CDS 1 - 318 /gene="1" /product="gp1" /function="hypothetical protein" /locus tag="MortySmith_1" /note=Original Glimmer call @bp 1 has strength 7.52; Genemark calls start at 1 /note=SSC: 1-318 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_1 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 6.0522E-65 GAP: 0 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.844, -5.132255893439239, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_1 [Microbacterium phage Aesir]],,QNN98567,100.0,6.0522E-65 SIF-HHPRED: ARL17 ; ADP-ribosylation factor-like protein 17,,,PF15840.8,22.8571,31.5 SIF-Syn: none /note=start: 1 /note=Gl/Gm favored: both /note=Gap: 517 with last gene /note=CP: Yes /note=most annotated: yes /note=most conserved: yes /note=SD Z=1.8. Final= -5.1, not best /note=Q1:S1: yes /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: top hit had 31.5% probability CDS 322 - 759 /gene="2" /product="gp2" /function="hypothetical protein" /locus tag="MortySmith_2" /note=Original Glimmer call @bp 322 has strength 10.76; Genemark calls start at 322 /note=SSC: 322-759 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_2 [Microbacterium phage TinyMiny]],,NCBI, q5:s3 84.1379% 1.37874E-12 GAP: 3 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_2 [Microbacterium phage TinyMiny]],,UAJ16093,57.1429,1.37874E-12 SIF-HHPRED: NADH:ubiquinone oxidoreductase subunit B4; complex, respiration, NADH, proton pump, mitochondria, iron-sulphur cluster, oxidoreductase, membrane protein, ELECTRON TRANSPORT; HET: AMP, ZMP, NAI, 3PE, 2MR, PC1, FMN, FME, MYR, AYA, SF4, DCQ, NDP, SEP, CDL; 2.6A {Ovis aries},,,6ZKE_p,33.7931,32.7 SIF-Syn: none /note=start: 322 /note=Gl/Gm favored: both /note=Gap: 3 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=3. Final= -2.4, best score: Yes /note=Q1:S1: yes /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: No functional hits above 90% Probability, top hit had 32.7% probability (cd14363) CDS 756 - 1187 /gene="3" /product="gp3" /function="hypothetical protein" /locus tag="MortySmith_3" /note=Original Glimmer call @bp 759 has strength 7.07; Genemark calls start at 759 /note=SSC: 756-1187 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_3 [Microbacterium phage TinyMiny]],,NCBI, q2:s1 99.3007% 7.50442E-15 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.206, -4.756595489459033, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_3 [Microbacterium phage TinyMiny]],,UAJ16094,47.9532,7.50442E-15 SIF-HHPRED: JAB ; JAB1/Mov34/MPN/PAD-1 ubiquitin protease,,,PF01398.24,66.4336,92.1 SIF-Syn: none /note=start: 756 /note=Gl/Gm favored: neither, but longest orf /note=Gap: -4 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.2 Final= -4.7, best- no but close /note=Q1:S1: yes /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: top hit had 92% probability (pf01398224)- ubiquitin protease family in eukaryotes CDS 1180 - 1641 /gene="4" /product="gp4" /function="terminase, small subunit" /locus tag="MortySmith_4" /note=Original Glimmer call @bp 1180 has strength 12.64; Genemark calls start at 1180 /note=SSC: 1180-1641 CP: yes SCS: both ST: SS BLAST-Start: [terminase small subunit [Microbacterium phage Hager]],,NCBI, q1:s1 100.0% 5.59809E-96 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.895, -4.946058559219759, no F: terminase, small subunit SIF-BLAST: ,,[terminase small subunit [Microbacterium phage Hager]],,UYL85297,96.1538,5.59809E-96 SIF-HHPRED: small terminase subunit; viral genome packaging motor, small terminase, Pseudomonas phage PaP3, DNA BINDING PROTEIN, VIRAL PROTEIN; 3.01A {Pseudomonas virus PaP3},,,6W7T_E,72.549,97.9 SIF-Syn: none /note=start: 1180 /note=Gl/Gm favored: both /note=Gap: -8 /note=CP: all /note=most annotated: yes /note=most conserved: other conserved starts not in our phage /note=SD Z=1.9. Final= -4.9, best- no but close /note=Q1:S1: yes with Aesir and several others /note=SIF-BLASTp: terminase small subunit, phage Hager, eval= e-96, 100% coverage /note=SIF-HHPRED: top hit had 97.9% probability, 72% coverage (6W7T_H) with Pseudomonas phage small terminase CDS 1634 - 1936 /gene="5" /product="gp5" /function="hypothetical protein" /locus tag="MortySmith_5" /note=Original Glimmer call @bp 1634 has strength 9.64; Genemark calls start at 1634 /note=SSC: 1634-1936 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_5 [Microbacterium phage TinyMiny]],,NCBI, q1:s1 97.0% 3.5697E-8 GAP: -8 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.634, -3.389881189012514, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_5 [Microbacterium phage TinyMiny]],,UAJ16096,58.8889,3.5697E-8 SIF-HHPRED: Type IV secretion system unknown protein fragment; Secretion, T4SS, Dot, PROTEIN TRANSPORT;{Legionella pneumophila},,,6X62_EX,71.0,76.0 SIF-Syn: none /note=start: 1634 /note=Gl/Gm favored: both /note=Gap: -8 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.6 Final= -3.4, best- no but best score has large overlap /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: No functional hits above 90% Probability, top hit had 76% probability CDS 1933 - 2079 /gene="6" /product="gp6" /function="hypothetical protein" /locus tag="MortySmith_6" /note=Original Glimmer call @bp 1933 has strength 6.85; Genemark calls start at 1933 /note=SSC: 1933-2079 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_8 [Microbacterium phage TinyMiny]],,NCBI, q6:s8 81.25% 2.30494E-11 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.224, -4.331668843916977, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_8 [Microbacterium phage TinyMiny]],,UAJ16099,73.3333,2.30494E-11 SIF-HHPRED: PPTA ; Protein prenyltransferase alpha subunit repeat,,,PF01239.25,12.5,46.7 SIF-Syn: none /note=start: 1933 /note=Gl/Gm favored: both /note=Gap: -4 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.2 Final= -4, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: No functional hits above 90% Probability, top hit had 46.7% probability CDS 2069 - 2266 /gene="7" /product="gp7" /function="hypothetical protein" /locus tag="MortySmith_7" /note=Original Glimmer call @bp 2069 has strength 5.72; Genemark calls start at 2102 /note=SSC: 2069-2266 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_KARATE_8 [Microbacterium phage Karate]],,NCBI, q1:s1 100.0% 5.93298E-33 GAP: -11 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.129, -4.918506487131662, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_KARATE_8 [Microbacterium phage Karate]],,QLF84332,95.3846,5.93298E-33 SIF-HHPRED: DUF3917 ; Protein of unknown function (DUF3917),,,PF13055.9,13.8462,45.0 SIF-Syn: none /note=start: 2069 /note=Gl/Gm favored: Glimmer /note=Gap: -11 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.12 Final= -4.9, best- no but best has too short of gene /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: No functional hits above 90% Probability, top hit had 45% probability CDS 2256 - 2579 /gene="8" /product="gp8" /function="hypothetical protein" /locus tag="MortySmith_8" /note=Original Glimmer call @bp 2256 has strength 16.37; Genemark calls start at 2256 /note=SSC: 2256-2579 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_9 [Microbacterium phage TinyMiny]],,NCBI, q1:s1 98.1308% 1.1903E-58 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.901, -2.827683592113848, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_9 [Microbacterium phage TinyMiny]],,UAJ16100,88.785,1.1903E-58 SIF-HHPRED: a.238.1.0 (B:5-273) automated matches {Human (Homo sapiens) [TaxId: 9606]},,,d5c5bb1,28.0374,65.5 SIF-Syn: none /note=start: 2256 /note=Gl/Gm favored: both /note=Gap: -11 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.9 Final= -2.8, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: No functional hits above 90% Probability, top hit had 65% probability CDS 2576 - 2839 /gene="9" /product="gp9" /function="hypothetical protein" /locus tag="MortySmith_9" /note=Original Glimmer call @bp 2576 has strength 7.78; Genemark calls start at 2576 /note=SSC: 2576-2839 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_HAUNTER_10 [Microbacterium phage Haunter]],,NCBI, q1:s1 100.0% 5.16644E-55 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.053, -4.692527399714444, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HAUNTER_10 [Microbacterium phage Haunter]],,QPL15024,98.8506,5.16644E-55 SIF-HHPRED: Heterocyst differentiation control protein; single helix, loop packing around, heterocyst development, heterocyst patterning, TRANSCRIPTION; 2.049A {Nostoc},,,4LH9_A,42.5287,52.6 SIF-Syn: none /note=start: 2576 /note=Gl/Gm favored: both /note=Gap: -4 /note=CP: all /note=most annotated: no- does not contain most annotated start /note=most conserved: no /note=SD Z=2 Final= -4.6, best- no but gap is best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: No functional hits above 90% Probability, top hit had 52% probability CDS 2836 - 4296 /gene="10" /product="gp10" /function="terminase, large subunit" /locus tag="MortySmith_10" /note=Original Glimmer call @bp 2836 has strength 11.85; Genemark calls start at 2836 /note=SSC: 2836-4296 CP: yes SCS: both ST: SS BLAST-Start: [terminase [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.222, -2.0895162839948163, yes F: terminase, large subunit SIF-BLAST: ,,[terminase [Microbacterium phage Aesir]],,QNN98576,100.0,0.0 SIF-HHPRED: Large subunit terminase; large terminase, VIRAL PROTEIN; 2.2A {Deep-sea thermophilic phage D6E},,,5OE8_B,91.358,100.0 SIF-Syn: two genes downstream is portal in Aesir /note=start: 2836 /note=Gl/Gm favored: both /note=Gap: -4 /note=CP: all /note=most annotated: yes for cluster EF and most annotated overall is not present in our genome /note=most conserved: yes /note=SD Z=3.2 Final= -2, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: terminase, eval=0 with Aesir terminase, 100% coverage /note=SIF-HHPRED: large subunit terminase, PDB, Bacteriophage T4, 3CPE_A, 90% alignment, 100% probability CDS 4426 - 4515 /gene="11" /product="gp11" /function="hypothetical protein" /locus tag="MortySmith_11" /note=Genemark calls start at 4426 /note=SSC: 4426-4515 CP: yes SCS: genemark ST: NI BLAST-Start: [hypothetical protein SEA_KARATE_11 [Microbacterium phage Karate] ],,NCBI, q1:s27 100.0% 8.19244E-9 GAP: 129 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.979, -2.6013996449736907, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_KARATE_11 [Microbacterium phage Karate] ],,QLF84335,52.7273,8.19244E-9 