CDS 10 - 270 /note=GM start, No GL, coding potential, blast matches, all guiding principles (gp) good, likely gene /note= /note=GM picked start 4. Start 3 was autoannnotated in 9 phages in starterator (including this one?). no human call. CrystalP is not included on starterator but uses start 2 and is very similar to Bilbo for all genes. start 2 has the best least negative RBS, highest Z score of the longer ORFs, good spacer, includes all coding potential (although there is no coding potential going back to 10. Best blast scores suggest start 2 at length of 261NTs. chose start 2 /note= /note=Function: /note=BLAST: Bench 1 function unknown 86 187 7e-48 /note=HHPRED shows best alignment with zinc finger domain from multiple microbial species CDS 267 - 449 /note=GL (Glimmer) and GM start agree, coding potential, blast matches, all gp good, likely gene /note= /note=Start 1 has highest z-score, least neg RBS, longest ORF, Starterator agrees (human called), BlastP: hypothetical protein Kostya_2 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 122 122 100% 2e-34 100.00% 60 YP_002014470 , keep at current start /note= /note=Function: /note=PhageaDB: Adnama 2 function unknown 60 119 3e-27 E 1181 /note= /note=HHPRED: No quality match PF19999.4 fvmX3 ; FtsH ternary system domain X3 80.5 35 1 22 29 50 5.3 /note= /note=not transmembrane protein, globular according to SOSUI and deepTMHMM /note= /note=Is on approved function list CDS 446 - 604 /note=GL and GM start agree, coding potential, blast matches, 159 bp length, likely gene /note= /note=Least neg RBS, highest Z value, reasonable spacer, 159 bp length, starterator agrees (human reviewed) /note=Blast P: hypothetical protein Porky_2 [Mycobacterium phage Porky] Mycobacterium phage Porky 105 105 100% 3e-28 100.00% 52 YP_002014323.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 2 function unknown 52 103 1e-22 E 85359 /note= /note=HHPred: No Quality Match PF11592.13 AvrPto ; Central core of the bacterial effector protein AvrPto 68.2 57.6923 11 41 19 49 6.8 /note= /note=Disagreement between SOSUI and DeepTMHMM, Phamerator shoes as TM /note= /note=Is on approved function list CDS 601 - 786 /note=GL and GM start agree, coding potential, blast matches, 186 bp length, likely gene /note= /note=Least neg RBS, highest Z value, long spacer, 186 bp length, starterator agrees (human reviewed), /note=Blast P: hypothetical protein Kostya_4 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 124 124 100% 4e-35 100.00% 61 YP_002014472, keep current start /note= /note=Function: /note=PhagesDB: ABCat 3 function unknown 61 134 1e-31 E 837 /note= /note=HHPRED:No Quality Match PF09930.14 DUF2162 ; Predicted transporter (DUF2162) 79 8.19672 104 109 49 54 1.1 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 783 - 1064 /note=GL and GM start agree, coding potential, blast matches, all gp good, likely gene /note= /note=Least neg RBS, highest z value, reasonable spacer, longest ORF, 282 bp length, starterator agrees (human reviewed) /note=Blast P: hypothetical protein SEA_DUSK_5 [Mycobacterium phage Dusk] Mycobacterium phage Dusk 181 181 100% 5e-57 100.00% 93 YP_009224273.1, keep current start /note= /note=Function: /note=PhagesDB:ABCat 4 function unknown 93 190 1e-48 E 85283 /note= /note=HHPRED:No Quality Match 4UPH_A SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN; HYDROLASE; HET: DDZ; 2.5A {AGROBACTERIUM RADIOBACTER K84} 45.5 62.3656 489 546 28 86 79 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved functions list CDS 1057 - 1518 /note=GL and GM start agree, coding potential, blast matches, all gp good, likely gene /note= /note=Least neg RBS, highest z value, slightly high spacer, longest ORF, 462 bp length, starterator agrees (human reviewed) /note=Blast P: terminase small subunit [Mycobacterium phage Kostya] Mycobacterium phage Kostya 316 316 100% 1e-108 100.00% 153 YP_002014474.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 5 terminase small subunit 153 324 6e-89 E 204823 /note= /note=HHPRED: PF05119.17 Terminase_4 ; Phage terminase, small subunit 99.8 59.4771 2 94 47 138 3.9e-18 /note= /note=Not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 1511 - 1855 /note=GL and GM start agree, coding potential, blast matches, all gp good, likely gene /note= /note=Least neg RBS, highest z value, slightly high spacer, 345 bp length, starterator agrees (human reviewed) /note=Blast P: hypothetical protein Kostya_7 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 231 231 100% 3e-76 100.00% 114 YP_002014475.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 6 function unknown 114 244 8e-65 E 210788 /note= /note=HHPRED: No Quality Match 9C3C_B Beta-dystroglycan; beta-helix, sarcolemma, glycosylation, muscular dystrophy, membrane protein; HET: BMA, NAG;{Oryctolagus cuniculus} 52 24.5614 94 122 4 32 85 /note= /note=Transmembrane/alpha TM protein according to SOSUI and deepTMHMM /note= /note=is on approved functions list CDS complement (1956 - 2267) /note=GL and GM start agree, coding potential, Blast matches, all gp good, switch in gene orientation, likely gene /note= /note=not least neg RBS, high z value, slightly high spacer, longest ORF, 312 bp length, starterator agrees (human reviewed) /note=Blast P: hypothetical protein Kostya_8 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 211 211 100% 1e-68 100.00% 103 YP_002014476.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 7 function unknown 103 210 1e-54 E 196319 /note= /note=HHPRED: No Quality Match PF06925.16 MGDG_synth ; Monogalactosyldiacylglycerol (MGDG) synthase 73.2 21.3592 2 24 62 84 11 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 2303 - 4966 /note=GL and GM start agree, coding potential, blast matches, all gp good, switch in gene orientation, likely gene /note= /note=Least neg RBS, high z value, reasonable spacer, longest ORF, 2664 bp length, starterator agrees (human reviewed) /note=Blast P: exonuclease [Mycobacterium phage Kostya] Mycobacterium phage Kostya 1845 1845 100% 0.0 100.00% 887 YP_002014477.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 8 terminase large subunit 887 1825 0 E 85489 /note= /note=HHPRED: 6Z6D_A Terminase large subunit; genome packaging, bacteriophage, ATPase, nuclease, VIRAL PROTEIN; HET: BR; 2.2A {Enterobacteria phage HK97} 100 51.6347 64 500 417 875 2.9e-33 /note= /note=Not transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 4978 - 5199 /note=GL and GM start agree, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, reasonable spacer, longest ORF, 222 bp length, starterator agrees (human reviewed), /note=Blast P: gp9 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 150 150 100% 1e-45 100.00% 73 NP_817459.1, keep current start /note= /note=Function: /note=PhagesDB: Dumbo 9 function unknown 73 154 1e-37 E 834 /note= /note=HHPRED:1YCY_C Conserved hypothetical protein; Structural Genomics, Southeast Collaboratory for Structural Genomics, SECSG, Protein Structure Initiative, PSI, conserved hypothetical protein, Pyrococcus; HET: MSE; 2.8A {Pyrococcus furiosus} SCOP: b.38.1.4 98.1 87.6712 7 70 4 68 0.00011 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 5186 - 6742 /note=GL and GM start disagree, coding potential, blast matches, all gp good, likely gene /note= /note=1 is not least neg RBS, highest z value, reasonable spacer, longest ORF, 1560 bp length, starterator agrees (human reviewed), 2 has least negative RBC value and same high Z score. Change to start 2 /note=Blast P: portal protein [Mycobacterium phage Contagion] Mycobacterium phage Contagion 1076 1076 100% 0.0 100.00% 519 YP_008410028.1, keep current start /note= /note=Function: /note=PhagesDB: Contagion 10 portal protein 519 1038 0 E 212409 /note= /note=HHPRED: 8FQL_D Portal protein; Prohead I, icosahedral symmetry, HK97, phage, capsid, VIRUS; 3.6A {Escherichia phage HK97} 100 69.7495 54 413 44 406 2.5e-37 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved functions list CDS 6745 - 7839 /note=GL and GM start agree, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, high z value, slightly high spacer, longest ORF, 1095 bp length, starterator agrees (human reviewed) /note=Blast P: head maturation protease [Mycobacterium phage Kostya] Mycobacterium phage Kostya 728 728 100% 0.0 100.00% 364 YP_002014480.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 11 capsid maturation protease 364 723 0 E 85136 /note= /note=HHPRED: PF04586.22 Peptidase_S78 ; Caudovirus prohead serine protease 99.5 34.8901 12 156 21 148 4.9e-12 /note= /note=not a transmembrane protein, soluble/globular according tp SOSUI and deepTMHMM /note= /note=is on approved list CDS 7927 - 9420 /note=GL and GM start, coding potential, blast matches, 90 bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, slightly high spacer, Longest ORF, 1494 bp length, starterator agrees (human reviewed), /note=Blast P: major head protein [Mycobacterium phage Toto] Mycobacterium phage Toto 1004 1004 100% 0.0 100.00% 497 YP_009208421.1, keep current start /note= /note= /note=Function /note=PhagesDB: CrystalP 13 major capsid protein 497 971 0 E 160236 /note= /note=HHPRED: (not top choice) 7RWZ_C Major capsid protein; HK97-like fold, capsid size redirection, major capsid protein, VIRUS; 4.0A {Staphylococcus aureus} 100 99.1952 22 399 3 496 5.1e-28 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on the approved functions list CDS 9488 - 9679 /note=GL and GM start agree, coding potential, blast matches, 192 bp length, 68 bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, reasonable spacer, longest ORF,192 bp length, starterator agrees (human reviewed) /note=Blast P:head-tail connector protein [Mycobacterium phage Kostya] Mycobacterium phage Kostya 124 124 100% 3e-35 100.00% 63 YP_002014482.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 13 function unknown 63 130 1e-30 E 812 /note= /note=HHPRED:No Quality Match 7UX9_B Probable histone H2A.7; Chromatin remodeler, Helicase, ATPase, Complex, Gene regulation;{Arabidopsis thaliana} 67 19.0476 1 13 1 13 7.4 /note= /note=is not a transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=is on approved functions list CDS 9679 - 10245 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, slightly high spacer, longest ORF, 567 length, starterator agrees (human reviewed) /note=Blast P: head-tail adaptor [Mycobacterium phage NelitzaMV] Mycobacterium phage NelitzaMV 386 386 100% 3e-135 100.00% 188 YP_009197683.1, keep current start /note= /note=Function: /note=PhagesDB: Toto_15, head-to-tail adaptor, 188 387 e-108 /note= /note=HHPRED: 8HQO_Q Head completion protein; Neck, Portal, T5, VIRUS, VIRAL PROTEIN; 3.2A {Escherichia phage DT57C} 99.9 97.8723 3 170 1 185 2.9e-22 /note= /note=is not transmembrane, soluble/globular according to SOSUI and deepTMHMM CDS 10258 - 10593 /note=GL and GM start agree, coding potential, blast matches, all gp good, likely gene /note= /note=not least neg RBS, high z value, reasonable spacer, longest ORF, 336 bp length, starterator agrees (human reviewed), /note=Blast P: head closure [Mycobacterium phage Kostya] Mycobacterium phage Kostya 229 229 100% 2e-75 100.00% 111 YP_002014484.1, keep current start /note= /note=Function: /note=PhagesDB:ABCat 15 head-to-tail stopper 111 237 7e-63 E 208327 /note= /note=HHPRED: 9D94_Hc Head-to-tail stopper; Bacteriophage, portal, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 99.7 90.991 18 125 7 108 3.4e-15 /note= /note=no transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 10590 - 10970 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, reasonable spacer, 381 bp length, starterator agrees (human call), /note=Blast P: minor tail protein [Mycobacterium phage Kostya] Mycobacterium phage Kostya 259 259 100% 1e-86 100.00% 126 YP_002014485.1, keep current start /note= /note=Function: /note=PhagesDB:ABCat 16 function unknown 126 263 2e-70 E 213864 /note=HHPRED: PF11114.13 Minor_capsid_2 ; Minor capsid protein 99.1 92.0635 6 103 9 125 3e-10 /note=highest PhagesdB function frequency is head-to-tail connector and HHPREDshows an alignment to an accepted crystal structure HK97 to make the call /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 10948 - 11352 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least neg RBS, highest z value, reasonable spacer, 405 bp length, starterator (human reviewed) /note=Blast P: head-tail adaptor [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 280 280 100% 7e-95 100.00% 134 NP_817467.1, keep current start /note= /note=Function: /note=PhagesDB:CrystalP 18 tail terminator 134 288 5e-78 E 166357 /note= /note=HHPRED: 9D94_Ic Tail terminator; Bacteriophage, portal, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 99.8 95.5224 1 146 4 132 2.1e-1 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 11379 - 12350 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, slightly high spacer, longest ORF, 972 bp length, atg start codon, no starterator call, other similar tracks human call first start /note=Blast P: major tail protein [Mycobacterium phage Kostya] Mycobacterium phage Kostya 647 647 100% 0.0 100.00% 323 YP_002014487.1, change start to 11379 /note= /note=Function: /note=PhagesDB:ABCat 18 major tail subunit 323 657 0 E 213947 /note= /note=HHPRED:9D9L_J Major tail protein; Bacteriophage, tail tube, VIRUS, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 100 82.0433 1 241 9 274 1.6e-27 /note= /note=is not a transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 12470 - 12931 /note=ribosomal slippage /note=CDS join(12470..12922;12922..13341) /note=GL and GM start, coding potential, blast matches, 120bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, slightly high spacer, 462 bp length, starterator agrees (human reviewed) /note=Blast P: tail assembly chaperone [Mycobacterium phage Dusk] Mycobacterium phage Dusk 317 317 100% 1e-108 100.00% 177 YP_009224288.1, keep current start /note= /note=Function: /note=PhagesDB:ABCat 19 tail assembly chaperone 177 309 2e-84 E 84650 /note= /note=HHPRED: PF17388.7 GP24_25 ; Mycobacteriophage tail assembly protein 96.3 88.2353 1 122 9 144 0.21 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 13334 - 18067 /note=GL and GM start, coding potential, blast matches, 192 bp length, likely gene /note= /note=low RBS,high z value, good spacer, 192 bp length, ATG start, starterator agrees (human reviewed), /note=Blast P: hypothetical protein SEA_MURICA_38 [Mycobacterium phage Murica] Mycobacterium phage Murica 136 136 100% 8e-40 100.00% 76 ATN91073.1, keep current start /note= /note=Function: /note=PhagesDB:CrystalP 22 tape measure protein 1577 3130 0 E 816 /note= /note=HHPRED: 8VJH_Q Tape measure; Flagellotropic bacteriophage, Siphophage, Tail-tip, VIRUS;{Chivirus chi} 99.5 10.1458 369 510 173 333 1e-7 /note= /note=Transmembrane protein, membrane/alpha TM according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 18097 - 19758 /note=GL and GM good, coding potential, blast matches, all gp good, likely gene /note= /note=not least neg RBS, high z value, high spacer, 1662 bp length, starterator agrees (human reviewed), longest ORF /note=Blast P: minor tail protein [Mycobacterium phage NelitzaMV] Mycobacterium phage NelitzaMV 1142 1142 100% 0.0 100.00% 553 YP_009197691.1, keep current start /note= /note=Function: /note=PhagesDB:BadStone 22 minor tail protein 553 1154 0 E 59 /note= /note=HHPRED:9D93_Mf Minor tail protein; Bacteriophage, tail tip, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 99.8 28.9331 3 161 5 165 1.4e-16 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 19830 - 21425 /note=GL and GM start disagree, coding potential, blast matches, 71 bp gap from previous, likely gene /note= /note=not Least neg RBS, low z value, 1596 bp length, 71 bp gap, slightly high spacer, starterator agrees (human called), ATG start /note=Blast P: minor tail protein [Mycobacterium phage Kostya] Mycobacterium phage Kostya 1037 1037 100% 0.0 99.80% 559 YP_002014492.1, change start to 19908 /note= /note=Function: /note=PhagesDB: Cjw1 24 minor tail protein 505 1038 0 E 213831 /note= /note=HHPRED: 9D93_Mf Minor tail protein; Bacteriophage, tail tip, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 99.8 28.9331 3 161 5 165 1.4e-16 