CDS 1 - 525
  /gene="1"
  /product="gp1"
  /function="Hypothetical Protein"
  /locus tag="Symere_1"
    /note=Original Glimmer call @bp 1 has strength 14.27; Genemark calls start at 1
    /note=SSC: 1-525 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_AXIPUP_1 [Microbacterium phage AxiPup] ],,NCBI, q1:s1 100.0% 3.08585E-121 GAP: 0 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.786, -5.135095111895543, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_AXIPUP_1 [Microbacterium phage AxiPup] ],,AUX82650,100.0,3.08585E-121 SIF-HHPRED:  SIF-Syn: Syntenic to pham of no known function in Sedgewig, StirFryIV, Ilzat, and Han Solo.
    /note=No significant sequence or structural homology to proteins of known function identified by BLASTP and HHPred respectively.

CDS 522 - 1922
  /gene="2"
  /product="gp2"
  /function="terminase"
  /locus tag="Symere_2"
    /note=Original Glimmer call @bp 522 has strength 11.66; Genemark calls start at 522
    /note=SSC: 522-1922 CP: yes SCS: both ST: SS BLAST-Start: [terminase [Microbacterium phage Raptor] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.931, -5.035742295039811, no F: terminase SIF-BLAST: ,,[terminase [Microbacterium phage Raptor] ],,AVR56419,100.0,0.0 SIF-HHPRED: DNA MATURASE B; HYDROLASE, ATPASE, DNA TRANSLOCATION, SINGLE-PARTICLE RECONSTRUCTION; 16.0A {ENTEROBACTERIA PHAGE T7},,,4BIJ_E,89.0558,100.0 SIF-Syn: Terminase annotated at this location in Ilzat, StirfryIV, and Sedgewig
    /note=HHpred predicts substantial structural homology to well characterized T-even and T-odd terminase proteins. BLASTp predicts substantial sequency homology to annotated terminases in related phages.

CDS 1953 - 3350
  /gene="3"
  /product="gp3"
  /function="portal protein"
  /locus tag="Symere_3"
    /note=Original Glimmer call @bp 1953 has strength 16.8; Genemark calls start at 1953
    /note=SSC: 1953-3350 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Microbacterium phage Sedgewig] ],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.913, -2.5823297389851954, yes F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage Sedgewig] ],,QJD49665,100.0,0.0 SIF-HHPRED:  SIF-Syn: Syntenic to predicted portal protein of Sedgewig, StirFryIV, and Ilzat.
    /note=HHPred predicts very strong structural homology to well characterized portal proteins of gram positive phages. Blast finds significant sequence homology to its syntenic phages.

CDS 3356 - 4024
  /gene="4"
  /product="gp4"
  /function="Hypothetical Protein"
  /locus tag="Symere_4"
    /note=Original Glimmer call @bp 3356 has strength 12.09; Genemark calls start at 3356
    /note=SSC: 3356-4024 CP: yes SCS: both ST: SS BLAST-Start: [head morphogenesis [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 3.43743E-161 GAP: 5 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.113, -4.645163458565996, no F: Hypothetical Protein SIF-BLAST: ,,[head morphogenesis [Microbacterium phage Ilzat] ],,YP_009623168,100.0,3.43743E-161 SIF-HHPRED:  SIF-Syn: Related phages Sedgewig and Ilzat call a MuF-like minor capsid protein for this fam but StirFryIV calls a capsid maturation protease, Synteny not too informative.
    /note=HHPred found a high structural homology to three distinct phams, and only over a short stretch of protein (~35 aa). Not compelling evidence of functional homology. BlastP found no significant homology to any proteins that would allow assignment of capsid maturation protease. Calling hypothetical protein.

CDS 4108 - 4668
  /gene="5"
  /product="gp5"
  /function="scaffolding protein"
  /locus tag="Symere_5"
    /note=Original Glimmer call @bp 4108 has strength 16.69; Genemark calls start at 4108
    /note=SSC: 4108-4668 CP: yes SCS: both ST: SS BLAST-Start: [scaffolding protein [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 7.83084E-130 GAP: 83 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.038, -3.222210725506937, yes F: scaffolding protein SIF-BLAST: ,,[scaffolding protein [Microbacterium phage Ilzat] ],,YP_009623169,99.4624,7.83084E-130 SIF-HHPRED:  SIF-Syn: Syntenic to scaffolding protein of Ilzat, StirFryIV and Sedgewig.
    /note=HHPred did not predict structural homology to any phams with biochemically characterized functions.  BLAST found consistent high sequence homology to annotated scaffolding proteins, but again, we could not with confidence find a BLAST hit with biochemical data supporting a functional call.  We used AlphaFold to generate a predicted tertiatry structure for Stop-4668.  The alpha-fold Stop-4668 structure is similar to the published structure of a scaffolding protein (Guo et al,  https://doi.org/10.1101/2024.11.01.621488), in that it has a long stretch of protein with no secondary structure, followed by a number of alpha-helices.  To be consistent with the community, we are calling a scaffolding protein.

CDS 4708 - 5634
  /gene="6"
  /product="gp6"
  /function="major capsid protein"
  /locus tag="Symere_6"
    /note=Original Glimmer call @bp 4708 has strength 14.85; Genemark calls start at 4708
    /note=SSC: 4708-5634 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: 39 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.207, -2.305049668942183, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Microbacterium phage Ilzat] ],,YP_009623170,100.0,0.0 SIF-HHPRED: Major capsid protein; HK97-fold, T=7, tailed bacteriophage, VIRUS; 2.2A {Microbacterium phage Oxtober96},,,8ECO_D,99.6753,100.0 SIF-Syn: There was synteny with StirfryIv, Ilzat, and Sedgewig in the phamerator map. All called for a major capsid protein.
    /note=HHPred suggests major capsid protein. Ncbi blast also calls for a major capsid protein.

CDS 5631 - 5882
  /gene="7"
  /product="gp7"
  /function="Hypothetical Protein"
  /locus tag="Symere_7"
    /note=Original Glimmer call @bp 5631 has strength 10.27; Genemark calls start at 5631
    /note=SSC: 5631-5882 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp07 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 2.97092E-47 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.894, -4.9056006736197375, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp07 [Microbacterium phage Ilzat] ],,YP_009623171,100.0,2.97092E-47 SIF-HHPRED:  SIF-Syn: Sedgewig, StirFryIV, Ilzat, and HanSolo did not make a call for this gene.
    /note=HHPred was inconsistent with low probability and coverage numbers. NCBI BLAST shows structural homology to hypothetical proteins.

CDS 5952 - 6377
  /gene="8"
  /product="gp8"
  /function="Hypothetical Protein"
  /locus tag="Symere_8"
    /note=Original Glimmer call @bp 5952 has strength 12.8; Genemark calls start at 5952
    /note=SSC: 5952-6377 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_AUBERGINE_8 [Microbacterium phage Aubergine] ],,NCBI, q1:s9 100.0% 8.09169E-102 GAP: 69 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.112, -2.5074698667202133, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_AUBERGINE_8 [Microbacterium phage Aubergine] ],,AUX82595,94.6309,8.09169E-102 SIF-HHPRED:  SIF-Syn: Synteny found in Strfry IV, Sedwig, Han Solo, and Ilzat.
    /note=No significant homology found by HHpred or NCBI Blast P.