SIF-HHPRED: Protein fem-1 homolog B,Guanine nucleotide exchange protein SMCR8; ubiquitination E3 ligase, PEPTIDE BINDING PROTEIN; 2.802A {Homo sapiens},,,7EL6_A,96.5517,61.8 SIF-Syn: yes- terminase before and portal after in Aesir /note=start: 4426 /note=Gl/Gm favored: Genemark /note=Gap: 129 /note=CP: all /note=most annotated: does not have it /note=most conserved: only start possible /note=SD Z=2.9 Final= -2.6, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no functional hits with eval below e-7 /note=SIF-HHPRED: No functional hits above 90% Probability, top hit had 52% probability /note=Only 90 aa but if not present would lead to large gap and is called by other cluster EF so kept it CDS 4517 - 6118 /gene="12" /product="gp12" /function="portal protein" /locus tag="MortySmith_12" /note=Original Glimmer call @bp 4517 has strength 13.37; Genemark calls start at 4517 /note=SSC: 4517-6118 CP: yes SCS: both ST: SS BLAST-Start: [portal protein [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.165, -4.9668027763900575, no F: portal protein SIF-BLAST: ,,[portal protein [Microbacterium phage Aesir]],,QNN98578,99.8124,0.0 SIF-HHPRED: PORTAL PROTEIN; BACTERIOPHAGE SPP1, DNA TRANSLOCATION, MOLECULAR MOTOR, VIRAL PORTAL PROTEIN, VIRAL PROTEIN; HET: CA, HG; 3.4A {BACTERIOPHAGE SPP1},,,2JES_Q,87.6173,100.0 SIF-Syn: yes, followed by capsid maturation protease in Aesir /note=start: 4517 /note=Gl/Gm favored: both /note=Gap: 1 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2 Final= -4.9, best- no but best has large gap /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: portal, eval=0 with Aesir portal, 100% coverage /note=SIF-HHPRED: portal protein, PDB, SPP1 phage, 2JES_Q, 87% alignment, 100% probability CDS 6156 - 7571 /gene="13" /product="gp13" /function="capsid maturation protease" /locus tag="MortySmith_13" /note=Original Glimmer call @bp 6156 has strength 11.96; Genemark calls start at 6192 /note=SSC: 6156-7571 CP: yes SCS: both-gl ST: SS BLAST-Start: [capsid maturation protease [Microbacterium phage Anakin] ],,NCBI, q1:s1 100.0% 0.0 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.681, -5.475274199998584, no F: capsid maturation protease SIF-BLAST: ,,[capsid maturation protease [Microbacterium phage Anakin] ],,QDF18066,99.3644,0.0 SIF-HHPRED: Phage_min_cap2 ; Phage minor capsid protein 2,,,PF06152.14,52.8662,99.8 SIF-Syn: yes, after portal and before scaffold protein in Aesir /note=start: 6156 /note=Gl/Gm favored: glimmer only /note=Gap: 38 /note=CP: all /note=most annotated: Yes /note=most conserved: yes for the cluster /note=SD Z=1.7 Final= -5.5, best /note=Q1:S1: yes with Anakin /note=SIF-BLASTp: capsid maturation protease, eval=0 with Anakin, 100% coverage /note=SIF-HHPRED: Phage minor capsid protein 2, Pfam, 52% alignment, 99.8% probability CDS 7697 - 8425 /gene="14" /product="gp14" /function="scaffolding protein" /locus tag="MortySmith_14" /note=Original Glimmer call @bp 7697 has strength 17.47; Genemark calls start at 7697 /note=SSC: 7697-8425 CP: yes SCS: both ST: SS BLAST-Start: [scaffolding protein [Microbacterium phage Anakin] ],,NCBI, q1:s1 100.0% 1.58542E-167 GAP: 125 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.442961286954254, yes F: scaffolding protein SIF-BLAST: ,,[scaffolding protein [Microbacterium phage Anakin] ],,QDF18068,100.0,1.58542E-167 SIF-HHPRED: Scaffold protein; major capsid protein, HK97-like fold, scaffolding protein, procapsid, VIRUS; 3.72A {Staphylococcus phage 80alpha},,,6B0X_f,57.8512,98.9 SIF-Syn: yes, after capsid maturation protease in Aesir /note=start: 7697 /note=Gl/Gm favored: both /note=Gap: 125 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=3 Final= -2.4, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: scaffold, eval=-167 with Anakin, 100% coverage /note=SIF-HHPRED: Scaffold, PDB, 6BOX-f, Staphylococcus phage 80alpha, 57% alignment, 98.9% probability CDS 8461 - 8820 /gene="15" /product="gp15" /function="head fiber protein" /locus tag="MortySmith_15" /note=Original Glimmer call @bp 8461 has strength 15.49; Genemark calls start at 8461 /note=SSC: 8461-8820 CP: yes SCS: both ST: SS BLAST-Start: [minor capsid protein [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 1.26151E-76 GAP: 35 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.583959800616441, yes F: head fiber protein SIF-BLAST: ,,[minor capsid protein [Microbacterium phage Hiddenleaf] ],,QGH73967,100.0,1.26151E-76 SIF-HHPRED: Capsid fiber protein; bacteriophage, phi29, prohead, VIRUS; HET: SO4; 1.8A {Bacillus phage phi29},,,6QYY_E,72.2689,90.9 SIF-Syn: between scaffold and major capsid protein /note=start: 8461 /note=Gl/Gm favored: both /note=Gap: 35 /note=CP: yes /note=most annotated: yes /note=most conserved: yes /note=SD Z=3.1 Final= -2.6, best /note=Q1:S1: yes with Hiddenleaf /note=SIF-BLASTp: minor capsid protein, Hiddenleaf, eval= -76, 100% coverage /note=SIF-HHPRED: Capsid fiber protein, PDB, 6QYY_E, Bacillus phage phi29, 72.3% alignment, 90.9 % probability /note=Note: head fiber protein designation seems more specific than minor capsid protein CDS 8835 - 9986 /gene="16" /product="gp16" /function="major capsid protein" /locus tag="MortySmith_16" /note=Original Glimmer call @bp 8835 has strength 14.53; Genemark calls start at 8835 /note=SSC: 8835-9986 CP: yes SCS: both ST: SS BLAST-Start: [major capsid protein [Microbacterium phage Aesir] ],,NCBI, q1:s1 100.0% 0.0 GAP: 14 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.144, -2.905625766045924, yes F: major capsid protein SIF-BLAST: ,,[major capsid protein [Microbacterium phage Aesir] ],,QNN98583,100.0,0.0 SIF-HHPRED: Major capsid protein; capsid, HK97-fold, dsDNA-phage, icosahedral, VIRUS; 3.8A {Escherichia phage T5},,,6OMC_A,78.5901,98.6 SIF-Syn: yes scaffolding and head fiber protein upstream and minor tail proteins a few genes down in other EF phages /note=start: 8835 /note=Gl/Gm favored: both /note=Gap: 14 /note=CP: yes /note=most annotated: yes /note=most conserved: yes /note=SD Z=3.1 Final= -2.9, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: major capsid, eval=0 with Aesir, 100% coverage /note=SIF-HHPRED: major capsid, PDB, 6OMC_A, Ecoli T5, 78.6% alignment, 98.6% probability CDS 10060 - 10443 /gene="17" /product="gp17" /function="hypothetical protein" /locus tag="MortySmith_17" /note=Original Glimmer call @bp 10060 has strength 19.81; Genemark calls start at 10060 /note=SSC: 10060-10443 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_20 [Microbacterium phage TinyMiny]],,NCBI, q1:s1 96.8504% 3.26365E-15 GAP: 73 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.144, -2.3335289980954053, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_20 [Microbacterium phage TinyMiny]],,UAJ16111,52.8662,3.26365E-15 SIF-HHPRED: a.140.2.1 (A:1-37) Heterogeneous nuclear ribonucleoprotein U-like protein 1 {Human (Homo sapiens) [TaxId: 9606]},,,d1zrja1,26.7717,97.9 SIF-Syn: none /note=start: 10060 /note=Gl/Gm favored: both /note=Gap: 73 /note=CP: yes /note=most annotated: yes /note=most conserved: yes /note=SD Z=3.1 Final= -2.3, best /note=Q1:S1: yes with DannyDe /note=SIF-BLASTp: no hit below eval=e-7 /note=SIF-HHPRED: no functional hits with probability over 90%, Top Hits over 90% were with eukaryotic organisms CDS 10521 - 10829 /gene="18" /product="gp18" /function="hypothetical protein" /locus tag="MortySmith_18" /note=Original Glimmer call @bp 10521 has strength 15.82; Genemark calls start at 10521 /note=SSC: 10521-10829 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_21 [Microbacterium phage TinyMiny] ],,NCBI, q1:s1 100.0% 1.67075E-17 GAP: 77 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.807, -2.9625409806968013, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_21 [Microbacterium phage TinyMiny] ],,UAJ16112,59.0476,1.67075E-17 SIF-HHPRED: Adaptor protein gp12; PHAGE, PHAGE TAIL, CRYOEM, VIRUS, VIRAL PROTEIN; 3.6A {Helicobacter phage KHP30},,,7WMP_t,33.3333,80.2 SIF-Syn: none /note=start: 10521 /note=Gl/Gm favored: both /note=Gap: 77 /note=CP: yes /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.8 Final= -2.9, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no hits below eval= -7 /note=SIF-HHPRED: no functional hits above 90% prob, best was 80% with H pylori phage tail protein CDS 10831 - 11199 /gene="19" /product="gp19" /function="head-to-tail stopper" /locus tag="MortySmith_19" /note=Original Glimmer call @bp 10831 has strength 14.73; Genemark calls start at 10831 /note=SSC: 10831-11199 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_ANNASERENA_21 [Microbacterium phage AnnaSerena] ],,NCBI, q1:s1 100.0% 6.67325E-79 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.259, -6.28590320515415, no F: head-to-tail stopper SIF-BLAST: ,,[hypothetical protein SEA_ANNASERENA_21 [Microbacterium phage AnnaSerena] ],,AWY04477,97.541,6.67325E-79 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,84.4262,94.9 SIF-Syn: yes before tail terminator in DannyDe /note=start: 10831 /note=Gl/Gm favored: both /note=Gap: 1 /note=CP: all /note=most annotated: Yes /note=most conserved: Yes /note=SD Z=1.3 Final= -6.3, not best but others have too big of a gap /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: head to tail stopper, eval=-79 with DannyDe, 100% coverage /note=SIF-HHPRED: head completion protein, PDB 5A21_E, Bacillus SPP1, 84% alignment, 94.9% probability CDS 11189 - 11575 /gene="20" /product="gp20" /function="hypothetical protein" /locus tag="MortySmith_20" /note=Original Glimmer call @bp 11189 has strength 4.56; Genemark calls start at 11189 /note=SSC: 11189-11575 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 6.08722E-88 GAP: -11 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.129, -4.4536196888290105, no F: hypothetical protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Aesir]],,QNN98587,100.0,6.08722E-88 SIF-HHPRED: HK97-gp10_like ; Bacteriophage HK97-gp10, putative tail-component,,,PF04883.15,62.5,99.3 SIF-Syn: None /note=start: 11189 /note=Gl/Gm favored: both /note=Gap: -11 /note=CP: all /note=most annotated: Yes /note=most conserved: yes /note=SD Z=2.1 Final= -4.5, not best but best gap /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: minor tail protein, eval=-88 with Aesir, 100% coverage /note=SIF-HHPRED: Putative tail component, Pf004833.15, 62.5% alignment, 99.3% probability /note=HHpred not strong enough to call minor tail protein even