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 21446 - 22267 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, reasonable spacer, 834 bp length, starterator does not agree, it chose start 4 /note=Blast P: minor tail protein [Mycobacterium phage Kostya] Mycobacterium phage Kostya 561 561 100% 0.0 100.00% 277 YP_002014493.1 , Change start to 21434 /note= /note=Function: /note=PhagesDB:AmericanBeauty 27 minor tail protein 277 570 1e-162 E 213854 /note= /note=HHPRED:No Quality Match PF09244.15 Suc_Porlyase_C ; Sucrose phosphorylase, C-terminal 32.9 12.6354 2 37 5 40 140 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 22284 - 24680 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, high z value, reasonable spacer, longest ORF, 2397 bp length, starterator agrees (human called), /note=Blast P: minor tail protein [Mycobacterium phage CrystalP] Mycobacterium phage CrystalP 1590 1590 100% 0.0 100.00% 798 APU02850.1, keep current start /note= /note=Function: /note=PhagesDB:CrystalP 26 minor tail protein 798 1599 0 E 213869 /note= /note=HHPRED: 9D93_Pb Minor tail protein; Bacteriophage, tail tip, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 100 75.4386 12 616 196 798 0 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved functions list CDS 24677 - 27523 /note=GL and GM start, coding potential, but does not stop until 28450, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, slightly high spacer, longest ORF, 2847 bp length, starterator agrees (human reviewed), /note=Blast P: minor tail protein [Mycobacterium phage CrystalP] Mycobacterium phage CrystalP 1905 1905 100% 0.0 100.00% 948 APU02851.1, keep current start /note= /note=Function: /note=PhagesDB:CrystalP 27 minor tail protein 948 1927 0 E 85018 /note= /note=HHPRED:(not top choice) 9D93_Sa Minor tail protein; Bacteriophage, tail tip, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 100 45.7806 8 466 1 435 7.8e-33 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 27524 - 28468 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, slightly high spacer, longest ORF, 945 bp length, starterator agrees (human reviewed), /note=Blast P: minor tail protein [Mycobacterium phage Toto] Mycobacterium phage Toto 603 603 100% 0.0 100.00% 314 YP_009208436.1, keep current start /note= /note=Function: /note=PhagesDB: CrystalP 28 function unknown 314 629 1e-180 E 206617 /note= /note=HHPRED:No Quality Match 5XOJ_G Nup42p; exportin, nucleoporin, GTP BINDING PROTEIN; HET: GTP; 2.2A {Saccharomyces cerevisiae (strain AWRI796)} 21.9 10.5096 4 35 21 54 200 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved functions list CDS 28549 - 28977 /note=GL and GM start, coding potential, blast matches, 81 bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, reasonable spacer, 429 bp length, starterator agrees (human reviewed), /note=Blast P: hypothetical protein Kostya_30 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 265 265 100% 1e-88 100.00% 142 YP_002014498.1, keep current start /note= /note=Function: /note=PhagesDB: CrystalP 29 function unknown 142 284 7e-77 E 213903 /note= /note=HHPRED: 9D93_Rc Minor tail protein; Bacteriophage, tail tip, VIRAL PROTEIN;{Mycobacterium phage Bxb1} 99.7 76.7606 1 106 32 141 2e-15 /note= /note=Transmembrane according to SOSUI but not deepTMHMM /note= /note=is on approved functions list CDS complement (28974 - 29150) /note=GL and GM start, coding potential, blast matches, switch in gene orientation, 177bp length, likely gene /note= /note=reasonable spacer, starterator agrees (human reviewed), longest ORF, 177 bp length, smallest gap, /note=Blast P: HTH DNA binding protein [Mycobacterium phage Kostya] Mycobacterium phage Kostya 117 117 100% 6e-33 100.00% 58 YP_002014499.1, keep current start /note= /note=Function: /note=PhagesDB: CrystalP 30 helix-turn-helix DNA binding protein 58 119 4e-27 E 204688 /note= /note=HHPRED: 5CLV_J TrfB transcriptional repressor protein; Helix-turn-helix, complex, transcription; 2.5A {Escherichia coli} 97.4 86.2069 7 56 5 55 0.0021 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved functions list CDS 29283 - 29567 /note=GL and GM start, coding potential, blast matches, 133 bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, slightly high spacer, longest ORF, 285 bp length, starterator agrees (human reviewed), /note=Blast P: gp31 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 194 194 100% 6e-62 100.00% 94 NP_817481.1 , keep current start /note= /note=Function: /note=PhagesDB:DoctorDiddles 31 function unknown 94 201 5e-52 E 163226 /note= /note=HHPRED:No Quality Match 7W13_A Alginate lyase; PL7 family, alginate lyase, complex, LYASE; HET: BEM; 1.65A {Neopyropia yezoensis} 80.4 27.6596 1 30 1 27 6.6 /note= /note=not transmembrane protein, globular+SP/soluble according to SOSUI and deepTMHMM but phamerator shows as TM /note= /note=is on approved functions list CDS 29641 - 31143 /note=GL and GM start, coding potential, blast matches, 143 bp gap from previous, likely gene /note= /note=low RBS, low z value, longest orf, reasonable spacer, starterator does not agree, it chose start 2, 1503 bp length, /note=Blast P: endolysin [Mycobacterium phage SirDuracell] Mycobacterium phage SirDuracell 1036 1036 100% 0.0 100.00% 500 YP_009607961.1, change start to 29641 /note= /note=Function: /note=PhagesDB:CrystalP 32 lysin A 500 1048 0 E 212200 /note= /note=HHPRED: (Not top choice) 5A6S_A ENDOLYSIN; STRUCTURAL PROTEIN, ENDOLYSIN, SECONDARY TRANSLATION PRODUCT, BACTERIOPHAGE; HET: GOL, 1PE; 1.9A {CLOSTRIDIUM PHAGE PHICTP1} 99.3 38.8 18 203 172 366 1.7e-9 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 31147 - 31530 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=ok z value, ok RBS, reasonable spacer, starterator agrees (human reviewed), longest ORF, 384 bp length, /note=Blast P: holin [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 247 247 100% 6e-82 100.00% 127 NP_817483.1, keep current start /note= /note=Function: /note=PhagesDB: Dumbo 33 holin 127 241 7e-64 E 210675 /note= /note=HHPRED: PF16081.10 Phage_holin_7_1 ; Mycobacterial 2 TMS Phage Holin (M2 Hol) Family 100 93.7008 1 121 3 122 1.2e-36 /note= /note=Transmembrane protein, membrane/Alpha TM according to SOSUI and deepTMHMM /note= /note=is on list of approved functions CDS 31523 - 31861 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=starterator agrees (human reviewed), longest ORF, no large gap, 339 bp length, /note=Blast P: gp34 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 229 229 100% 3e-75 100.00% 112 NP_817484.1 /note= /note=Function: /note=PhagesDB:Cactus 35 function unknown 112 233 2e-61 E 210871 /note= /note=HHPRED:No Quality Match PF09081.15 AMT4_dom_C ; Glucan 1,4-alpha-maltotetraohydrolase, domain C 38.7 14.2857 5 21 90 106 56 /note= /note=not a transmembrane protein, globular/soluble according to SOSUi and deepTMHMM /note= /note=is on approved function list CDS 31858 - 32715 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, longest orf, 858 bp length, reasonable spacer, starterator agrees (human reviewed), /note=Blast P: lysin B [Mycobacterium phage Kostya] Mycobacterium phage Kostya 583 583 100% 0.0 100.00% 285 YP_002014504.1, keep current start /note= /note=Function: /note=PhagesDB:Balomoji 34 lysin B 285 583 1e-166 E 208221 /note= /note=HHPRED: 3HC7_A Gene 12 protein; alpha/beta sandwich, CELL ADHESION; 2.0A {Mycobacterium phage D29} 100 90.8772 2 254 17 276 4.3e-29 /note= /note=not a transmembrane protein, soluble/globular+SP according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 32712 - 33128 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=longer ORF, 417 bp length, good spacer, ATG start, starterator agrees (human review), /note=Blast P: hypothetical protein Porky_36 [Mycobacterium phage Porky] Mycobacterium phage Porky 280 280 100% 7e-95 100.00% 138 YP_002014357.1, keep current start /note= /note=Function: /note=PhagesDB: Buck 35 function unknown 138 290 1e-78 E 213859 /note= /note=HHPRED: PF06667.17 PspB ; Phage shock protein B 93.2 50 2 62 14 83 2.6 /note= /note=transmembrane protein, membrane/Alpha TM according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 33135 - 33380 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=ok RBS, high z value, good spacer, Longest orf, 246 bp length, starterator agrees (human reviewed), /note=Blast P: thioredoxin domain [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 165 165 100% 5e-51 100.00% 81 NP_817487.1, keep current start /note= /note=Function: /note=PhagesDB:Argent26 39 NrdH-like glutaredoxin 81 170 1e-42 E 213834 /note= /note=HHPRED:(Not Top Choice) 1H75_A GLUTAREDOXIN-LIKE PROTEIN NRDH; ELECTRON TRANSPORT, NRDH, THIOREDOXIN, GLUTAREDOXIN, REDOX PROTEIN; 1.7A {ESCHERICHIA COLI} SCOP: c.47.1.1 99.4 96.2963 1 74 1 79 1.8e-10 /note= /note=not transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS complement (33542 - 34129) /note=GM start, No GL start, coding potential, blast matches, switch in gene orientation, 162 bp gap from previous, likely gene /note= /note=ok z value, starterator agrees (human reviewed), longest orf, 588 bp length, /note=Blast P: HNH endonuclease [Mycobacterium phage Dusk] Mycobacterium phage Dusk 405 405 100% 2e-142 100.00% 195 YP_009224305.1 , keep current start /note= /note=Function: /note=PhagesDB: ABCat 37 HNH endonuclease 195 420 1e-117 E 213882 /note= /note=HHPRED: (Not Top Choice) 1U3E_M HNH homing endonuclease; HNH catalytic motif, Helix-turn-helix DNA binding domain, protein-DNA complex, DNA binding protein-DNA COMPLEX; HET: EDO; 2.92A {Bacillus phage SPO1} SCOP: d.285.1.1, d.4.1.3 99.7 53.8462 1 107 36 141 8.2e-16 /note= /note=Not transmembrane, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS complement (34252 - 34638) /note=GL and GM start, coding potential, blast matches, 123 bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, good spacer, longest orf, 387 bp length, starterator agrees (human reviewed), /note=Blast P: nucloid associated Lsr2-like [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 261 261 100% 8e-88 100.00% 128 NP_817489.1, keep current start /note= /note=Function: /note=PhagesDB:Bench 41 Lsr2-like DNA bridging protein 128 264 6e-71 E 84708 /note= /note=HHPRED: (not top choice) PF11774.13 Lsr2 ; Lsr2 100 82.8125 1 113 1 107 1.9e-27 /note= /note=not transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS complement (34686 - 34877) /note=GL and GM start, coding potential, blast matches, 192 bp length, likely gene /note= /note=low RBS,high z value, good spacer, 192 bp length, ATG start, starterator agrees (human reviewed), /note=Blast P: hypothetical protein SEA_MURICA_38 [Mycobacterium phage Murica] Mycobacterium phage Murica 136 136 100% 8e-40 100.00% 76 ATN91073.1, keep current start /note= /note=Function: /note=PhagesDB:244 43 function unknown 65 140 9e-34 E 1036 /note= /note=HHPRED: No Quality Match PF20745.2 TSP_Ig-like ; Tailspike protein-like, Ig-like domain 83.3 57.1429 27 76 4 40 12 /note= /note=not transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS complement (34880 - 35347) /note=GM start, No GL start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, good spacer, 468 bp length, starterator agrees (human reviewed), /note=Blast P: hypothetical protein SEA_TOTO_41 [Mycobacterium phage Toto] Mycobacterium phage Toto 318 318 100% 2e-109 100.00% 155 YP_009208449.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 40 function unknown 155 336 1e-92 E 214145 /note= /note=HHPRED: No Quality Match PF08815.15 Nuc_rec_co-act ; Nuclear receptor coactivator 42.2 4.51613 24 31 52 59 42 /note= /note=not transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS complement (35344 - 35832) /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least neg RBS, highest z value, longest orf, 489 bp length, good spacer, ATG start, starterator agrees (human reviewed), /note=Blast P: hypothetical protein PBI_ABCAT_41 [Mycobacterium phage ABCat] Mycobacterium phage ABCat 320 320 100% 7e-110 100.00% 162 AGR48881.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 41 function unknown 162 330 1e-90 E 214179 /note= /note=HHPRED: No Quality Match 5U59_A Designed dimeric coiled coil peptide with two terpyridine side chains; designed peptide, synthetic, metal coordination framework, supramolecular assembly, DE NOVO PROTEIN; HET: CIT, 7WJ; 2.2A {N/A} 83.2 11.7284 3 22 102 121 5.7 /note= /note=not a transmembrane, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS complement (35825 - 36121) /note=GM and GL start, coding potential, blast matches, all gp good, likely gene /note= /note=good RBS, high z value, good spacer, longest orf, 297 bp length, starterator agrees (human reviewed), /note=Blast P: hypothetical protein SEA_TOTO_43 [Mycobacterium phage Toto] Mycobacterium phage Toto 204 204 100% 7e-66 100.00% 98 YP_009208451.1 , keep current start /note= /note=Function: /note=PhagesDB: ABCat 42 function unknown 98 211 7e-55 E 213912 /note= /note=HHPRED: No Quality Match PF08815.15 Nuc_rec_co-act ; Nuclear receptor coactivator 60.9 7.14286 24 31 57 64 14 /note= /note=not transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS complement (36229 - 36357) /note=GL and GM start, coding potential, blast matches, 108 bp gap from previous, 129 bp length, likely gene /note= /note=good RBS, high z value, good spacer, 129 bp length, starterator agrees (human reviewed), /note=Blast P: hypothetical protein SEA_TOTO_44 [Mycobacterium phage Toto] Mycobacterium phage Toto 83.6 83.6 100% 1e-19 100.00% 42 YP_009208452.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 43 function unknown 42 85 8e-17 E 1247 /note= /note=HHPRED: No Quality match 4XJC_A Deoxycytidine triphosphate deaminase; bifunctional, TTP binding, complex, hydrolase; HET: TTP; 2.35A {Bacillus halodurans C-125} SCOP: b.85.4.0 79.9 35.7143 1 16 19 34 2.8 /note= /note=Not transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=is on approved list of functions CDS complement (36357 - 36524) /note=GL and GM start, coding potential, blast matches, 168 bp length, likely gene /note= /note=least neg RBS, best z value, good spacer, longest orf, ATG start,168 bp length, starterator agree (human reviewed) /note=Blast P: site-specific recombination directionality factor RDF [Mycobacterium phage Toto] Mycobacterium phage Toto 109 109 100% 8e-30 100.00% 55 YP_009208453.1, keep current start /note= /note=Functions: /note=PhagesDB: ABCat 44 function unknown 55 110 1e-24 E 84692 /note= /note=HHPRED: No Quality Match 6MQU_B PL5, designed TM pentamer; designed, engineered, transmembrane, pentamer, phospholamban, DE NOVO PROTEIN; 3.17A {N/A} 75.9 14.5455 3 11 13 21 5.7 /note= /note=Not transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved functions list CDS complement (36521 - 36757) /note=GL and GM start, coding potential, blast matches, 171 bp length, likely gene /note= /note=good RBS, high z value, good spacer, 237 bp length, Starterator does not agree it chose start 5, /note=Blast P: gp48 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 160 160 100% 5e-49 100.00% 78 NP_817497.1 , change start to 36757 /note= /note=Function: /note=PhagesDB:244 48 function unknown 78 167 1e-41 E 85211 /note= /note=HHPRED: No quality Match 5SVY_A MORC family CW-type zinc finger protein 3; reader, histone, chromatin, methylation, methyllysine, TRANSCRIPTION; HET: MLZ; 1.05A {Homo sapiens} 77.6 16.6667 1 14 30 43 2 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS complement (36750 - 36965) /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, high spacer, longest orf, 216 bp length, starterator agrees (human reviewed), /note=Blast P: hypothetical protein SEA_TOTO_47 [Mycobacterium phage Toto] Mycobacterium phage Toto 142 142 100% 2e-42 100.00% 71 YP_009208455.1, keep current start /note= /note=Function /note=PhagesDB: CrystalP 48 function unknown 71 147 8e-36 E 85132 /note= /note=HHPRED: No Quality Match 8WXS_A FI02030p; piRNA, Tudor domain-containing protein, RNA BINDING PROTEIN; 2.0A {Drosophila melanogaster} 35.8 46.4789 50 80 18 51 93 /note= /note=not transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is in approved function list CDS complement (36984 - 37130) /note=GL and GM start, coding potential, blast matches, 147 bp length, likely gene /note= /note=starterator agree (human reviewed), good spacer, 147 bp length, no large gap, ATG start, /note=Blast P: gp50 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 100 100 100% 2e-26 100.00% 48 NP_817499.1, keep current start /note= /note=Function: /note=PhagesDB: AmericanBeauty 53 function unknown 48 108 5e-24 E 85134 /note= /note=HHPRED: No Quality Match 6Y7G_B Ras-related protein Rab-3C; RAB3C, human Ras-related protein Rab-3C, Structural Genomics, Structural Genomics Consortium, SGC; HET: GDP, BTB; 2.3A {Homo sapiens} SCOP: c.37.1.0 74.9 20.8333 217 227 2 12 6.1 /note= /note=not a transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS complement (37130 - 37525) /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=good RBS, highest z value, good spacer, longest orf, 396 bo length, starterator agree (human reviewed), ATG start, /note=Blast P: hypothetical protein SEA_TOTO_49 [Mycobacterium phage Toto] Mycobacterium phage Toto 267 267 100% 1e-89 100.00% 131 YP_009208457.