CDS 6404 - 6817
  /gene="9"
  /product="gp9"
  /function="Hypothetical Protein"
  /locus tag="Symere_9"
    /note=Original Glimmer call @bp 6404 has strength 9.94; Genemark calls start at 6395
    /note=SSC: 6404-6817 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PAPAFRITTA_9 [Microbacterium phage Papafritta] ],,NCBI, q1:s1 100.0% 1.25468E-95 GAP: 26 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.099, -4.6767843745817785, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PAPAFRITTA_9 [Microbacterium phage Papafritta] ],,AXH48520,100.0,1.25468E-95 SIF-HHPRED:  SIF-Syn: Syntenic to Phams of unknown function in Ilzat, StirFryIV and Sedgewig.
    /note=No significant structural or sequence homology predicted by HHPred or BLAST.

CDS 6783 - 7199
  /gene="10"
  /product="gp10"
  /function="Hypothetical Protein"
  /locus tag="Symere_10"
    /note=Original Glimmer call @bp 6783 has strength 15.43; Genemark calls start at 6795
    /note=SSC: 6783-7199 CP: yes SCS: both-gl ST: NI BLAST-Start: [hypothetical protein PBI_STINGRAY_10 [Microbacterium phage StingRay] ],,NCBI, q1:s1 100.0% 3.91734E-91 GAP: -35 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.281, -3.934452679007171, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_STINGRAY_10 [Microbacterium phage StingRay] ],,AVJ51455,100.0,3.91734E-91 SIF-HHPRED:  SIF-Syn: Synteny to phams in StirfryIV, Ilzat, and Sedgewig. They all do not call a function.
    /note=HHPred showed no significant score other than one. That score called for an unknown function. Blast calls for hypothetical protein.

CDS 7196 - 7537
  /gene="11"
  /product="gp11"
  /function="Hypothetical Protein"
  /locus tag="Symere_11"
    /note=Original Glimmer call @bp 7196 has strength 13.49; Genemark calls start at 7196
    /note=SSC: 7196-7537 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp11 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 7.54602E-76 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.979, -3.3503726477288405, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp11 [Microbacterium phage Ilzat] ],,YP_009623175,100.0,7.54602E-76 SIF-HHPRED:  SIF-Syn: Synteny of proteins with no known function found in Sedgewig, Stirfry IV, and Ilzat.
    /note=We looked through HHpred results and found some results connecting to H97 but no compelling evidence was found. NCBI Blast came up with hypothetical proteins. We`ll settle with this for now but further research may prove useful.

CDS 7540 - 7896
  /gene="12"
  /product="gp12"
  /function="tail terminator"
  /locus tag="Symere_12"
    /note=Original Glimmer call @bp 7540 has strength 13.48; Genemark calls start at 7540
    /note=SSC: 7540-7896 CP: yes SCS: both ST: SS BLAST-Start: [tail terminator [Microbacterium phage StingRay] ],,NCBI, q1:s1 100.0% 2.09491E-78 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.327, -3.978223840957539, yes F: tail terminator SIF-BLAST: ,,[tail terminator [Microbacterium phage StingRay] ],,AVJ51457,100.0,2.09491E-78 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,70.339,97.2 SIF-Syn: NCBI BLAST finds structural homology to tail terminator. HHPred confirms tail terminator with an SPP1
    /note=Function list says that SPP1 confirms tail terminator.

CDS 7896 - 8132
  /gene="13"
  /product="gp13"
  /function="Hypothetical Protein"
  /locus tag="Symere_13"
    /note=Original Glimmer call @bp 7896 has strength 14.68; Genemark calls start at 7896
    /note=SSC: 7896-8132 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp13 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 4.32394E-48 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.133, -2.17469248771465, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp13 [Microbacterium phage Ilzat] ],,YP_009623177,100.0,4.32394E-48 SIF-HHPRED:  SIF-Syn: Synteny found with a protein of no known function in Ilzat, Sedgewig, and Stirfry IV.
    /note=No significant homology found by HHPred or NCBI blast.

CDS 8145 - 8645
  /gene="14"
  /product="gp14"
  /function="major tail protein"
  /locus tag="Symere_14"
    /note=Original Glimmer call @bp 8145 has strength 16.72; Genemark calls start at 8145
    /note=SSC: 8145-8645 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 5.64023E-115 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.112, -2.2364030944336752, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Ilzat] ],,YP_009623178,100.0,5.64023E-115 SIF-HHPRED:  SIF-Syn: Syntenic to major tail protein of Sedgwig, StirFryIV and Ilzat.  Magritte has a major tail protein proceeding tail assembly chaperone and tape measure protein, and this structure would be conserved in EA1s if this is a major tail protein.
    /note=HHPred found compelling structural homology to a "phage-tail like" protein from Listeria, but since this is a bacterial protein and not a phage protein, we declined to note it as evidence.  No other significant structural homology predicted.  BLAST finds significant sequence homology to other annotated Major Tail Proteins.

CDS 8674 - 9243
  /gene="15"
  /product="gp15"
  /function="tail assembly chaperone"
  /locus tag="Symere_15"
    /note=Original Glimmer call @bp 8674 has strength 14.18; Genemark calls start at 8674
    /note=SSC: 8674-9243 CP: no SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.29806E-134 GAP: 28 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.979, -2.794070146961553, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Ilzat] ],,YP_009623179,100.0,1.29806E-134 SIF-HHPRED:  SIF-Syn: Syntenic to TAC of Sedgewig, StirFryIV and Ilzat.
    /note=No significant structural homology predicted by HHPred.  Blast finds significant sequence homology to tail assembly chaperones of microbacterium phages (mostly), all likely annotated on the basis of synteny.

CDS 9267 - 9629
  /gene="16"
  /product="gp16"
  /function="tail assembly chaperone"
  /locus tag="Symere_16"
    /note=Original Glimmer call @bp 9480 has strength 5.45; Genemark calls start at 9258
    /note=SSC: 9267-9629 CP: yes SCS: both-cs ST: NI BLAST-Start: [tail assembly chaperone [Microbacterium Phage Clancy] ],,NCBI, q1:s1 100.0% 3.17053E-83 GAP: 23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.02, -4.845715258040838, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium Phage Clancy] ],,QDM57688,100.0,3.17053E-83 SIF-HHPRED:  SIF-Syn: Syntenic to TACs of Ilzat, Sedgewig and StirFryIV.  This functional call based upon synteny alone as the Pham precedes the Tape Measure Protein.
    /note=No significant structural homology predicted by HHPred.  BLAST finds sequence homology to annotated TACs, but no BLAST hits to biochemically characterized proteins.
    /note=
    /note=Searched long and hard for an unambiguous slippery sequence to tie this to the upstream Pham, but did not find a ss.

