Detailed information
Bioinformatically predicted
Overview
| Name | ssb | Type | Machinery gene |
| Locus tag | R6U75_RS04380 | Genome accession | NZ_CP137627 |
| Coordinates | 848309..848791 (+) | Length | 160 a.a. |
| NCBI ID | WP_199875575.1 | Uniprot ID | - |
| Organism | Pediococcus pentosaceus strain LA0061 | ||
| Function | ssDNA binding (predicted from homology) DNA processing |
||
Related MGE
Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.
Gene-MGE association summary
| MGE type | MGE coordinates | Gene coordinates | Relative position | Distance (bp) |
|---|---|---|---|---|
| Prophage | 838417..877900 | 848309..848791 | within | 0 |
Gene organization within MGE regions
Location: 838417..877900
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| R6U75_RS04305 (R6U75_04300) | - | 838417..839589 (-) | 1173 | WP_199875583.1 | site-specific integrase | - |
| R6U75_RS04310 (R6U75_04305) | - | 839686..839988 (-) | 303 | WP_029257881.1 | hypothetical protein | - |
| R6U75_RS04315 (R6U75_04310) | - | 840077..841147 (-) | 1071 | WP_199875582.1 | DUF4236 domain-containing protein | - |
| R6U75_RS04320 (R6U75_04315) | - | 841262..842242 (-) | 981 | WP_199875581.1 | hypothetical protein | - |
| R6U75_RS04325 (R6U75_04320) | - | 842304..842711 (-) | 408 | WP_199875580.1 | ImmA/IrrE family metallo-endopeptidase | - |
| R6U75_RS04330 (R6U75_04325) | - | 842723..843094 (-) | 372 | WP_176932925.1 | helix-turn-helix domain-containing protein | - |
| R6U75_RS04335 (R6U75_04330) | - | 843246..843497 (+) | 252 | WP_249704015.1 | helix-turn-helix domain-containing protein | - |
| R6U75_RS04340 (R6U75_04335) | - | 843494..843715 (+) | 222 | WP_199875579.1 | hypothetical protein | - |
| R6U75_RS04345 (R6U75_04340) | - | 843789..844247 (+) | 459 | WP_229572679.1 | helix-turn-helix domain-containing protein | - |
| R6U75_RS04350 (R6U75_04345) | - | 844248..844523 (+) | 276 | WP_199875578.1 | helix-turn-helix domain-containing protein | - |
| R6U75_RS04355 (R6U75_04350) | - | 844761..845042 (+) | 282 | WP_141822573.1 | hypothetical protein | - |
| R6U75_RS04360 (R6U75_04355) | bet | 845035..845799 (+) | 765 | WP_094104559.1 | phage recombination protein Bet | - |
| R6U75_RS04365 (R6U75_04360) | - | 845759..846604 (+) | 846 | WP_234417758.1 | PD-(D/E)XK nuclease-like domain-containing protein | - |
| R6U75_RS04370 (R6U75_04365) | - | 846615..847445 (+) | 831 | WP_199875577.1 | helix-turn-helix domain-containing protein | - |
| R6U75_RS04375 (R6U75_04370) | - | 847449..848144 (+) | 696 | WP_199875576.1 | putative HNHc nuclease | - |
| R6U75_RS04380 (R6U75_04375) | ssb | 848309..848791 (+) | 483 | WP_199875575.1 | single-stranded DNA-binding protein | Machinery gene |
| R6U75_RS04385 (R6U75_04380) | - | 848867..849268 (+) | 402 | WP_234417756.1 | hypothetical protein | - |