though several EF phages call it minor tail protein CDS 11572 - 12000 /gene="21" /product="gp21" /function="tail terminator" /locus tag="MortySmith_21" /note=Original Glimmer call @bp 11572 has strength 9.89; Genemark calls start at 11572 /note=SSC: 11572-12000 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_22 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 3.5896E-96 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.983, -4.760712055653865, no F: tail terminator SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_22 [Microbacterium phage Hiddenleaf] ],,QGH73973,99.2958,3.5896E-96 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,97.8873,98.5 SIF-Syn: Yes, two downstream of head to tail stopper in Aesir /note=start: 11572 /note=Gl/Gm favored: both /note=Gap: -4 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.0 Final= -4.8, not best but has best overlap and longest orf /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: tail terminator eval=-96 with DannyDe, 100% coverage /note=SIF-HHPRED: tail to head joining protein, 5A21_G, Bacillus phage SPP1, 97.8% alignment, 98.5% probability CDS 12036 - 12407 /gene="22" /product="gp22" /function="hypothetical protein" /locus tag="MortySmith_22" /note=Original Glimmer call @bp 12036 has strength 17.05; Genemark calls start at 12036 /note=SSC: 12036-12407 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_TINYMINY_25 [Microbacterium phage TinyMiny]],,NCBI, q51:s38 52.8455% 7.99433E-17 GAP: 35 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.286, -1.953940808934884, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_TINYMINY_25 [Microbacterium phage TinyMiny]],,UAJ16116,43.1193,7.99433E-17 SIF-HHPRED: DUF1838 ; Protein of unknown function (DUF1838),,,PF08894.14,34.1463,61.9 SIF-Syn: none /note=start: 12036 /note=Gl/Gm favored: both /note=Gap: 35 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=3.3 Final= -1.9, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no hits below eval= -7 /note=SIF-HHPRED: no functional hits with prob above 90%, highest was 61.9% probability CDS 12410 - 12613 /gene="23" /product="gp23" /function="hypothetical protein" /locus tag="MortySmith_23" /note=Genemark calls start at 12410 /note=SSC: 12410-12613 CP: yes SCS: genemark ST: SS BLAST-Start: [gp27 [Mycobacterium phage Konstantine] ],,NCBI, q2:s3 91.0448% 6.75122E-9 GAP: 2 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.572, -5.704875679872614, no F: hypothetical protein SIF-BLAST: ,,[gp27 [Mycobacterium phage Konstantine] ],,YP_002242084,59.1549,6.75122E-9 SIF-HHPRED: Transcription initiation factor TFIID subunit 14; YEATS domain, Ig fold, Nucleus, NUCLEAR PROTEIN; HET: PGE; 1.7A {Saccharomyces cerevisiae},,,3QRL_A,71.6418,55.9 SIF-Syn: none /note=start: 12410 /note=Gl/Gm favored: genemark /note=Gap: 2 /note=CP: all but very little /note=most annotated: yes /note=most conserved: yes /note=SD Z=1.6 Final= -5.7, not best but best gap /note=Q1:S1: yes with Krampus /note=SIF-BLASTp: no functional hits below eval= e-7 /note=SIF-HHPRED: no functional hits above 90% probability, highest was 56% CDS 12600 - 13178 /gene="24" /product="gp24" /function="major tail protein" /locus tag="MortySmith_24" /note=Original Glimmer call @bp 12600 has strength 14.24; Genemark calls start at 12600 /note=SSC: 12600-13178 CP: yes SCS: both ST: SS BLAST-Start: [major tail protein [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 1.02103E-137 GAP: -14 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.876, -2.8170432709374893, yes F: major tail protein SIF-BLAST: ,,[major tail protein [Microbacterium phage Aesir]],,QNN98591,100.0,1.02103E-137 SIF-HHPRED: Phage_TTP_1 ; Phage tail tube protein,,,PF04630.15,86.4583,99.9 SIF-Syn: yes with multiple EF phages upstream of tail assembly chaperone /note=start: 12600 /note=Gl/Gm favored: both /note=Gap: -14 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.9 Final= -2.8, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: major tail protein, eval=-137 with Aesir, 100% coverage /note=SIF-HHPRED: Major tail protein, PDB 6XGR_M, phage sp., 97.4% alignment, 97.5% probability CDS 13216 - 13818 /gene="25" /product="gp25" /function="tail assembly chaperone" /locus tag="MortySmith_25" /note=Original Glimmer call @bp 13216 has strength 14.1; Genemark calls start at 13216 /note=SSC: 13216-13818 CP: yes SCS: both ST: SS BLAST-Start: [tail assembly chaperone [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 2.11191E-141 GAP: 37 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.297, -1.993391246735709, yes F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Aesir]],,QNN98592,99.5,2.11191E-141 SIF-HHPRED: PsbW; PSII-FCP supercomplex, PLANT PROTEIN; HET: DD6, CLA, OEX, LMG, A86, PL9, HEM, DGD, KC2, KC1, BCR, SQD, LHG, PHO; 3.02A {Chaetoceros gracilis},,,6JLU_w,9.5,13.8 SIF-Syn: yes, downstream of major tail, Upstream of Tape Measure /note=start: 13216 /note=Gl/Gm favored: both /note=Gap: 37 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=3.3 Final= -2.0, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: tail assembly chaperone, eval=-141 with Aesir, 100% coverage /note=SIF-HHPRED: no functional hits above 90%, only hit with plant protein 13% probability /note=Note: Frameshift was called a -2 for Aesir (adding in an amino acid) and others called it a +1 CDS 13769 - 14044 /gene="26" /product="gp26" /function="tail assembly chaperone" /locus tag="MortySmith_26" /note=Original Glimmer call @bp 13769 has strength 2.95 /note=SSC: 13769-14044 CP: yes SCS: glimmer ST: NI BLAST-Start: [tail assembly chaperone [Microbacterium phage Rachella]],,NCBI, q1:s1 100.0% 1.38954E-58 GAP: -50 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.602, -6.028440224479473, no F: tail assembly chaperone SIF-BLAST: ,,[tail assembly chaperone [Microbacterium phage Rachella]],,QCQ57390,98.9011,1.38954E-58 SIF-HHPRED: LLCFC1 ; LLLL and CFNLAS motif-containing protein 1,,,PF15838.8,35.1648,69.0 SIF-Syn: between major tail protein and tapemeasure in Aesir /note=start: see previous gene (second half of tail assembly chaperone) /note=Gl/Gm favored: see previous gene /note=Gap: see previous gene /note=CP: all /note=most annotated: see previous gene /note=most conserved: see previous gene /note=SD see previous gene /note=Q1:S1: see previous gene /note=SIF-BLASTp: tail assembly chaperone, Rachella, eval: e-58, 99% Alignment /note=SIF-HHPRED: no functional hit above 90%, top hit: 69% /note=Frame shift (-2) with previous gene at postion 13790. CDS 14047 - 16923 /gene="27" /product="gp27" /function="tape measure protein" /locus tag="MortySmith_27" /note=Original Glimmer call @bp 14047 has strength 12.44; Genemark calls start at 14047 /note=SSC: 14047-16923 CP: yes SCS: both ST: SS BLAST-Start: [tape measure protein [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: 2 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.255, -4.125189544139167, no F: tape measure protein SIF-BLAST: ,,[tape measure protein [Microbacterium phage Aesir]],,QNN98594,98.8518,0.0 SIF-HHPRED: Tape Measure Protein, gp57; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_AF,95.0939,99.8 SIF-Syn: yes, Downstream of Tail Assembly Chaperone, Upstream of Minor Tail /note=start: 14047 /note=Gl/Gm favored: both /note=Gap: 2 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=2.3 Final= -4.1, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: tape measure, eval=-0 with Aesir, 100% coverage /note=SIF-HHPRED: Tape measure, PDB 6V8I_AF, Staphylococcus phage 80alpha, 95% alignment, 99.8% probability CDS 16923 - 17813 /gene="28" /product="gp28" /function="minor tail protein" /locus tag="MortySmith_28" /note=Original Glimmer call @bp 16923 has strength 10.63; Genemark calls start at 16923 /note=SSC: 16923-17813 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.133, -2.417348306996335, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Aesir]],,QNN98595,100.0,0.0 SIF-HHPRED: Distal Tail Protein, gp58; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_BD,97.973,100.0 SIF-Syn: yes, Downstream of Tape Measure, Upstream of Minor Tail /note=start: 16923 /note=Gl/Gm favored: both /note=Gap: -1 /note=CP: all /note=most annotated: Yes /note=most conserved: yes /note=SD Z=3.1 Final= -2.4, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: minor tail protein, eval=0 with Aesir, 100% coverage /note=SIF-HHPRED: distal tail protein, PDB 6V8I_BD, Staph phage 80alpha, 97.9% coverage, 100% probability CDS 17815 - 19581 /gene="29" /product="gp29" /function="minor tail protein" /locus tag="MortySmith_29" /note=Original Glimmer call @bp 17815 has strength 9.28; Genemark calls start at 17815 /note=SSC: 17815-19581 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage FreddieHg] ],,NCBI, q1:s1 100.0% 0.0 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.923, -4.887586077132851, no F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage FreddieHg] ],,QNJ55652,95.9253,0.0 SIF-HHPRED: Tail-Associated Lysin, gp59; phage tail, tail tip, tape measure protein, VIRAL PROTEIN; 3.7A {Staphylococcus virus 80alpha},,,6V8I_CE,61.5646,99.8 SIF-Syn: yes between two minor tail proteins with FreddieHg /note=start: 17815 /note=Gl/Gm favored: both /note=Gap: 1 /note=CP: all /note=most annotated: no do not have /note=most conserved: yes /note=SD Z=1.9 Final= -4.9, not best but the best gap /note=Q1:S1: yes with FreddieHg /note=SIF-BLASTp: minor tail protein, eval=0 with FreddyHg, 100% coverage /note=SIF-HHPRED: tail associated lysin, PDB 6V8I_CE, Staph phage 80alpha, 61.6% coverage, 99.8% probability CDS 19625 - 20569 /gene="30" /product="gp30" /function="minor tail protein" /locus tag="MortySmith_30" /note=Original Glimmer call @bp 19625 has strength 8.86; Genemark calls start at 19625 /note=SSC: 19625-20569 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage DannyDe]],,NCBI, q1:s1 100.0% 0.0 GAP: 43 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.133, -2.2763497933341483, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage DannyDe]],,QPX61875,99.0446,0.0 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,49.3631,99.8 SIF-Syn: yes between two minor tail proteins in DannyDe /note=start: 19625 /note=Gl/Gm favored: both /note=Gap: 43 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=3.1 Final= -2.3, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: minor tail protein, eval=0 with DannyDe, 