Detailed information
Bioinformatically predicted
Overview
| Name | ssb | Type | Machinery gene |
| Locus tag | S100424_RS04230 | Genome accession | NZ_CP021484 |
| Coordinates | 875803..876249 (+) | Length | 148 a.a. |
| NCBI ID | WP_065124802.1 | Uniprot ID | - |
| Organism | Pediococcus acidilactici strain SRCM100424 | ||
| 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 | 865345..905768 | 875803..876249 | within | 0 |
Gene organization within MGE regions
Location: 865345..905768
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| S100424_RS04150 (S100424_00829) | - | 865345..866256 (-) | 912 | WP_232457162.1 | integrase | - |
| S100424_RS04155 (S100424_00830) | - | 866354..867160 (-) | 807 | WP_065124812.1 | DUF3037 domain-containing protein | - |
| S100424_RS04160 (S100424_00831) | - | 867162..867986 (-) | 825 | WP_081276413.1 | HipA family kinase | - |
| S100424_RS04165 (S100424_00832) | - | 868028..869224 (-) | 1197 | WP_081276412.1 | Ltp family lipoprotein | - |
| S100424_RS04170 (S100424_00833) | - | 869297..869704 (-) | 408 | WP_065124811.1 | ImmA/IrrE family metallo-endopeptidase | - |
| S100424_RS04175 (S100424_00834) | - | 869716..870078 (-) | 363 | WP_008840853.1 | helix-turn-helix domain-containing protein | - |
| S100424_RS04180 (S100424_00835) | - | 870221..870451 (+) | 231 | WP_065124810.1 | helix-turn-helix transcriptional regulator | - |
| S100424_RS10390 (S100424_00836) | - | 870448..870585 (+) | 138 | WP_008840855.1 | hypothetical protein | - |
| S100424_RS04185 (S100424_00837) | - | 870588..870812 (-) | 225 | WP_065124809.1 | hypothetical protein | - |
| S100424_RS04190 (S100424_00838) | - | 870879..871094 (+) | 216 | WP_065124808.1 | hypothetical protein | - |
| S100424_RS04195 (S100424_00839) | - | 871179..871643 (+) | 465 | WP_232457163.1 | helix-turn-helix domain-containing protein | - |
| S100424_RS04200 (S100424_00840) | - | 871644..871925 (+) | 282 | WP_065124807.1 | hypothetical protein | - |
| S100424_RS10395 (S100424_00841) | - | 871927..872070 (+) | 144 | WP_157420393.1 | hypothetical protein | - |
| S100424_RS04205 (S100424_00843) | - | 872163..873056 (+) | 894 | WP_065124806.1 | DUF1351 domain-containing protein | - |
| S100424_RS04210 (S100424_00844) | - | 873059..873895 (+) | 837 | WP_065124805.1 | ERF family protein | - |
| S100424_RS04215 (S100424_00845) | - | 873888..874721 (+) | 834 | WP_065124804.1 | helix-turn-helix domain-containing protein | - |
| S100424_RS04220 (S100424_00846) | - | 874726..875448 (+) | 723 | WP_021361655.1 | putative HNHc nuclease | - |
| S100424_RS04225 (S100424_00847) | - | 875393..875800 (+) | 408 | WP_065124803.1 | hypothetical protein | - |
| S100424_RS04230 (S100424_00848) | ssb | 875803..876249 (+) | 447 | WP_065124802.1 | single-stranded DNA-binding protein | Machinery gene |
| S100424_RS04235 (S100424_00849) | - | 876260..876607 (+) | 348 | WP_065124801.1 | DUF1642 domain-containing protein | - |
| S100424_RS04240 (S100424_00850) | - | 876604..876828 (+) | 225 | WP_065124800.1 | hypothetical protein | - |