| R6U75_RS04390 (R6U75_04385) | - | 849280..849573 (+) | 294 | WP_199875574.1 | hypothetical protein | - |
| R6U75_RS04395 (R6U75_04390) | - | 849574..850140 (+) | 567 | WP_199875573.1 | DUF1642 domain-containing protein | - |
| R6U75_RS04400 (R6U75_04395) | - | 850133..850300 (+) | 168 | WP_199875572.1 | hypothetical protein | - |
| R6U75_RS04405 (R6U75_04400) | - | 850448..850690 (+) | 243 | WP_199875571.1 | hypothetical protein | - |
| R6U75_RS04410 (R6U75_04405) | - | 851062..851505 (+) | 444 | WP_094104548.1 | hypothetical protein | - |
| R6U75_RS04420 (R6U75_04415) | - | 851841..852665 (+) | 825 | WP_199875570.1 | DUF5677 domain-containing protein | - |
| R6U75_RS04425 (R6U75_04420) | - | 852662..852838 (+) | 177 | WP_199875569.1 | hypothetical protein | - |
| R6U75_RS04430 (R6U75_04425) | - | 852838..853518 (+) | 681 | WP_199875568.1 | terminase gpP N-terminus-related DNA-binding protein | - |
| R6U75_RS04435 (R6U75_04430) | - | 853515..854888 (+) | 1374 | WP_234417754.1 | PBSX family phage terminase large subunit | - |
| R6U75_RS04440 (R6U75_04435) | - | 854942..856438 (+) | 1497 | WP_234417752.1 | phage portal protein | - |
| R6U75_RS04445 (R6U75_04440) | - | 856435..857568 (+) | 1134 | WP_199875566.1 | phage minor capsid protein | - |
| R6U75_RS04450 (R6U75_04445) | - | 857668..858225 (+) | 558 | WP_199875565.1 | phage scaffolding protein | - |
| R6U75_RS04455 (R6U75_04450) | - | 858238..859146 (+) | 909 | WP_199875564.1 | hypothetical protein | - |
| R6U75_RS04460 (R6U75_04455) | - | 859214..859630 (+) | 417 | WP_199875563.1 | hypothetical protein | - |
| R6U75_RS04465 (R6U75_04460) | - | 859627..859974 (+) | 348 | WP_199875562.1 | putative minor capsid protein | - |
| R6U75_RS04470 (R6U75_04465) | - | 859974..860324 (+) | 351 | WP_199875561.1 | minor capsid protein | - |
| R6U75_RS04475 (R6U75_04470) | - | 860311..860706 (+) | 396 | WP_199875560.1 | minor capsid protein | - |
| R6U75_RS04480 (R6U75_04475) | - | 860709..861149 (+) | 441 | Protein_856 | phage tail tube protein | - |
| R6U75_RS04485 (R6U75_04480) | - | 861358..861795 (+) | 438 | WP_199875559.1 | hypothetical protein | - |
| R6U75_RS04490 (R6U75_04485) | - | 861802..862434 (+) | 633 | WP_199875558.1 | Gp15 family bacteriophage protein | - |
| R6U75_RS04495 (R6U75_04490) | - | 862438..868014 (+) | 5577 | WP_199875557.1 | glycine zipper domain-containing protein | - |
| R6U75_RS04500 (R6U75_04495) | - | 868067..868864 (+) | 798 | WP_199875556.1 | phage tail domain-containing protein | - |
| R6U75_RS04505 (R6U75_04500) | - | 868873..870009 (+) | 1137 | WP_199875555.1 | phage tail protein | - |
| R6U75_RS04510 (R6U75_04505) | - | 869999..870208 (+) | 210 | WP_199875554.1 | hypothetical protein | - |
| R6U75_RS04515 (R6U75_04510) | - | 870314..870610 (+) | 297 | WP_199875553.1 | hypothetical protein | - |
