TABLE 2.
List of annotated ORFs of jumbo phage RsoM2USA with predicted functions and proteins, and their BLASTp results.
| Function | ORF | Strand | Start nt | Stop nt | Length (aa) | Similarity to best functional homologs | E-Value | Homolog accession no. |
| Replication, recombination and repair | ORF28 | − | 21,854 | 23,371 | 506 | SpoVR family protein [Vibrio parahaemolyticus] | 0 | WP_025610357 |
| ORF129 | − | 85,243 | 85,968 | 242 | Homing endonuclease [Escherichia phage vB_EcoM_112] | 1.00E-23 | YP_009030743.1 | |
| ORF195 | − | 121,703 | 122,092 | 130 | DUF2493 domain-containing protein [Bacillus pumilus] | 3.00E-25 | WP_074041829.1 | |
| ORF213 | − | 135,426 | 136,346 | 307 | Hypothetical protein DRJ15_13365 [Bacteroidetes bacterium] | 8.00E-93 | RLD77522.1 | |
| ORF234 | − | 149,131 | 150,414 | 428 | DNA helicase-like protein [Salicola phage SCTP-2] | 7.00E-87 | ASV44158.1 | |
| ORF253 | + | 162,753 | 164,330 | 526 | Terminase large subunit [Xanthomonas phage XacN1] | 7.00E-136 | BBA65403.1 | |
| ORF358 | − | 225,112 | 226,089 | 326 | GDP-mannose 4,6-dehydratase [Enterobacter hormaechei] | 1.00E-92 | WP_190319761 | |
| ORF371 | + | 248,317 | 250,059 | 581 | Endonuclease subunit [uncultured Caudovirales phage] | 2.00E-87 | CAB4241474.1 | |
| ORF435 | − | 307,406 | 308,074 | 223 | Putative exonuclease [Serratia phage phiMAM1] | 6.00E-40 | YP_007349054.1 | |
| ORF441 | − | 312,188 | 313,516 | 443 | DNA primase-helicase subunit [Agrobacterium phage Atu_ph07] | 4.00E-95 | ASV44692.1 | |
| ORF448 | − | 319,603 | 320,598 | 332 | DNA polymerase I [Syntrophomonadaceae bacterium] | 3.00E-93 | AVH85376.1 | |
| ORF451 | − | 321,631 | 324,054 | 808 | DNA polymerase [Xanthomonas phage XacN1] | 8.00E-167 | BBA65491.1 | |
| ORF458 | − | 326,884 | 327,468 | 195 | DNA polymerase III epsilon subunit [Xanthomonas phage XacN1] | 3.00E-32 | BBA65371.1 | |
| Translation, ribosomal structure and biogenesis | ORF8 | − | 6,927 | 7,346 | 140 | Cytidine and deoxycytidylate deaminase zinc-binding region [uncultured Eubacterium sp.] | 1.00E-26 | SCI18574.1 |
| ORF22 | − | 16,776 | 17,813 | 346 | Bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase [Chitinivorax tropicus] | 1.00E-96 | WP_184035971.1 | |
| ORF157 | − | 103,724 | 104,122 | 133 | Aminoacyl-tRNA hydrolase [Steroidobacter agaridevorans] | 7.00E-53 | WP_202623994.1 | |
| ORF161 | − | 105,942 | 106,757 | 272 | DUF4343 domain-containing protein [Polaromonas sp. CF318] | 2.00E-68 | WP_007869793.1 | |
| ORF183 | − | 114,961 | 115,776 | 272 | Putative Thg1 [Pseudomonas phage 201phi2-1] | 5.00E-67 | YP_001957040.1 | |
| ORF204 | − | 129,120 | 130,403 | 428 | ATP-dependent DNA ligase [Bacillus phage SP-10] | 2.00E-38 | YP_007003455.1 | |