| S100424_RS10400 (S100424_00851) | - | 876848..877006 (+) | 159 | WP_153903504.1 | hypothetical protein | - |
| S100424_RS04245 (S100424_00853) | - | 877346..877777 (+) | 432 | WP_065124799.1 | ArpU family phage packaging/lysis transcriptional regulator | - |
| S100424_RS04255 (S100424_00855) | - | 878390..879058 (+) | 669 | WP_065124798.1 | hypothetical protein | - |
| S100424_RS04260 (S100424_00856) | - | 879127..879813 (+) | 687 | WP_032540563.1 | terminase gpP N-terminus-related DNA-binding protein | - |
| S100424_RS04265 (S100424_00857) | - | 879797..881110 (+) | 1314 | WP_021361666.1 | PBSX family phage terminase large subunit | - |
| S100424_RS04270 (S100424_00858) | - | 881122..882651 (+) | 1530 | WP_050585101.1 | phage portal protein | - |
| S100424_RS04275 (S100424_00859) | - | 882648..883781 (+) | 1134 | WP_081276410.1 | phage minor capsid protein | - |
| S100424_RS04280 (S100424_00860) | - | 883881..884453 (+) | 573 | WP_021361667.1 | phage scaffolding protein | - |
| S100424_RS04285 (S100424_00861) | - | 884466..885335 (+) | 870 | WP_065124797.1 | capsid protein | - |
| S100424_RS04290 (S100424_00862) | - | 885406..885822 (+) | 417 | WP_065124796.1 | hypothetical protein | - |
| S100424_RS04295 (S100424_00863) | - | 885819..886169 (+) | 351 | WP_065124795.1 | putative minor capsid protein | - |
| S100424_RS04300 (S100424_00864) | - | 886169..886513 (+) | 345 | WP_065124794.1 | minor capsid protein | - |
| S100424_RS04305 (S100424_00865) | - | 886513..886908 (+) | 396 | WP_065124793.1 | phage tail terminator protein | - |
| S100424_RS04310 (S100424_00866) | - | 887032..887463 (+) | 432 | Protein_819 | phage tail tube protein | - |
| S100424_RS04315 (S100424_00867) | - | 887537..888004 (+) | 468 | WP_065124791.1 | Ig-like domain-containing protein | - |
| S100424_RS04320 (S100424_00868) | - | 888080..888472 (+) | 393 | WP_065124790.1 | hypothetical protein | - |
| S100424_RS04325 (S100424_00869) | - | 888482..889102 (+) | 621 | WP_065124789.1 | Gp15 family bacteriophage protein | - |
| S100424_RS04330 (S100424_00870) | - | 889136..894253 (+) | 5118 | WP_065124788.1 | tape measure protein | - |
| S100424_RS04335 (S100424_00871) | - | 894255..895079 (+) | 825 | WP_065124787.1 | phage tail domain-containing protein | - |
| S100424_RS04340 (S100424_00872) | - | 895091..896206 (+) | 1116 | WP_065124786.1 | prophage endopeptidase tail family protein | - |
| S100424_RS04345 (S100424_00873) | - | 896199..896429 (+) | 231 | WP_065124785.1 | hypothetical protein | - |
| S100424_RS04350 (S100424_00874) | - | 896410..896820 (+) | 411 | WP_065124784.1 | hypothetical protein | - |
| S100424_RS04355 (S100424_00875) | - | 896810..897847 (+) | 1038 | WP_065124783.1 | BppU family phage baseplate upper protein | - |
| S100424_RS04360 (S100424_00876) | - | 897860..898681 (+) | 822 | WP_065124782.1 | collagen-like protein | - |
| S100424_RS04365 (S100424_00877) | - | 898697..900187 (+) | 1491 | WP_065124781.1 | hypothetical protein | - |
| S100424_RS04370 (S100424_00878) | - | 900245..900508 (+) | 264 | WP_065124780.1 | hypothetical protein | - |