100% coverage /note=SIF-HHPRED: receptor binding protein, PDB 4L9B_A, lactococcus phage, 49.4% coverage, 99.8% probability CDS 20579 - 21391 /gene="31" /product="gp31" /function="minor tail protein" /locus tag="MortySmith_31" /note=Original Glimmer call @bp 20579 has strength 7.68; Genemark calls start at 20579 /note=SSC: 20579-21391 CP: yes SCS: both ST: SS BLAST-Start: [minor tail protein [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: 9 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.042, -4.654324162979347, yes F: minor tail protein SIF-BLAST: ,,[minor tail protein [Microbacterium phage Aesir]],,QNN98598,99.6296,0.0 SIF-HHPRED: DUF859 ; Siphovirus protein of unknown function (DUF859),,,PF05895.15,43.7037,99.2 SIF-Syn: yes between tapemeasure and endolysin in Aesir /note=start: 20579 /note=Gl/Gm favored: both /note=Gap: 9 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=2.0 Final= -4.7, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: minor tail protein, eval=0 with Aesir, 100% coverage /note=SIF-HHPRED: no functional hits above 90% with phage or bacterial proteins, top 250 hits all over 90% with eukaryotic receptor proteins /note=Note: SEA forum post indicates that genes between tapemeasure and endolysiin encode minor tail proteins CDS 21413 - 21748 /gene="32" /product="gp32" /function="minor tail protein" /locus tag="MortySmith_32" /note=Original Glimmer call @bp 21413 has strength 15.22; Genemark calls start at 21413 /note=SSC: 21413-21748 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_33 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 8.08786E-75 GAP: 21 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.19, -2.2364030944336752, yes F: minor tail protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_33 [Microbacterium phage Aesir]],,QNN98599,100.0,8.08786E-75 SIF-HHPRED: DUF6651 ; Family of unknown function (DUF6651),,,PF20356.1,58.5586,72.4 SIF-Syn: between tapemeasure and endolysin in region with other minor tail proteins /note=start: 21413 /note=Gl/Gm favored: both /note=Gap: 21 /note=CP: all /note=most annotated: yes /note=most conserved: yes /note=SD Z=3.2 Final= -2.2, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no hits below eval= e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 72.4% /note=Note: SEA forum post indicates that genes between tapemeasure and endolysiin encode minor tail proteins CDS 21753 - 22877 /gene="33" /product="gp33" /function="endolysin" /locus tag="MortySmith_33" /note=Original Glimmer call @bp 21753 has strength 10.72; Genemark calls start at 21753 /note=SSC: 21753-22877 CP: yes SCS: both ST: NI BLAST-Start: [lysin A [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 0.0 GAP: 4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.001, -4.741344217713455, no F: endolysin SIF-BLAST: ,,[lysin A [Microbacterium phage Hiddenleaf] ],,QGH73985,100.0,0.0 SIF-HHPRED: d.65.1.5 (B:2-149) L-alanyl-D-glutamate peptidase Ply {Listeria phage A500 [TaxId: 40522]},,,d1xp2b1,40.9091,99.6 SIF-Syn: yes holin is 3 downstream in Aesir /note=start: 21753 /note=Gl/Gm favored: both /note=Gap: 4 /note=CP: all /note=most annotated: no, doesn`t contain /note=most conserved: yes for cluster /note=SD Z=2 Final= -4.7, not best but LOR /note=Q1:S1: yes with HiddenLeaf /note=SIF-BLASTp: lysin A, HiddenLeaf, 100% coverage and eval= 0 /note=SIF-HHPRED: endolysin, Bacillus phage B4, PDB 6AKV_A, 99.1% prob, coverage 37% CDS 22946 - 23491 /gene="34" /product="gp34" /function="membrane protein" /locus tag="MortySmith_34" /note=Original Glimmer call @bp 22946 has strength 7.18; Genemark calls start at 22946 /note=SSC: 22946-23491 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 1.78171E-123 GAP: 68 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.15, -4.426679849915311, no F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Hiddenleaf] ],,QGH73986,99.4475,1.78171E-123 SIF-HHPRED: SHR3_chaperone ; ER membrane protein SH3,,,PF08229.14,63.5359,76.2 SIF-Syn: yes downstream of lysin A and 2 upstream of holin in Aesir /note=start: 22946 /note=Gl/Gm favored: both /note=Gap: 68 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=2.2 Final= -4.4, best /note=Q1:S1: yes with HiddenLeaf /note=SIF-BLASTp: membrane protein, Hidden leaf, 100% coverage, eval= e-123 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 76% with ER membrane protein pfam /note=TmHHm: 4 TMHs CDS 23488 - 23829 /gene="35" /product="gp35" /function="membrane protein" /locus tag="MortySmith_35" /note=Original Glimmer call @bp 23488 has strength 13.23; Genemark calls start at 23488 /note=SSC: 23488-23829 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Rachella]],,NCBI, q1:s1 100.0% 1.71966E-70 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.585, -3.430952136556091, no F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Rachella]],,QCQ57399,98.2143,1.71966E-70 SIF-HHPRED: LapA_dom ; Lipopolysaccharide assembly protein A domain,,,PF06305.14,32.7434,87.7 SIF-Syn: yes, 2 downstream of lysin A, Upstream of holin in Aesir /note=start: 23488 /note=Gl/Gm favored: both /note=Gap: -4 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=2.5 Final= -3.4, best /note=Q1:S1: yes with Rachella /note=SIF-BLASTp: membrane protein, Rachella, 100% coverage, eval= e-70 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 87% /note=only one TMH called and SOSUI called it a membrane protein CDS 23859 - 24260 /gene="36" /product="gp36" /function="holin" /locus tag="MortySmith_36" /note=Original Glimmer call @bp 23859 has strength 15.01; Genemark calls start at 23859 /note=SSC: 23859-24260 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 1.33412E-85 GAP: 29 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.442961286954254, yes F: holin SIF-BLAST: ,,[membrane protein [Microbacterium phage Hiddenleaf] ],,QGH73988,100.0,1.33412E-85 SIF-HHPRED: DUF2279 ; Predicted periplasmic lipoprotein (DUF2279),,,PF10043.12,54.8872,89.0 SIF-Syn: yes most cluster EF call the third gene downstream of lysin the holin gene, downstream of membrane protein /note=start: 23859 /note=Gl/Gm favored: both /note=Gap: 29 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=3.1 Final= -2.4, best /note=Q1:S1: yes with Rachella /note=SIF-BLASTp: Holin protein, Aesir, 100% coverage, eval= e-85 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 89% /note=3 TMHs CDS 24387 - 24977 /gene="37" /product="gp37" /function="hypothetical protein" /locus tag="MortySmith_37" /note=Original Glimmer call @bp 24387 has strength 12.15; Genemark calls start at 24387 /note=SSC: 24387-24977 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_39 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 8.22161E-142 GAP: 126 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.807, -3.0248543014571307, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_39 [Microbacterium phage Hiddenleaf] ],,QGH73990,99.4898,8.22161E-142 SIF-HHPRED: DUF6011 ; Family of unknown function (DUF6011),,,PF19474.2,17.3469,98.9 SIF-Syn: none /note=start: 24387 /note=Gl/Gm favored: both /note=Gap: 126, LORF /note=CP: all /note=most annotated: Yes /note=most conserved: yes for cluster /note=SD Z=2.8 Final= -3.0, best /note=Q1:S1: yes with Hidden leaf /note=SIF-BLASTp: no hits below eval= e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 98% with DUF CDS 24974 - 26881 /gene="38" /product="gp38" /function="DNA helicase" /locus tag="MortySmith_38" /note=Original Glimmer call @bp 24974 has strength 11.37; Genemark calls start at 25037 /note=SSC: 24974-26881 CP: yes SCS: both-gl ST: NI BLAST-Start: [helicase [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.473, -4.194122423817307, no F: DNA helicase SIF-BLAST: ,,[helicase [Microbacterium phage Aesir]],,QNN98605,100.0,0.0 SIF-HHPRED: ATP-dependent DNA helicase uvsW; ATP-dependant helicase, T4-bacteriophage, Recombination, HYDROLASE; 2.7A {Enterobacteria phage T4},,,2OCA_A,82.5197,100.0 SIF-Syn: yes, downstream of holin in EF phages /note=Start: 522 /note=Gl/Gm favored: Yes /note=Gap: -4 /note=Cp: Yes /note=Most Annotated: does not have most annotated /note=Most Conserved: Yes for our cluster /note=SD: Z = 2.4 Final = -4.1, best /note=Q1s1: yes /note=SIF-BLASTp: helicase, evalue: 0, 100% coverage, with Aesir /note=SIF-HHPRED: DNA helicase, 2OCA_A, Enterobacteria phage T4, 100% probability, 82.5% alignment CDS 26881 - 27153 /gene="39" /product="gp39" /function="membrane protein" /locus tag="MortySmith_39" /note=Original Glimmer call @bp 26881 has strength 8.63; Genemark calls start at 26881 /note=SSC: 26881-27153 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_40 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 5.38697E-58 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.133, -2.338663114094478, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_40 [Microbacterium phage Aesir]],,QNN98606,100.0,5.38697E-58 SIF-HHPRED: DUF6479 ; Family of unknown function (DUF6479),,,PF20087.2,64.4444,78.8 SIF-Syn: yes this pham downstream of helicase in many EF phages /note=start: 26881 /note=Gl/Gm favored: both /note=Gap: -1 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=3.1 Final= -2.4, best /note=Q1:S1: yes /note=SIF-BLASTp: no hits above eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 78% /note=only one TMH called and SOSUI called it a membrane protein CDS 27276 - 27806 /gene="40" /product="gp40" /function="hypothetical protein" /locus tag="MortySmith_40" /note=Original Glimmer call @bp 27276 has strength 14.83; Genemark calls start at 27276 /note=SSC: 27276-27806 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_41 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 3.12334E-110 GAP: 122 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -3.095100142625534, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_41 [Microbacterium phage Aesir]],,QNN98607,99.4318,3.12334E-110 SIF-HHPRED: HTH_ABP1_N ; Fission yeast centromere protein N-terminal domain,,,PF18107.4,26.7045,90.0 SIF-Syn: none /note=start: 27276 /note=Gl/Gm favored: both /note=Gap: 122 /note=CP: all /note=most annotated: Yes /note=most conserved: yes /note=SD Z=3 Final= -3.1, best /note=Q1:S1: yes /note=SIF-BLASTp: no hits above eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 90% with yeast CDS 27877 - 29034 /gene="41" /product="gp41" /function="RecB-like exonuclease/helicase" /locus tag="MortySmith_41" /note=Original Glimmer call @bp 27877 has