CDS 9654 - 11921
  /gene="17"
  /product="gp17"
  /function="tape measure protein"
  /locus tag="Symere_17"
    /note=Original Glimmer call @bp 9654 has strength 17.18; Genemark calls start at 9654
    /note=SSC: 9654-11921 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Microbacterium phage Espinosa] ],,NCBI, q1:s1 100.0% 0.0 GAP: 24 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.207, -1.953940808934884, yes F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage Espinosa] ],,AUX82791,98.9418,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BF,16.4238,99.9 SIF-Syn: Syntenic to StirFryIV, Sedgewig, Ilzat, and HanSolo calling tape measure protein. Next upstream pham from tail assembly chaperone.
    /note=HHPred calls for a tape measure protein with a high probability, homologous to gp57 of staph 80 alpha and Bxb1. NCBI BLAST also calls for tape measure protein on all pages.

CDS 11918 - 12691
  /gene="18"
  /product="gp18"
  /function="minor tail protein"
  /locus tag="Symere_18"
    /note=Original Glimmer call @bp 11918 has strength 15.68; Genemark calls start at 11918
    /note=SSC: 11918-12691 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.635, -3.318900340397143, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Sedgewig]],,QJD49680,100.0,0.0 SIF-HHPRED: HYPOTHETICAL PROTEIN 19.1; VIRAL PROTEIN, DISTAL TAIL PROTEIN; 2.95A {BACILLUS PHAGE SPP1},,,2X8K_A,99.2218,100.0 SIF-Syn: Synteny to pham in Sedgewig, StirfryIV, and Izat. They all call a minor tail protien.
    /note=HHPred showed homology to minor tail proteins more specifically distal tail proteins. Blast showed homology to minor tail protein as well.

CDS 12691 - 15117
  /gene="19"
  /product="gp19"
  /function="minor tail protein"
  /locus tag="Symere_19"
    /note=Original Glimmer call @bp 12691 has strength 17.48; Genemark calls start at 12691
    /note=SSC: 12691-15117 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.828, -2.7653702713535186, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Ilzat] ],,YP_009623183,100.0,0.0 SIF-HHPRED: Tail-Associated Lysin, gp59; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AE,38.9851,99.9 SIF-Syn: Syntenic and structural homology to StirFryIV, Sedgewig, HanSolo, and Ilzat calling minor tail protein.
    /note=Two hits on HHPred and NCBI BLAST predicts structural homology to minor tail proteins. gp59, the tail protein region, sialic acid, and sugar-binding proteins.

tRNA complement (13536 - 13621)
  /gene="20"
  /product="tRNA-Val(gac)"
  /locus tag="SYMERE_20"
    /note=tRNA-Val(gac)

CDS 15117 - 15302
  /gene="21"
  /product="gp21"
  /function="Hypothetical Protein"
  /locus tag="Symere_21"
    /note=Original Glimmer call @bp 15117 has strength 13.17; Genemark calls start at 15117
    /note=SSC: 15117-15302 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp20 [Microbacterium phage Ilzat] ],,NCBI, q1:s2 100.0% 3.99156E-35 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.491, -3.5660483139923818, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp20 [Microbacterium phage Ilzat] ],,YP_009623184,98.3871,3.99156E-35 SIF-HHPRED:  SIF-Syn: Syntenic to StirFryIV, Sedgewig, Ilzat, and HanSolo calling hypothetical protein.
    /note=HHPred had inconsistent data with numbers that are not high enough to look into. NCBI BLAST finds homology to hypothetical proteins.

CDS 15299 - 15895
  /gene="22"
  /product="gp22"
  /function="Hypothetical Protein"
  /locus tag="Symere_22"
    /note=Original Glimmer call @bp 15299 has strength 12.59; Genemark calls start at 15299
    /note=SSC: 15299-15895 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_SEDGEWIG_21 [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 2.76277E-140 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.036, -4.601664605840989, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SEDGEWIG_21 [Microbacterium phage Sedgewig]],,QJD49683,99.4949,2.76277E-140 SIF-HHPRED:  SIF-Syn: Syntenic to StirFryIV, Sedgewig, Ilzat, and HanSolo calling hypothetical protein.
    /note=HHPred numbers did not meet the 90% cutoff and did not contain any useful data. NCBI BLAST finds homology to hypothetical proteins on all pages.

CDS 15895 - 16374
  /gene="23"
  /product="gp23"
  /function="minor tail protein"
  /locus tag="Symere_23"
    /note=Original Glimmer call @bp 15895 has strength 17.02; Genemark calls start at 15895
    /note=SSC: 15895-16374 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_SEDGEWIG_22 [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 7.84366E-111 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.565, -3.389881189012514, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein SEA_SEDGEWIG_22 [Microbacterium phage Sedgewig]],,QJD49684,100.0,7.84366E-111 SIF-HHPRED: Gp15 protein; Listeria, homotrimeric, receptor binding protein, Bacteriophage, VIRAL PROTEIN; HET: 1PE, ACT; 1.7A {Listeria phage PSA},,,6R5W_B,72.327,99.0 SIF-Syn: Syntenic to Sedgewig, Stirfry IV, and Ilzat which dont call a funtion but are nested in a region of minor tail protiens.
    /note=HHPred shows significant scores to GP 15 protein in listeria phage as well as receptor binding protiens in lactococcus phage. Blast showed significant scores for hypothetical protien.

CDS 16374 - 18509
  /gene="24"
  /product="gp24"
  /function="minor tail protein"
  /locus tag="Symere_24"
    /note=Original Glimmer call @bp 16374 has strength 10.07; Genemark calls start at 16374
    /note=SSC: 16374-18509 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Papafritta] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.845, -4.868688382016774, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Papafritta] ],,AXH48534,100.0,0.0 SIF-HHPRED:  SIF-Syn: Syntenic to Stirfry IV, Ilzat, and Sedgewig. They all call for a minor tail protein. This pham is also in the region of other phams calling for minor tail proteins.
    /note=HHPred shows significant scores to sugar binding proteins. Interesting scores to levanase hydrolase in bacillus from query 381 to 556. Blast shows significant homology to minor tail proteins. Significant scores to chitinase from query 2 to 346. Also goood scores for glycoside hydrolase from query 438 to 556.

CDS 18540 - 19346
  /gene="25"
  /product="gp25"
  /function="endolysin"
  /locus tag="Symere_25"
    /note=Original Glimmer call @bp 18540 has strength 13.92; Genemark calls start at 18540
    /note=SSC: 18540-19346 CP: yes SCS: both ST: SS BLAST-Start: [endolysin [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: 30 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.979, -2.442961286954254, yes F: endolysin SIF-BLAST: ,,[endolysin [Microbacterium phage Ilzat] ],,YP_009623188,100.0,0.0 SIF-HHPRED: Putative carboxypeptidase YodJ; LAS family, LD-carboxypeptidase, Cell wall modifying enzyme, HYDROLASE; 2.0A {Bacillus subtilis},,,4OX3_A,39.1791,98.4 SIF-Syn: Syntenic to lysin A of Sedgewig, Ilzat and HanSolo, and to endolysin of StirFryIV.
    /note=HHPred finds compelling structural homology to carboxypeptidases, consistent with an endolysin function.  We have not identified a lysin B pham, and therefore we are annotating this pham as an endolysin.