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 48 function unknown 131 263 2e-70 E 814 /note= /note=HHPRED: No Quality Match PF07865.16 DUF1652 ; Protein of unknown function (DUF1652) 89.8 37.4046 13 64 9 58 4.8 /note= /note=not transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS complement (37812 - 38114) /note=GL and GM start, coding potential, blast matches, 287 bp gap from previous,, likely gene /note= /note=least neg RBS, highest z value, good spacer, 303 bp length, starterator agrees (human reviewed), /note=Blast P: gp52 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 194 194 100% 7e-62 100.00% 100 NP_817501.1, keep current start /note= /note=Function: /note=PhagesDB:244 52 function unknown 100 201 6e-52 E 85144 /note= /note=HHPRED:No Quality Match 4Z3N_A Putative drug/sodium antiporter; transporter, TRANSPORT PROTEIN; HET: OLC, CAC; 2.7A {Escherichia coli} 88 83 406 491 6 89 10 /note= /note=Transmembrane protein, membrane/alpha TM according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 38365 - 39246 /note=GL and GM start, coding potential, blast matches, 251 bp gap from previous, switch in gene orientation, unlikely gene /note= /note=good RBS, highest z value, longest orf, 882 bp length, starterator agree (human reviewed), /note=Blast P: integrase [Mycobacterium phage Toto] Mycobacterium phage Toto 596 596 100% 0.0 100.00% 293 YP_009208459.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 50 tyrosine integrase 293 580 1e-165 E 213960 /note= /note=HHPRED: Not best Choice 5C6K_A Integrase; Integrase, tyrosine recombinase, integration, site-specific recombination, hydrolase; 1.9A {Enterobacteria phage P2} SCOP: d.163.1.1 100 99.6587 11 279 1 293 4.7e-31 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 39385 - 39624 /note=GL and GM start, coding potential, blast matches,139 bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, ATG start, longest orf, 240 bp length, starterator agrees (human reviewed), good spacer, /note=Blast P:gp54 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 157 157 100% 6e-48 100.00% 79 NP_817503.1, keep current start /note= /note=Function: /note=PhagesDB:Dusk 51 function unknown 79 159 3e-39 E 800 /note= /note=HHPRED: No quality match 4F3Q_A Transcriptional regulatory protein CBU_1566; YebC family, TRANSCRIPTION; HET: MSE; 2.15A {Coxiella burnetii} SCOP: e.39.1.1 24.9 59.4937 3 64 11 58 130 /note= /note=not transmembrane protein, soluble/globular according to SOSUI and deep TMHMM /note= /note=is on approved function list CDS complement (39602 - 40375) /note=GL and GM start disagree, coding potential, blast matches, switch in gene orientation, likely gene /note= /note=least neg RBS, highest z value, high spacer, ATG start, longest orf, 774 bp length, smallest gap, similar starterator tracks agree (human reviewed) /note=Blast P: hypothetical protein Porky_53 [Mycobacterium phage Porky] Mycobacterium phage Porky 517 517 100% 0.0 100.00% 257 YP_002014374.1, change start to 40375 /note= /note=Function: /note=PhagesDB: BaboJay 50 function unknown 257 521 1e-148 E 213906 /note= /note=HHPRED: No Quality Match 7QHM_W Hypothetical membrane protein; supercomplex, respiratory chain, cytochrome bcc-aa3 supercomplex, proton translocation, bioenergetics, membrane protein, electron transport, OXIDOREDUCTASE; HET: LYC, 3PE, SMA, DGA, HAS, IZL, IX7, 9YF, LMT, HEC, PLM, HEM, MQ9, CDL;{Corynebacterium glutamicum ATCC 13032} 68.1 28.7938 36 106 179 253 130 /note= /note=Is a transmembrane protein, membrane/alpha TM according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS complement (40470 - 40901) /note=GL and GM start disagree, coding potential, blast matches, 257 bp gap from previous, likely gene /note= /note=Start 4 has good rbs, good z value, good spacer, ATG start, 300 bp length, starterator agrees (human reviewed), but doesn`t cover all GM potential. CrystalP calls start 2 (human). /note=Blast P: immunity repressor [Mycobacterium phage Murica] Mycobacterium phage Murica 206 206 100% 1e-66 100.00% 115 ATN91092.1, Change to start 2 /note= /note=Function: /note=PhagesDB: BaboJay 51 helix-turn-helix DNA binding protein 146 206 2e-53 E 34502 /note=HHPRED: No Quality Match PF19615.4 DUF6120 ; Family of unknown function (DUF6120) 61.1 58.5859 21 68 17 75 56 ALSO has similarity to lambda repressor proteins /note= /note=not transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 41127 - 41225 /note=GM start, No GL start, No coding potential, blast matches, switch in gene orientation, 358 bp gap from previous, 92 bp length, unlikely gene except that it seems to have been called in many E phages. Could also be the start of the next gene except no coding capacity in GM. /note= /note=least neg RBS, highest z score, ATG start, longest orf, 99 bp length, good spacer, starterator agree (human reviewed), /note=Blast P: gp57 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 65.1 65.1 100% 1e-12 100.00% 32 NP_817506.1, keep current start /note= /note=Function: /note=PhagesDB:Asriel 56 function unknown 32 65 7e-11 E 900 /note= /note=HHPRED: No Quality Match 6ZJ3_L6 Ribosomal protein eLEgr2; Single particle cryo-EM RNA modifications, RIBOSOME; HET: 1MA, 6MZ, MIA, B8N, 5MC, OMU, B8H, MA6, OMC, PSU, OMG, JMH, A2M, UR3, JMC, 7MG; 3.15A {Euglena gracilis} 43.2 50 45 61 8 24 110 /note= /note=Not a transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 41222 - 41359 /note=GL and GM start, coding potential, blast matches, 138 bp length, likely gene /note= /note=least neg RBS, highest z value, small gap, 138 bp length, ATG start, starterator agrees (human reviewed), /note=Blast P: gp58 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 92.0 92.0 100% 5e-23 100.00% 45 NP_817507.1, keep current start /note= /note=Function: /note=PhagesDB:Daikon_Draft 59 function unknown 45 89 3e-18 E 866 /note= /note=HHPRED: PF03345.19 DDOST_48kD ; Oligosaccharyltransferase 48 kDa subunit beta 96.3 82.2222 388 427 5 42 0.03 /note= /note=is a transmembrane protein, membrane/alphaTM according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 41356 - 42201 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, highest z value, good spacer, longest orf, 846 bp length, ATG start, starterator agrees (human reviewed), /note=Blast P: pentapeptide repeat protein [Mycobacterium phage NelitzaMV] Mycobacterium phage NelitzaMV 566 566 100% 0.0 100.00% 281 YP_009197723.1, keep current start /note= /note=Function: /note=PhagesDB: BadStone 56 pentapeptide repeat protein 281 552 1e-157 E 808 /note= /note=HHPRED: Not Top Choice 6FLS_A Pentapeptide repeat family protein; Pentapeptide repeat protein Clostridium botulinum, UNKNOWN FUNCTION; HET: GOL; 2.8A {Clostridium botulinum} 99.7 43.0605 82 208 43 164 2.8e-17 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 42203 - 42349 /note=GL and GM start, coding potential, blast matches, 147 bp length, likely gene /note= /note=least neg RBS, highest z value, ATG start, 147 bp length, good spacer, starterator agrees (human reviewed), /note=Blast P: hypothetical protein Kostya_60 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 97.8 97.8 100% 3e-25 100.00% 48 YP_002014528.1 , keep current start /note= /note=Function: /note=PhagesDB:ABCat 57 function unknown 48 99 3e-21 E 757 /note= /note=HHPRED: No Quality Match 2MRL_A Uncharacterized protein BTH I2711; UNKNOWN FUNCTION, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID; NMR {Burkholderia thailandensis E264} 77.9 87.5 6 51 1 43 29 /note= /note=not a transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 42346 - 42624 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg RBS, ok z value, ATG start, smallest gap, 279 bp length, good spacer, starterator agrees (human reviewed), /note=Blast P gp61 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 192 192 100% 2e-61 100.00% 92 NP_817510.1, keep current start /note= /note=Function: /note=PhagesDB: DrDrey 59 function unknown 92 199 2e-51 E 830 /note= /note=HHPRED: Not Top Choice PF19126.5 DUF5810 ; Family of unknown function (DUF5810) 92.9 19.5652 2 19 69 87 0.15 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 43168 - 43473 /note=GL and GM start, coding potential, blast matches, 544 bp gap from previous, likely gene /note= /note=least neg RBS, highest z value, longest orf, 306 bp length, good spacer, ATG start, starterator agrees (human reviewed), /note=Blast P: gp62 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 202 202 100% 3e-65 100.00% 101 NP_817511.1, keep current start /note= /note=Function: /note=PhagesDB:Command613 63 function unknown 101 207 8e-54 E 822 /note= /note=HHPRED: No Quality Match 5NUS_B p44; RING finger domain, von Willebrand factor A like, transcription; 2.2A {Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)} 47 6.93069 5 12 65 72 22 /note= /note=not a transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 43492 - 43599 /note=GM start, No GL start, coding potential, blast matches, 108 bp length, unlikely gene /note= /note=Only start, high z value, least neg RBSm longest orf, 108 bp length, ATG start, starterator agree (human reviewed), /note=Blast P: gp63 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 71.2 71.2 100% 5e-15 100.00% 35 NP_817512.1 , keep current start /note= /note=Function: /note=PhagesDB: 244 63 function unknown 35 77 2e-14 E 1067 /note= /note=HHPRED: No Quality Match 2XZE_Q CHARGED MULTIVESICULAR BODY PROTEIN 3; HYDROLASE-PROTEIN TRANSPORT COMPLEX; 1.75A {HOMO SAPIENS} 58 20 31 38 1 8 15 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 43607 - 43840 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=only start, longest orf, least neg rbs, highest z value, 234 bp length, ATG start, starterator has human call. /note=Blast P: hypothetical protein SEA_TOMASZEWSKI_58 [Mycobacterium phage Tomaszewski] Mycobacterium phage Tomaszewski 162 162 100% 1e-49 100.00% 103 QDK02130.1, keep current start /note= /note=Function: /note=PhagesDB:ABCat 61 function unknown 77 179 2e-45 E 206634 /note= /note=HHPRED: PF09538.15 FYDLN_acid ; Protein of unknown function (FYDLN_acid) 95.5 41.5584 2 36 1 33 0.039 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=in approved function list CDS 43840 - 44001 /note=GL and GM start, coding potential, blast matches, switch in gene orientation, 117 bp gap from previous, 162 bp length, unlikely gene /note= /note=least neg RBS, highest z value, 162 bp length, good spacer, ATG start, starterator agree (human reviewed), /note=Blast P: gp65 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 113 113 100% 4e-31 100.00% 53 NP_817514.1, keep current start /note= /note=Function: /note=PhagesDB: 244 65 function unknown 53 122 3e-28 E 85029 /note= /note=HHPRED: No Quality Match SCOP_d5hs7a1 a.4.5.0 (A:5-105) automated matches {Bacillus subtilis [TaxId: 224308]} | CLASS: All alpha proteins, FOLD: DNA/RNA-binding 3-helical bundle, SUPFAM: `Winged helix` DNA-binding domain, FAM: automated matches 76.5 69.8113 67 101 8 45 9.7 /note= /note=not a transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=in approved function list CDS 44222 - 44551 /note=GL and GM start, coding potential, blast matches, 221 bp gap from previous, likely gene /note= /note=starterator agree (human reviewed), least neg rbs, high z value, 330 bp length, /note=Blast P: hypothetical protein SEA_TOTO_64 [Mycobacterium phage Toto] Mycobacterium phage Toto 227 227 100% 1e-74 100.00% 109 YP_009208472.1 , keep current start /note= /note=Function: /note=PhagesDB:ABCat 63 function unknown 109 221 7e-58 E 212298 /note= /note=HHPRED: PF19698.4 DUF6197 ; Family of unknown function (DUF6197) 99.9 98.1651 8 137 1 108 3.4e-21 /note= /note=not a transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 44548 - 45516 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=ATG start, longest orf, 969 bp length, starterator agree (human reviewed), /note=Blast P: exonuclease [Mycobacterium phage Porky] Mycobacterium phage Porky 664 664 100% 0.0 100.00% 322 YP_002014387.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 64 exonuclease 322 655 0 E 212237 /note= /note=HHPRED: PF19698.4 DUF6197 ; Family of unknown function (DUF6197) 99.9 98.1651 8 137 1 108 3.4e-21 /note= /note=not a transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 45513 - 45923 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=ATG start, starterator agrees (human reviewed), 411 bp length, small gap /note=Blast P: hypothetical protein SEA_TOTO_66 [Mycobacterium phage Toto] Mycobacterium phage Toto 280 280 100% 1e-94 100.00% 136 YP_009208474.1, keep current start /note= /note=Function: /note=PhagesDB:Adnama 72 function unknown 136 284 7e-77 E 213850 /note= /note=HHPRED: No Quality Match PF01611.21 Filo_glycop ; Filovirus glycoprotein 51 25.7353 112 143 21 56 14 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 45916 - 46638 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least neg RBS, high z value, ATG start, starterator agrees (human reviewed), good spacer, 723 bp length, /note=Blast P: ERF family ssDNA binding protein [Mycobacterium phage Porky] Mycobacterium phage Porky 494 494 100% 4e-176 100.00% 240 YP_002014389.1, keep current start /note= /note=Function: /note=PhagesDB: ABCat 66 ERF family ssDNA binding protein 240 489 1e-138 E 195402 /note= /note=HHPRED: PF04404.17 ERF ; ERF superfamily 99.9 57.0833 1 147 21 158 1.7e-23 /note= /note=not a transmembrane protein, soluble/globular according to SOSUI and deepTMHMM /note= /note=is on approved function list CDS 46631 - 46942 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=high z value, longest orf, 312 bp length, ATG start, good spacer, starterator agrees (human reviewed), /note=Blast P: hypothetical protein SEA_TOTO_68 [Mycobacterium phage Toto] Mycobacterium phage Toto 220 220 100% 4e-72 100.00% 103 YP_009208476.1, keep current start /note= /note=Function: /note=PhagesDB: BaboJay 67 function unknown 103 225 3e-59 E 826 /note= /note=HHPRED: not top choice PF19126.5 DUF5810 ; Family of unknown function (DUF5810) 93.1 15.534 2 18 81 97 0.2 /note= /note=not a transmembrane protein, soluble/globular according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 46942 - 47412 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least neg rbs, high z value, ATG start, 471 bp length, good spacer, starterator agree (human reviewed) /note=Blast P: hypothetical protein Kostya_71 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 322 322 100% 7e-111 100.00% 156 YP_002014539.1, keep current start /note= /note=Function: /note=PhagesDB:ABCat 68 function unknown 156 344 6e-95 E 829 /note= /note=HHPRED: No quality match 8IUJ_5B COX5b-2; Electron transport chain, supercomplex, membrane protein, Euglena gracilis, ELECTRON TRANSPORT; HET: HEC, HEA, CDL, 3PE, PX2, HEM, S12, PC1;{Euglena gracilis} 48.6 26.2821 124 166 7 48 45 /note= /note=not a transmembrane protein, globular/soluble according to deepTMHMM and SOSUI /note= /note=is on approved function list CDS 47412 - 47780 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Not least negative RBS, Z-score slightly under 2. spacer in correct range, 369 bp length, starterator agrees (human called), Blast P: hypothetical protein Kostya_72 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 