| ORF222 | − | 141,515 | 142,111 | 199 | Alpha/beta fold hydrolase [Verrucomicrobiaceae bacterium] | 1.00E-32 | RYD62074.1 | |
| ORF397 | + | 266,707 | 267,747 | 347 | RNA ligase [Caulobacter phage Cr30] | 5.00E-98 | YP_009098789.1 | |
| ORF470 | − | 332,504 | 333,007 | 168 | Macro domain-containing protein [Paraburkholderia sp. UCT31] | 2.00E-35 | WP_187631037.1 | |
| ORF480 | − | 336,962 | 338,041 | 360 | 2’-5’ RNA ligase [Paraburkholderia sp. C35] | 2.00E-84 | WP_109482880.1 | |
| Transcription | ORF14 | − | 10,780 | 12,177 | 466 | Nicotinate phosphoribosyltransferase [Variovorax paradoxus] | 0 | WP_081267491.1 |
| ORF57 | − | 43,612 | 45,078 | 489 | TROVE domain-containing protein [Candidatus Woesebacteria bacterium RBG_13_36_22] | 5.00E-143 | OGM09089.1 | |
| ORF193 | − | 119,483 | 121,156 | 558 | gp73 [Bacillus virus G] | 3.00E-109 | YP_009015384.1 | |
| ORF194 | − | 121,156 | 121,710 | 185 | Dihydrofolate reductase [Bacillus sp. VT-16-64] | 1.00E-30 | WP_077113372.1 | |
| ORF217 | − | 138,548 | 139,012 | 155 | CMP deaminase [Mariniphaga anaerophila] | 1.00E-44 | WP_073001946.1 | |
| ORF248 | − | 159,734 | 160,165 | 144 | Adenylylsulfate kinase [Beijerinckia sp. 28-YEA-48] | 8.00E-53 | SEB56588.1 | |
| ORF446 | − | 317963 | 319,018 | 352 | CobS [Synechococcus phage S-WAM2] | 8.00E-49 | YP_009324303.1 | |
| ORF485 | − | 341,063 | 342,979 | 639 | GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [uncultured Caudovirales phage] | 0.00E + 00 | CAB4159554.1 | |
| Posttranslational modification, protein turnover and chaperones | ORF3 | − | 3,079 | 3,714 | 212 | Heat-shock protein [Microvirga sp. BSC39] | 5.00E-22 | WP_036354424.1 |
| ORF112 | − | 77,678 | 78,244 | 189 | NAD-dependent deacylase [Thermococcus gorgonarius] | 1.00E-43 | WP_088885183.1 | |
| ORF223 | − | 142,171 | 142,503 | 111 | Thioredoxin [Crenothrix sp. D3] | 1.00E-25 | OTE97860.1 | |
| Nucleotide transport and metabolism | ORF10 | − | 7,607 | 8,443 | 279 | Putative thymidylate synthase [Xanthomonas phage Xp15] | 2.00E-50 | YP_239304.1 |
| ORF225 | − | 142,794 | 143,939 | 382 | Ribonucleotide-diphosphate reductase subunit beta [Shewanella colwelliana] | 3.00E-141 | WP_028763880.1 | |
| ORF226 | − | 144,040 | 146,370 | 777 | Ribonucleoside-diphosphate reductase subunit alpha [Comamonas sp. B-9] | 0 | WP_027011154.1 | |
| ORF473 | − | 334,304 | 335,233 | 310 | Td thymidylate synthetase [Acinetobacter phage Acj61] | 3.00E-167 | YP_004009838.1 | |
| Amino acid transport and metabolism | ORF5 | − | 5,117 | 5,956 | 280 | Nitrate reductase [Herbaspirillum chlorophenolicum] | 6.00E-69 | WP_050467745.1 |
| ORF477 | − | 336,023 | 336,469 | 149 | NTP-PPase [Caudovirales sp. ctOwN3] | 3.00E-32 | QGH72159.1 | |