CDS 19381 - 19770
  /gene="26"
  /product="gp26"
  /function="membrane protein"
  /locus tag="Symere_26"
    /note=Original Glimmer call @bp 19381 has strength 13.44; Genemark calls start at 19381
    /note=SSC: 19381-19770 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 5.4004E-88 GAP: 34 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.979, -2.970161406017234, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Ilzat] ],,YP_009623189,100.0,5.4004E-88 SIF-HHPRED: Peptidase M23; membrane protein, enzyme, TRANSPORT PROTEIN; HET: ADP;{Vibrio cholerae},,,8TZL_E,79.0698,90.9 SIF-Syn: Syntenic to phams of no known function in Ilzat, Sedgewig, StirfryIV and HanSolo.
    /note=DeepTMHMM predicts high likelihood of a membrane-spanning domain.  HHPred predicts compelling structural homology to FtsX from Vibrio cholorea.

CDS 19775 - 20116
  /gene="27"
  /product="gp27"
  /function="holin"
  /locus tag="Symere_27"
    /note=Original Glimmer call @bp 19775 has strength 16.74; Genemark calls start at 19775
    /note=SSC: 19775-20116 CP: yes SCS: both ST: SS BLAST-Start: [holin [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 2.7174E-68 GAP: 4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.089, -4.87383788125753, no F: holin SIF-BLAST: ,,[holin [Microbacterium phage Ilzat] ],,YP_009623190,100.0,2.7174E-68 SIF-HHPRED: Phage_holin_5_1 ; Bacteriophage A118-like holin, Hol118,,,PF06946.16,75.2212,99.7 SIF-Syn: Syntenic to StirFryIV, Ilzat, HanSolo, and Sedgewig calling holin. Region of genome involving lysis.
    /note=HHPred shows evidence for holin. DeepTMHMM shows three passes through the membrane.

CDS complement (20172 - 20360)
  /gene="28"
  /product="gp28"
  /function="Hypothetical Protein"
  /locus tag="Symere_28"
    /note=Original Glimmer call @bp 20360 has strength 20.08; Genemark calls start at 20360
    /note=SSC: 20360-20172 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp27 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.62979E-36 GAP: 63 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.979, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp27 [Microbacterium phage Ilzat] ],,YP_009623191,100.0,1.62979E-36 SIF-HHPRED:  SIF-Syn: Syntenic on pham of no known function with Sedgewig, Izlat, Stirfry IV, and Han Solo.
    /note=No significant results from HHpred or others. Settling on hypothetical protein, no known function.

CDS complement (20424 - 20576)
  /gene="29"
  /product="gp29"
  /function="Hypothetical Protein"
  /locus tag="Symere_29"
    /note=Original Glimmer call @bp 20576 has strength 12.89; Genemark calls start at 20576
    /note=SSC: 20576-20424 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_AUBERGINE_28 [Microbacterium phage Aubergine] ],,NCBI, q1:s7 100.0% 7.18654E-29 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.854, -5.50074291708362, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_AUBERGINE_28 [Microbacterium phage Aubergine] ],,AUX82615,89.2857,7.18654E-29 SIF-HHPRED:  SIF-Syn: Syntenic to StirFryIV, Sedgewig, HanSolo, and Ilzat all calling hypothetical protein.
    /note=HHPred and NCBI BLAST both call for a hypothetical protein. There was not much useful data.

CDS complement (20591 - 20749)
  /gene="30"
  /product="gp30"
  /function="Hypothetical Protein"
  /locus tag="Symere_30"
    /note=Original Glimmer call @bp 20749 has strength 8.28; Genemark calls start at 20749
    /note=SSC: 20749-20591 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_SEDGEWIG_29 [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 7.38096E-28 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.281, -4.075451192669358, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SEDGEWIG_29 [Microbacterium phage Sedgewig]],,QJD49691,100.0,7.38096E-28 SIF-HHPRED:  SIF-Syn: Syntenic to Pham of no known function in Ilzat, Sedgewig and StirFry IV.
    /note=No significant structural or sequence homology to Phams of known function predicted by HHPred or BLAST.

CDS complement (20746 - 21588)
  /gene="31"
  /product="gp31"
  /function="Hypothetical Protein"
  /locus tag="Symere_31"
    /note=Original Glimmer call @bp 21588 has strength 14.37; Genemark calls start at 21588
    /note=SSC: 21588-20746 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp30 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: 44 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.508, -6.242072432500853, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp30 [Microbacterium phage Ilzat] ],,YP_009623194,100.0,0.0 SIF-HHPRED: TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN-INHIBITORY PROTEIN; TRANSCRIPTION REGULATION, ANTI-TRAP; HET: ZN; 2.8A {BACILLUS SUBTILIS},,,2BX9_A,17.5,93.9 SIF-Syn: Syntenic to Pham of no known function in
    /note=Interesting HHPred results.  From amino acid 24 to 66 roughly very high homology predicted to an anti-termination Protein Q (Shield et al 2019 Nat. Comm) and an inhibitor of the Tryptophan RNA-binding attenuator protein.  Further along, from about 88 to 187 more or less, structural homology to nucleic acid binding proteins is predicted.  Compelling and interesting, but not a clear function.  BLAST found little beyond hypothetical proteins other than two SS-DNA binding proteins.  Hypothetical Protein.

CDS complement (21633 - 21896)
  /gene="32"
  /product="gp32"
  /function="membrane protein"
  /locus tag="Symere_32"
    /note=Original Glimmer call @bp 21896 has strength 18.48; Genemark calls start at 21896
    /note=SSC: 21896-21633 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp31 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.0349E-57 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.262, -4.327759218808925, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp31 [Microbacterium phage Ilzat] ],,YP_009623195,100.0,1.0349E-57 SIF-HHPRED:  SIF-Syn: Syntenic to Pham of no known function in StirFryIV, Sedgewig and Ilzat.
    /note=No significant structural homology predicted by HHPred.  BLAST found significant sequence homology to several phage Phams annotated as membrane proteins.  DeepTMHmm agrees, predicting a membrane spanning protein.

CDS complement (21896 - 22105)
  /gene="33"
  /product="gp33"
  /function="membrane protein"
  /locus tag="Symere_33"
    /note=Original Glimmer call @bp 22105 has strength 15.5; Genemark calls start at 22105
    /note=SSC: 22105-21896 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 2.20237E-41 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.828, -2.9063687850157054, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Sedgewig]],,QJD49694,100.0,2.20237E-41 SIF-HHPRED:  SIF-Syn: Syntenic to Pham of no known function in Ilzat, Sedgewig and StirFry IV.
    /note=No significant structural homology predicted by HHPred.  BLAST finds significant sequence homology to Phage Phams annotated as membrane proteins, and DeepTMHMM finds an extensive transmembrane region.