245 245 100% 2e-81 100.00% 122 YP_002014540., keep current start. /note= /note=Function: /note= Blast P/NCBI match: hypothetical protein Kostya_72 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 245 245 100% 2e-81 100.00% 122 YP_002014540. /note= /note=Phages db: 244 73 function unknown 122 241 7e-64 E 180 /note= /note=HHPred: 4ZWQ_C Recombination protein uvsY; recombination, DNA binding, homo-heptamer, asymmetry, alpha barrel, VIRAL PROTEIN; 2.351A {Enterobacteria phage T4} /note= /note= /note=Not transmembrane (slouble, globular) via SOUSI and DEEPTHMM /note= /note=is on the function list CDS 47783 - 48154 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, good spacer length, 372 bp length, Starterator agrees, Blast P: hypothetical protein DRDREY_73 [Mycobacterium phage DrDrey] Mycobacterium phage DrDrey 257 257 100% 5e-86 100.00% 125 YP_008409466.1, keep gene start /note= /note=Function: /note= /note=Phages db: ABCat 70 function unknown 125 259 1e-69 E 213850 /note=HHPred: 8V3T_L Collar (CD1362); Phage tail-like, bacteriocin, collar, pre-contraction, VIRUS LIKE PARTICLE;{Clostridioides difficile} /note= /note=not transmembrane protein (globular and soluble via SOUSI and DEEPTHMM) CDS 48154 - 48327 /note=GL and GM start, coding potential, blast matches, 174 bp length, likely gene /note= /note=Least negative RBS, z-score under 2 (1.604), appropriate spacer length, 174 bp length, starterator agrees (human called), Blast P: gp75 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 116 116 100% 2e-32 100.00% 57 NP_817524.1, keep gene start /note= /note=Function: /note= /note=Phages db: Argent26 78 function unknown 57 115 4e-26 E /note= /note=HHPred: no quality matches 6GVW_J BRCA1-A complex subunit RAP80; Deubiquitinase complex, DUB, Lysine-63 linkage specific, BRCC36-containing, BRCA1A binding, SIGNALING PROTEIN; 3.75A {Mus musculus} /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=likely hypothetical protien (in approved function list) CDS 48330 - 48563 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer length, 234 bp, starterator agrees (human called), Blast P: gp76 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 153 153 100% 2e-46 100.00% 77 NP_817525.1, keep gene start /note= /note=Function: /note=PhagesDB:Buck 76 function unknown 77 155 4e-38 E 820 /note= /note=HHPRED: No Quality Match PF12022.13 COG2_C ; COG complex component, COG2, C-terminal 61.5 53.2468 227 273 2 43 31 /note= /note=not a transmembrane protein, globular/soluble according to SOSUI and deepTMHMM /note= /note=is on approved functions list CDS 48560 - 48973 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score under 2 (1.476), appropriate spacers, 414 bp, starterator agrees, Blast P: gp77 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 285 285 100% 6e-97 100.00% 137 NP_817526.1, keep gene start /note= /note=Function: /note= /note=Phages db: 244 77 function unknown 137 292 3e-79 E /note= /note=HHPred: high quality match 3UQZ_A DNA processing protein DprA; SAM and Rossmann Fold, DNA processing protein A, DNA BINDING PROTEIN; HET: SO4, MSE; 2.7A {Streptococcus pneumoniae} SCOP: a.60.17.1, l.1.1.1, c.129.1.4 /note= /note=Not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=Is on approved function list CDS 48970 - 49287 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Not least negative RBS (highest value), z-score less than 2 (0.59), appropriate spacer, 318 bp length, starterator agrees, Blast P: HNH endonuclease [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 220 220 100% 3e-72 100.00% 105 NP_817527.1, /note= /note=Function: /note= /note=NCBI: >ref|YP_008409470.1| HNH endonuclease [Mycobacterium phage DrDrey] >ref|YP_008410091.1| HNH endonuclease [Mycobacterium phage Contagion] >ref|YP_008531156.1| HNH endonuclease [Mycobacterium phage Quink] >ref|YP_008857568.1| HNH endonuclease [Mycobacterium phage PhatBacter] >ref|YP_008858359.1| HNH endonuclease [Mycobacterium phage Nala] /note= /note=HHPred: 6GHC_B 5-methylcytosine-specific restriction enzyme A; HNH ENDONUCLEASE, MODIFICATION DEPENDENT RESTRICTION, 5-METHYLCYTOSINE, 5MC, 5-HYDROXYMETHYLCYTOSINE, 5HMC, BBA-ME NUCLEASE, ScoMcrA, HYDROLASE; 2.85A {Escherichia coli (strain K12)} /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=is on approved function list CDS 49277 - 49513 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, lowest spacer but still high (14), 237 bp, starterator agrees (human generated), /note=Blast P: gp79 [Mycobacterium phage 244] Mycobacterium phage 244 159 159 100% 6e-48 100.00% 135 YP_654834.1, keep gene start /note= /note=Function: /note= /note=NCBI: YP_654834 gp79 [Mycobacterium phage 244] >gb|ABD58054.1| hypothetical protein PBI_244_79 [Mycobacterium phage 244] /note= /note=HHPred: no quality matches- PF18495.6 VbhA ; Antitoxin VbhA 85.2 26.9231 23 44 46 67 2.6 /note= /note=not transmembrane protein (Soluble and Globular via SOUSI and DeepTHMM) /note= /note=in approved function list CDS 49510 - 50160 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Not least negative RBS, z-score below 2 (0.895), appropriate spacer, 651 bp, starterator agrees (human generated), Blast P: gp80 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 441 441 100% 4e-156 100.00% 216 NP_817529.1, keep gene start /note= /note=Function: /note= /note=NCBI: gp80 [Mycobacterium phage Cjw1] >ref|YP_002014399.1| hypothetical protein Porky_78 [Mycobacterium phage Porky] >ref|YP_002014547.1| hypothetical protein Kostya_79 [Mycobacterium phage Kostya] >ref|YP_008051558.1| hypothetical protein PBI_MURPHY_79 [Mycobacterium phage Murphy] >ref|YP_008051704.1| hypothetical protein PBI_DUMBO_79 /note= /note=HHPred: PF09681.15 Phage_rep_org_N ; N-terminal phage replisome organiser (Phage_rep_org_N) 97.9 /note= /note=not transmembrane protien (soluble and globular via SOUSI and DeepTHMM) /note= /note=is in approved function list CDS 50157 - 50489 /note=GL and GM start disagree, coding potential, blast matches, all gp good, likely gene /note= /note=Not least negative RBS, Z-score under 2 (1.956), appropriate spacer, starterator report picked start 2, Change gene start to 50157. New RBS is the least neg, new z-score 3.072, slightly low spacer, 333 bp, Blast P: hypothetical protein PBI_MURPHY_80 [Mycobacterium phage Murphy] Mycobacterium phage Murphy 228 228 100% 7e-75 100.00% 110 YP_008051559.1 /note= /note=Function: /note= /note=NCBI: hypothetical protein PBI_MURPHY_80 [Mycobacterium phage Murphy] >ref|YP_008052013.1| hypothetical protein PBI_PHRUX_77 [Mycobacterium phage Phrux] >ref|YP_009011841.1| hypothetical protein LILAC_82 [Mycobacterium phage Lilac] >ref|YP_009208486.1| hypothetical protein SEA_TOTO_78 [Mycobacterium phage Toto] >ref|YP_009225366.1| hypothetical protein SEA_MINDY_79 /note= /note=HHPred: no quality matches- PF01611.21 Filo_glycop ; Filovirus glycoprotein /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=is in approved function list CDS 50536 - 51744 /note=GL and GM start disagree, coding potential, blast matches, all gp good, likely gene /note= /note=Not least negative RBS, z-score above 2, too high spacer (15), 1209 bp, starterator agrees (human generated), Blast P: Select seq ref|NP_817531.1| DnaB-like replicative helicase [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 827 827 100% 0.0 100.00% 420 NP_817531.1, keep gene start /note= /note=Function: /note= /note=NCBI: DnaB-like replicative helicase [Mycobacterium phage Cjw1] >ref|YP_002014401.1| DnaB-like replicative helicase [Mycobacterium phage Porky] >ref|YP_008051706.1| DnaB-like replicative helicase [Mycobacterium phage Dumbo] >ref|YP_008052014.1| DnaB-like replicative helicase [Mycobacterium phage Phrux] >ref|YP_008409474.1| DnaB-like replicative helicase [Mycobacterium phage DrDrey] /note= /note=HHPred: 3BGW_B DNAB-Like Replicative Helicase; ATPase, REPLICATION; 3.91A {Bacillus phage SPP1} 100% /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) CDS 51741 - 51929 /note=GL and GM start, coding potential, blast matches, 189 bp length, likely gene /note= /note=Not least negative RBS, z-score above 2, low spacer, 189 bp, starterator agrees, Blast P: Select seq ref|YP_008430596.1| hypothetical protein GOKU_80 [Mycobacterium phage Goku] Mycobacterium phage Goku 127 127 100% 1e-36 100.00% 67 YP_008430596.1. Keep gene start /note= /note= /note=Function; /note= /note=NCBI: hypothetical protein GOKU_80 [Mycobacterium phage Goku] >ref|YP_009591620.1| hypothetical protein FDG60_gp080 [Mycobacterium phage Eureka] >gb|AYQ99070.1| hypothetical protein PBI_BABOJAY_79 /note= /note=HHPred: no quality matches PF22564.1 HAAS ; HAAS 57.4 /note= /note=not transmembrane protein (Soluble and globular via SOUSI and DeepTHMM) /note= /note=in approved function list CDS 51926 - 52186 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Not least negative RBS, z-score below 2 (1.764), spacer above 12, 261 bp, starterator agrees (human generated), Blast P: transcriptional regulator WhiB-like [Mycobacterium phage Phrux] Mycobacterium phage Phrux 181 181 100% 5e-57 100.00% 86 YP_008052016.1. Keep gene start /note= /note=Function: /note= /note=NCBI: transcriptional regulator WhiB-like [Mycobacterium phage Phrux] >ref|YP_009011844.1| transcriptional regulator WhiB-like [Mycobacterium phage Lilac] >ref|YP_009225369.1| transcriptional regulator WhiB-like [Mycobacterium phage Mindy] >ref|YP_009613708.1| transcriptional regulator WhiB-like [Mycobacterium phage Pumpkin] >gb|AEK08932.1| WhiB family transcription factor [Mycobacterium phage Henry] /note= /note=HHPred: quality match- Probable transcriptional regulator WhiB7; Redox-sensitive, Iron-sulfur cluster, transcription, activator; HET: SF4, MSE; 1.55A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)} /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=in approved function list CDS 52161 - 52382 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 222 bp, starterator agrees (human generated), Blast P: Select seq ref|NP_817534.1| gp85 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 149 149 100% 9e-45 100.00% 73 NP_817534.1 /note= /note=Function; /note= /note=NCBI: gp85 [Mycobacterium phage Cjw1] >ref|YP_002014404.1| hypothetical protein Porky_83 [Mycobacterium phage Porky] >ref|YP_002014552.1| hypothetical protein Kostya_84 [Mycobacterium phage Kostya] >ref|YP_008051563.1| hypothetical protein PBI_MURPHY_84 [Mycobacterium phage Murphy] >ref|YP_008052017.1| hypothetical protein PBI_PHRUX_81 [Mycobacterium phage Phrux] /note= /note=HHPred: no quality match- SCOP_d1nxia1 d.58.47.1 (A:1-124) Hypothetical protein VC0424 {Vibrio cholerae [TaxId: 666]} | CLASS: Alpha and beta proteins (a+b), FOLD: Ferredoxin-like, SUPFAM: Hypothetical protein VC0424, FAM: Hypothetical protein VC0424 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=in approved function list CDS 52375 - 52701 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, appropriate spacers, 327 bp, starterator agrees (human generated), Blast P: hypothetical protein PBI_PHRUX_82 [Mycobacterium phage Phrux] Mycobacterium phage Phrux 220 220 100% 5e-72 100.00% 108 YP_008052018.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein PBI_PHRUX_82 [Mycobacterium phage Phrux] >ref|YP_009208491.1| hypothetical protein SEA_TOTO_83 [Mycobacterium phage Toto] >ref|YP_009225371.1| hypothetical protein SEA_MINDY_84 [Mycobacterium phage Mindy] >ref|YP_654841.1| gp86 [Mycobacterium phage 244] >gb|AEK08934.1| hypothetical protein PBI_HENRY_83 [Mycobacterium phage Henry] >gb|APU02900.1| /note= /note=HHPred: no quality matches- PF11740.13 KfrA_N ; Plasmid replication region DNA-binding N-term /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=in approved function list CDS 52698 - 53060 /note=GL and GM start disagree, coding potential, blast matches, all gp good, likely gene /note= /note=Not least negative RBS, z-score under 2 (1.277), spacer above 12 (16), 384 bp, Starterator disagrees (called start 1). Changed start to 52698. Least negative RBS, z-score under 2 (1.866), apropriate spacer, Blast P: hypothetical protein Porky_85 [Mycobacterium phage Porky] Mycobacterium phage Porky 244 244 100% 4e-81 100.00% 120 YP_002014406.1 /note= /note=Function: /note= /note=NCBI: hypothetical protein Porky_85 [Mycobacterium phage Porky] >ref|YP_008051711.1| hypothetical protein PBI_DUMBO_86 [Mycobacterium phage Dumbo] >ref|YP_008052019.1| hypothetical protein PBI_PHRUX_83 [Mycobacterium phage Phrux] >ref|YP_008409479.1| hypothetical protein DRDREY_86 [Mycobacterium phage DrDrey] >ref|YP_008430601.1| hypothetical protein GOKU_85 [Mycobacterium phage Goku] /note= /note=phages db: AmericanBeauty 90 Holliday junction resolvase 120 241 7e-64 E /note= /note=HHPred: Holliday junction resolvase; archeal holliday junction resolvase helicase DNA binding enzyme phage 15-6 thermus thermophilus, RECOMBINATION; HET: SO4, MSE; 2.5A {Thermus thermophilus phage 15-6} /note= /note=is a transmembrane protein? (membrane and globular) /note= /note=in approved function list CDS 53057 - 53251 /note=GL and GM start, coding potential, blast matches, 195 bp length, likely gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 195 bp, Starterator agrees (human generated), Blast P: hypothetical protein Porky_86 [Mycobacterium phage Porky] Mycobacterium phage Porky 130 130 100% 1e-37 100.00% 64 YP_002014407.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein Porky_86 [Mycobacterium phage Porky] >ref|YP_002014555.1| hypothetical protein Kostya_87 [Mycobacterium phage Kostya] >ref|YP_008051712.1| hypothetical protein PBI_DUMBO_87 [Mycobacterium phage Dumbo] >ref|YP_008409480.1| hypothetical protein DRDREY_87 [Mycobacterium phage DrDrey] >ref|YP_008410101.1| hypothetical protein PBI_CONTAGION_83 [Mycobacterium phage Contagion] /note= /note=HHPred: no quality matches- PF06785.16 Monovalent cation/H+ antiporter subunit E; cryoEM, membrane protein, respiratory system; HET: SF4; 4.0A {Pyrococcus furiosus COM1} /note= /note=is a transmembrane protein (membrane and alpha TM via SOSUI and DeepTHMM) /note= /note=in approved function list CDS 53406 - 54347 /note=GL and GM start, coding potential, blast matches, 155 bp gap from previous, likely gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 942 bp, starterator agrees (human generated), Blast P: polynucleotide kinase [Mycobacterium phage Murphy] Mycobacterium phage Murphy 639 639 100% 0.0 100.00% 313 YP_008051567.1. Keep gene start /note= /note=Function: /note= /note=Phages db: AmericanBeauty 92 polynucleotide kinase /note= /note=NCBI: polynucleotide kinase [Mycobacterium phage Murphy] >ref|YP_008409481.1| polynucleotide kinase [Mycobacterium phage DrDrey] >ref|YP_009208494.1| polynucleotide kinase [Mycobacterium phage Toto] >ref|YP_009225374.1| polynucleotide kinase [Mycobacterium phage Mindy] >gb|AEJ92607.1| polynucleotide kinase [Mycobacterium phage Rakim] /note= /note=HHPred: 4XRP_D Pnkp1; RNA repair, kinase, phosphatase, methyltransferase, ligase, PROTEIN BINDING; HET: GOL, SO4, PO4; 3.3A {Capnocytophaga gingivalis} /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=in approved function list CDS 54454 - 54822 /note=GL and GM start, coding potential, blast matches, 107 bp gap from previous, likely gene /note= /note=Least negative RBS, z-score over 2, appropriate space, 369 bp, starterator agrees (human generated), Blast P: hypothetical protein PBI_MURPHY_89 [Mycobacterium phage Murphy] Mycobacterium phage Murphy 254 254 100% 4e-85 100.00% 122 YP_008051568.