strength 12.0; Genemark calls start at 27898 /note=SSC: 27877-29034 CP: yes SCS: both-gl ST: SS BLAST-Start: [exonuclease [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 0.0 GAP: 70 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -2.442961286954254, yes F: RecB-like exonuclease/helicase SIF-BLAST: ,,[exonuclease [Microbacterium phage Hiddenleaf] ],,QGH73994,98.1333,0.0 SIF-HHPRED: ATP-dependent DNA helicase (UvrD/REP); DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; 3.5A {Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)},,,6PPU_A,91.9481,99.8 SIF-Syn: yes two genes upstream of RecA-like DNA recombinase in HiddenLeaf /note=start: 27877 /note=Gl/Gm favored: only glimmer /note=Gap: 70 /note=CP: all /note=most annotated: does not have /note=most conserved: yes for cluster /note=SD Z=3.1 Final= -2.4, best /note=Q1:S1: yes /note=SIF-BLASTp: exonuclease, HiddenLeaf, coverage= 100 %, eval+0 /note=SIF-HHPRED: DNA binding protein- helicase, M. smegmatis, 6PPU_N, 99.8% prob, 91% coverage /note=Note: has both exonuclease and helicase based on HHpred CDS 29034 - 29204 /gene="42" /product="gp42" /function="hypothetical protein" /locus tag="MortySmith_42" /note=Original Glimmer call @bp 29034 has strength 18.28; Genemark calls start at 29034 /note=SSC: 29034-29204 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT40_gp44 [Microbacterium phage Krampus] ],,NCBI, q1:s1 100.0% 2.59883E-31 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.086, -4.482213237254482, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT40_gp44 [Microbacterium phage Krampus] ],,YP_009802634,100.0,2.59883E-31 SIF-HHPRED: a.137.12.1 (C:) Glu-tRNAGln amidotransferase C subunit, GatC {Staphylococcus aureus [TaxId: 158878]},,,d3ip4c_,60.7143,60.1 SIF-Syn: none /note=start: 29034 /note=Gl/Gm favored: both /note=Gap: -1 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=2.1 Final= -4.5, best /note=Q1:S1: yes with Krampus /note=SIF-BLASTp: no functional hits above eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 60% CDS 29204 - 30049 /gene="43" /product="gp43" /function="RecA-like DNA recombinase" /locus tag="MortySmith_43" /note=Original Glimmer call @bp 29204 has strength 14.56; Genemark calls start at 29204 /note=SSC: 29204-30049 CP: yes SCS: both ST: SS BLAST-Start: [RecA-like DNA recombinase [Microbacterium phage Aesir] ],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.133, -2.356391881054909, yes F: RecA-like DNA recombinase SIF-BLAST: ,,[RecA-like DNA recombinase [Microbacterium phage Aesir] ],,QNN98610,100.0,0.0 SIF-HHPRED: Protein RecA, 1st part, 2nd part; HOMOLOGOUS RECOMBINATION, DNA REPAIR, ATPASE, RECOMBINASE, DNA BINDING PROTEIN, PLOOP CONTAINING NTPASE FOLD, ATP BINDING, HYDROLYSIS; HET: FLC, EDO; 2.3A {Mycobacterium tuberculosis} SCOP: d.48.1.0, c.37.1.11,,,4PPF_A,74.7331,99.3 SIF-Syn: yes downstream of exonuclease and two upstream of DNA primase/helicase in Aesir /note=start: 29204 /note=Gl/Gm favored: both /note=Gap: -1 /note=CP: all /note=most annotated: Yes /note=most conserved: yes for cluster /note=SD Z=3.1 Final= -2.4, best /note=Q1:S1: yes /note=SIF-BLASTp: RecA-like DNA recombinase, Aesir, 100% coverage, eval= 0 /note=SIF-HHPRED: RecA recombinase, 4PPF_A, M. tuberculosis, 99.3% prob, 75% coverage CDS 30049 - 31080 /gene="44" /product="gp44" /function="hypothetical protein" /locus tag="MortySmith_44" /note=Original Glimmer call @bp 30049 has strength 21.02; Genemark calls start at 30049 /note=SSC: 30049-31080 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_45 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.958, -2.996490344739583, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_45 [Microbacterium phage Aesir]],,QNN98611,100.0,0.0 SIF-HHPRED: U3 small nucleolar RNA-associated protein 5; ribosome assembly, 90S to pre-40S transition, cryo-EM, Dhr1, RIBOSOME; HET: GTP; 3.2A {Saccharomyces cerevisiae S288C},,,6LQP_A5,34.6939,95.5 SIF-Syn: none /note=start: 30049 /note=Gl/Gm favored: both /note=Gap: -1 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=3 Final= -3, best /note=Q1:S1: yes /note=SIF-BLASTp: no functional hits above eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hits with over 90% probability with eukaryotic proteins CDS 31568 - 34453 /gene="45" /product="gp45" /function="DNA primase/helicase" /locus tag="MortySmith_45" /note=Original Glimmer call @bp 31568 has strength 15.92; Genemark calls start at 31568 /note=SSC: 31568-34453 CP: yes SCS: both ST: SS BLAST-Start: [DNA primase/helicase [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: 487 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -2.5052746077145835, yes F: DNA primase/helicase SIF-BLAST: ,,[DNA primase/helicase [Microbacterium phage Aesir]],,QNN98612,100.0,0.0 SIF-HHPRED: DNA primase/helicase; helicase, ATPase, hexamer, DNA replication, HYDROLASE, TRANSFERASE-DNA complex; HET: TTP; 3.2A {Enterobacteria phage T7},,,6N7I_D,30.6972,99.8 SIF-Syn: two downstream of RecA-like recombinase in Aesir /note=start: 31568 /note=Gl/Gm favored: both /note=Gap: 487 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z=3.1 Final= -2.5, best /note=Q1:S1: yes /note=SIF-BLASTp: DNA primase/helicase, Aesir, 100% coverage, eval= 0 /note=SIF-HHPRED: DNA primase/helicase, phage T7, 99.8% prob, only 30% coverage CDS 34450 - 34659 /gene="46" /product="gp46" /function="hypothetical protein" /locus tag="MortySmith_46" /note=Original Glimmer call @bp 34450 has strength 9.35; Genemark calls start at 34450 /note=SSC: 34450-34659 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_FREDDIEHG_48 [Microbacterium phage FreddieHg] ],,NCBI, q1:s1 100.0% 3.88891E-41 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.805, -3.875201829906135, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_FREDDIEHG_48 [Microbacterium phage FreddieHg] ],,QNJ55670,100.0,3.88891E-41 SIF-HHPRED: Cytosolic 5`-nucleotidase 3; SUBSTRATE COMPLEX, HAD-like, NUCLEOTIDASE, PROTEIN BINDING; HET: U5P; 1.74A {Mus musculus} SCOP: l.1.1.1, c.108.1.21,,,4FE3_A,88.4058,82.5 SIF-Syn: none /note=start: 34450 /note=Gl/Gm favored: both /note=Gap: -4 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD: Z = 2.9, Final = -3.9, not best score, but LORF /note=Q1:S1: yes /note=SIF-BLASTp: no functional hits above eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 82% CDS 34735 - 34968 /gene="47" /product="gp47" /function="hypothetical protein" /locus tag="MortySmith_47" /note=Original Glimmer call @bp 34735 has strength 16.5; Genemark calls start at 34735 /note=SSC: 34735-34968 CP: no SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_48 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 1.28639E-47 GAP: 75 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.807, -2.9625409806968013, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_48 [Microbacterium phage Aesir]],,QNN98614,100.0,1.28639E-47 SIF-HHPRED: Elongation Factor G; L11, EF-G, cryo-EM, 70S E.coli ribosome, GTP state, RIBOSOME; 18.0A {Escherichia coli} SCOP: i.1.1.1,,,1JQS_B,33.7662,43.7 SIF-Syn: none /note=start: 34735 /note=Gl/Gm favored: both /note=Gap: 75 /note=CP: no but small amount missed, but lor /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z: 2.8, Final: -3.0, best /note=Q1:S1: yes with Aesir /note=SIF-BLASTp: no functional hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 43% CDS 35090 - 35623 /gene="48" /product="gp48" /function="hypothetical protein" /locus tag="MortySmith_48" /note=Original Glimmer call @bp 35090 has strength 15.2; Genemark calls start at 35090 /note=SSC: 35090-35623 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT40_gp50 [Microbacterium phage Krampus] ],,NCBI, q1:s1 100.0% 2.03982E-116 GAP: 121 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.807, -2.9625409806968013, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT40_gp50 [Microbacterium phage Krampus] ],,YP_009802640,96.6102,2.03982E-116 SIF-HHPRED: ZapB ; Cell division protein ZapB,,,PF06005.15,25.9887,87.5 SIF-Syn: none /note=start: 35090 /note=Gl/Gm favored: both /note=Gap: 121 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD Z: 2.8, Final: -3.0, best /note=Q1:S1: yes /note=SIF-BLASTp: no functional hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 87.5% CDS 35704 - 36249 /gene="49" /product="gp49" /function="hypothetical protein" /locus tag="MortySmith_49" /note=Original Glimmer call @bp 35704 has strength 10.19; Genemark calls start at 35704 /note=SSC: 35704-36249 CP: yes SCS: both ST: SS BLAST-Start: [endonuclease [Microbacterium phage Neptune] ],,NCBI, q1:s1 100.0% 4.63676E-128 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.807, -3.3136498407041004, yes F: hypothetical protein SIF-BLAST: ,,[endonuclease [Microbacterium phage Neptune] ],,UDG78671,98.895,4.63676E-128 SIF-HHPRED: ENDONUCLEASE V; ENDONUCLEASE; 1.45A {Enterobacteria phage T4} SCOP: a.18.1.1,,,2END_A,43.6464,93.0 SIF-Syn: no /note=start: 35704 /note=Gl/Gm favored: both /note=Gap: 80 /note=CP: all /note=most annotated: yes /note=most conserved: yes for cluster /note=SD : Z= 2.8, final= -3.3, best /note=Q1:S1: yes /note=SIF-BLASTp: endonuclease, Neptune, 100% coverage, eval=e-128 /note=SIF-HHPRED: endonuclease V, 2END_A, phage T4, 93% prob, 44% coverage /note=Note: endonuclease is not listed as a function in the functions list and this HHpred hit does not match any of the specific types of endonucleases found in the functions list. CDS 36246 - 37049 /gene="50" /product="gp50" /function="oxidoreductase" /locus tag="MortySmith_50" /note=Original Glimmer call @bp 36285 has strength 12.37; Genemark calls start at 36285 /note=SSC: 36246-37049 CP: yes SCS: both-cs ST: SS BLAST-Start: [oxidoreductase [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.756, -3.0713502170045657, yes F: oxidoreductase SIF-BLAST: ,,[oxidoreductase [Microbacterium phage Hiddenleaf] ],,QGH74003,99.6255,0.0 SIF-HHPRED: D-Arginine Dehydrogenase; D-Arginine Dehydrogenase, FAD, Imino-Arginine, oxidoreductase; HET: IAR, FAD; 1.06A {Pseudomonas aeruginosa},,,3NYC_A,72.6592,99.4 SIF-Syn: Yes, upstream of ThyX-like thymidylate synthase in cluster EF phages /note=Start: 36246 /note=Glimmer/Genemark favored: no /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: Yes for our cluster /note=SD score: Z= 2.756 Final= -3.071 Best Score /note=Q1:S1 yes /note=Function: oxidoreductase /note=Blast: oxidoreductase, Hiddenleaf, evalue: 0, 100% coverage /note=HHpred: oxidoreductase, 3NYC_A, Pseudomonas aeruginosa, 99.4% probability, 73% alignment CDS 37046 - 38386 /gene="51" /product="gp51" /function="ThyX-like thymidylate synthase" /locus tag="MortySmith_51" /note=Original Glimmer call @bp 37046 has strength 12.81; Genemark calls start at 37046 /note=SSC: 37046-38386 CP: yes SCS: both ST: SS BLAST-Start: [ThyX-like thymidylate synthase [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.644, -5.4744737427355155, no F: ThyX-like thymidylate synthase SIF-BLAST: ,,[ThyX-like thymidylate synthase [Microbacterium phage Aesir]],,QNN98618,99.1031,0.0 SIF-HHPRED: Thymidylate synthase thyX; ThyX, FAD, FdUMP, Flavoprotein, Methyltransferase, Nucleotide biosynthesis, Transferase, Structural Genomics, Seattle Structural Genomics Center for Infectious; HET: FAD, UFP; 1.9A {Mycobacterium tuberculosis},,,3GWC_F,56.7265,100.0 SIF-Syn: Yes, follows oxidoreductase in Aesir /note=Start: 37046 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated Start based on Starterator: Yes (42 out of 56) /note=Most Conserved Start: Yes, 75.7% for our cluster also /note=SD score: Z= 1.644 Final= -5.474. Not the best score, but best gap. /note=Q1:S1 yes /note=Function: ThyX-like thymidylate synthase /note=HHpred: Thymidylate synthase thyX, 3GWC_F, M. tuberculosis, 100% probability, 56.7% alignment /note=Blast: ThyX-like thymidylate synthase, Aesir, evalue: 0, 100% coverage CDS 38383 - 39036 /gene="52" /product="gp52" /function="hypothetical protein" /locus tag="MortySmith_52" /note=Original Glimmer call @bp 38386 has strength 14.37; Genemark calls start at 38386 /note=SSC: 38383-39036 CP: yes SCS: both-cs ST: SS BLAST-Start: [hypothetical protein HOT40_gp54 [Microbacterium phage Krampus] ],,NCBI, q2:s3 99.5392% 1.77131E-143 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -3.493040151297572, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT40_gp54 [Microbacterium phage Krampus] ],,YP_009802644,93.578,1.77131E-143 SIF-HHPRED: DUF1599 ; Nucleotide modification associated domain 1,,,PF07659.14,30.4147,99.7 SIF-Syn: none /note=Start: 38383 /note=Glimmer/Genemark favored: no /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved Start: Yes /note=SD score: Z= 3.054 Final= -3.493 Not best but close and called by starterator /note=Q1:S1 yes /note=Function: NKF /note=SIF-HHPRED: hit on nucleotide modification associated domain, 99.7% probability but 30% alignment /note=SIF-BLASTp: no functional hits below eval=e-7 CDS 39036 - 39263 /gene="53" /product="gp53" /function="hypothetical protein" /locus tag="MortySmith_53" /note= /note=SSC: 39036-39263 CP: yes SCS: neither ST: NI BLAST-Start: [hypothetical protein SEA_AESIR_54 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 9.7361E-46 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.498, -5.72026482151185, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_54 [Microbacterium phage Aesir]],,QNN98620,100.0,9.7361E-46 SIF-HHPRED: DUF6331 ; Family of unknown function (DUF6331),,,PF19856.2,40.0,70.5 SIF-Syn: none /note=Start: 39036 /note=Glimmer/Genemark favored: no, added gene based on coding potential present and present in other cluster EF phages /note=Gap/Overlap: -1 /note=Contains all CP: Yes /note=Most Annotated: no pham info- added gene based on coding potential present and present in other cluster EF phages /note=Most Conserved Start: no pham info /note=SD score: Z= 1.5 Final= -5.7 /note=Q1:S1 yes /note=Function: NKF /note=SIF-HHPRED: no functional hits above 90% probability, top hit is 70.5% prob /note=SIF-BLASTp: no functional hits below eval=e-7 /note=Note: added gene based on coding potential present and present in other cluster EF phages on phamerator (pham 5064) CDS 39260 - 40297 /gene="54" /product="gp54" /function="DnaE-like DNA polymerase III (alpha)" /locus tag="MortySmith_54" /note=Original Glimmer call @bp 39260 has strength 12.58; Genemark calls start at 39302 /note=SSC: 39260-40297 CP: yes SCS: both-gl ST: SS BLAST-Start: [DnaE-like DNA polymerase III [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 0.0 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.133, -2.2763497933341483, yes F: DnaE-like DNA polymerase III (alpha) SIF-BLAST: ,,[DnaE-like DNA polymerase III [Microbacterium phage Hiddenleaf] ],,QGH74008,99.1304,0.0 SIF-HHPRED: DNA polymerase III alpha subunit; DNA polymerase III, DNA replication, nucleotidyltransferase, Pol beta, PHP, TRANSFERASE; HET: PO4; 2.3A {Escherichia coli},,,2HNH_A,97.3913,100.0 SIF-Syn: upstream of DnaE-like DNA polymerase III /note=Start: 39260 /note=Glimmer/Genemark favored: Glimmer only /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved Start: Yes, 89.4% (for our cluster also) /note=SD score: Z= 3.133 Final= -2.276 Best Score /note=Q1:S1 yes /note=Function: DnaE-like DNA polymerase III (alpha) /note=HHpred: DNA polymerase III alpha subunit, E.coli, 2HNH_A, 100% probability, 97.4% alignment /note=Blast: DnaE-like DNA polymerase III (alpha), Hiddenleaf, evalue: 0, 100% coverage CDS 40308 - 42608 /gene="55" /product="gp55" /function="DnaE-like DNA polymerase III (alpha)" /locus tag="MortySmith_55" /note=Original Glimmer call @bp 40308 has strength 17.46; Genemark calls start at 40314 /note=SSC: 40308-42608 CP: yes SCS: both-gl ST: NI BLAST-Start: [DnaE-like DNA polymerase III alpha [Microbacterium phage Haunter]],,NCBI, q1:s1 100.0% 0.0 GAP: 10 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.44, -4.264132201270119, no F: DnaE-like DNA polymerase III (alpha) SIF-BLAST: ,,[DnaE-like DNA polymerase III alpha [Microbacterium phage Haunter]],,QPL15070,99.8695,0.0 SIF-HHPRED: DNA POLYMERASE III ALPHA; TRANSFERASE, DNA REPLICATION, DNA POLYMERASE III ALPHA, DNA POLYMERASE III BETA, DNA POLYMERASE III EPSILON; 7.3A {ESCHERICHIA COLI K-12},,,5FKW_A,98.564,100.0 SIF-Syn: downstream of DnaE-like DNA polymerase III (alpha) /note=Start: 40308 /note=Glimmer/Genemark favored: glimmer only /note=Gap/Overlap: 10 /note=Contains all CP: Yes /note=Most Annotated: No, Doesn`t contain /note=Most Conserved: yes, in cluster /note=SD score: Z= 2.44 Final= -4.264 Best Score? No, but the best gap. /note=Q1:S1 yes /note=Function: DnaE-like DNA polymerase III (alpha) /note=HHpred: DNA polymerase III alpha, 5FKW_A, E.coli, 100% probability, 98.6% alignment /note=Blast: DnaE-like DNA polymerase III (alpha), Haunter, evalue: 0, 100% coverage, CDS 42725 - 44356 /gene="56" /product="gp56" /function="membrane protein" /locus tag="MortySmith_56" /note=Original Glimmer call @bp 42725 has strength 17.4; Genemark calls start at 42725 /note=SSC: 42725-44356 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: 116 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.115, -3.921180729842956, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Aesir]],,QNN98623,99.4475,0.0 SIF-HHPRED: DUF6520 ; Family of unknown function (DUF6520),,,PF20130.2,5.15654,88.9 SIF-Syn: Yes, Downstream of DnaE-like DNA Polymerase III (Alpha) /note=Start: 42725 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 116 /note=Contains all CP: Yes /note=Most Annotated: Yes (38 out of 47) /note=Most Conserved: Yes, 81.8% (also for our cluster) /note=SD score: Z= 3.115 Final= -3.921 Best Score /note=Q1:S1 1:1 aligned with Aesir /note=Function: Membrane protein /note=HHpred: no probability above 90% (top hit 88.9%) /note=Blast: membrane protein, with Aesir, evalue: 0, 100% coverage /note=TmHHm: 2 TMHs CDS 44479 - 44760 /gene="57" /product="gp57" /function="hypothetical protein" /locus tag="MortySmith_57" /note=Original Glimmer call @bp 44479 has strength 14.86; Genemark calls start at 44479 /note=SSC: 44479-44760 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HAUNTER_59 [Microbacterium phage Haunter]],,NCBI, q1:s1 100.0% 1.3562E-59 GAP: 122 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.807, -2.9625409806968013, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HAUNTER_59 [Microbacterium phage Haunter]],,QPL15072,98.9247,1.3562E-59 SIF-HHPRED: UipA; Native, membrane protein, metal binding, METAL BINDING PROTEIN; 2.343A {Microbacterium sp.},,,7ATH_AAA,97.8495,80.2 SIF-Syn: none /note=Start: 44479 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 122 /note=Contains all CP: Yes /note=Most Annotated: Yes (14 out of 16) /note=Most Conserved: Yes, 100% (cluster 14 times) /note=SD score: Z= 2.807 Final= -2.963 Best Score /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 80% with metal binding protein in Microbacterium ssp CDS 44851 - 46098 /gene="58" /product="gp58" /function="hypothetical protein" /locus tag="MortySmith_58" /note=Original Glimmer call @bp 44851 has strength 12.64; Genemark calls start at 44851 /note=SSC: 44851-46098 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_59 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 0.0 GAP: 90 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.807, -2.9625409806968013, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_59 [Microbacterium phage Aesir]],,QNN98625,99.759,0.0 SIF-HHPRED: CCDC47 ; PAT complex subunit CCDC47,,,PF07946.17,16.1446,69.8 SIF-Syn: None /note=Start: 44851 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 90 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: yes, Called 93.5% of time when present /note=SD score: Z= 2.807 Final= -2.963 Best Score /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top functional hit was 69.8% CDS 46267 - 46914 /gene="59" /product="gp59" /function="hypothetical protein" /locus tag="MortySmith_59" /note=Original Glimmer call @bp 46267 has strength 14.55; Genemark calls start at 46267 /note=SSC: 46267-46914 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_60 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 9.74593E-158 GAP: 168 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.807, -3.0248543014571307, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_60 [Microbacterium phage Aesir]],,QNN98626,99.5349,9.74593E-158 SIF-HHPRED: FYDLN_acid ; Protein of unknown function (FYDLN_acid),,,PF09538.13,23.2558,84.3 SIF-Syn: None /note=Start: 46267 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 168 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: 11.2%, yes for our cluster (14) /note=SD score: Z= 2.807 Final= -3.025 Best Score /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no functional hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 84% CDS 46965 - 47573 /gene="60" /product="gp60" /function="hypothetical