TABLE 1.
General features of the putative ORFs encoded by ΨM100 and comparison to the corresponding ORFs of ΨM2 and to other proteins in databases
| ORF | Fa | Start/end | Size (aa) | Motifb | Related
ORF in ΨM2
|
Other related protein in database
|
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ORF | Size (aa)c | Proposed function | % aa identityd | Name | Accession no.e | Size (aa) | % aa identity | |||||
| orf29 | 2 | 65/1273 | 402 | orf29 | 402 | Integrase or recombinase | 63.8 (406) | Integrase or recombinase RipX (Bacillus subtilis) | sp P46352 | 296 | 28.0 (416) | |
| orf30 | 1 | 1489/1791 | 100 | orf30 | 124 | 44.8 (137) | Hypothetical protein (Emericella nidulans mitochondrion) | sp P03883 | 228 | 24.2 (230) | ||
| orf31 | 2 | 1826/2278 | 150 | orf31 | 150 | 39.9 (153) | ||||||
| orf1 | 1 | 2578/3102 | 174 | orf1 | 177 | 73.0 (178) | ||||||
| orfA | 2 | 3287/3754 | 155 | NA | NA | |||||||
| orf2 | 3 | 3828/4085 | 85 | orf2 | 95 | 95.3 (95) | ||||||
| orf3 | 1 | 4324/4608 | 94 | orf3 | 94 | 98.9 (94) | ||||||
| orf4 | 3 | 4605/5069 | 154 | HTH | orf4 | 154 | 100 (154) | |||||
| orfB | 3 | 5577/6335 | 252 | NA | NA | Hypothetical protein MTH315 (Methanothermobacter thermautotrophicus ΔH) | pir D69140 | 254 | 62.9 (258) | |||
| orfC | 1 | 6385/6708 | 107 | NA | NA | Hypothetical protein MTH316 (Methanothermobacter thermautotrophicus ΔH) | pir E69140 | 114 | 56.9 (119) | |||
| orfD | 3 | 6720/8198 | 492 | NA | NA | |||||||
| orf5 | 1 | 8176/8565 | 129 | orf5 | 127 | 89.1 (129) | Hypothetical protein APE1779 (Aeropyrum pernix K1) | pir A72562 | 158 | 26.4 (158) | ||
| orf6 | 1 | 8665/9000 | 111 | HTH | orf6 | 117 | 66.7 (119) | ORF6 of plasmid pME2200 (Methanothermobacter marburgensis ZH3) | gb AAF00129 | 135 | 40.5 (136) | |
| orf7 | 2 | 9389/9661 | 90 | orf7 | 90 | 97.8 (90) | ||||||
| orf8 | 3 | 9702/10223 | 173 | HTH | orf8 | 173 | Small terminase subunit | 100 (173) | Prophage PBSX small terminase subunit (Bacillus subtilis) | sp P39785 | 265 | 21.5 (276) |
| orf9 | 1 | 10168/11571 | 467 | ATP or GTP binding motif A | orf9 | 468 | Large terminase subunit | 91.5 (468) | Unknown protein of bacteriophage Felix 01 | gb AAC24136.1 | 533 | 36.0 (540) |
| orf10 | 2 | 11564/13186 | 540 | orf10 | 542 | Portal protein | 78.2 (542) | Portal protein of temperate phage HP1 (Haemophilus influenzae) | sp P51717 | 345 | 24.9 (561) | |
| orf11 | 1 | 13327/13932 | 201 | orf11 | 216 | 60.3 (220) | ||||||
| orf12 | 2 | 14003/15223 | 406 | orf12 | 351 | Structural protein | 55.8 (416) | Unknown protein of a cryptic prophage (Bacillus subtilis) | sp P45920 | 322 | 26.0 (424) | |
| orf13 | 1 | 15238/16182 | 314 | orf13 | 315 | Structural protein | 57.1 (321) | Unknown protein of a cryptic prophage (Bacillus subtilis) | sp P45921 | 311 | 30.2 (327) | |
| orf14 | 3 | 16254/16574 | 106 | orf14 | 110 | 53.9 (114) | ||||||
| orf15 | 1 | 16561/16902 | 113 | orf15 | 112 | 41.1 (114) | ||||||
| orf16 | 3 | 16908/17309 | 133 | orf16 | 133 | 63.9 (133) | Unknown protein of phage SPP1 (Bacillus subtilis) | pir T42287 | 144 | 31.0 (148) | ||
| orf17 | 2 | 17294/17710 | 138 | orf17 | 139 | 54.0 (140) | ||||||
| orf18 | 1 | 17707/18423 | 238 | orf18 | 243 | Structural protein | 64.4 (245) | |||||
| orf19 | 3 | 18435/18986 | 183 | orf19 | 189 | 59.2 (193) | ||||||
| orfE | 6 | 19613/19185 | 142 | NA | NA | Hypothetical protein MTH1518 (Methanothermobacter thermautotrophicus ΔH) | pir E69069 | 133 | 28.1 (147) | |||
| orf21 | 2 | 19679/23152 | 1,157 | orf21 | 1,186 | Tail protein | 49.8 (1,222) | Hypothetical protein M151.4 (Caenorhabditis elegans) | pir T32297 | 1,034 | 20.0 (1,686) | |
| orf22 | 1 | 23149/23583 | 144 | ATP or GTP binding motif A | orf22 | 144 | ATP or GTP binding protein | 100 (144) | ||||
| orf23 | 2 | 23588/24373 | 261 | orf23 | 268 | 92.7 (268) | ||||||
| orf24 | 1 | 24370/25068 | 232 | orf24 | 232 | 98.3 (232) | ||||||
| orf25 | 2 | 25070/26101 | 343 | orf25 | 354 | 86.2 (357) | ||||||
| orf26 | 3 | 26280/26912 | 210 | orf26 | 216 | 81.8 (217) | ||||||
| orf27 | 2 | 26909/27631 | 240 | orf27 | 206 | 41.9 (248) | ORFA of phage ΨM1 element DR1 (Methanothermobacter marburgensis Marburg) | gb AAC27071 | 217 | 38.5 (249) | ||
| orf28 | 3 | 27780/28634 | 284 | orf28 | 305 | Pseudomurein endoisopeptidase PeiP | 53.4 (306) | Conserved hypothetical protein MTH412 (Methanothermobacter thermautotrophicus ΔH) | pir F69153 | 583 | 20.0 (602) | |
a
F, reading frame in which an ORF was defined.
b
HTH, helix-turn-helix motif.
c
NA, not available.
d
The percentages of amino acid (aa) identity were calculated using the GAP program of GCG. The numbers in parentheses are the sizes (in amino acids) of the alignment overlap. NA, not available.
e
The database sources are shown before the accession numbers as follows: sp, SWISSPROT; pir, PIR database; gb, GenBank.