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein PBI_MURPHY_89 [Mycobacterium phage Murphy] >ref|YP_008409482.1| hypothetical protein DRDREY_89 [Mycobacterium phage DrDrey] >ref|YP_008410103.1| hypothetical protein PBI_CONTAGION_85 [Mycobacterium phage Contagion] >ref|YP_008430604.1| hypothetical protein GOKU_88 [Mycobacterium phage Goku] >ref|YP_008859523.1| hypothetical protein BRUIN_86 /note= /note=HHPred: no quality matches 7JZW_J Type I-F anti-CRISPR protein; CRISPR, HYDROLASE;{Pseudomonas aeruginosa} /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 54795 - 54917 /note=GL and GM start disagree, some coding potential, blast matches, 123 bp length, likely gene /note= /note=Least negative RBS, z-score above 2, spacer under 8 (5), 123 bp, starterator agrees (human generated), Blast P: Select seq ref|YP_002014558.1| hypothetical protein Kostya_90 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 79.3 79.3 100% 5e-18 100.00% 40 YP_002014558.1. Keep gene start. /note= /note=Function: /note= /note=NCBI: hypothetical protein Kostya_90 [Mycobacterium phage Kostya] >ref|YP_008409483.1| hypothetical protein DRDREY_90 [Mycobacterium phage DrDrey] >ref|YP_008410104.1| hypothetical protein PBI_CONTAGION_86 [Mycobacterium phage Contagion] >ref|YP_008430605.1| hypothetical protein GOKU_89 [Mycobacterium phage Goku] >ref|YP_008859524.1| hypothetical protein BRUIN_87 [Mycobacterium phage Bruin] /note= /note=HHPred: not quality match- SCOP_d4pv1e_ f.23.24.1 (E:) PetL subunit of the cytochrome b6f complex {Mastigocladus laminosus [TaxId: 83541]} | CLASS: Membrane and cell surface proteins and peptides, FOLD: Single transmembrane helix, SUPFAM: PetL subunit of the cytochrome b6f complex, FAM: PetL subunit of the cytochrome b6f complex /note= /note=membrane protein? (globular + SP and membrane via DeepTHMM and SOUSI) CDS 54914 - 56239 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, spacer above 12 (13), 1326 bp, starterator agrees (human generated), Blast P: RNA ligase [Mycobacterium phage Contagion] Mycobacterium phage Contagion 920 920 100% 0.0 100.00% 441 YP_008410105.1. Keep gene start /note= /note=Function: /note= /note=NCBI: RNA ligase [Mycobacterium phage Contagion] >ref|YP_008859525.1| RNA ligase [Mycobacterium phage Bruin] >ref|YP_009208497.1| RNA ligase [Mycobacterium phage Toto] >ref|YP_009225377.1| RNA ligase [Mycobacterium phage Mindy] >gb|AEJ92610.1| RNA ligase [Mycobacterium phage Rakim] /note= /note=HHPred: 6VTB_A RNA ligase; RNA repair, adenylyltransferase, LIGASE; HET: ATP; 1.547A {Naegleria gruberi} /note= /note=not a transmembrane protien (soluble and globular via SOUSI and DeepTHMM /note= /note=on approved function list CDS 56276 - 57097 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2.84, spacer above 12 (13), 822 bp, starterator agrees (human generated), Blast P: hypothetical protein PBI_DUMBO_92 [Mycobacterium phage Dumbo] Mycobacterium phage Dumbo 553 553 100% 0.0 100.00% 273 YP_008051717.1. Keep gene start /note= /note=Function: /note= /note=phages db: CrystalP 91 helix-turn-helix DNA binding protein 273 537 1e-152 E /note= /note=NCBI: hypothetical protein PBI_DUMBO_92 [Mycobacterium phage Dumbo] >ref|YP_008052026.1| hypothetical protein PBI_PHRUX_90 [Mycobacterium phage Phrux] >ref|YP_008052269.1| hypothetical protein M039_gp095 [Mycobacterium phage Phaux] >ref|YP_008409485.1| hypothetical protein DRDREY_92 [Mycobacterium phage DrDrey] >ref|YP_008410106.1| hypothetical protein PBI_CONTAGION_88 [Mycobacterium phage Contagion] /note= /note=HHPred: 8VD6_A CAP REPEAT; diffusion, generation, de novo, RoseTTAFold, sequence, ProteinGenerator, PROTEIN GENERATOR, deep learning, machine learning, generative model, DE; 3.7A {synthetic construct} /note= /note=not transmembrane protien (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 57094 - 57354 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score over 2, appropriate spacer, 261 bp, starterator agrees (human generated), Blast P: gp95 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 179 179 100% 1e-56 100.00% 86 NP_817544.1. Keep gene start /note= /note=Function: /note= /note=NCBI: gp95 [Mycobacterium phage Cjw1] >ref|YP_002014413.1| WhiB/HNH endonuclease [Mycobacterium phage Porky] >ref|YP_002014561.1| WhiB/HNH endonuclease [Mycobacterium phage Kostya] >ref|YP_008051572.1| WhiB [Mycobacterium phage Murphy] >ref|YP_008051718.1| WhiB [Mycobacterium phage Dumbo] /note= /note=Phages db: CrystalP 92 WhiB family transcription factor 86 186 3e-47 E /note= /note=HHPred: Transcriptional regulator WhiB1; nitric oxide, sigmaA, iron-sulfur, tuberculosis, Wbl protein, SIGNALING PROTEIN; HET: SF4; NMR {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)} 99.9 /note= /note=Not a transmembrane protien (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 57371 - 57529 /note=GL and GM start, coding potential, blast matches, 159 bp length, likely gene /note= /note=Least negative RBS, z-score above 2, spacer above 12 (13), 246 bp, starterator agrees (human generated), Blast P: hypothetical protein SEA_RIVERMONSTER_95 [Mycobacterium phage RiverMonster] Mycobacterium phage RiverMonster 109 109 100% 2e-29 100.00% 81 AVO23626.1. Keep gene start /note= /note=Function: /note= /note=NCBI: gp96 [Mycobacterium phage Cjw1] >ref|YP_002014414.1| hypothetical protein Porky_93 [Mycobacterium phage Porky] >ref|YP_002014562.1| hypothetical protein Kostya_94 [Mycobacterium phage Kostya] >ref|YP_008051573.1| hypothetical protein PBI_MURPHY_94 [Mycobacterium phage Murphy] >ref|YP_008051719.1| hypothetical protein PBI_DUMBO_94 [Mycobacterium phage Dumbo] >ref|YP_008052028.1| /note= /note=HHPred: no quality matches- PF11782.13 DUF3319 ; Protein of unknown function (DUF3319) 79.6 /note= /note=not a transmembrane protien (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 57526 - 57978 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=not least negative RBS, z-score under 2 (1.63), appropriate spacer, 453 bp, starterator agrees (human generated), Blast P: hypothetical protein DRDREY_95 [Mycobacterium phage DrDrey] Mycobacterium phage DrDrey 309 309 100% 8e-106 100.00% 150 YP_008409488.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein DRDREY_95 [Mycobacterium phage DrDrey] >ref|YP_009208501.1| hypothetical protein SEA_TOTO_93 [Mycobacterium phage Toto] >gb|AOT23974.1| hypothetical protein SEA_PHARSALUS_92 [Mycobacterium phage Pharsalus] >gb|APU02908.1| hypothetical protein SEA_CRYSTALP_94 [Mycobacterium phage CrystalP] >gb|AXH47638.1| hypothetical protein SEA_IHOP_93 /note= /note= /note=HHPred: no quality matches- PF12668.12 DUF3791 ; Protein of unknown function (DUF3791) 61.1 /note= /note=not a transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 57982 - 58104 /note=GL and GM start, coding potential, blast matches, 123 bp length, likely gene /note= /note=Least negative RBS, z-score above 2, appropriate space, 123 bp, starterator agrees (human generated), Blast P: hypothetical protein Kostya_96 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 78.6 78.6 100% 1e-17 100.00% 40 YP_002014564.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein Kostya_96 [Mycobacterium phage Kostya] >ref|YP_008051575.1| hypothetical protein PBI_MURPHY_96 [Mycobacterium phage Murphy] >ref|YP_008409489.1| hypothetical protein DRDREY_96 [Mycobacterium phage DrDrey] >ref|YP_008430611.1| hypothetical protein GOKU_95 [Mycobacterium phage Goku] >ref|YP_009197762.1| hypothetical protein SEA_NELITZAMV_94 [Mycobacterium phage NelitzaMV] >ref|YP_009208502.1| /note= /note=HHPred: no quality matches- PF07319.16 DnaI_N ; Primosomal protein DnaI N-terminus 82.4 /note= /note=not a transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 58106 - 58441 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=least negative RBS, z-score over 2, spacer a over 12 (15), 336 bp, starterator agrees (human generated), Blast P: hypothetical protein SEA_TOTO_95 [Mycobacterium phage Toto] Mycobacterium phage Toto 230 230 100% 1e-75 100.00% 111 YP_009208503.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_TOTO_95 [Mycobacterium phage Toto] >gb|AOY11951.1| hypothetical protein SEA_GOLDILOCKS_100 [Mycobacterium phage Goldilocks] >gb|APU02910.1| hypothetical protein SEA_CRYSTALP_96 [Mycobacterium phage CrystalP] >gb|QYC54740.1| /note= /note=HHPred: no quality matches- SCOP_d1j8ba_ d.222.1.1 (A:) Hypothetical protein HI0442 {Haemophilus influenzae [TaxId: 727]} | CLASS: Alpha and beta proteins (a+b), FOLD: YbaB-like, SUPFAM: YbaB-like, FAM: YbaB-like 78.7 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 58474 - 58980 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 507 bp, starterator agrees (human generated), Blast P: DNA binding protein [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 348 348 100% 7e-121 100.00% 168 NP_817548.1. Keep gene start /note= /note=Function: /note= /note=Only significant BLASTp/BLAST hits to NKF /note=NCBI: DNA binding protein [Mycobacterium phage Cjw1] >ref|YP_002014418.1| DNA binding protein [Mycobacterium phage Porky] >ref|YP_008430613.1| DNA binding protein [Mycobacterium phage Goku] >ref|YP_008857588.1| DNA binding protein [Mycobacterium phage PhatBacter] >ref|YP_008858380.1| DNA binding protein [Mycobacterium phage Nala] >ref|YP_008858829.1| DNA binding protein [Mycobacterium phage HufflyPuff] >ref|YP_009011859.1| DNA binding protein [Mycobacterium phage Lilac] /note= /note=HHPred: 8Q5B_A Small CPxCG-related zinc finger protein; zinc-finger, METAL BINDING PROTEIN; NMR {Haloferax volcanii DS2} 95.7 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 58977 - 60200 /note=GL and GM start, coding potential, blast potential, all gp good, likely gene /note= /note=least negative RBS, z-score above 2, spacer below 8 (7), 1224 bp, starterator agrees (human generated), Blast P; DNA methylase [Mycobacterium phage Emmina] Mycobacterium phage Emmina 830 830 100% 0.0 100.00% 421 AXQ60903.1. Keep gene start /note= /note=Function: /note= /note=Phages db: CrystalP 98 methyltransferase 407 824 0 E 213956 /note= /note=NCBI: DNA methyltransferase [Mycobacterium phage Quink] >ref|YP_009208505.1| DNA methyltransferase [Mycobacterium phage Toto] >gb|AEK08947.1| methyltransferase [Mycobacterium phage Henry] >gb|AEL21841.1| DNA methyltransferase [Mycobacterium phage Elph10] >gb|AKU42538.1| DNA methylase [Mycobacterium phage NoSleep] >gb|APU02912.1| methyltransferase [Mycobacterium phage CrystalP] >gb|AQP30819.1| DNA methylase [Mycobacterium phage Maxxinista] >gb|AVO23628.1| RNA ligase [Mycobacterium phage RiverMonster] /note= /note=HHPred: 1EG2_A MODIFICATION METHYLASE RSRI; Rossmann Fold, exocyclic amino DNA methyltransferase RsrI, DNA binding, DNA modification, DNA methylation, Structural Genomics, PSI; HET: MTA; 1.75A {Rhodobacter sphaeroides} SCOP: c.66.1.11 99.9 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 60193 - 60633 /note=GL and GM start, coding potential, blast matches, all gp good, likely gene /note= /note=Least negative RBS, z-score above 2, spacer above 12 (14), 441 bp, starterator agrees (human generated), Blast P: SSB protein [Mycobacterium phage Kostya] Mycobacterium phage Kostya 300 300 100% 2e-102 100.00% 146 YP_002014568.1. Keep gene start /note= /note=Function: /note= /note=Phages db: CrystalP 99 ssDNA binding protein 146 299 2e-81 E /note= /note=NCBI: SSB protein [Mycobacterium phage Kostya] >ref|YP_008052276.1| ssDNA binding protein [Mycobacterium phage Phaux] >ref|YP_008409493.1| ssDNA binding protein [Mycobacterium phage DrDrey] >ref|YP_008410114.1| ssDNA binding protein [Mycobacterium phage Contagion] >ref|YP_008430615.1| ssDNA binding domain protein [Mycobacterium phage Goku] >ref|YP_008857590.1| ssDNA binding protein [Mycobacterium phage PhatBacter] >ref|YP_008858382.1| ssDNA binding protein [Mycobacterium phage Nala] >ref|YP_008859534.1| ssDNA binding protein [Mycobacterium phage Bruin] /note= /note=HHPred: 7F5Y_A Single-stranded DNA-binding protein; DNA binding, quaternary structure, plasticity, inhibitor development, DNA BINDING PROTEIN; HET: FMT; 1.92A {Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)} 100 /note= /note=not transmembrane protien (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 60749 - 61528 /note=GL and GM start disagree, coding potential, blast matches, 116 bp gap from previous, likely gene /note= /note=least negative RBS , z-score above 2, appropriate spacer, 780 bp, starterator agrees (human generated), Blast P: ClpP-like protease [Mycobacterium phage RiverMonster] Mycobacterium phage RiverMonster 539 539 100% 0.0 99.61% 304 AVO23629.1. Keep gene start /note= /note=Function: /note= /note=Phages db: CrystalP 100 ClpP-like protease 259 526 1e-149 E /note= /note=NCBI: head maturation protease [Mycobacterium phage Lilac] >ref|YP_009197766.1| head maturation protease [Mycobacterium phage NelitzaMV] >ref|YP_009208507.1| head maturation protease [Mycobacterium phage Toto] >ref|YP_009225387.1| head maturation protease [Mycobacterium phage Mindy] >gb|AEJ92619.1| ClpP-like protease [Mycobacterium phage Rakim] >gb|AEL21843.1| ClpP-like protease [Mycobacterium phage Elph10] >gb|AKU42540.1| ClpP-like protease [Mycobacterium phage NoSleep] >gb|APU02914.1| ClpP-like protease [Mycobacterium phage CrystalP] >gb|AQP30821.1| ClpP-like protease [Mycobacterium phage Maxxinista] >gb|AVE00182.1| ClpP-like protease [Mycobacterium phage Kimchi] /note= /note=HHPred: 1TG6_G Putative ATP-dependent Clp protease proteolytic subunit; mitochondrial ClpP, Clp/Hsp 100, ATP-dependent protease, HYDROLASE; HET: DIO, FME, EDO, GOL; 2.1A {Homo sapiens} SCOP: c.14.1.1 99.9 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 61530 - 61727 /note=GL and GM disagree, coding potential, BLAST matches, 197 bp length, all gp good, likely a gene /note= /note=not least negative RBS, z-score above 2, spacer above 12 (17), 198 bp, starterator agrees (human generated), Blast P: hypothetical protein Kostya_102 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 132 132 100% 2e-38 100.00% 65 YP_002014570.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein Kostya_102 [Mycobacterium phage Kostya] >ref|YP_008052278.1| hypothetical protein M039_gp104 [Mycobacterium phage Phaux] >ref|YP_008430617.1| hypothetical protein GOKU_101 [Mycobacterium phage Goku] >ref|YP_009208508.1| hypothetical protein SEA_TOTO_100 [Mycobacterium phage Toto] >ref|YP_009591262.1| hypothetical protein FDG56_gp102 [Mycobacterium phage Bask21] >ref|YP_009591641.1| hypothetical protein FDG60_gp101 [Mycobacterium phage Eureka] >ref|YP_009608032.1| hypothetical protein FDI14_gp102 [Mycobacterium phage SirDuracell] >gb|AEK08950.1| hypothetical protein PBI_HENRY_99 [Mycobacterium phage Henry] >gb|AGR48939.1| hypothetical protein PBI_ABCAT_99 [Mycobacterium phage ABCat] >gb|AMS01901.1| hypothetical protein SEA_TEARDROPMSU_98 [Mycobacterium phage TeardropMSU] /note= /note=HHpred: 7UQ2_F Vs.4; Binds 3`, 3`-cGAMP, VIRAL PROTEIN; HET: 4BW; 2.0A {Tequatrovirus} 99.8 /note= /note=not a transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 61724 - 62080 /note=GL GM disagree, large gap before, BLAST matches, coding potential, doesn`t meet the requirements of all gp, possibly not a gene /note= /note=Glimmer (start 3) has Least negative RBS, z-score above 2, appropriate spacer, 273 bp, starterator has no human called start, but 9 auto annotations with start 3. Blast P: hypothetical protein Porky_101 [Mycobacterium phage Porky] Mycobacterium phage Porky 180 180 100% 3e-56 100.00% 118 YP_002014422.1. Change to GM start which has human-called starterator starts in other phages but not in the same track. BLASTp alignment supports the longer ORF and there is -4 overlap /note= /note=Function: /note= /note=NCBI: no quality matches- hypothetical protein Porky_101 [Mycobacterium phage Porky] >ref|YP_002014571.1| hypothetical protein Kostya_103 [Mycobacterium phage Kostya] >ref|YP_008051581.1| hypothetical protein PBI_MURPHY_102 [Mycobacterium phage Murphy] >ref|YP_008051727.1| hypothetical protein PBI_DUMBO_102 [Mycobacterium phage Dumbo] >ref|YP_008052035.1| hypothetical protein PBI_PHRUX_99 [Mycobacterium phage Phrux] >ref|YP_008052279.1| hypothetical protein M039_gp105 [Mycobacterium phage Phaux] >ref|YP_008409496.1| hypothetical protein DRDREY_103 [Mycobacterium phage DrDrey] >ref|YP_008410117.1| hypothetical protein PBI_CONTAGION_99 [Mycobacterium phage Contagion] >ref|YP_008531181.1| hypothetical protein P755_gp105 [Mycobacterium phage Quink] >ref|YP_008857593.1| hypothetical protein PHATBACTER_106 [Mycobacterium phage PhatBacter] /note= /note=HHPred: no quality matches- 3REB_B Tyrosine-protein kinase HCK; HIV-1 Nef, SH3 domain binding, signaling, Hck SH3 domain, PROTEIN BINDING; 3.45A {HIV-1 M:B_ARV2/SF2} 79.3 /note= /note=Not a transmembrane protein (soluble and globular according to SOUSI and DeepTHMM) /note= /note=on approved function list CDS 62081 - 62329 /note=GL GM start, BLAST matches, coding potential, all gp good, likely a gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 249 bp, starterator agrees (human generated, Blast P: hypothetical protein SEA_TOTO_102 [Mycobacterium phage Toto] Mycobacterium phage Toto 166 166 100% 2e-51 100.00% 82 YP_009208510.