| ORF262 | + | 169,665 | 170,243 | 193 | Phospholipase D family protein [Chlorobaculum limnaeum] | 1.00E-33 | WP_069809568.1 | |
| Signal transduction mechanisms | ORF2 | − | 1,890 | 3,020 | 377 | Beta glucosyl transferase [Enterobacter phage CC31] | 5.00E-38 | YP_004009897.1 |
| ORF17 | − | 13,266 | 13,880 | 205 | General stress protein 16U [Pseudomonas phage VCM] | 2.00E-45 | YP_009222754.1 | |
| ORF18 | − | 13867 | 14,931 | 355 | DUF475 domain-containing protein [Sphingomonas sanguinis] | 7.00E-98 | WP_058733334.1 | |
| ORF19 | − | 14,888 | 15,565 | 226 | Von Willebrand factor type A domain-containing protein [Rhizobium phage RHph_TM30] | 6.00E-86 | QIG71336.1 | |
| ORF30 | − | 24,727 | 26,670 | 648 | PrkA family serine protein kinase [Alcanivorax sp. CP2C] | 0 | WP_067606528.1 | |
| ORF35 | − | 28,475 | 29,101 | 209 | Metallophosphoesterase [Bacillus phage Troll] | 7.00E-32 | YP_008430899.1 | |
| ORF43 | − | 34,664 | 35,284 | 207 | Putative Hef-like homing endonuclease [Acinetobacter virus 133] | 1.00E-06 | YP_004300760.1 | |
| ORF237 | − | 151,481 | 152,338 | 286 | Serine/threonine protein phosphatase 1 [Methylocaldum sp. 175] | 1.00E-39 | SMF95613.1 | |
| ORF239 | − | 153,493 | 154,359 | 289 | Single-stranded DNA binding protein [Xanthomonas phage XacN1] | 4.00E-44 | BBA65400.1 | |
| Cell wall/membrane/envelope biogenesis | ORF33 | − | 27,527 | 28,144 | 206 | Restriction endonuclease [Betaproteobacteria bacterium RIFCSPLOWO2_12_FULL_62_13] | 5.00E-55 | OGA37234.1 |
| ORF60 | − | 46,489 | 47,295 | 269 | Putative family 9 glycosyl transferase [Caulobacter phage CcrColossus] | 5.00E-17 | YP_006988365.1 | |
| ORF155 | − | 101,717 | 103,162 | 482 | VCBS repeat-containing protein [Loktanella vestfoldensis] | 7.00E-28 | WP_087211375.1 | |
| ORF425 | + | 299,739 | 301,409 | 557 | Murein DD-endopeptidase MepM [Syntrophomonadaceae bacterium] | 8.00E-61 | MBT9137488.1 | |
| ORF426 | + | 301,412 | 301,699 | 96 | PaaR repeat-containing protein [Ruegeria mobilis] | 8.00E-10 | WP_074712575.1 | |
| ORF486 | − | 343,044 | 343,793 | 250 | Bifunctional protein GlmU [bacterium BMS3Bbin11] | 8.00E-06 | GBE46073.1 | |
| Structure | ORF356 | − | 223,631 | 224,212 | 194 | Structural protein [Xanthomonas phage XacN1] | 4.00E-44 | BBA65499.1 |
| ORF359 | − | 226,174 | 227,745 | 524 | Tail sheath protein [Xanthomonas phage XacN1] | 8.00E-94 | BBA65515.1 | |
| ORF361 | − | 229,048 | 236,670 | 2541 | Structural protein [Pectobacterium phage CBB] | 2.00E-17 | AMM43801.1 | |
| ORF362 | − | 236,776 | 240,420 | 1215 | Baseplate wedge [Cronobacter phage vB_CsaM_GAP32] | 2.00E-93 | YP_006987336.1 | |