CDS complement (22102 - 23772)
  /gene="34"
  /product="gp34"
  /function="DNA primase/helicase"
  /locus tag="Symere_34"
    /note=Original Glimmer call @bp 23703 has strength 12.91; Genemark calls start at 23703
    /note=SSC: 23772-22102 CP: yes SCS: both-cs ST: NI BLAST-Start: [DNA recombinase [Microbacterium phage Aubergine] ],,NCBI, q1:s1 100.0% 0.0 GAP: -25 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.049, -2.4329349954350334, yes F: DNA primase/helicase SIF-BLAST: ,,[DNA recombinase [Microbacterium phage Aubergine] ],,AUX82620,100.0,0.0 SIF-HHPRED: Replication protein B; primase, Nucleotidyltransferase, helix-bundle-domain, replication, RSF1010; HET: SO4; 1.99A {Plasmid RSF1010},,,3H20_A,46.5827,99.4 SIF-Syn: Syntenic to called DNA recombinase of Ilzat, RecA-like DNA recombinase of Sedgewig and NKF in StirFryIV.
    /note=HHPred did predict substantive structural homology to RecA DNA recombinase of E. coli.  However, the sequence did not align to the E. coli RecA gene sequence well.  Moreover, the predicted protein for this pham is quite a bit larger than the E. coli RecA, and the structural homology to RecA predicted by HHPred only occurs across the C-terminal half of this Pham.  Across this same region of Stop 22102, HHPred also finds substantial structural homology to well characterized DNA helicases.  And in the preceeding N-terminal region of Stop 22102, HHPred finds substantial structural homology to biochemically characterized primases.

CDS complement (23748 - 24041)
  /gene="35"
  /product="gp35"
  /function="VRR-Nuc domain protein"
  /locus tag="Symere_35"
    /note=Original Glimmer call @bp 24041 has strength 5.92; Genemark calls start at 24041
    /note=SSC: 24041-23748 CP: yes SCS: both ST: SS BLAST-Start: [endonuclease [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.9725E-65 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.163, -6.678258492274136, no F: VRR-Nuc domain protein SIF-BLAST: ,,[endonuclease [Microbacterium phage Ilzat] ],,YP_009623198,100.0,1.9725E-65 SIF-HHPRED: Nuclease; Nuclease, HYDROLASE; HET: SO4; 1.85A {Salmonella phage SETP3} SCOP: c.52.1.35,,,4QBN_A,94.8454,99.8 SIF-Syn: Syntenic to phams in Ilzat,Sedgewig, and StirfryIV who all called for a nuclease.
    /note=HHPred shows biochemical synteny to VRR-Nuc domain protein in Fan1 from query 1 to 93.

CDS complement (24045 - 24890)
  /gene="36"
  /product="gp36"
  /function="DNA binding protein"
  /locus tag="Symere_36"
    /note=Original Glimmer call @bp 24890 has strength 18.23; Genemark calls start at 24890
    /note=SSC: 24890-24045 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp35 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: 32 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.685, -3.2123487306667524, yes F: DNA binding protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp35 [Microbacterium phage Ilzat] ],,YP_009623199,100.0,0.0 SIF-HHPRED: Transcription termination factor Rho; transcription termination factor, RNA helicase, ATP-dependent, molecular motor, TRANSCRIPTION; HET: ATP;{Mycobacterium tuberculosis},,,7OQH_D,10.6762,91.1 SIF-Syn: Syntenic to phams in Sedgewig, Ilzat, and Stirfry IV who dont call a fuunction.
    /note=HHPred shows biochemical synteny to DNA binding protein in OB Fold from query 2 to 132. This looks at Bredienstein Et.al (2024) Life Sci Alliance 7. This paper talks about how this protein can also grab onto double stranded DNA.

CDS complement (24923 - 25591)
  /gene="37"
  /product="gp37"
  /function="Hypothetical Protein"
  /locus tag="Symere_37"
    /note=Original Glimmer call @bp 25591 has strength 18.34; Genemark calls start at 25591
    /note=SSC: 25591-24923 CP: yes SCS: both ST: SS BLAST-Start: [AAA-ATPase [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.14731E-161 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.104, -4.455662434380964, no F: Hypothetical Protein SIF-BLAST: ,,[AAA-ATPase [Microbacterium phage Ilzat] ],,YP_009623200,100.0,1.14731E-161 SIF-HHPRED: P4; HYDROLASE, NTPASE, CYSTOVIRIDAE; 3.1A {PSEUDOMONAS PHAGE PHI8},,,4BWY_D,84.2342,98.8 SIF-Syn: Syntenic to AAA-ATPase of Sedgewig, StirFryIV and Ilzat.  AAA-ATPase is no longer on the approved function list.
    /note=HHPred predicts substantial structural homology to a number of proteins that fall under the category of ASCE ATPases.  HOWEVER, we cannot identify with confidence sequence that is unambiguously either Walker A or Walker B motif, and we have looked extensively through several alignments to well characterized ASCE ATPases.  This pham clearly has a relationship to ASCE ATPases, but we are not comfortable calling it an ASCE ATPase.  Hypothetical protein.

CDS complement (25588 - 26763)
  /gene="38"
  /product="gp38"
  /function="Cas4 exonuclease"
  /locus tag="Symere_38"
    /note=Original Glimmer call @bp 26763 has strength 13.27; Genemark calls start at 26772
    /note=SSC: 26763-25588 CP: yes SCS: both-gl ST: SS BLAST-Start: [exonuclease [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: -14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.405, -3.670670413150579, no F: Cas4 exonuclease SIF-BLAST: ,,[exonuclease [Microbacterium phage Ilzat] ],,YP_009623201,100.0,0.0 SIF-HHPRED:  SIF-Syn: No function assigned to syntenic Pham of StirFryIV.  Ilzat and Sedgewig assign a function of exonuclease to this Pham.
    /note=HHPred predicts substantive structural homology between aas 33 to 365 to aas 791-1045 of the unbound form of the AdnA protein, a well characterized helicase/exonuclease (see Jia et al 2019 PNAS 116 p24507).  Digging into the supplementary materials of Jia et al, we found that aas 791-1045 of AdnA correspond to the RecB-like nuclease domain, and exclude the preceding helicase domain.  From the current function list for Cas4 exonuclease ("	This family of exonucleases is similar to the exonuclease domain of RecB. The Cas4 label should be used if the gene includes only the exonuclease region.")  Therefore we are calling a Cas4 exonuclease.

CDS complement (26750 - 28615)
  /gene="39"
  /product="gp39"
  /function="DNA polymerase I"
  /locus tag="Symere_39"
    /note=Original Glimmer call @bp 28615 has strength 13.87; Genemark calls start at 28606
    /note=SSC: 28615-26750 CP: yes SCS: both-gl ST: SS BLAST-Start: [DNA polymerase I [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 0.0 GAP: 199 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.905, -2.6013996449736907, yes F: DNA polymerase I SIF-BLAST: ,,[DNA polymerase I [Microbacterium phage Sedgewig]],,QJD49700,100.0,0.0 SIF-HHPRED: DNA polymerase I; mycobacteria, DNA polymerase, Flap endonuclease, TRANSFERASE; 2.713A {Mycolicibacterium smegmatis},,,6VDE_A,99.0338,100.0 SIF-Syn: Syntenic homology with Ilzat, Sedgewig, Han Solo, and Stirfry IV.
    /note=HHpred comes up with DNA polymerase I with great scores, whats not to love?