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_TOTO_102 [Mycobacterium phage Toto] >gb|AEJ92482.1| hypothetical protein SEA_TOTO_102 [Mycobacterium phage Toto] >gb|AEK08952.1| hypothetical protein PBI_HENRY_101 [Mycobacterium phage Henry] >gb|APU02917.1| hypothetical protein SEA_CRYSTALP_103 [Mycobacterium phage CrystalP] >gb|QYC54747.1| hypothetical protein SEA_SHAMWOW_104 [Mycobacterium phage ShamWow] /note= /note=HHPred: PF13870.11 DUF4201 ; Domain of unknown function (DUF4201) 96.5 /note= /note=not a transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 62334 - 62645 /note=GL GM start, coding potential, BLAST matches, all gp good, likely a gene /note= /note=not Least negative RBS, z-score under 2 (1.068), appropriate spacer, 312 bp, starterator agrees (human generated), Blast P: gp106 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 216 216 100% 2e-70 100.00% 103 NP_817555.1. Keep gene start. /note= /note=function: /note= /note=Phages db: CrystalP 104 helix-turn-helix DNA binding protein 103 219 2e-57 E /note= /note=NCBI: hypothetical protein BRUIN_102 [Mycobacterium phage Bruin] >ref|YP_009197770.1| HTH DNA binding protein [Mycobacterium phage NelitzaMV] >ref|YP_009591644.1| hypothetical protein FDG60_gp104 [Mycobacterium phage Eureka] >gb|AOY11959.1| HTH DNA binding protein [Mycobacterium phage Goldilocks] >gb|ATN91710.1| helix-turn-helix DNA binding domain protein [Mycobacterium phage Sassay] >gb|AYQ99093.1| helix-turn-helix DNA binding protein [Mycobacterium phage BaboJay] >gb|AYQ99787.1| helix-turn-helix DNA binding protein [Mycobacterium phage Manda] >gb|QIQ63542.1| helix-turn-helix DNA binding domain protein [Mycobacterium phage BadStone] >gb|UKH48244.1| hypothetical protein SEA_GOLDENSPARK_109 [Mycobacterium phage GoldenSpark] /note= /note=HHPred; SCOP_d6hn7b1 a.6.1.5 (B:1-69) automated matches {Escherichia phage [TaxId: 10710]} | CLASS: All alpha proteins, FOLD: Putative DNA-binding domain, SUPFAM: Putative DNA-binding domain, FAM: Terminase gpNU1 subunit domain 99 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 62827 - 62988 /note=GL GM start, coding potential, BLAST matches, 161 bp length, large gap before, doesn`t adhere to all gp rules. unsure if gene or not /note= /note=Not Least negative RBS, z-score above 2, appropriate spacer, 162 bp, starterator agrees (human generated), Blast P: HNH endonuclease [Mycobacterium phage Quallification] Mycobacterium phage Quallification 112 112 100% 6e-31 100.00% 53 UVK62215.1. Keep gene start /note= /note=Function: /note= /note=NCBI: UVK62215 No 2022-08-31 HNH endonuclease HNH endonuclease [Mycobacterium phage Quallification] >gb|XCH43186.1| HNH endonuclease [Mycobacterium Phage Xandras] >gb|XKC22130.1| HNH endonuclease [Mycobacterium phage AmericanBeauty] /note= /note=HHpred: PF13392.11 HNH_3 ; HNH endonuclease 99.7 /note= /note=not a transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 63562 - 63786 /note=GL GM start, coding potential, BLAST matches, large gap before gene, likely gene /note= /note=Gene codes for tRNA not protein. Least negative RBS, z-score over 2, appropriate spacer, 225 length, Keep gene start /note= /note=Function: /note= /note=NCBI: AXH68580 hypothetical protein SEA_XKCD_113 [Mycobacterium phage xkcd] >gb|QLF84774.1| hypothetical protein SEA_MISFIT_110 [Mycobacterium phage Misfit] /note= /note=HHPred: no quality mathes- PF22910.1 EDR4-like_1st ; Enhanced disease resistance 4-like, N-terminal domain 88.5 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 63813 - 64046 /note=GL GM disagree, coding potential, BLAST Matches, all gp good, may be a gene /note= /note=Suggested start is close but not least negative RBS, z-score over 2, appropriate spacer, 234 length, starterator human agreement. Keep current start. /note= /note=Function: /note= /note=NCBI: gp112 [Mycobacterium phage Cjw1] >ref|YP_002014427.1| hypothetical protein Porky_108 [Mycobacterium phage Porky] >ref|YP_002014576.1| hypothetical protein Kostya_110 [Mycobacterium phage Kostya] >ref|YP_008051586.1| hypothetical protein PBI_MURPHY_109 [Mycobacterium phage Murphy] >ref|YP_008051733.1| hypothetical protein PBI_DUMBO_110 [Mycobacterium phage Dumbo] >ref|YP_008052040.1| hypothetical protein PBI_PHRUX_106 [Mycobacterium phage Phrux] >ref|YP_008052284.1| hypothetical protein M039_gp144 [Mycobacterium phage Phaux] >ref|YP_008409501.1| hypothetical protein DRDREY_110 [Mycobacterium phage DrDrey] >ref|YP_008410123.1| hypothetical protein PBI_CONTAGION_107 [Mycobacterium phage Contagion] >ref|YP_008430623.1| hypothetical protein GOKU_109 [Mycobacterium phage Goku] /note= /note=HHPred: no quality matches- PF10671.14 TcpQ ; Toxin co-regulated pilus biosynthesis protein Q 64 /note= /note=not a transmembrane protein (Soluble and globular via SOUSI and DeepTHMM) but phamerator shows as membrane /note= /note=on approved function list CDS 64057 - 64431 /note=GL GM start, some coding potential (incomplete), BLAST matches, adheres to all gp, likely a gene /note= /note=not least negative RBS, z-score under 2 (1.98), appropriate spacer, 375 bp, starterator disagrees (picked third start). Blast P: hydrolase [Mycobacterium phage DrDrey] Mycobacterium phage DrDrey 255 255 100% 2e-85 100.00% 124 YP_008409502.1. Human-picked starterator. Keep gene start /note= /note=Function: /note=BLASTp most significant - hydrolase score 263, 1e-70 /note=NCBI: hydrolase [Mycobacterium phage DrDrey] >ref|YP_009225395.1| hydrolase [Mycobacterium phage Mindy] >gb|AGR48946.1| hypothetical protein PBI_ABCAT_108 [Mycobacterium phage ABCat] >gb|AMS01908.1| hydrolase [Mycobacterium phage TeardropMSU] >gb|APC44053.1| hydrolase [Mycobacterium phage Tuco] >gb|APU02920.1| hypothetical protein SEA_CRYSTALP_111 [Mycobacterium phage CrystalP] >gb|AVI04563.1| hydrolase [Mycobacterium phage Sotrice96] >gb|AXH47651.1| hydrolase [Mycobacterium phage IHOP] >gb|QIQ63546.1| hypothetical protein SEA_BADSTONE_108 [Mycobacterium phage BadStone] >gb|QNJ58599.1| nucleoside deoxyribosyltransferase [Mycobacterium phage Cactus] /note= /note=HHPred: 1T1J_A hypothetical protein; structural genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, unknown function; 1.7A {Pseudomonas aeruginosa} SCOP: l.1.1.1, c.23.14.2 /note= /note=HHPred(2): 4MEJ_A Nucleoside deoxyribosyltransferase; purine deoxyribosyl transferase (PDT), transferase-transferase inhibitor complex; HET: SO4, 28Y; 2.1A {Lactobacillus helveticus} SCOP: c.23.14.1 99.6 /note= /note= /note=not a membrane protein (Soluble and globular via SOUSI and DeppTHMM) /note= /note=on approved function list CDS 64431 - 64748 /note=GL GM start, coding potential, BLAST matches, adheres to all gp, likely a gene /note= /note=Only one gene start, z-score below 2 (1.63), 318 bp, starterator agrees. Blast P: hypothetical protein Kostya_112 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 213 213 100% 2e-69 100.00% 105 YP_002014578.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein Kostya_112 [Mycobacterium phage Kostya] >ref|YP_008409503.1| DUF550 domain-containing protein [Mycobacterium phage DrDrey] >ref|YP_009208516.1| DUF550 domain-containing protein [Mycobacterium phage Toto] >ref|YP_009224375.1| DUF550 domain-containing protein [Mycobacterium phage Dusk] >ref|YP_009225396.1| DUF550 domain-containing protein [Mycobacterium phage Mindy] >ref|YP_009591270.1| DUF550 domain-containing protein [Mycobacterium phage Bask21] >ref|YP_009608040.1| DUF550 domain-containing protein [Mycobacterium phage SirDuracell] >gb|AEJ92628.1| hypothetical protein SEA_RAKIM_113 [Mycobacterium phage Rakim] >gb|AEK08958.1| hypothetical protein PBI_HENRY_110 [Mycobacterium phage Henry] >gb|AGR48947.1| hypothetical protein PBI_ABCAT_109 [Mycobacterium phage ABCat] /note= /note=HHPred: PF04447.17 dATP-dGTP_PPHyd ; dATP/dGTP pyrophosphohydrolase 99.2 /note= /note=Not a transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 64738 - 65331 /note=GL GM start, coding potential, BLAST matches, adheres to all gp, likely a gene /note= /note=not least negative RBS, z-score above 2, spacer above 12 (14), 594 bp, starterator agrees, Blast P: hypothetical protein Porky_111 [Mycobacterium phage Porky] Mycobacterium phage Porky 406 406 100% 1e-142 100.00% 197 YP_002014430.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein Porky_111 [Mycobacterium phage Porky] >ref|YP_009208517.1| hypothetical protein SEA_TOTO_111 [Mycobacterium phage Toto] >ref|YP_009591271.1| hypothetical protein FDG56_gp143 [Mycobacterium phage Bask21] >ref|YP_009608041.1| hypothetical protein FDI14_gp141 [Mycobacterium phage SirDuracell] >ref|YP_654867.1| gp114 [Mycobacterium phage 244] >gb|AEJ92629.1| hypothetical protein SEA_RAKIM_114 [Mycobacterium phage Rakim] >gb|AOY11964.1| hypothetical protein SEA_GOLDILOCKS_116 [Mycobacterium phage Goldilocks] >gb|APU02922.1| hypothetical protein SEA_CRYSTALP_113 [Mycobacterium phage CrystalP] >gb|AVE00149.1| hypothetical protein SEA_KIMCHI_117 [Mycobacterium phage Kimchi] >gb|AVI03347.1| hypothetical protein SEA_ASRIEL_111 [Mycobacterium phage Asriel] /note= /note=HHPRED: PF18909.5 dGTP_diPhyd_N ; dATP/dGTP diphosphohydrolase, N-terminal 100 /note= /note=on approved function list /note=not transmembrane protein (soluble and globular via SOSUI and DeepTHMM) CDS 65342 - 66127 /note=GL GM start, coding potential, BLAST matches, all gp good, likely a gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 786 bp, starterator agrees (human selected), Blast P: DNA polymerase exonuclease subunit [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 546 546 100% 0.0 100.00% 261 NP_817562.1. Keep gene start /note= /note=Function: /note= /note=Phages db: CrystalP 114 DnaQ-like DNA polymerase III subunit 261 547 1e-156 E /note= /note=NCBI: DNA polymerase exonuclease subunit [Mycobacterium phage Cjw1] >ref|YP_002014431.1| DNA polymerase exonuclease subunit [Mycobacterium phage Porky] >ref|YP_008051589.1| DNA polymerase exonuclease subunit [Mycobacterium phage Murphy] >ref|YP_008051736.1| DNA polymerase exonuclease subunit [Mycobacterium phage Dumbo] >ref|YP_008052043.1| DNA polymerase exonuclease subunit [Mycobacterium phage Phrux] >ref|YP_008052287.1| DNA polymerase exonuclease subunit [Mycobacterium phage Phaux] >ref|YP_008410126.1| DNA polymerase exonuclease subunit [Mycobacterium phage Contagion] >ref|YP_008430627.1| DNA polymerase exonuclease subunit [Mycobacterium phage Goku] >ref|YP_008531190.1| DNA polymerase exonuclease subunit [Mycobacterium phage Quink] >ref|YP_008857601.1| DNA polymerase exonuclease subunit [Mycobacterium phage PhatBacter] /note= /note=HHPred: 8UN9_A Exonuclease MrfB; exonuclease, DNA, HYDROLASE; 2.103A {Bacillus subtilis} 99.6 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 66124 - 66366 /note=GL and GM start, coding potential, BLAST Matches, all gp good, likely a gene /note= /note=least negative RBS, z-score above 2, spacer above 12 (15), 243 bp, starterator agrees, Blast P: gp116 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 168 168 100% 2e-52 100.00% 80 NP_817563.1. Keep current start /note= /note=Function; /note= /note=NCBI: gp116 [Mycobacterium phage Cjw1] >ref|YP_002014432.1| hypothetical protein Porky_113 [Mycobacterium phage Porky] >ref|YP_008051590.1| hypothetical protein PBI_MURPHY_113 [Mycobacterium phage Murphy] >ref|YP_008051737.1| hypothetical protein PBI_DUMBO_114 [Mycobacterium phage Dumbo] >ref|YP_008052044.1| RecA [Mycobacterium phage Phrux] >ref|YP_008052288.1| hypothetical protein M039_gp140 [Mycobacterium phage Phaux] >ref|YP_008410127.1| hypothetical protein PBI_CONTAGION_111 [Mycobacterium phage Contagion] >ref|YP_008430628.1| hypothetical protein GOKU_114 [Mycobacterium phage Goku] >ref|YP_008531191.1| hypothetical protein P755_gp146 [Mycobacterium phage Quink] >ref|YP_008858394.1| hypothetical protein NALA_116 [Mycobacterium phage Nala] /note= /note=HHPred: no quality matches- PF18634.6 RXLR_WY ; RXLR phytopathogen effector protein /note= /note=Not a transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 66374 - 67336 /note=GL GM start, coding potential, BLAST matches, all gp good, likely a gene /note= /note=Least negative RBS, z-score above 2, spacer under 8 (7), 963 bp, starterator agrees (humans generated), Blast P: UvsX-like recombinase [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 647 647 100% 0.0 100.00% 320 NP_817564.1. Keep current start /note= /note=Function: /note= /note=Phages db: CrystalP 116 RecA-like DNA recombinase 320 626 1e-179 E /note= /note=NCBI: UvsX-like recombinase [Mycobacterium phage Cjw1] >ref|YP_002014433.1| UvsX-like recombinase [Mycobacterium phage Porky] >ref|YP_008051591.1| UvsX-like recombinase [Mycobacterium phage Murphy] >ref|YP_008051738.1| UvsX-like recombinase [Mycobacterium phage Dumbo] >ref|YP_008052045.1| UvsX-like recombinase [Mycobacterium phage Phrux] >ref|YP_008052289.1| UvsX-like recombinase [Mycobacterium phage Phaux] >ref|YP_008410128.1| UvsX-like recombinase [Mycobacterium phage Contagion] >ref|YP_008430629.1| UvsX-like recombinase [Mycobacterium phage Goku] >ref|YP_008531192.1| UvsX-like recombinase [Mycobacterium phage Quink] >ref|YP_008857603.1| UvsX-like recombinase [Mycobacterium phage PhatBacter] /note= /note=HHPred: 3HR8_A Protein recA; Alpha and beta proteins (a/b, a+b), ATP-binding, Cytoplasm, DNA damage, DNA recombination, DNA repair, DNA-binding, Nucleotide-binding; 1.95A {Thermotoga maritima} 100 /note= /note=Not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 67333 - 67470 /note=GL start but no GM, coding potential but no bar, BLAST matches, 137 bp only, adheres to gp, possible gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 138 bp, starterator agrees (human generated), Blast P: hypothetical protein Porky_115 [Mycobacterium phage Porky] Mycobacterium phage Porky 89.7 89.7 100% 4e-22 100.00% 45 YP_002014434.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein Porky_115 [Mycobacterium phage Porky] >ref|YP_008051592.1| hypothetical protein PBI_MURPHY_115 [Mycobacterium phage Murphy] >ref|YP_008051739.1| hypothetical protein PBI_DUMBO_116 [Mycobacterium phage Dumbo] >ref|YP_008052290.1| hypothetical protein M039_gp138 [Mycobacterium phage Phaux] >ref|YP_008410129.1| hypothetical protein PBI_CONTAGION_113 [Mycobacterium phage Contagion] >ref|YP_008430630.1| hypothetical protein GOKU_116 [Mycobacterium phage Goku] >ref|YP_008857604.1| hypothetical protein PHATBACTER_119 [Mycobacterium phage PhatBacter] >ref|YP_008858396.1| hypothetical protein NALA_118 [Mycobacterium phage Nala] >ref|YP_008858845.1| hypothetical protein HUFFLYPUFF_118 [Mycobacterium phage HufflyPuff] >ref|YP_008859548.1| hypothetical protein BRUIN_113 [Mycobacterium phage Bruin] /note= /note=HHPred: no quality matches - PF21830.1 DUF6890 ; Family of unknown function (DUF6890) 44.4 /note= /note=Not transmembrane ? (soluble and globular + SP via SOSUI and DeepTHMM). phamerator shows as membrane. /note= /note=on approved function list CDS 67457 - 67630 /note=GL GM Start, coding potential, BLAST matches, 173 bp only, all gp good, likely a gene /note= /note=not least negative RBS, z-score under 2 (1.604), spacer above 12 (16), 174 bp, starterator agrees (human generated), Blast P: gp119 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 117 117 100% 1e-32 100.00% 57 NP_817566.1. Keep gene start /note= /note=Function: /note= /note=NCBI: gp119 [Mycobacterium phage Cjw1] >ref|YP_002014435.1| hypothetical protein Porky_116 [Mycobacterium phage Porky] >ref|YP_002014587.1| hypothetical protein Kostya_121 [Mycobacterium phage Kostya] >ref|YP_008051593.1| hypothetical protein PBI_MURPHY_116 [Mycobacterium phage Murphy] >ref|YP_008051740.1| hypothetical protein PBI_DUMBO_117 [Mycobacterium phage Dumbo] >ref|YP_008052291.1| hypothetical protein M039_gp137 [Mycobacterium phage Phaux] >ref|YP_008409512.1| hypothetical protein DRDREY_121 [Mycobacterium phage DrDrey] >ref|YP_008410130.1| hypothetical protein PBI_CONTAGION_114 [Mycobacterium phage Contagion] >ref|YP_008430631.1| hypothetical protein GOKU_117 [Mycobacterium phage Goku] >ref|YP_008531194.1| hypothetical protein P755_gp143 [Mycobacterium phage Quink] /note= /note=HHPred: no quality matches- PF17471.7 GP63 ; Gene product 63 88.5 /note= /note=Not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (67620 - 67730) /note=GM but no GL, has coding potential concurrent with 116, BLAST matches, reversal of direction, 110 bp, doesn`t adhere to all gp, likely not a gene /note= /note=least negative RBS, z-core above 2, spacer under 8 (6), 111 bp, starterator agrees), Blast P: hypothetical protein SEA_BUCK_119 [Mycobacterium phage Buck] Mycobacterium phage Buck 72.4 72.4 100% 2e-15 100.00% 36 QGJ95425.