| S100424_RS04375 (S100424_00879) | - | 900508..900762 (+) | 255 | WP_065124779.1 | phage holin | - |
| S100424_RS04380 (S100424_00880) | - | 900746..902113 (+) | 1368 | WP_065124778.1 | GH25 family lysozyme | - |
| S100424_RS04385 (S100424_00881) | - | 902141..902740 (+) | 600 | WP_065124777.1 | GH25 family lysozyme | - |
| S100424_RS04395 (S100424_00882) | - | 903199..903519 (+) | 321 | WP_065124775.1 | acetyl-CoA carboxylase | - |
| S100424_RS10555 (S100424_00883) | - | 903864..904748 (-) | 885 | WP_232457164.1 | hypothetical protein | - |
| S100424_RS04405 (S100424_00884) | - | 904869..905768 (-) | 900 | WP_065124774.1 | hypothetical protein | - |
Sequence
Protein
Download Length: 148 a.a. Molecular weight: 16646.32 Da Isoelectric Point: 5.7209
>NTDB_id=230947 S100424_RS04230 WP_065124802.1 875803..876249(+) (ssb) [Pediococcus acidilactici strain SRCM100424]
MINRTVLVGRLTKDPEIRYTQSGMAVANFTMAVNRQFTNANGEREADFISCIVWRKAAENFCNFTHKGSLVGIDGRIQTS
SYEKEGQRVYATQVVVDSFSLLEPKQQSQQRGQQSNASDALHNNFGQPTNNYSQNNNDFGIDDNDLPF
MINRTVLVGRLTKDPEIRYTQSGMAVANFTMAVNRQFTNANGEREADFISCIVWRKAAENFCNFTHKGSLVGIDGRIQTS
SYEKEGQRVYATQVVVDSFSLLEPKQQSQQRGQQSNASDALHNNFGQPTNNYSQNNNDFGIDDNDLPF
Nucleotide
Download Length: 447 bp
>NTDB_id=230947 S100424_RS04230 WP_065124802.1 875803..876249(+) (ssb) [Pediococcus acidilactici strain SRCM100424]
ATGATTAATCGAACCGTATTAGTCGGACGCCTAACCAAGGATCCAGAAATCCGTTATACCCAATCAGGGATGGCGGTGGC
CAACTTTACTATGGCCGTGAACCGGCAGTTCACCAACGCTAATGGCGAGCGAGAAGCGGACTTTATCAGCTGTATTGTCT
GGAGAAAGGCGGCCGAAAACTTCTGTAATTTTACCCACAAAGGATCATTGGTCGGGATTGATGGTCGGATTCAAACTAGT
TCGTACGAAAAGGAAGGTCAACGCGTGTATGCTACACAAGTGGTTGTAGATAGTTTCTCGTTGCTTGAACCAAAGCAACA
AAGCCAACAACGTGGCCAGCAATCCAACGCTAGCGATGCTTTGCATAACAATTTCGGACAACCTACTAACAATTATAGCC
AGAATAATAACGATTTCGGCATCGACGATAATGATTTGCCGTTTTAG
ATGATTAATCGAACCGTATTAGTCGGACGCCTAACCAAGGATCCAGAAATCCGTTATACCCAATCAGGGATGGCGGTGGC
CAACTTTACTATGGCCGTGAACCGGCAGTTCACCAACGCTAATGGCGAGCGAGAAGCGGACTTTATCAGCTGTATTGTCT
GGAGAAAGGCGGCCGAAAACTTCTGTAATTTTACCCACAAAGGATCATTGGTCGGGATTGATGGTCGGATTCAAACTAGT
TCGTACGAAAAGGAAGGTCAACGCGTGTATGCTACACAAGTGGTTGTAGATAGTTTCTCGTTGCTTGAACCAAAGCAACA
AAGCCAACAACGTGGCCAGCAATCCAACGCTAGCGATGCTTTGCATAACAATTTCGGACAACCTACTAACAATTATAGCC
AGAATAATAACGATTTCGGCATCGACGATAATGATTTGCCGTTTTAG
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 |
54.706 |
100 |
0.628 |
| ssbA | Bacillus subtilis subsp. subtilis str. 168 |
48.837 |
100 |
0.568 |
| ssbB | Bacillus subtilis subsp. subtilis str. 168 |
55.455 |
74.324 |
0.412 |
| ssbB | Streptococcus sobrinus strain NIDR 6715-7 |
38.514 |
100 |
0.385 |
| ssbB/cilA | Streptococcus pneumoniae TIGR4 |
37.838 |
100 |
0.378 |
| ssbB/cilA | Streptococcus mitis NCTC 12261 |
37.838 |
100 |
0.378 |
| ssb | Vibrio cholerae strain A1552 |
31.977 |
100 |
0.372 |
| ssbB/cilA | Streptococcus pneumoniae Rx1 |
37.162 |
100 |
0.372 |
| ssbB/cilA | Streptococcus pneumoniae D39 |
37.162 |
100 |
0.372 |
| ssbB/cilA | Streptococcus pneumoniae R6 |
37.162 |
100 |
0.372 |
| ssbB/cilA | Streptococcus mitis SK321 |
37.162 |
100 |
0.372 |