CDS complement (28815 - 29240)
  /gene="40"
  /product="gp40"
  /function="Hypothetical Protein"
  /locus tag="Symere_40"
    /note=Original Glimmer call @bp 29240 has strength 17.81; Genemark calls start at 29240
    /note=SSC: 29240-28815 CP: yes SCS: both ST: SS BLAST-Start: [ABC transporter [Microbacterium sp. HM58-2]],,NCBI, q26:s21 46.0993% 4.47798E-26 GAP: 170 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.979, -2.442961286954254, yes F: Hypothetical Protein SIF-BLAST: ,,[ABC transporter [Microbacterium sp. HM58-2]],,GAT74858,51.4019,4.47798E-26 SIF-HHPRED:  SIF-Syn: Synetnic homology in hypothetical protein to Stirfry IV, Sedgwig, Ilzat, and Han Solo.
    /note=HHpred gives no results with good results. BLAST shows a result of an ABC transporter but we aren`t totally on board with that, we see no indication that there is biochemical evidence for it.

CDS complement (29411 - 30799)
  /gene="41"
  /product="gp41"
  /function="Hypothetical Protein"
  /locus tag="Symere_41"
    /note=Original Glimmer call @bp 30799 has strength 10.38; Genemark calls start at 30799
    /note=SSC: 30799-29411 CP: yes SCS: both ST: SS BLAST-Start: [DNA helicase [Microbacterium phage Superfresh] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.084, -4.497860114175419, no F: Hypothetical Protein SIF-BLAST: ,,[DNA helicase [Microbacterium phage Superfresh] ],,AUX83317,100.0,0.0 SIF-HHPRED: RNA polymerase-associated protein RapA; hydrolase, TRANSCRIPTION; HET: SO4, MSE; 3.205A {Escherichia coli O45:K1},,,6BOG_A,97.8355,100.0 SIF-Syn: Syntenic to helicase of StirFryIV and to DNA helicase of Sedgewig and Ilzat.
    /note=We predict a protein of about 463 amino acids.  HHPred predicts substantial structural homology across most of this stretch (generally leaving off the N-terminal 40 aas or so) to...
    /note=
    /note=The RecA-like domains 1A and 2A, linker 2 region and Swi2/Snf2-specific domains of E. coli RapA protein (Shaw et al Structure 16 p 1417), an RNA-polymerase recycling protein.  We aligned the predicted protein sequence of Stop-29,411 with an E. coli RecA and Spud gp205 and found no clear Walker A or B sequence motifs so Stop-29,411 seems not be a RecA protein or an ASCE ATPase.  
    /note=
    /note=Amino acids 577 to 1064 of the E. coli Zorb protein, the C-terminal domain of Zorb which has ATPase and nuclease functions (Hu et al, Nature Vol 639 p1093).  
    /note=
    /note=Amino acids 111 to 490 of the E. coli DEAD-box helicase DbpA of E. coli, a dsRNA helicase involved in ribosome maturation.  
    /note=
    /note=So we appear to have a nucleotide-binding ATPase, but beyond that, the evidence is not clear.  Stop-29,411 does not appear to be unambiguously a helicase.  We are calling hypothetical protein.

CDS complement (30799 - 31392)
  /gene="42"
  /product="gp42"
  /function="phosphoesterase"
  /locus tag="Symere_42"
    /note=Original Glimmer call @bp 31392 has strength 18.83; Genemark calls start at 31392
    /note=SSC: 31392-30799 CP: yes SCS: both ST: SS BLAST-Start: [phosphoesterase [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 1.01979E-139 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.972, -4.738143471880277, no F: phosphoesterase SIF-BLAST: ,,[phosphoesterase [Microbacterium phage Sedgewig]],,QJD49703,100.0,1.01979E-139 SIF-HHPRED: RNA 2`,3`-cyclic phosphodiesterase; Enzyme, 2H phosphoesterase/ligase, hydrolase; HET: NAP, 1PE; 1.7A {Escherichia coli BL21(DE3)} SCOP: d.61.1.0,,,5LDQ_B,77.665,99.4 SIF-Syn: Syntenic to phams in Ilzat and Sedgewig which call it phosphoesterase. Also syntenic to pham in Stirfry IV which calls it a hypothetical protein.
    /note=HHPred shows significant scores for a phosphoesterase. Blast did as well. Looked at Myllykoski and Kursula`s paper Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase (2017).

CDS complement (31389 - 31697)
  /gene="43"
  /product="gp43"
  /function="Hypothetical Protein"
  /locus tag="Symere_43"
    /note=Original Glimmer call @bp 31697 has strength 15.03; Genemark calls start at 31697
    /note=SSC: 31697-31389 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp42 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 5.83082E-58 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.979, -2.523003374675015, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp42 [Microbacterium phage Ilzat] ],,YP_009623206,100.0,5.83082E-58 SIF-HHPRED:  SIF-Syn: Syntenic homology with hypothetical protein with Ilzat, Sedgwig, Stirfry IV, and Han Solo.
    /note=HHpred gives no results with higher scores. NCBI BLAST gives us all hypothetical proteins.

CDS complement (31697 - 31975)
  /gene="44"
  /product="gp44"
  /function="Hypothetical Protein"
  /locus tag="Symere_44"
    /note=Original Glimmer call @bp 31975 has strength 15.16; Genemark calls start at 31975
    /note=SSC: 31975-31697 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein H3N90_gp44 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 7.05219E-61 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.01, -4.59534204625343, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein H3N90_gp44 [Microbacterium phage Teagan] ],,YP_009908746,100.0,7.05219E-61 SIF-HHPRED:  SIF-Syn: Syntenic hypothetical protein homology with Stirfry IV, Sedgwig, Ilzat, and Han Solo.
    /note=HHpred gives us no results above our desired 90%. BLAST gives us all hypothetical proteins.

CDS complement (31975 - 32784)
  /gene="45"
  /product="gp45"
  /function="MazG-like nucleotide pyrophosphohydrolase"
  /locus tag="Symere_45"
    /note=Original Glimmer call @bp 32784 has strength 16.77; Genemark calls start at 32784
    /note=SSC: 32784-31975 CP: yes SCS: both ST: SS BLAST-Start: [nucleotide pyrophosphohydrolase [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.709, -3.1604619823777065, yes F: MazG-like nucleotide pyrophosphohydrolase SIF-BLAST: ,,[nucleotide pyrophosphohydrolase [Microbacterium phage Ilzat] ],,YP_009623208,100.0,0.0 SIF-HHPRED: MAZG-LIKE NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE; HYDROLASE, DIMERIC DUTPASE; HET: GOL, SO4; 1.7A {DEINOCOCCUS RADIODURANS},,,2YF4_C,61.3383,100.0 SIF-Syn: Syntenic to Sedgewig and StirFryIV calling a MazG-like nucleotide pyrophosphohydrolase.
    /note=HHPred had a very probable hit on MazG-like nucleotide pyrophosphohydrolase with the query from 99 to 264. HHPred had another hit on a PGDYG Protein with the query from 1 to 81.

CDS complement (32781 - 33506)
  /gene="46"
  /product="gp46"
  /function="Hypothetical Protein"
  /locus tag="Symere_46"
    /note=Original Glimmer call @bp 33506 has strength 10.98; Genemark calls start at 33506
    /note=SSC: 33506-32781 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp45 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 1.02495E-175 GAP: -23 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.491, -4.138145081942901, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp45 [Microbacterium phage Ilzat] ],,YP_009623209,100.0,1.02495E-175 SIF-HHPRED:  SIF-Syn: Syntenic phages call hypothetical protein.
    /note=HHPred did not have any solid hits. NCBI BLAST calls for hypothetical protein.

