815 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BUBBABEAR_61 [Microbacterium phage BubbaBear] ],,NCBI, q1:s1 100.0% 2.36774E-29 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.474, -5.973594388290967, no F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_BUBBABEAR_61 [Microbacterium phage BubbaBear] ],,QCG77322,98.4375,2.36774E-29 SIF-HHPRED: DUF2530 ; Protein of unknown function (DUF2530),,,PF10745.12,64.0625,74.6 SIF-Syn: No synteny
    /note=Start: 38621 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 1.47 Final= -5.97, 2nd best score, but best overlap 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: membrane protein, Burritobowl, eval= 2e-29, 100% coverage
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 75%
    /note=TmHmm: 2 TMHs

CDS 38959 - 39099
  /gene="62"
  /product="gp62"
  /function="hypothetical protein"
  /locus tag="Johnathan_62"
    /note=Original Glimmer call @bp 38959 has strength 11.28; Genemark calls start at 38893
    /note=SSC: 38959-39099 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_DICKRICHARDS_61 [Microbacterium phage DickRichards] ],,NCBI, q1:s1 100.0% 8.28438E-24 GAP: 143 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.972, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DICKRICHARDS_61 [Microbacterium phage DickRichards] ],,QOP66378,100.0,8.28438E-24 SIF-HHPRED: d.15.4.2 (A:3-81) Carbone monoxide (CO) dehydrogenase iron-sulfur protein, N-domain {Hydrogenophaga pseudoflava [TaxId: 47421]},,,d1ffva2,67.3913,66.7 SIF-Syn: No synteny
    /note=Start: 38959
    /note=GI/GM favored: Glimmer
    /note=Gap/Overlap: 143 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.97 Final= -2.44, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 67%

CDS 39092 - 39298
  /gene="63"
  /product="gp63"
  /function="hypothetical protein"
  /locus tag="Johnathan_63"
    /note=Original Glimmer call @bp 39092 has strength 12.96; Genemark calls start at 39092
    /note=SSC: 39092-39298 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_BURRITOBOWL_65 [Microbacterium phage Burritobowl]],,NCBI, q1:s1 100.0% 4.18213E-41 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.972, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_BURRITOBOWL_65 [Microbacterium phage Burritobowl]],,QNJ56223,100.0,4.18213E-41 SIF-HHPRED: OR494; Structural Genomics, PSI-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, De Novo, OR494, DE NOVO; HET: ACY; 1.471A {synthetic construct},,,4PWW_A,26.4706,80.3 SIF-Syn: no synteny
    /note=Start: 39092 
    /note=GI/GM favored: both
    /note=Gap/Overlap : -8 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.97  Final= -2.51, best scores 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 80%

CDS 39298 - 39480
  /gene="64"
  /product="gp64"
  /function="hypothetical protein"
  /locus tag="Johnathan_64"
    /note=Original Glimmer call @bp 39298 has strength 12.29; Genemark calls start at 39298
    /note=SSC: 39298-39480 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ANNALIE_64 [Microbacterium phage AnnaLie] ],,NCBI, q1:s1 100.0% 2.20406E-33 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.82, -2.8454123590742793, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ANNALIE_64 [Microbacterium phage AnnaLie] ],,QOC59513,100.0,2.20406E-33 SIF-HHPRED: Phosphoglycolate phosphatase; np_784602.1, putative phosphoglycolate phosphatase, Structural Genomics, PSI-2, Protein Structure Initiative, Joint Center for Structural Genomics, JCSG; HET: PO4, MSE; 1.5A {Lactobacillus plantarum} SCOP: c.108.1.6,,,2HDO_A,55.0,75.8 SIF-Syn: No synteny
    /note=Start: 39298
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -1 
    /note=Contains all CP: yes
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.82 Final= -2.84, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 75%

CDS 39493 - 39723
  /gene="65"
  /product="gp65"
  /function="hypothetical protein"
  /locus tag="Johnathan_65"
    /note=Original Glimmer call @bp 39493 has strength 16.04; Genemark calls start at 39493
    /note=SSC: 39493-39723 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AVOCADOMAN_65 [Microbacterium phage Avocadoman] ],,NCBI, q1:s1 100.0% 9.38208E-43 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.213, -2.0720764396375664, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AVOCADOMAN_65 [Microbacterium phage Avocadoman] ],,QOP64893,100.0,9.38208E-43 SIF-HHPRED: DUF6422 ; Family of unknown function (DUF6422),,,PF19986.2,52.6316,74.4 SIF-Syn: No synteny
    /note=Start: 39493 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: 12, LORF
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 3.21  Final= -2.07, best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 74%