| R6U75_RS04520 (R6U75_04515) | - | 870610..872418 (+) | 1809 | WP_199875552.1 | BppU family phage baseplate upper protein | - |
| R6U75_RS04525 (R6U75_04520) | - | 872437..873201 (+) | 765 | WP_199875551.1 | hypothetical protein | - |
| R6U75_RS04530 (R6U75_04525) | - | 873215..873526 (+) | 312 | WP_199875550.1 | DUF2977 domain-containing protein | - |
| R6U75_RS04535 (R6U75_04530) | - | 873526..873657 (+) | 132 | WP_199875549.1 | XkdX family protein | - |
| R6U75_RS04540 (R6U75_04535) | - | 873993..874232 (+) | 240 | WP_199875548.1 | phage holin | - |
| R6U75_RS04545 (R6U75_04540) | - | 874216..875340 (+) | 1125 | WP_199875547.1 | peptidoglycan recognition family protein | - |
| R6U75_RS04550 (R6U75_04545) | - | 876524..877900 (+) | 1377 | WP_199875546.1 | amino acid permease | - |
Sequence
Protein
Download Length: 160 a.a. Molecular weight: 18151.89 Da Isoelectric Point: 6.4638
>NTDB_id=899499 R6U75_RS04380 WP_199875575.1 848309..848791(+) (ssb) [Pediococcus pentosaceus strain LA0061]
MINRTVLVGRLTNGPELKYTGSGVAVATFTVAVNRQFTNSQGEREADFIRCQMWRKAAENFCNFTHKGSLVGIDGRIQTR
SYDNQQGTRIFVTEVVAENFSLLESKNSNQNNQNEQFEQNRPQNNGQNYQNQQNGQSSHSINPNDPFKSMPDIKDDDLPF
MINRTVLVGRLTNGPELKYTGSGVAVATFTVAVNRQFTNSQGEREADFIRCQMWRKAAENFCNFTHKGSLVGIDGRIQTR
SYDNQQGTRIFVTEVVAENFSLLESKNSNQNNQNEQFEQNRPQNNGQNYQNQQNGQSSHSINPNDPFKSMPDIKDDDLPF
Nucleotide
Download Length: 483 bp
>NTDB_id=899499 R6U75_RS04380 WP_199875575.1 848309..848791(+) (ssb) [Pediococcus pentosaceus strain LA0061]
ATGATTAATCGAACAGTATTAGTCGGGCGGTTAACTAACGGTCCAGAACTAAAATACACAGGCAGCGGTGTAGCAGTTGC
AACCTTCACAGTAGCCGTTAATCGGCAATTTACTAATTCGCAAGGCGAACGTGAAGCAGATTTTATTAGATGCCAAATGT
GGCGCAAAGCTGCTGAAAACTTCTGTAACTTTACTCACAAAGGTTCACTGGTTGGCATCGACGGACGCATTCAAACTCGT
TCATACGATAATCAGCAAGGTACACGAATTTTTGTTACTGAGGTCGTAGCTGAGAACTTCTCGCTACTTGAATCTAAAAA
TAGCAATCAAAATAACCAAAATGAACAATTTGAACAAAATAGACCTCAAAATAATGGACAAAATTATCAGAATCAACAAA
ATGGTCAATCATCACATAGCATAAATCCTAACGACCCATTTAAAAGCATGCCGGATATCAAGGATGACGATTTACCATTC
TAG
ATGATTAATCGAACAGTATTAGTCGGGCGGTTAACTAACGGTCCAGAACTAAAATACACAGGCAGCGGTGTAGCAGTTGC
AACCTTCACAGTAGCCGTTAATCGGCAATTTACTAATTCGCAAGGCGAACGTGAAGCAGATTTTATTAGATGCCAAATGT
GGCGCAAAGCTGCTGAAAACTTCTGTAACTTTACTCACAAAGGTTCACTGGTTGGCATCGACGGACGCATTCAAACTCGT
TCATACGATAATCAGCAAGGTACACGAATTTTTGTTACTGAGGTCGTAGCTGAGAACTTCTCGCTACTTGAATCTAAAAA
TAGCAATCAAAATAACCAAAATGAACAATTTGAACAAAATAGACCTCAAAATAATGGACAAAATTATCAGAATCAACAAA
ATGGTCAATCATCACATAGCATAAATCCTAACGACCCATTTAAAAGCATGCCGGATATCAAGGATGACGATTTACCATTC
TAG
3D structure
| Source | ID | Structure |
|---|
Similar proteins
Only experimentally validated proteins are listed.
| Protein | Organism | Identities (%) | Coverage (%) | Ha-value |
|---|---|---|---|---|
| ssb | Latilactobacillus sakei subsp. sakei 23K |
56.471 |
100 |
0.6 |
| ssbA | Bacillus subtilis subsp. subtilis str. 168 |
55.172 |
100 |
0.6 |