CDS complement (33484 - 34083)
  /gene="47"
  /product="gp47"
  /function="thymidylate kinase"
  /locus tag="Symere_47"
    /note=Original Glimmer call @bp 34083 has strength 17.57; Genemark calls start at 34083
    /note=SSC: 34083-33484 CP: yes SCS: both ST: SS BLAST-Start: [thymidylate kinase [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 3.02673E-144 GAP: 12 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.218, -2.0720764396375664, yes F: thymidylate kinase SIF-BLAST: ,,[thymidylate kinase [Microbacterium phage Ilzat] ],,YP_009623210,100.0,3.02673E-144 SIF-HHPRED: THYMIDYLATE KINASE; TRANSFERASE, TRANSFERASE (ATP:TMP PHOSPHOTRANSFERASE), KINASE; HET: SO4, ACT, TYD, TMP; 1.55A {MYCOBACTERIUM TUBERCULOSIS} SCOP: c.37.1.1,,,1GTV_B,84.9246,99.5 SIF-Syn: Syntenic to phams in Sedgewig and Stirfry IV which call for thymidylate kinase. Syntenic to pham in Ilzat that calls an aaa-atpase.
    /note=HHPred shows hits from query 1 to 170 calling for a thymidylate kinase. No other hits were found.

CDS complement (34096 - 35028)
  /gene="48"
  /product="gp48"
  /function="glycosyltransferase"
  /locus tag="Symere_48"
    /note=Original Glimmer call @bp 35028 has strength 14.71; Genemark calls start at 35028
    /note=SSC: 35028-34096 CP: yes SCS: both ST: SS BLAST-Start: [glycosyltransferase [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: -8 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.993, -6.157910251162862, no F: glycosyltransferase SIF-BLAST: ,,[glycosyltransferase [Microbacterium phage Ilzat] ],,YP_009623211,100.0,0.0 SIF-HHPRED: Glycosyltransferase; Glycosyltransferase, TRANSFERASE; HET: GOL, TRH, TAR; 2.2A {Listeria monocytogenes},,,8BZ7_E,84.8387,98.8 SIF-Syn: Syntenic function homology with Sedgwig.
    /note=HHpred comes up with hit for glycosyltransferase that has good scores and a query from 1 to 264.

CDS complement (35021 - 35254)
  /gene="49"
  /product="gp49"
  /function="Hypothetical Protein"
  /locus tag="Symere_49"
    /note=Original Glimmer call @bp 35254 has strength 5.97; Genemark calls start at 35254
    /note=SSC: 35254-35021 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_CLANCY_48 [Microbacterium Phage Clancy] ],,NCBI, q1:s1 100.0% 4.29595E-51 GAP: 62 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.099, -4.325675514574479, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_CLANCY_48 [Microbacterium Phage Clancy] ],,QDM57720,100.0,4.29595E-51 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Ilzat, Sedgewig, and Stirfry IV that dont call a function.
    /note=HHPred shows no significant scores. Blast calls for hypothetical protein.

CDS complement (35317 - 35613)
  /gene="50"
  /product="gp50"
  /function="membrane protein"
  /locus tag="Symere_50"
    /note=Original Glimmer call @bp 35613 has strength 12.88; Genemark calls start at 35613
    /note=SSC: 35613-35317 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp49 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 4.93732E-62 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.133, -2.253377680616507, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp49 [Microbacterium phage Ilzat] ],,YP_009623213,100.0,4.93732E-62 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Ilzat, Sedgewig, and Stirfry IV that dont call a function.
    /note=HHPred shows no significant scores. Blast shows homology to hypothetical proteins and membrane proteins. DeepTMHMM finds a membrane hit. Calling this membrane protein based off of the deep TMHMM hit.

CDS complement (35610 - 36377)
  /gene="51"
  /product="gp51"
  /function="thymidylate synthase"
  /locus tag="Symere_51"
    /note=Original Glimmer call @bp 36377 has strength 13.14; Genemark calls start at 36377
    /note=SSC: 36377-35610 CP: yes SCS: both ST: SS BLAST-Start: [thymidylate synthase [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 0.0 GAP: 119 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.979, -2.523003374675015, yes F: thymidylate synthase SIF-BLAST: ,,[thymidylate synthase [Microbacterium phage Ilzat] ],,YP_009623214,100.0,0.0 SIF-HHPRED: CMP 5-hydroxymethylase; CMP hydroxymethylase, TRANSFERASE; HET: C5P; 1.65A {Streptomyces rimofaciens},,,5B6D_A,87.8431,100.0 SIF-Syn: Syntenic phages such as Sedgewig, StirFryIV, and Ilzat call thymidylate synthase.
    /note=HHPred has a solid hit on a thymidylate synthase. BLAST also calls for a thymidylate synthase.

CDS complement (36497 - 36727)
  /gene="52"
  /product="gp52"
  /function="Hypothetical Protein"
  /locus tag="Symere_52"
    /note=Original Glimmer call @bp 36709 has strength 10.29; Genemark calls start at 36709
    /note=SSC: 36727-36497 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein PBI_KNOX_52 [Microbacterium phage Knox] ],,NCBI, q1:s1 100.0% 3.68289E-48 GAP: 60 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.612, -6.672171187999036, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_KNOX_52 [Microbacterium phage Knox] ],,AUX83013,100.0,3.68289E-48 SIF-HHPRED:  SIF-Syn: Syntenic to Pham of no known function in Ilzat, Sedgewig and SitrFryIV
    /note=HHPred predicts no structural homology to genes of known function.  BLAST finds no significant sequence homology to genes of known function.

CDS complement (36788 - 37054)
  /gene="53"
  /product="gp53"
  /function="Hypothetical Protein"
  /locus tag="Symere_53"
    /note=Original Glimmer call @bp 37012 has strength 19.77; Genemark calls start at 37012
    /note=SSC: 37054-36788 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein PBI_PEEP_53 [Microbacterium phage Peep] ],,NCBI, q1:s1 100.0% 7.60653E-58 GAP: 22 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.433, -4.517920812149203, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_PEEP_53 [Microbacterium phage Peep] ],,AUX83139,100.0,7.60653E-58 SIF-HHPRED:  SIF-Syn: Syntenic to Pham of no predicted function in Ilzat, Sedgewig, and StirFryIV.
    /note=HHPred predicts no significant structural homology to proteins of known function.  BLAST finds no significant sequence homology to proteins of known function.

CDS complement (37077 - 37343)
  /gene="54"
  /product="gp54"
  /function="Hypothetical Protein"
  /locus tag="Symere_54"
    /note=Original Glimmer call @bp 37343 has strength 19.91; Genemark calls start at 37343
    /note=SSC: 37343-37077 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp53 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 3.07531E-52 GAP: 71 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.133, -2.1123791669543204, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp53 [Microbacterium phage Ilzat] ],,YP_009623217,100.0,3.07531E-52 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Ilzat, Sedgewig, and StirfryIV that call no function.
    /note=HHPred shows no significant scores above 90%. Blast shows sequence homology to no known functions.