protein" /locus tag="MortySmith_60" /note=Original Glimmer call @bp 46965 has strength 20.83; Genemark calls start at 46965 /note=SSC: 46965-47573 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DANNYDE_63 [Microbacterium phage DannyDe]],,NCBI, q1:s1 100.0% 8.09983E-144 GAP: 50 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -2.442961286954254, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DANNYDE_63 [Microbacterium phage DannyDe]],,QPX61907,99.505,8.09983E-144 SIF-HHPRED: Metabotropic GABA-B receptor subtype 3, isoform A; GABAB receptor, Drosophila, coiled-coil, SIGNALING PROTEIN; NMR {Drosophila melanogaster},,,5GWM_B,18.3168,89.0 SIF-Syn: none /note=Start: 46965 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 50 gap (smallest) /note=Contains all CP: Yes /note=Most Annotated: Yes (16 out of 16) /note=Most Conserved: Yes, 100% /note=SD score: Z= 3.054 Final= -2.443 Best Score /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no functional hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 89% CDS 47654 - 47815 /gene="61" /product="gp61" /function="hypothetical protein" /locus tag="MortySmith_61" /note=Original Glimmer call @bp 47654 has strength 23.53; Genemark calls start at 47654 /note=SSC: 47654-47815 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_62 [Microbacterium phage Aesir] ],,NCBI, q1:s1 100.0% 1.92916E-28 GAP: 80 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.807, -3.0425830684175623, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_62 [Microbacterium phage Aesir] ],,QNN98628,100.0,1.92916E-28 SIF-HHPRED: cortexillin I/GCN4 hybrid peptide; coiled-coil, UNKNOWN FUNCTION; 1.17A {N/A} SCOP: h.1.10.1,,,1P9I_A,52.8302,92.8 SIF-Syn: none /note=Start: 47654 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 80 (smallest of two) /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: Yes, 100% /note=SD score: Z= 2.807 Final= -3.043 Best Score /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no functional hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 92.8% probability with protein of unknown function CDS 47815 - 48162 /gene="62" /product="gp62" /function="hypothetical protein" /locus tag="MortySmith_62" /note=Original Glimmer call @bp 47815 has strength 10.0; Genemark calls start at 47815 /note=SSC: 47815-48162 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_63 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 1.04766E-80 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.647, -5.468788754841594, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_63 [Microbacterium phage Aesir]],,QNN98629,100.0,1.04766E-80 SIF-HHPRED: a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: Transcription factor E/IIe-alpha, N-terminal domain,,,SCOP_d1q1ha_,42.6087,94.2 SIF-Syn: none /note=Start: 47815 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -1 overlap /note=Contains all CP: Yes /note=Most Annotated: Yes (16 out of 16) /note=Most Conserved: Yes /note=SD score: Z= 1.647 Final= -5.469 Best Score? Not the best score, but the best gap. /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no relevant functional hits above 90% prob, top hit was 95.8% probability with Solfolobus transcription factor, SCOP_d1q1ha_ CDS 48254 - 48415 /gene="63" /product="gp63" /function="membrane protein" /locus tag="MortySmith_63" /note=Original Glimmer call @bp 48254 has strength 19.65; Genemark calls start at 48254 /note=SSC: 48254-48415 CP: yes SCS: both ST: SS BLAST-Start: [membrane protein [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 6.8922E-26 GAP: 91 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.807, -2.9625409806968013, yes F: membrane protein SIF-BLAST: ,,[membrane protein [Microbacterium phage Hiddenleaf] ],,QGH74017,100.0,6.8922E-26 SIF-HHPRED: DUF6131 ; Family of unknown function (DUF6131),,,PF19626.2,79.2453,95.8 SIF-Syn: none /note=Start: 48254 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 91 (only option) /note=Contains all CP: Yes /note=Most Annotated: Yes (18 out of 18) /note=Most Conserved: Yes /note=SD score: Z= 2.807 Final= -2.963 Best Score? Yes, only option /note=Q1:S1 yes /note=Function: membrane protein /note=SIF-BLASTp: membrane protein, multiple phages, 100% coverage, e-value: e-26 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 95.8% with unknown function, PF19626.2 /note=Number of predicted TMHs: 2 CDS 48412 - 48708 /gene="64" /product="gp64" /function="hypothetical protein" /locus tag="MortySmith_64" /note=Original Glimmer call @bp 48412 has strength 15.11; Genemark calls start at 48412 /note=SSC: 48412-48708 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_67 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 5.20757E-65 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -2.523003374675015, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_67 [Microbacterium phage Hiddenleaf] ],,QGH74018,100.0,5.20757E-65 SIF-HHPRED: d.391.1.0 (B:266-348) automated matches {Escherichia coli [TaxId: 83333]},,,d4xgab2,56.1224,70.3 SIF-Syn: none /note=Start: 48412 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: Yes (16 out of 16) /note=Most Conserved: Yes /note=SD score: Z= 3.054 Final= -2.523 Best Score? Yes, the best score. /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 70.3% CDS 48708 - 49112 /gene="65" /product="gp65" /function="hypothetical protein" /locus tag="MortySmith_65" /note=Original Glimmer call @bp 48708 has strength 11.66; Genemark calls start at 48708 /note=SSC: 48708-49112 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_68 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 1.86041E-92 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.43, -3.8970005018578204, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_68 [Microbacterium phage Hiddenleaf] ],,QGH74019,99.2537,1.86041E-92 SIF-HHPRED: Lipocalin AI-4; lipocalin, Rhodnius, salivary, TRANSPORT PROTEIN; HET: LTX; 1.28A {Rhodnius prolixus},,,5H9N_A,48.5075,69.5 SIF-Syn: none /note=Start: 48708 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -1 /note=Contains all CP: Yes /note=Most Annotated: Yes (16 out of 16) /note=Most Conserved: Yes /note=SD score: Z= 2.43 Final= -3.897 Best Score? Yes, the best score /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 69.5% CDS 49112 - 49453 /gene="66" /product="gp66" /function="membrane protein" /locus tag="MortySmith_66" /note=Original Glimmer call @bp 49112 has strength 9.83; Genemark calls start at 49112 /note=SSC: 49112-49453 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_69 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 2.57302E-75 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -2.794070146961553, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_69 [Microbacterium phage Hiddenleaf] ],,QGH74020,99.115,2.57302E-75 SIF-HHPRED: DUF6480 ; Family of unknown function (DUF6480),,,PF20088.2,39.823,72.5 SIF-Syn: none /note=Start: 49112 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -1 /note=Contains all CP: Yes /note=Most Annotated: Yes (15 out of 16) /note=Most Conserved: Yes /note=SD score: Z= 3.054 Final= -2.794 Best Score? Yes, the best score /note=Q1:S1 yes /note=Function: membrane protein /note=SIF-BLASTp: membrane protein, Chivey, eval= 2.6e-75, 98.2% identity /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 72.5% /note=membrane: 1 TMH predicted by TmHmm and predicted to be membrane protein by SOSUI CDS 49453 - 49575 /gene="67" /product="gp67" /function="hypothetical protein" /locus tag="MortySmith_67" /note=Original Glimmer call @bp 49453 has strength 6.44; Genemark calls start at 49453 /note=SSC: 49453-49575 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_70 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 2.68044E-21 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 1.745, -5.340269015678895, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_70 [Microbacterium phage Hiddenleaf] ],,QGH74021,100.0,2.68044E-21 SIF-HHPRED: g.37.1.1 (A:8-35) automated matches {Human (Homo sapiens) [TaxId: 9606]},,,d2em6a1,50.0,85.7 SIF-Syn: none /note=Start: 49453 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -1 /note=Contains all CP: Yes /note=Most Annotated: Yes (16 out of 16) /note=Most Conserved: Yes /note=SD score: Z= 1.745 Final= -5.340 Best Score? no but best score has big gap /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 85.7% CDS 49575 - 49979 /gene="68" /product="gp68" /function="hypothetical protein" /locus tag="MortySmith_68" /note=Original Glimmer call @bp 49575 has strength 11.17; Genemark calls start at 49575 /note=SSC: 49575-49979 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_DANNYDE_71 [Microbacterium phage DannyDe]],,NCBI, q1:s1 100.0% 1.93887E-93 GAP: -1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.481, -3.790975366313636, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DANNYDE_71 [Microbacterium phage DannyDe]],,QPX61915,100.0,1.93887E-93 SIF-HHPRED: PLDc_Tdp1_2; Catalytic domain, repeat 2, of tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat 2, of Tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.,,,cd09123,5.22388,58.2 SIF-Syn: none /note=Start: 49575 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -1 /note=Contains all CP: Yes /note=Most Annotated: No does not have most annotated /note=Most Conserved: Yes for the cluster EF /note=SD score: Z= 2.481 Final= -3.791 Best Score? yes /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 58.2% CDS 49981 - 50670 /gene="69" /product="gp69" /function="hypothetical protein" /locus tag="MortySmith_69" /note=Original Glimmer call @bp 49981 has strength 13.76; Genemark calls start at 49981 /note=SSC: 49981-50670 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_72 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 1.71742E-162 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.988, -2.6623718267059564, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_72 [Microbacterium phage Hiddenleaf] ],,QGH74023,100.0,1.71742E-162 SIF-HHPRED: MNT REPRESSOR; TRANSCRIPTION REGULATION; NMR {Enterobacteria phage P22} SCOP: a.43.1.1,,,1MNT_B,27.5109,64.8 SIF-Syn: none /note=Start: 49981 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 1 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: Yes /note=SD score: Z= 2.988 Final= -2.662 Best Score? yes /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 64.8% CDS 50667 - 