CDS 39723 - 40073
  /gene="66"
  /product="gp66"
  /function="hypothetical protein"
  /locus tag="Johnathan_66"
    /note=Original Glimmer call @bp 39723 has strength 12.03; Genemark calls start at 39723
    /note=SSC: 39723-40073 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_ALBRIGHT_66 [Microbacterium phage Albright]],,NCBI, q1:s1 100.0% 6.54063E-76 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.869, -5.690486437352653, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_ALBRIGHT_66 [Microbacterium phage Albright]],,QTF82241,100.0,6.54063E-76 SIF-HHPRED: NFU1 iron-sulfur cluster scaffold homolog, mitochondrial; Structural Genomics, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, Mitochondrial Protein Partnership, MPP, PSI-Biology, Protein Structure Initiative, ELECTRON; NMR {Homo sapiens},,,2LTM_A,51.7241,65.8 SIF-Syn: No synteny
    /note=Start: 39723 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: -1 
    /note=Contains all CP: yes 
    /note=Most annotated: no
    /note=Most conserved: yes 
    /note=SD score: z= 1.869 Final= -5.690, not best score, but best overlap 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: no functional hit below e-7 
    /note=SIF-HHPRED: no functional hit above 90% probability, top hit 66%

tRNA 40222 - 40294
  /gene="67"
  /product="tRNA-Asn(gtt)"
  /locus tag="JOHNATHAN_67"
    /note=tRNA-Asn(gtt)

tRNA 40354 - 40425
  /gene="68"
  /product="tRNA-Gln(ctg)"
  /locus tag="JOHNATHAN_68"
    /note=tRNA-Gln(ctg)

tRNA 40432 - 40504
  /gene="69"
  /product="tRNA-Lys(ctt)"
  /locus tag="JOHNATHAN_69"
    /note=tRNA-Lys(ctt)

CDS 40508 - 40783
  /gene="70"
  /product="gp70"
  /function="HNH endonuclease"
  /locus tag="Johnathan_70"
    /note=Original Glimmer call @bp 40508 has strength 4.5; Genemark calls start at 40508
    /note=SSC: 40508-40783 CP: yes SCS: both ST: SS BLAST-Start: [HNH endonuclease [Microbacterium phage Arroyo] ],,NCBI, q1:s1 100.0% 6.65992E-62 GAP: 434 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.227, -4.086372157395013, yes F: HNH endonuclease SIF-BLAST: ,,[HNH endonuclease [Microbacterium phage Arroyo] ],,QDH93484,100.0,6.65992E-62 SIF-HHPRED: HNH endonuclease domain protein; CRISPR-Cas, Cas9, HNH, RuvC, RNA-guided DNA endonuclease, cytoplasmic, Hydrolase; HET: SPD; 2.201A {Actinomyces naeslundii},,,4OGE_A,80.2198,98.4 SIF-Syn: No synteny
    /note=Start: 40508 
    /note=GI/GM favored: both 
    /note=Gap/Overlap: 434 
    /note=Contains all CP: yes 
    /note=Most annotated: no
    /note=Most conserved: yes for EB
    /note=SD score: z= 2.23 Final= -4.09 (only score) 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: HNH endonuclease, Genbank, Arroyo, QDH93484, 100% alignment, evalue= 6.66e-62 
    /note=SIF-HHPRED: HNH endonuclease, Actinomyces naeslundii, 4OGE_A, 80.218% alignment, 98.4% probability

CDS 40783 - 40911
  /gene="71"
  /product="gp71"
  /function="membrane protein"
  /locus tag="Johnathan_71"
    /note=Genemark calls start at 40783
    /note=SSC: 40783-40911 CP: yes SCS: genemark ST: SS BLAST-Start: [hypothetical protein SEA_SANSAFET_73 [Microbacterium phage SansAfet] ],,NCBI, q1:s1 100.0% 2.80325E-20 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.82, -2.8454123590742793, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_SANSAFET_73 [Microbacterium phage SansAfet] ],,QFP94324,100.0,2.80325E-20 SIF-HHPRED: DUF2062 ; Uncharacterized protein conserved in bacteria (DUF2062),,,PF09835.12,76.1905,89.9 SIF-Syn: No synteny
    /note=Start: 40783 
    /note=GI/GM favored: Genemark
    /note=Gap/Overlap : -1 
    /note=Contains all CP: yes 
    /note=Most annotated: yes 
    /note=Most conserved: yes 
    /note=SD score: z= 2.82 Final= -2.84 best score 
    /note=Q1:s1: yes 
    /note=SIF-BLASTp: membrane protein, Abigail, eval= 2e-20, 100% coverage
    /note=SIF-HHPRED: no functional hit above 90% probability
    /note=1 TMH, SOSUI calls it a membrane protein