CDS complement (37415 - 37717)
  /gene="55"
  /product="gp55"
  /function="Hypothetical Protein"
  /locus tag="Symere_55"
    /note=Original Glimmer call @bp 37717 has strength 16.87; Genemark calls start at 37717
    /note=SSC: 37717-37415 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp54 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 8.01803E-66 GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.067, -2.253486910374644, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp54 [Microbacterium phage Ilzat] ],,YP_009623218,100.0,8.01803E-66 SIF-HHPRED: Hydrogenase/urease nickel incorporation protein hypA; metallochaperone, hydrogenase, Metal-binding, Nickel, METAL-BINDING PROTEIN, METAL BINDING PROTEIN; HET: ZN; NMR {Helicobacter pylori},,,2KDX_A,77.0,97.5 SIF-Syn: Syntentic structural homology to Sedgewig, StirfryIV, and Ilzat.
    /note=Interesting top hits on HHPred, all seem to be connected to zinc binding. But none of these were listed on the approved function list, so we`re going with hypothetical protein.

CDS complement (37809 - 38003)
  /gene="56"
  /product="gp56"
  /function="Hypothetical Protein"
  /locus tag="Symere_56"
    /note=Original Glimmer call @bp 38003 has strength 17.11; Genemark calls start at 38003
    /note=SSC: 38003-37809 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein FDJ36_gp55 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 3.19909E-39 GAP: 38 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.7, -5.830816207622988, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp55 [Microbacterium phage Ilzat] ],,YP_009623219,100.0,3.19909E-39 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Sedgewig, Ilzat, and StirFryIV that call a hypothetical protein
    /note=No hits on HHPred. NCBI BLAST calls for a hypothetical protein.

CDS complement (38042 - 38347)
  /gene="57"
  /product="gp57"
  /function="Hypothetical Protein"
  /locus tag="Symere_57"
    /note=Original Glimmer call @bp 38347 has strength 6.57; Genemark calls start at 38347
    /note=SSC: 38347-38042 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp56 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 4.80597E-67 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.849, -5.386343183173524, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp56 [Microbacterium phage Ilzat] ],,YP_009623220,100.0,4.80597E-67 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Sedgewig, StirFryIV, Ilzat, and HanSolo which all called hypothetical protein.
    /note=No significant HHPred hits and BLAST calls for a hypothetical protein.

CDS complement (38344 - 38529)
  /gene="58"
  /product="gp58"
  /function="Hypothetical Protein"
  /locus tag="Symere_58"
    /note=Original Glimmer call @bp 38529 has strength 10.26; Genemark calls start at 38529
    /note=SSC: 38529-38344 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein H3N90_gp58 [Microbacterium phage Teagan] ],,NCBI, q1:s1 100.0% 5.06966E-37 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.447, -5.78257814227218, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein H3N90_gp58 [Microbacterium phage Teagan] ],,YP_009908760,100.0,5.06966E-37 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Sedgewig, StirFryIV, Ilzat, and HanSolo which all called hypothetical protein.
    /note=HHPred did not have any significant hits and BLAST calls for a hypothetical protein.

CDS complement (38531 - 39262)
  /gene="59"
  /product="gp59"
  /function="Hypothetical Protein"
  /locus tag="Symere_59"
    /note=Original Glimmer call @bp 39262 has strength 14.58; Genemark calls start at 39262
    /note=SSC: 39262-38531 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp58 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 2.33668E-175 GAP: 93 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.067, -2.253486910374644, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp58 [Microbacterium phage Ilzat] ],,YP_009623222,100.0,2.33668E-175 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Sedgewig, StirFryIV, Ilzat, and HanSolo which all called hypothetical protein.
    /note=No significant HHPred hits and BLAST calls for a hypothetical protein.

CDS complement (39356 - 39742)
  /gene="60"
  /product="gp60"
  /function="Hypothetical Protein"
  /locus tag="Symere_60"
    /note=Original Glimmer call @bp 39694 has strength 20.25; Genemark calls start at 39742
    /note=SSC: 39742-39356 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein FDJ36_gp59 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 2.3585E-88 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.433, -3.9616183113819163, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp59 [Microbacterium phage Ilzat] ],,YP_009623223,100.0,2.3585E-88 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Sedgewig, StirFryIV, Ilzat, and HanSolo which all called hypothetical protein.
    /note=No significant HHPred hits and BLAST calls for a hypothetical protein.

CDS complement (39739 - 40098)
  /gene="61"
  /product="gp61"
  /function="Hypothetical Protein"
  /locus tag="Symere_61"
    /note=Original Glimmer call @bp 40098 has strength 4.9; Genemark calls start at 40098
    /note=SSC: 40098-39739 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein FDJ36_gp60 [Microbacterium phage Ilzat] ],,NCBI, q1:s1 100.0% 4.26512E-78 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.519, -6.393143906827662, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein FDJ36_gp60 [Microbacterium phage Ilzat] ],,YP_009623224,100.0,4.26512E-78 SIF-HHPRED:  SIF-Syn: Syntenic to StirFryIV, Ilzat, and Sedgewig calling hypothetical protein.
    /note=HHPred did not show good probability or coverage. BLAST shows hypothetical protein.

CDS complement (40095 - 40277)
  /gene="62"
  /product="gp62"
  /function="Hypothetical Protein"
  /locus tag="Symere_62"
    /note=Original Glimmer call @bp 40277 has strength 3.93; Genemark calls start at 40277
    /note=SSC: 40277-40095 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein PBI_AUBERGINE_61 [Microbacterium phage Aubergine] ],,NCBI, q1:s18 100.0% 1.94169E-36 GAP: 610 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.133, -2.1123791669543204, yes F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein PBI_AUBERGINE_61 [Microbacterium phage Aubergine] ],,AUX82648,77.9221,1.94169E-36 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Ilzat, Sedgewig, and Stirfry IV, who dont call a function.
    /note=HHPred showed no significant scores. Blast shows homology to hypothetical proteins. Calling a hypothetical protein.

CDS 40888 - 41331
  /gene="63"
  /product="gp63"
  /function="Hypothetical Protein"
  /locus tag="Symere_63"
    /note=Original Glimmer call @bp 40888 has strength 13.17; Genemark calls start at 40690
    /note=SSC: 40888-41331 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_SEDGEWIG_62 [Microbacterium phage Sedgewig]],,NCBI, q1:s1 100.0% 1.71996E-99 GAP: 610 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.979, -2.442961286954254, no F: Hypothetical Protein SIF-BLAST: ,,[hypothetical protein SEA_SEDGEWIG_62 [Microbacterium phage Sedgewig]],,QJD49724,100.0,1.71996E-99 SIF-HHPRED:  SIF-Syn: Syntenic to phams in Sedgewig and Stirfry IV but they do not call a function. An alternative pham is called in Ilzat but we suspect that its due to a mistake of the start site.
    /note=HHPred showed no significant scores. Blast shows homology to hypothetical proteins. Calling this a hypothetical protein.