51047 /gene="70" /product="gp70" /function="hypothetical protein" /locus tag="MortySmith_70" /note=Original Glimmer call @bp 50667 has strength 16.15; Genemark calls start at 50667 /note=SSC: 50667-51047 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT40_gp72 [Microbacterium phage Krampus] ],,NCBI, q1:s1 100.0% 2.71884E-83 GAP: -4 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 2.471, -3.75071250087134, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT40_gp72 [Microbacterium phage Krampus] ],,YP_009802662,100.0,2.71884E-83 SIF-HHPRED: eS8; Microsporidia, Ribosome, Intracellular Parasite; HET: MG; 3.4A {Vairimorpha necatrix},,,6RM3_SI0,22.2222,68.7 SIF-Syn: none /note=Start: 50667 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: Yes /note=SD score: Z= 2.471 Final= -3.751 Best Score? no but best score has big gap /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 68.7% CDS 51047 - 51757 /gene="71" /product="gp71" /function="RuvC-like resolvase" /locus tag="MortySmith_71" /note=Original Glimmer call @bp 51047 has strength 10.72; Genemark calls start at 51125 /note=SSC: 51047-51757 CP: yes SCS: both-gl ST: NI BLAST-Start: [RuvC-like resolvase [Microbacterium phage DannyDe]],,NCBI, q1:s1 100.0% 5.67053E-175 GAP: -1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.008, -4.726225951355071, no F: RuvC-like resolvase SIF-BLAST: ,,[RuvC-like resolvase [Microbacterium phage DannyDe]],,QPX61918,100.0,5.67053E-175 SIF-HHPRED: HOLLIDAY JUNCTION RESOLVASE (RUVC); SITE-SPECIFIC RECOMBINASE; 2.5A {Escherichia coli} SCOP: c.55.3.6,,,1HJR_D,69.9153,99.7 SIF-Syn: none /note=Start: 51047 /note=Glimmer/Genemark favored: only glimmer /note=Gap/Overlap: -1 /note=Contains all CP: Yes /note=Most Annotated: No second most annotated start, (10 MAs vs 11 MAs) /note=Most Conserved Start: Yes, found in 100% genes in pham /note=SD score: Z= 2.008 Final= -4.726 Best Score? no second best /note=Q1:S1 yes /note=Function: RuvC-like resolvase /note=SIF-BLASTp: RuvC-like resolvase, DannyDe, eval=5.6e-175, 100% identity /note=SIF-HHPRED: RuvC in E.coli, 1HJR_D , 99.7% probability, 69.9% coverage CDS 51754 - 52038 /gene="72" /product="gp72" /function="hypothetical protein" /locus tag="MortySmith_72" /note=Original Glimmer call @bp 51754 has strength 11.65; Genemark calls start at 51745 /note=SSC: 51754-52038 CP: yes SCS: both-gl ST: SS BLAST-Start: [hypothetical protein SEA_DANNYDE_75 [Microbacterium phage DannyDe]],,NCBI, q1:s1 100.0% 1.01391E-63 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.901, -3.6727816321281046, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_DANNYDE_75 [Microbacterium phage DannyDe]],,QPX61919,100.0,1.01391E-63 SIF-HHPRED: NCD3G ; Nine Cysteines Domain of family 3 GPCR,,,PF07562.17,13.8298,78.2 SIF-Syn: none /note=Start: 51754 /note=Glimmer/Genemark favored: Glimmer only /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: Yes /note=SD score: Z= 2.901 Final= -3.673 Best Score? yes /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 78.2% CDS 52035 - 52508 /gene="73" /product="gp73" /function="hypothetical protein" /locus tag="MortySmith_73" /note=Original Glimmer call @bp 52038 has strength 9.93; Genemark calls start at 52038 /note=SSC: 52035-52508 CP: yes SCS: both-cs ST: NI BLAST-Start: [hypothetical protein SEA_HAUNTER_76 [Microbacterium phage Haunter]],,NCBI, q1:s1 99.3631% 8.83602E-102 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.133, -2.356391881054909, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HAUNTER_76 [Microbacterium phage Haunter]],,QPL15089,94.9045,8.83602E-102 SIF-HHPRED: DUF3788 ; Protein of unknown function (DUF3788),,,PF12663.10,17.1975,85.0 SIF-Syn: none /note=Start: 52035 /note=Glimmer/Genemark favored: neither, favored start does not have Q1:S1 /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: does not contain /note=Most Conserved: does not contain /note=SD score: Z= 3.1 Final= -2.4 Best Score? yes /note=Q1:S1 yes /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 85% CDS 52505 - 52693 /gene="74" /product="gp74" /function="hypothetical protein" /locus tag="MortySmith_74" /note=Original Glimmer call @bp 52505 has strength 4.79 /note=SSC: 52505-52693 CP: yes SCS: glimmer ST: SS BLAST-Start: [hypothetical protein SEA_HIDDENLEAF_77 [Microbacterium phage Hiddenleaf] ],,NCBI, q1:s1 100.0% 3.28397E-36 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.303, -4.3751676966419835, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_HIDDENLEAF_77 [Microbacterium phage Hiddenleaf] ],,QGH74028,100.0,3.28397E-36 SIF-HHPRED: g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]},,,d1x64a1,59.6774,91.0 SIF-Syn: none /note=Start: 52505 /note=Glimmer/Genemark favored: only glimmer /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: yes /note=Most Conserved: yes /note=SD score: Z= 2.303 Final= -4.375 Best Score? yes /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, hits above 90% were to human and mouse proteins CDS 52681 - 52896 /gene="75" /product="gp75" /function="hypothetical protein" /locus tag="MortySmith_75" /note=Original Glimmer call @bp 52651 has strength 9.17; Genemark calls start at 52681 /note=SSC: 52681-52896 CP: yes SCS: both-gm ST: SS BLAST-Start: [hypothetical protein HOT40_gp77 [Microbacterium phage Krampus] ],,NCBI, q1:s1 100.0% 7.62913E-43 GAP: -13 bp gap LO: no RBS: Kibler 6, Karlin Medium, 2.048, -5.468747614834752, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein HOT40_gp77 [Microbacterium phage Krampus] ],,YP_009802667,100.0,7.62913E-43 SIF-HHPRED: Nudix_Hydrolase_11; Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X.,,,cd04669,45.0704,73.4 SIF-Syn: none /note=Start: 52681 /note=Glimmer/Genemark favored: only Genemark /note=Gap/Overlap: -13 /note=Contains all CP: little CP visible /note=Most Annotated: Yes /note=Most Conserved: Yes /note=SD score: Z= 2.048 Final= -5.469 Best Score? no /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 73.4% CDS 53065 - 53463 /gene="76" /product="gp76" /function="hypothetical protein" /locus tag="MortySmith_76" /note=Original Glimmer call @bp 53065 has strength 15.07; Genemark calls start at 53065 /note=SSC: 53065-53463 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_77 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 7.20334E-92 GAP: 168 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_77 [Microbacterium phage Aesir]],,QNN98643,100.0,7.20334E-92 SIF-HHPRED: PRD-containing transcription regulator; STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-BIOLOGY, TRANSCRIPTION, TRANSCRIPTION REGULATOR; HET: EDO, PG4, MSE; 1.38A {Lactobacillus casei},,,3NUF_B,39.3939,46.9 SIF-Syn: none /note=Start: 53065 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: 168, longest orf and no coding potential in the gap to add a gene /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: Yes /note=SD score: Z= 3.054 Final= -2.505 Best Score? yes /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 46.9% CDS 53460 - 53600 /gene="77" /product="gp77" /function="membrane protein" /locus tag="MortySmith_77" /note=Original Glimmer call @bp 53460 has strength 20.53; Genemark calls start at 53460 /note=SSC: 53460-53600 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein HOT40_gp80 [Microbacterium phage Krampus] ],,NCBI, q1:s1 100.0% 2.54005E-21 GAP: -4 bp gap LO: no RBS: Kibler 6, Karlin Medium, 3.054, -3.3503726477288405, yes F: membrane protein SIF-BLAST: ,,[hypothetical protein HOT40_gp80 [Microbacterium phage Krampus] ],,YP_009802670,100.0,2.54005E-21 SIF-HHPRED: Photosynthetic reaction center, H-chain; photosynthesis, light-harvesting complex, reaction centre, purple bacteria, membrane protein, STRUCTURAL PROTEIN; HET: BPH, CD4, PGW, 07D, FME, U10, RQ0, LMT, CRT;{Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)},,,7OY8_H,52.1739,93.2 SIF-Syn: none /note=Start: 53460 /note=Glimmer/Genemark favored: Both /note=Gap/Overlap: -4 /note=Contains all CP: Yes /note=Most Annotated: Yes /note=Most Conserved: Yes /note=SD score: Z= 3.054 Final= -3.35 Best Score? yes /note=Q1:S1 yes /note=Function: membrane protein /note=SIF-BLASTp: membrane protein, Chivey, 100% identity, eval=2.5e-21 /note=SIF-HHPRED: photosynthesis related membrane protein, Rhodospirillum, 93.2% prob, 53% coverage /note=membrane: 1TMH from TmHmm, membrane protein called by SOSUI CDS 53602 - 54462 /gene="78" /product="gp78" /function="hypothetical protein" /locus tag="MortySmith_78" /note=Original Glimmer call @bp 53602 has strength 17.51; Genemark calls start at 53602 /note=SSC: 53602-54462 CP: yes SCS: both ST: NI BLAST-Start: [hypothetical protein SEA_AESIR_80 [Microbacterium phage Aesir]],,NCBI, q1:s2 100.0% 0.0 GAP: 1 bp gap LO: yes RBS: Kibler 6, Karlin Medium, 3.054, -2.5052746077145835, yes F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_80 [Microbacterium phage Aesir]],,QNN98646,98.9547,0.0 SIF-HHPRED: NICKEL AND COBALT RESISTANCE PROTEIN CNRR; METAL BINDING PROTEIN, SENSOR PROTEIN, SIGNAL TRANSDUCTION; HET: GOL, PGE, PEG; 1.85A {CUPRIAVIDUS METALLIDURANS},,,3ZG1_A,25.5245,88.5 SIF-Syn: none /note=Start: 53602 /note=Glimmer/Genemark favored: both /note=Gap/Overlap: 1 /note=Contains all CP: Yes /note=Most Annotated: no, does not have most annotated start /note=Most Conserved: no /note=SD score: Z= 3.054 Final= -2.505 Best Score? yes /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 88.5% CDS 54464 - 54946 /gene="79" /product="gp79" /function="hypothetical protein" /locus tag="MortySmith_79" /note=Original Glimmer call @bp 54464 has strength 8.23; Genemark calls start at 54464 /note=SSC: 54464-54946 CP: yes SCS: both ST: SS BLAST-Start: [hypothetical protein SEA_AESIR_81 [Microbacterium phage Aesir]],,NCBI, q1:s1 100.0% 4.74595E-113 GAP: 1 bp gap LO: no RBS: Kibler 6, Karlin Medium, 1.612, -5.542591178556752, no F: hypothetical protein SIF-BLAST: ,,[hypothetical protein SEA_AESIR_81 [Microbacterium phage Aesir]],,QNN98647,99.375,4.74595E-113 SIF-HHPRED: g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]},,,d1a7ia2,22.5,84.7 SIF-Syn: none /note=Start: 54464 /note=Glimmer/Genemark favored: both /note=Gap/Overlap: 1 /note=Contains all CP: Yes /note=Most Annotated: yes /note=Most Conserved: Yes /note=SD score: Z= 1.612 Final= -5.543 Best Score? no but best gap /note=Q1:S1 yes /note=Function: NKF /note=SIF-BLASTp: no hits below eval=e-7 /note=SIF-HHPRED: no functional hits above 90% prob, top hit was 84.7%