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_BUCK_119 [Mycobacterium phage Buck] >gb|QGJ96307.1| hypothetical protein SEA_MYRALE_119 [Mycobacterium phage Myrale] >gb|UVK61919.1| hypothetical protein SEA_ARGENT26_122 [Mycobacterium phage Argent26] >gb|WNO26195.1| hypothetical protein SEA_SAINTS25_114 [Mycobacterium phage Saints25] >gb|WNO28081.1| hypothetical protein SEA_MARSHMALLOW_120 [Mycobacterium phage Marshmallow] >gb|WNO28557.1| hypothetical protein SEA_HIGHBURY_114 [Mycobacterium phage Highbury] /note= /note=HHPred: no quality matches- 8H0G_A AQEE-30; VGF, HFIP, NEUROPEPTIDE; NMR {Homo sapiens} 36.6 /note= /note=not transmembrane protein? (soluble and globular + SP via SOUSI and DeepTHMM). phamerator shows as membrane /note= /note=on approved function list CDS complement (67731 - 68003) /note=GL GM start, coding potential, BLAST matches, all gp good, likely a gene /note= /note=not least negative RBS, z-score less than 2 (1.975), appropriate spacer, 273 bp, starterator agrees, Blast P: hypothetical protein SEA_ORIONPAX_116 [Mycobacterium phage OrionPax] Mycobacterium phage OrionPax 186 186 100% 7e-59 100.00% 90 QGJ92372.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_ORIONPAX_116 [Mycobacterium phage OrionPax] >gb|QGJ94647.1| hypothetical protein SEA_GOOBERAZURE_121 [Mycobacterium phage GooberAzure] >gb|QGJ96275.1| hypothetical protein SEA_MYRALE_120 [Mycobacterium phage Myrale] >gb|UVK61920.1| hypothetical protein SEA_ARGENT26_123 [Mycobacterium phage Argent26] >gb|WNO28082.1| hypothetical protein SEA_MARSHMALLOW_121 [Mycobacterium phage Marshmallow] /note= /note=HHPred: no quality matches- 5ZJL_B Der f 23 allergen; Allergen; 1.7A {Dermatophagoides farinae} 36.2 /note= /note=might be membrane protein (Membrane and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 68019 - 68480 /note=GL GM start, coding potential, BLAST matches, reversal, violates 50 bp between starts for reverse genes, not all gp ashered, maybe a gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 462 bp, starterator agrees (human generated), Blast P: gp122 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 312 312 100% 7e-107 100.00% 153 NP_817569.1. Keep current start. /note= /note=Function: /note= /note=NCBI:gp122 [Mycobacterium phage Cjw1] >ref|YP_002014439.1| hypothetical protein Porky_120 [Mycobacterium phage Porky] >ref|YP_008052294.1| hypothetical protein M039_gp134 [Mycobacterium phage Phaux] >ref|YP_008531197.1| hypothetical protein P755_gp140 [Mycobacterium phage Quink] >ref|YP_008857608.1| hypothetical protein PHATBACTER_123 [Mycobacterium phage PhatBacter] >ref|YP_008858400.1| hypothetical protein NALA_122 [Mycobacterium phage Nala] >ref|YP_008858849.1| hypothetical protein HUFFLYPUFF_122 [Mycobacterium phage HufflyPuff] >ref|YP_008859552.1| hypothetical protein BRUIN_117 [Mycobacterium phage Bruin] >ref|YP_009011878.1| hypothetical protein LILAC_121 [Mycobacterium phage Lilac] >ref|YP_009208525.1| hypothetical protein SEA_TOTO_119 [Mycobacterium phage Toto] 100 /note= /note=HHPred: 3RHT_D (GATase1)-like protein; Structural Genomics, PSI-Biology, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION; HET: GOL, MSE, ACT; 1.83A {Planctomyces limnophilus} 91 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 68477 - 68644 /note=GL GM start, coding potential, BLAST matches, 167 bp, adheres to all gp, likely a gene /note= /note=least negative RBS, z-score above 2, appropriate spacer, 168 bp, starterator agrees Blast P: gp123 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 116 116 100% 1e-32 100.00% 55 NP_817570.1. Keep gene start /note= /note=Function: /note= /note=NCBI: gp123 [Mycobacterium phage Cjw1] >ref|YP_002014440.1| hypothetical protein Porky_121 [Mycobacterium phage Porky] >ref|YP_002014590.1| hypothetical protein Kostya_124 [Mycobacterium phage Kostya] >ref|YP_008051597.1| hypothetical protein PBI_MURPHY_120 [Mycobacterium phage Murphy] >ref|YP_008051746.1| hypothetical protein PBI_DUMBO_123 [Mycobacterium phage Dumbo] >ref|YP_008052051.1| hypothetical protein PBI_PHRUX_117 [Mycobacterium phage Phrux] >ref|YP_008052295.1| hypothetical protein M039_gp133 [Mycobacterium phage Phaux] >ref|YP_008409516.1| hypothetical protein DRDREY_125 [Mycobacterium phage DrDrey] >ref|YP_008410134.1| hypothetical protein PBI_CONTAGION_118 [Mycobacterium phage Contagion] >ref|YP_008430635.1| hypothetical protein GOKU_121 [Mycobacterium phage Goku] /note= /note=HHPred: no quality matches- 1JW9_B MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN; MoeB: modified Rossmann fold (2) Cys-X-X-Cys Zinc-binding motifs MoaD: ubiquitin-like fold, LIGASE; HET: SO4; 1.7A {Escherichia coli} SCOP: c.111.1.1 /note= /note=not transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 68628 - 68828 /note=GL GM start, coding potential, BLAST matches, adheres to all gp, likely a gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 201 bp, starterator agrees (human generated), Blast P: gp124 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 132 132 100% 2e-38 100.00% 66 NP_817571.1 /note= /note=Function: /note= /note=NCBI: gp124 [Mycobacterium phage Cjw1] >ref|YP_008051747.1| hypothetical protein PBI_DUMBO_124 [Mycobacterium phage Dumbo] >ref|YP_008052052.1| hypothetical protein PBI_PHRUX_118 [Mycobacterium phage Phrux] >ref|YP_008430636.1| hypothetical protein GOKU_122 [Mycobacterium phage Goku] >ref|YP_008531199.1| hypothetical protein P755_gp138 [Mycobacterium phage Quink] >ref|YP_009208527.1| hypothetical protein SEA_TOTO_121 [Mycobacterium phage Toto] >ref|YP_009591660.1| hypothetical protein FDG60_gp132 [Mycobacterium phage Eureka] >gb|AEL21861.1| hypothetical protein ELPH10_121 [Mycobacterium phage Elph10] >gb|ALA06347.1| hypothetical protein SEA_UKULELE_117 [Mycobacterium phage Ukulele] >gb|APU02930.1| hypothetical protein SEA_CRYSTALP_123 [Mycobacterium phage CrystalP] /note= /note=HHPred: no quality matches- PF11998.13 DUF3493 ; Low psii accumulation1 / Rep27 23.3 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 68828 - 68962 /note=GM but no GL, coding potential, BLAST matches, only 125 bp, all gp good, unsure if gene or not /note= /note=not least negative RBS, z-score lower than 2 (1.504), appropriate spacer, 126 bp, starterator agrees Change gene to 68828 start. New RBS is least negative, New z-score is above 2. Blast P: gp125 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 92.0 92.0 100% 4e-23 100.00% 45 NP_817572.1. /note= /note=Function: /note= /note=NCBI: gp125 [Mycobacterium phage Cjw1] >ref|YP_002014442.1| hypothetical protein Porky_123 [Mycobacterium phage Porky] >ref|YP_008051599.1| hypothetical protein PBI_MURPHY_122 [Mycobacterium phage Murphy] >ref|YP_008051748.1| hypothetical protein PBI_DUMBO_125 [Mycobacterium phage Dumbo] >ref|YP_008052053.1| hypothetical protein PBI_PHRUX_119 [Mycobacterium phage Phrux] >ref|YP_008052297.1| hypothetical protein M039_gp131 [Mycobacterium phage Phaux] >ref|YP_008409518.1| hypothetical protein DRDREY_127 [Mycobacterium phage DrDrey] >ref|YP_008410136.1| hypothetical protein PBI_CONTAGION_120 [Mycobacterium phage Contagion] >ref|YP_008531200.1| hypothetical protein P755_gp137 [Mycobacterium phage Quink] >ref|YP_008857611.1| hypothetical protein PHATBACTER_126 [Mycobacterium phage PhatBacter] /note= /note=HHPred: PF04606.17 Ogr_Delta ; Ogr/Delta-like zinc finger /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 68959 - 69138 /note=GL GM start, coding potential, BLAST matches, 179 bp, all gp good, likely a gene /note= /note=Least negative RBS, z-score under 2 (1.844), appropriate spacer, 180 bp, starterator agrees, Blast P: gp126 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 122 122 100% 9e-35 100.00% 59. Keep gene start. /note= /note=Function: /note= /note=NCBI: gp126 [Mycobacterium phage Cjw1] >ref|YP_002014443.1| hypothetical protein Porky_124 [Mycobacterium phage Porky] >ref|YP_008051600.1| hypothetical protein PBI_MURPHY_123 [Mycobacterium phage Murphy] >ref|YP_008051749.1| hypothetical protein PBI_DUMBO_126 [Mycobacterium phage Dumbo] >ref|YP_008052054.1| hypothetical protein PBI_PHRUX_120 [Mycobacterium phage Phrux] >ref|YP_008410137.1| hypothetical protein PBI_CONTAGION_121 [Mycobacterium phage Contagion] >ref|YP_008430638.1| hypothetical protein GOKU_124 [Mycobacterium phage Goku] >ref|YP_008531201.1| hypothetical protein P755_gp136 [Mycobacterium phage Quink] >ref|YP_008858404.1| hypothetical protein NALA_126 [Mycobacterium phage Nala] >ref|YP_008858853.1| hypothetical protein HUFFLYPUFF_126 [Mycobacterium phage HufflyPuff] /note= /note=HHPred: no quality matches- PF13535.11 ATP-grasp_4 ; ATP-grasp domain 76.4 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 69138 - 69269 /note=GL GM start, coding potential, BLAST matches, 131 bp, all gp good, likely a gene /note= /note=not least negative RBS, z-score less than 2 (1.705), appropriate spacer, 132 bp, starterator agrees, Blast P: gp127 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 85.9 85.9 100% 1e-20 100.00% 43 NP_817574.1. Keep gene start /note= /note=Function: /note= /note=NCBI; phage Cjw1] >ref|YP_002014444.1| hypothetical protein Porky_125 [Mycobacterium phage Porky] >ref|YP_002014593.1| hypothetical protein Kostya_127 [Mycobacterium phage Kostya] >ref|YP_008051750.1| hypothetical protein PBI_DUMBO_127 [Mycobacterium phage Dumbo] >ref|YP_008052055.1| hypothetical protein PBI_PHRUX_121 [Mycobacterium phage Phrux] >ref|YP_008052299.1| hypothetical protein M039_gp129 [Mycobacterium phage Phaux] >ref|YP_008409520.1| hypothetical protein DRDREY_129 [Mycobacterium phage DrDrey] >ref|YP_008410138.1| hypothetical protein PBI_CONTAGION_122 [Mycobacterium phage Contagion] >ref|YP_008430639.1| hypothetical protein GOKU_125 [Mycobacterium phage Goku] >ref|YP_008531202.1| RDF protein [Mycobacterium phage Quink] /note= /note=HHpred: PF00988.27 CPSase_sm_chain ; Carbamoyl-phosphate synthase small chain, CPSase domain 90.1 /note= /note=not a transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 69253 - 69414 /note=GL but no GM, some coding potential but not all, BLAST matches, 161 bp, all gp good, unsure if gene /note= /note=Least negative RBS , z-score above 2, spacer above 12 (14), 162 bp, starterator agrees , Blast P: gp128 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 111 111 100% 2e-30 100.00% 53 NP_817575.1. Keep gene start /note= /note=Function: /note= /note=NCBI: gp128 [Mycobacterium phage Cjw1] >ref|YP_002014445.1| hypothetical protein Porky_126 [Mycobacterium phage Porky] >ref|YP_002014594.1| hypothetical protein Kostya_128 [Mycobacterium phage Kostya] >ref|YP_008051602.1| hypothetical protein PBI_MURPHY_125 [Mycobacterium phage Murphy] >ref|YP_008051751.1| hypothetical protein PBI_DUMBO_128 [Mycobacterium phage Dumbo] >ref|YP_008052056.1| hypothetical protein PBI_PHRUX_122 [Mycobacterium phage Phrux] >ref|YP_008052300.1| hypothetical protein M039_gp128 [Mycobacterium phage Phaux] >ref|YP_008410139.1| hypothetical protein PBI_CONTAGION_123 [Mycobacterium phage Contagion] >ref|YP_009197789.1| hypothetical protein SEA_NELITZAMV_123 [Mycobacterium phage NelitzaMV] >ref|YP_009208531.1| hypothetical protein SEA_TOTO_125 [Mycobacterium phage Toto] /note= /note=HHPred: no quality matches- SCOP_d1p9ra1 c.37.1.11 (A:100-498) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: RecA protein-like (ATPase-domain) /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (69793 - 70056) /note=GM but no GL, large gap before gene, coding potential, BLAST matches, reversal of direction, 194 bp, missing some gp, unsure if gene /note= /note=Least negative RBS, z-score above 2, spacer below 8 (7), 195 bp, starterator disagrees (human called start 3 6/7 are drafts). Changing start to 70056. New RBS not least negative, New z-score above 2, appropriate spacer, 264 bp. Blast P: hypothetical protein Kostya_129 [Mycobacterium phage Kostya] Mycobacterium phage Kostya 179 179 100% 3e-56 100.00% 87 YP_002014595.1 /note= /note=Function: /note= /note=Phages DB: CrystalP 128 helix-turn-helix DNA binding protein 87 173 1e-43 E /note= /note=NCBI: hypothetical protein Kostya_129 [Mycobacterium phage Kostya] >ref|YP_008051603.1| hypothetical protein PBI_MURPHY_126 [Mycobacterium phage Murphy] >ref|YP_008052058.1| hypothetical protein PBI_PHRUX_124 [Mycobacterium phage Phrux] >ref|YP_008409522.1| hypothetical protein DRDREY_131 [Mycobacterium phage DrDrey] >ref|YP_008531205.1| hypothetical protein P755_gp132 [Mycobacterium phage Quink] >ref|YP_009197791.1| HTH DNA binding protein [Mycobacterium phage NelitzaMV] >ref|YP_009208532.1| hypothetical protein SEA_TOTO_126 [Mycobacterium phage Toto] >ref|YP_009224394.1| HTH DNA binding protein [Mycobacterium phage Dusk] >ref|YP_009225415.1| hypothetical protein SEA_MINDY_130 [Mycobacterium phage Mindy] >gb|AEJ92657.1| hypothetical protein SEA_RAKIM_129 [Mycobacterium phage Rakim] /note= /note=HHPred: 5CLV_J TrfB transcriptional repressor protein; Helix-turn-helix, complex, transcription; 2.5A {Escherichia coli} /note= /note=not transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS complement (70053 - 70442) /note=GM but no GL, large gap before, coding potential, BLAST matches, most gp good, likely gene /note= /note=Not least negative RBS, z-score above 2, spacer below 8 (6), 390 bp, starterator agrees (human generated), Blast P: ParB C-terminal domain [Mycobacterium phage Murphy] Mycobacterium phage Murphy 260 260 100% 4e-87 100.00% 129 YP_008051604.1. Keep gene start /note= /note=Function: /note= /note=NCBI: ParB C-terminal domain [Mycobacterium phage Murphy] >ref|YP_008052059.1| ParB C-terminal domain [Mycobacterium phage Phrux] >ref|YP_008409523.1| ParB C-terminal domain [Mycobacterium phage DrDrey] >ref|YP_008531206.1| ParB C-terminal domain [Mycobacterium phage Quink] >ref|YP_009011884.1| ParB C-terminal domain [Mycobacterium phage Lilac] >ref|YP_009197792.1| ParB C-terminal domain [Mycobacterium phage NelitzaMV] >ref|YP_009208533.1| ParB C-terminal domain [Mycobacterium phage Toto] >ref|YP_009224395.1| ParB C-terminal domain [Mycobacterium phage Dusk] >gb|AEK08975.1| ParB-like nuclease domain protein [Mycobacterium phage Henry] >gb|AEL21884.1| hypothetical protein ELPH10_127 [Mycobacterium phage Elph10] /note= /note=HHPred: no quality matches - 7UR8_A 170_h_ob; DE NOVO DESIGN, Beta-barrel, Protein binder, DE NOVO PROTEIN; 1.5A {synthetic construct} /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list (*** different terminal) CDS complement (70561 - 70794) /note=GM but no GL, some coding potential, BLAST matches, large gap before, adheres to most gp, unsure if gene /note= /note=not least negative RBS, z-score under 2 (1.482), appropriate spacer, 234 bp, starterator agrees (human generated. Blast P: gp130 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 155 155 100% 5e-47 98.70% 86 NP_817577.1. Keep gene start /note= /note=Function: /note= /note=NCBI: gp130 [Mycobacterium phage Cjw1] >ref|YP_008410142.1| hypothetical protein PBI_CONTAGION_126 [Mycobacterium phage Contagion] >ref|YP_008857618.1| hypothetical protein PHATBACTER_133 [Mycobacterium phage PhatBacter] >ref|YP_008858410.1| hypothetical protein NALA_132 [Mycobacterium phage Nala] >ref|YP_008858859.1| hypothetical protein HUFFLYPUFF_132 [Mycobacterium phage HufflyPuff] >ref|YP_008859562.1| hypothetical protein BRUIN_127 [Mycobacterium phage Bruin] >ref|YP_654884.1| gp131 [Mycobacterium phage 244] >gb|AHB32077.1| hypothetical protein PBI_MOSBY_127 [Mycobacterium phage Mosby] >gb|AKU42565.1| hypothetical protein SEA_NOSLEEP_129 [Mycobacterium phage NoSleep] >gb|AOT24006.1| hypothetical protein SEA_PHARSALUS_127 [Mycobacterium phage Pharsalus] /note= /note=HHPred: no quality matches- PF20537.3 DUF6752 ; Domain of unknown function (DUF6752) 71.5 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (71248 - 71706) /note=GL GM start, large gap before, coding potential, BLAST matches, adheres to most gp, likely a gene /note= /note=least negative RBS, z-score above 2, spacer under 8 (6), 459 bp, starterator agrees (human generated), Blast P: hypothetical protein SEA_CRYSTALP_132 [Mycobacterium phage CrystalP] Mycobacterium phage CrystalP 308 308 100% 2e-105 100.00% 152 APU02937.1. Keep gene start /note= /note=Function: /note= /note=NCBI: APU02937 No 2023-08-29 hypothetical protein SEA_CRYSTALP_132 [Mycobacterium phage CrystalP] /note= /note=HHPred: no quality matches- PF01812.25 5-FTHF_cyc-lig ; 5-formyltetrahydrofolate cyclo-ligase family 42.1 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (71721 - 72050) /note=GL GM start, coding potential, BLAST matches, adheres to most gp, likely a gene /note= /note=least negative RBS, z-score above 2, spacer above 12 (13), 330 bp, starterator agrees, Blast P: hypothetical protein SEA_CRYSTALP_133 [Mycobacterium phage CrystalP] Mycobacterium phage CrystalP 225 225 100% 7e-74 100.00% 109 APU02938.