| ORF363 | − | 240,586 | 240,963 | 126 | Baseplate wedge [Xanthomonas phage XacN1] | 2.00E-26 | BBA65471.1 | |
| ORF364 | − | 240,963 | 242,090 | 376 | Baseplate hub subunit and tail lysozyme [Pseudomonas phage vB_PaeM_PA5oct] | 2.00E-29 | QCG76015.1 | |
| ORF367 | − | 244,672 | 245,745 | 358 | Structural protein [Serratia phage BF] | 2.00E-17 | AQW88767.1 | |
| ORF375 | − | 253,025 | 253,825 | 267 | Baseplate hub subunit [Agrobacterium phage Atu_ph07] | 2.00E-23 | ASV44759.1 | |
| ORF378 | + | 257,102 | 258,826 | 575 | Portal vertex protein [Xanthomonas phage XacN1] | 4.00E-133 | BBA65449.1 | |
| ORF379 | + | 259,178 | 259,705 | 176 | Prohead core scaffolding protein and protease [Xanthomonas phage XacN1] | 1.00E-51 | BBA65445.1 | |
| ORF383 | + | 261286 | 262,521 | 412 | Major capsid protein [Salicola phage SCTP-2] | 7.00E-104 | ASV44110.1 | |
| ORF401 | + | 268,348 | 269,829 | 494 | Neck protein [Pectobacterium phage CBB] | 2.00E-23 | AMM43766.1 | |
| ORF406 | + | 274017 | 274,829 | 271 | Proximal tail sheath stabilization [uncultured Mediterranean phage uvMED] | 7.00E-22 | BAR27635.1 | |
| ORF410 | + | 278,320 | 279,018 | 233 | Putative tail fiber protein [Pseudomonas phage Noxifer] | 2.00E-07 | ARV77307.1 | |
| ORF415 | + | 283,386 | 285,101 | 572 | Phage-related tail fiber protein [uncultured Mediterranean phage uvMED] | 1.00E-29 | BAR25957.1 | |
| Integral component of membrane | ORF54 | − | 41,514 | 42,440 | 309 | Phage shock protein A [Lewinella agarilytica] | 1.00E-22 | SEQ17255.1 |
| ORF187 | − | 117,319 | 117,720 | 134 | DUF3307 domain-containing protein [Sulfitobacter sp. 20_GPM-1509m] | 4.00E-19 | WP_028956004.1 | |
| Coenzyme transport and metabolism | ORF271 | + | 174,077 | 174,772 | 232 | VWA domain-containing protein [Blautia hydrogenotrophica] | 8.00E-49 | WP_005952142.1 |
| ORF445 | − | 316,066 | 317,973 | 636 | Peptidase [uncultured Mediterranean phage uvMED] | 3.00E-25 | BAR35475.1 | |
| Mobilome: prophages, transposons | ORF37 | − | 29,535 | 29,810 | 92 | Hypothetical protein E4H12_13870 [Candidatus Thorarchaeota archaeon] | 1.00E-13 | TFG95161.1 |
| ORF228 | − | 147,097 | 147,360 | 88 | MULTISPECIES: DUF4326 domain-containing protein [Thioalkalivibrio] | 1.00E-31 | WP_013006599.1 | |
| ORF260 | − | 167,955 | 168,383 | 143 | Head completion protein [Synechococcus phage ACG-2014f] | 5.00E-37 | AIX21328.1 | |
| tRNA | ORF84 | − | 59,431 | 60,477 | 349 | tRNA(Ile)-lysidine synthase (tRNA(Ile)-lysidinesynthetase) (tRNA(Ile)-2-lysyl-cytidine synthase) [Rickettsiella grylli] | 2.00E-32 | EDP46981.1 |
| ORF156 | − | 103,221 | 103,724 | 168 | Glutaminyl-tRNA synthase (glutamine-hydrolyzing) subunit B [Candidatus Saccharibacteria bacterium 49-20] | 5.00E-08 | OJU87614.1 |