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_CRYSTALP_133 [Mycobacterium phage CrystalP] >gb|AVI03362.1| hypothetical protein SEA_ASRIEL_130 [Mycobacterium phage Asriel] >gb|AVI03501.1| hypothetical protein SEA_BARBARIAN_133 [Mycobacterium phage Barbarian] >gb|QDH91997.1| hypothetical protein SEA_FLYPOTENUSE_128 [Mycobacterium phage Flypotenuse] >gb|XEN17366.1| hypothetical protein SEA_BALOMOJI_133 [Mycobacterium phage Balomoji] /note= /note=HHPred: no quality matches- SCOP_d2od4a1 d.58.4.20 (A:1-100) Hypothetical protein GOS_3280838 {Environmental samples [TaxId: 33858]} | CLASS: Alpha and beta proteins (a+b), FOLD: Ferredoxin-like, SUPFAM: Dimeric alpha+beta barrel, FAM: Marine metagenome family DABB2 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (72056 - 72571) /note=GL GM start, coding potential, BLAST matches, all gp good, likely a gene /note= /note=Least negative RBS, z-score under 2 (1.956), spacer under 8 (7), 516 bp, Starterator agrees, Blast P: hypothetical protein FDI14_gp117 [Mycobacterium phage SirDuracell] Mycobacterium phage SirDuracell 344 344 100% 4e-119 100.00% 171 YP_009608065.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein FDI14_gp117 [Mycobacterium phage SirDuracell] >gb|APU02939.1| hypothetical protein SEA_CRYSTALP_134 [Mycobacterium phage CrystalP] >gb|AVI03363.1| hypothetical protein SEA_ASRIEL_131 [Mycobacterium phage Asriel] >gb|AVI03502.1| hypothetical protein SEA_BARBARIAN_134 [Mycobacterium phage Barbarian] >gb|AXC37853.1| hypothetical protein SEA_ICEE_139 [Mycobacterium phage Icee] >gb|QDH91998.1| hypothetical protein SEA_FLYPOTENUSE_129 [Mycobacterium phage Flypotenuse] >gb|QGJ91940.1| hypothetical protein SEA_TRAAWW1_130 [Mycobacterium phage Traaww1] >gb|XEN17367.1| hypothetical protein SEA_BALOMOJI_134 [Mycobacterium phage Balomoji] /note= /note=HHPred: no quality matches- PF10787.14 YfmQ ; Uncharacterised protein from bacillus cereus group 78.1 /note= /note=not transmembrane protein (Soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (72592 - 72903) /note=GM but no GL, coding potential, BLAST matches, all gp good, likely a gene /note= /note=Not least negative RBS, z-score above 2, spacer below 8 (5), 327 bp, starterator agrees (said start 1), Changing start to 72903. new RBS is least negative, z-score above 2, appropriate spacer, starterator agrees, Blast P: hypothetical protein SEA_MINDY_138 [Mycobacterium phage Mindy] Mycobacterium phage Mindy 210 210 100% 5e-68 100.00% 108 YP_009225423.1 /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_MINDY_138 [Mycobacterium phage Mindy] >gb|AEK08981.1| hypothetical protein PBI_HENRY_137 [Mycobacterium phage Henry] >gb|AVI03376.1| hypothetical protein SEA_ASRIEL_132 [Mycobacterium phage Asriel] >gb|QDH92014.1| hypothetical protein SEA_FLYPOTENUSE_130 [Mycobacterium phage Flypotenuse] >gb|QGJ94130.1| hypothetical protein SEA_COMMAND613_137 [Mycobacterium phage Command613] >gb|QGJ96288.1| hypothetical protein SEA_MYRALE_136 [Mycobacterium phage Myrale] >gb|WVX88976.1| hypothetical protein SEA_SOPHKB_133 [Mycobacterium phage SophKB] /note= /note=HHPred: no quality matches- 8H3Z_B NtcB; LysR-type transcription factor, TRANSCRIPTION, TRANSCRIPTION-DNA complex; HET: IOD; 2.35A {Anabaena} 79.1 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (73023 - 73229) /note=GL GM start, large gap before, coding potential, BLAST matches, all gp good, likely a gene /note= /note=Least negative RBS, z-score above 2, appropriate spacer, 207 bp, starterator agrees, Blast P: hypothetical protein SEA_CRYSTALP_136 [Mycobacterium phage CrystalP] Mycobacterium phage CrystalP 141 141 100% 5e-42 100.00% 68 APU02941.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_CRYSTALP_136 [Mycobacterium phage CrystalP] >gb|AVI03364.1| hypothetical protein SEA_ASRIEL_133 [Mycobacterium phage Asriel] >gb|AVI03504.1| hypothetical protein SEA_BARBARIAN_136 [Mycobacterium phage Barbarian] >gb|QDH91999.1| hypothetical protein SEA_FLYPOTENUSE_131 [Mycobacterium phage Flypotenuse] >gb|WNM73970.1| hypothetical protein SEA_HOLT_142 [Mycobacterium Phage Holt] /note= /note=HHPred: PF19837.4 DUF6316 ; Domain of unknown function (DUF6316) 96 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (73275 - 73793) /note=GL GM start, large gap before, coding potential, BLAST matches, adheres to most gp, likely a gene /note= /note=Lease negative RBS, z-score above 2, appropriate spacer, 519 bp, starterator agrees, Blast P: hypothetical protein SEA_CRYSTALP_137 [Mycobacterium phage CrystalP] Mycobacterium phage CrystalP 355 355 100% 3e-123 100.00% 184 APU02950.1. Keep gene start. /note= /note=Function: /note= /note=NCBI: APU02950 No 2023-08-29 hypothetical protein SEA_CRYSTALP_137 [Mycobacterium phage CrystalP] /note= /note=HHPred: no quality matches- 1VD4_A Transcription initiation factor IIE, alpha subunit; ZINC FINGER, Transcription; HET: ZN; NMR {Homo sapiens} SCOP: g.41.3.1 88.8 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (73833 - 74216) /note=GM start but no GL, coding potential, BLAST matches, all gp good, likely a gene /note= /note=not least negative RBS, z-score above 2, appropriate spacer, 384 length, starterator agrees, Blast P: hypothetical protein GOKU_137 [Mycobacterium phage Goku] Mycobacterium phage Goku 261 261 100% 9e-88 100.00% 127 YP_008430651.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein GOKU_137 [Mycobacterium phage Goku] >ref|YP_008859570.1| hypothetical protein BRUIN_135 [Mycobacterium phage Bruin] >ref|YP_009591300.1| hypothetical protein FDG56_gp114 [Mycobacterium phage Bask21] >ref|YP_009591676.1| hypothetical protein FDG60_gp116 [Mycobacterium phage Eureka] >ref|YP_009608069.1| hypothetical protein FDI14_gp113 [Mycobacterium phage SirDuracell] >gb|APU02942.1| hypothetical protein SEA_CRYSTALP_138 [Mycobacterium phage CrystalP] >gb|QAY06663.1| hypothetical protein SEA_COOKIES_140 [Mycobacterium phage Cookies] >gb|UVK62243.1| hypothetical protein SEA_QUALLIFICATION_139 [Mycobacterium phage Quallification] >gb|WNO26215.1| hypothetical protein SEA_SAINTS25_134 [Mycobacterium phage Saints25] >gb|WNO28577.1| hypothetical protein SEA_HIGHBURY_134 [Mycobacterium phage Highbury] /note= /note=HHPred: cd20474 Tudor_Agenet_FMR1_rpt2; second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins. 95 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (74221 - 74394) /note=GL start but no GM, incomplete coding potential, BLAST matches, all gp match, 159 bp length, unsure if gene or not /note= /note=Not least negative RBS, z-score under 2 (1.724), spacer over 12 (14), 159 bp, starterator agrees, Change start to74394, new RBS is least negative, new z-score is above 2, appropriate spacer, 174 bp, starterator agrees Blast P: hypothetical protein PBI_MURPHY_139 [Mycobacterium phage Murphy] Mycobacterium phage Murphy 119 119 100% 2e-33 100.00% 57 YP_008051616.1 /note= /note=Function: /note= /note=NCBI: hypothetical protein PBI_MURPHY_139 [Mycobacterium phage Murphy] >ref|YP_008052313.1| hypothetical protein M039_gp115 [Mycobacterium phage Phaux] >ref|YP_008409533.1| hypothetical protein DRDREY_142 [Mycobacterium phage DrDrey] >ref|YP_008857628.1| hypothetical protein PHATBACTER_143 [Mycobacterium phage PhatBacter] >ref|YP_008859571.1| hypothetical protein BRUIN_136 [Mycobacterium phage Bruin] >ref|YP_009224406.1| hypothetical protein SEA_DUSK_140 [Mycobacterium phage Dusk] >ref|YP_009608070.1| hypothetical protein FDI14_gp112 [Mycobacterium phage SirDuracell] >ref|YP_009613759.1| hypothetical protein FDI54_gp114 [Mycobacterium phage Pumpkin] >ref|YP_654893.1| gp140 [Mycobacterium phage 244] >gb|AGR48978.1| hypothetical protein PBI_ABCAT_140 [Mycobacterium phage ABCat] /note= /note=HHPred: no quality matches- 1RI9_A FYN-binding protein; SH3-LIKE, HELICALLY EXTENDED, SIGNALING PROTEIN; NMR {Homo sapiens} SCOP: b.34.2.1 73.6 /note= /note=not transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS complement (74391 - 74627) /note=GM but no GL, coding potential, BLAST matches, all gp good, likely a gene /note= /note=least negative RBS, z-score above 2, appropriate spacer, 237 bp, starterator agrees (human generated), Blast P: gp140 [Mycobacterium phage Cjw1] Mycobacterium phage Cjw1 157 157 100% 5e-48 100.00% 81 NP_817587.1. Keep gene start /note= /note=Function;: /note= /note=NCBI: gp140 [Mycobacterium phage Cjw1] >ref|YP_008410152.1| hypothetical protein PBI_CONTAGION_136 [Mycobacterium phage Contagion] >ref|YP_008858420.1| hypothetical protein NALA_142 [Mycobacterium phage Nala] >ref|YP_009011894.1| hypothetical protein LILAC_137 [Mycobacterium phage Lilac] >gb|AEK08985.1| hypothetical protein PBI_HENRY_142 [Mycobacterium phage Henry] >gb|ATN92126.1| hypothetical protein SEA_TERMINUS_143 [Mycobacterium phage Terminus] >gb|AXH49948.1| hypothetical protein SEA_GLEXAN_144 [Mycobacterium phage Glexan] >gb|AXH65545.1| hypothetical protein SEA_HOPEY_138 [Mycobacterium phage Hopey] >gb|QDK01873.1| hypothetical protein SEA_GATOR_142 [Mycobacterium phage Gator] >gb|QDK02195.1| hypothetical protein SEA_TOMASZEWSKI_134 [Mycobacterium phage Tomaszewski] /note= /note=HHPred: no quality matches- 2QF9_A Putative secreted protein; structural genomics, DUF305, Q8CK01, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics; HET: MSE; 1.69A {Streptomyces coelicolor A3(2)} /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (74630 - 74842) /note=GL and GM disagree, coding potential, BLAST matches, all gp good, likely a gene /note= /note=Start 2: Least negative RBS, z-score above 2, spacer above 12 (15), 204 bp, starterator agrees (human generated), Blast P: hypothetical protein SEA_NELITZAMV_136 [Mycobacterium phage NelitzaMV] Mycobacterium phage NelitzaMV 131 131 100% 5e-38 100.00% 70 YP_009197802.1. Start 1 is -4 and longest. Change to start 1. /note= /note=Function: /note= /note=NCBI: hypothetical protein SEA_NELITZAMV_136 [Mycobacterium phage NelitzaMV] >ref|YP_009208544.1| hypothetical protein SEA_TOTO_138 [Mycobacterium phage Toto] >gb|AOT24018.1| hypothetical protein SEA_PHARSALUS_139 [Mycobacterium phage Pharsalus] >gb|AOY11991.1| hypothetical protein SEA_GOLDILOCKS_147 [Mycobacterium phage Goldilocks] >gb|ASZ73627.1| hypothetical protein SEA_MADAMMONKFISH_142 [Mycobacterium phage MadamMonkfish] >gb|AVE00173.1| hypothetical protein SEA_KIMCHI_146 [Mycobacterium phage Kimchi] >gb|AVI04022.1| hypothetical protein SEA_GAGE_132 [Mycobacterium phage Gage] >gb|AVI04592.1| hypothetical protein SEA_SOTRICE96_146 [Mycobacterium phage Sotrice96] >gb|AXC35986.1| hypothetical protein SEA_ADNAMA_145 [Mycobacterium phage Adnama] >gb|AXC37519.1| hypothetical protein SEA_DOCTORDIDDLES_140 [Mycobacterium phage DoctorDiddles] /note= /note=HHPred: PF19944.4 DUF6406 ; Family of unknown function (DUF6406) 91.8 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS complement (74839 - 75036) /note=GL GM start, coding potential, BLAST matches, all gp good, likely a gene, 198 bp length /note= /note=Not least negative RBS, z-score above 2, appropriate spacer, 198 bp, starterator agrees (human generated), Blast P: hypothetical protein HUFFLYPUFF_144 [Mycobacterium phage HufflyPuff] Mycobacterium phage HufflyPuff 136 136 100% 5e-40 100.00% 78 YP_008858871.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein HUFFLYPUFF_144 [Mycobacterium phage HufflyPuff] >gb|AHB31310.1| hypothetical protein HUFFLYPUFF_144 [Mycobacterium phage HufflyPuff] /note= /note=HHPred: no quality matches - 7FEV_A FMN binding; Flavoenzyme, Ascochyta rabiei, FMN-binding, Fungal OYEs, OXIDOREDUCTASE; HET: FMN; 1.594A {Ascochyta rabiei} 83 /note= /note=not transmembrane protein (soluble and globular via SOSUI and DeepTHMM) /note= /note=on approved function list CDS 75269 - 75616 /note=GL GM start, reversal of direction, coding potential, BLAST matches, large gap before gene, all gp good, likely a gene /note= /note=Least negative RBS, z-score above 2, spacer below 8 (6), 348 bp, starterator agrees, Blast P: hypothetical protein PBI_MURPHY_145 [Mycobacterium phage Murphy] Mycobacterium phage Murphy 232 232 100% 1e-76 100.00% 115 YP_008051622.1. Keep gene start /note= /note=Function: /note= /note=NCBI: hypothetical protein PBI_MURPHY_145 [Mycobacterium phage Murphy] >ref|YP_008051770.1| hypothetical protein PBI_DUMBO_147 [Mycobacterium phage Dumbo] >ref|YP_008052316.1| hypothetical protein M039_gp112 [Mycobacterium phage Phaux] >ref|YP_008409536.1| hypothetical protein DRDREY_145 [Mycobacterium phage DrDrey] >ref|YP_008410156.1| hypothetical protein PBI_CONTAGION_140 [Mycobacterium phage Contagion] >ref|YP_008857633.1| hypothetical protein PHATBACTER_148 [Mycobacterium phage PhatBacter] >ref|YP_008859576.1| hypothetical protein BRUIN_141 [Mycobacterium phage Bruin] >ref|YP_009208547.1| hypothetical protein SEA_TOTO_141 [Mycobacterium phage Toto] >ref|YP_009224409.1| hypothetical protein SEA_DUSK_143 [Mycobacterium phage Dusk] >ref|YP_009591306.1| hypothetical protein FDG56_gp108 [Mycobacterium phage Bask21] /note= /note=HHPred: no quality matches- PF03698.18 UPF0180 ; Uncharacterised protein family (UPF0180) 77.5 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list CDS 75718 - 75912 /note=GL GM start disagree, large gap before gene, coding potential, BLAST matches, 194 bp only, all gp good, likely a gene /note= /note=Not least negative RBS, z-score below 2 (0.647), spacer under 8 (7), 195 bp, starterator did not call start Blast P: hypothetical protein GOKU_144 [Mycobacterium phage Goku] Mycobacterium phage Goku 127 127 100% 1e-36 100.00% 64 YP_008430658.1. Unsure about start /note= /note=Function: /note= /note=NCBI: hypothetical protein GOKU_144 [Mycobacterium phage Goku] >gb|ATN92566.1| hypothetical protein SEA_WILLEZ_143 [Mycobacterium phage Willez] >gb|ATW59695.1| hypothetical protein SEA_YOUNGBLOOD_149 [Mycobacterium phage Youngblood] >gb|QLF84809.1| hypothetical protein SEA_MISFIT_145 [Mycobacterium phage Misfit] >gb|XEN19162.1| hypothetical protein SEA_TEASPOON_129 [Mycobacterium phage Teaspoon] >gb|AGT14247.1| hypothetical protein GOKU_144 [Mycobacterium phage Goku] /note= /note=HHPred: no quality matches- PF09413.15 DUF2007 ; Putative prokaryotic signal transducing protein 88.1 /note= /note=not transmembrane protein (soluble and globular via SOUSI and DeepTHMM) /note= /note=on approved function list GAPS (old numbering) Gene 49-50: 287 bp gap, There is some coding potential but not called in other phages. Gene 50-51: 251 bp gap no coding potential not in other phages Genes 59-60: 544 bp gap, There is some coding potential is called in other phages. Genes 63-64: 221bp gap, No coding potential, not called. Genes 85-86: 155 bp gap, No coding potential, not called Genes 104-105: 574 bp gap, v little coding potential, not called. Genes 126-127: 454 bp gap, some coding potential, but this is a called gene in other phages Genes 137-138: 233 bp gap, somecoding potential but this is not called as a gene in in pother phages