Detailed information
Bioinformatically predicted
Overview
| Name | ssb | Type | Machinery gene |
| Locus tag | AB3223_RS04615 | Genome accession | NZ_OZ061351 |
| Coordinates | 894327..894767 (-) | Length | 146 a.a. |
| NCBI ID | WP_367365880.1 | Uniprot ID | - |
| Organism | Pediococcus parvulus isolate Pediococcus parvulus IOEB-8801 | ||
| 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 | 872578..909073 | 894327..894767 | within | 0 |
Gene organization within MGE regions
Location: 872578..909073
| Locus tag | Gene name | Coordinates (strand) | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| AB3223_RS04460 | - | 873038..873205 (-) | 168 | WP_367371028.1 | hypothetical protein | - |
| AB3223_RS04465 | - | 873210..874511 (-) | 1302 | WP_367365853.1 | LysM peptidoglycan-binding domain-containing protein | - |
| AB3223_RS04470 | - | 874508..874717 (-) | 210 | WP_250800166.1 | phage holin | - |
| AB3223_RS04475 | - | 874724..874981 (-) | 258 | WP_367365854.1 | hemolysin XhlA family protein | - |
| AB3223_RS04480 | - | 875086..876042 (+) | 957 | WP_367365855.1 | DUF6625 family protein | - |
| AB3223_RS04485 | - | 876338..876556 (-) | 219 | Protein_835 | phage holin | - |
| AB3223_RS04490 | - | 876546..876851 (-) | 306 | WP_367365856.1 | hypothetical protein | - |
| AB3223_RS04495 | - | 876896..878821 (-) | 1926 | WP_367365857.1 | glycosyl hydrolase family 28-related protein | - |
| AB3223_RS04500 | - | 878821..880347 (-) | 1527 | WP_367365858.1 | phage tail protein | - |
| AB3223_RS04505 | - | 880347..881075 (-) | 729 | WP_367365859.1 | phage tail protein | - |
| AB3223_RS04510 | - | 881059..883494 (-) | 2436 | WP_367365860.1 | phage tail protein | - |
| AB3223_RS04515 | - | 883494..883862 (-) | 369 | WP_367365861.1 | DUF5361 domain-containing protein | - |
| AB3223_RS04520 | - | 883874..884137 (-) | 264 | WP_367365862.1 | hypothetical protein | - |
| AB3223_RS04525 | - | 884143..884721 (-) | 579 | WP_367365863.1 | phage tail protein | - |
| AB3223_RS04530 | - | 884733..885065 (-) | 333 | WP_367365864.1 | hypothetical protein | - |
| AB3223_RS04535 | - | 885065..885301 (-) | 237 | WP_367365865.1 | hypothetical protein | - |
| AB3223_RS04540 | - | 885294..885632 (-) | 339 | WP_367365866.1 | hypothetical protein | - |
| AB3223_RS04545 | - | 885610..886014 (-) | 405 | WP_367365867.1 | phage Gp19/Gp15/Gp42 family protein | - |
| AB3223_RS04550 | - | 886017..886295 (-) | 279 | WP_367365868.1 | hypothetical protein | - |
| AB3223_RS04555 | - | 886300..887187 (-) | 888 | WP_367365869.1 | phage major capsid protein | - |
| AB3223_RS04560 | - | 887195..887665 (-) | 471 | WP_367366129.1 | DUF4355 domain-containing protein | - |
| AB3223_RS04565 | - | 887745..889142 (-) | 1398 | WP_367365870.1 | terminase | - |
| AB3223_RS04570 | - | 889193..889894 (-) | 702 | WP_367365871.1 | hypothetical protein | - |
| AB3223_RS04575 | - | 889887..891143 (-) | 1257 | WP_367365872.1 | hypothetical protein | - |
| AB3223_RS04580 | - | 891282..891587 (-) | 306 | WP_367365873.1 | HNH endonuclease | - |
| AB3223_RS04585 | - | 891759..892274 (-) | 516 | WP_367365874.1 | hypothetical protein | - |
| AB3223_RS04590 | - | 892321..892560 (-) | 240 | WP_367365875.1 | hypothetical protein | - |
| AB3223_RS04595 | - | 892579..892782 (-) | 204 | WP_367365876.1 | hypothetical protein | - |
| AB3223_RS04600 | - | 892775..893233 (-) | 459 | WP_367365877.1 | DUF1064 domain-containing protein | - |
| AB3223_RS04605 | - | 893230..893436 (-) | 207 | WP_367365878.1 | helix-turn-helix domain-containing protein | - |
| AB3223_RS04610 | - | 893426..894310 (-) | 885 | WP_367365879.1 | DnaD domain protein | - |
| AB3223_RS04615 | ssb | 894327..894767 (-) | 441 | WP_367365880.1 | single-stranded DNA-binding protein | Machinery gene |
| AB3223_RS04620 | - | 894778..895713 (-) | 936 | WP_367366130.1 | recombinase RecT | - |
| AB3223_RS04625 | - | 895721..896608 (-) | 888 | WP_367365881.1 | YqaJ viral recombinase family protein | - |
| AB3223_RS04630 | - | 896592..896720 (-) | 129 | WP_367365882.1 | hypothetical protein | - |
| AB3223_RS04635 | - | 896823..897017 (-) | 195 | WP_367365883.1 | helix-turn-helix domain-containing protein | - |
| AB3223_RS04640 | - | 897170..897334 (+) | 165 | WP_367365884.1 | YjzC family protein | - |
| AB3223_RS04645 | - | 897339..897485 (-) | 147 | WP_367371029.1 | hypothetical protein | - |
| AB3223_RS04650 | - | 897565..897732 (-) | 168 | WP_367365885.1 | hypothetical protein | - |
| AB3223_RS04655 | - | 897767..897985 (-) | 219 | WP_367365886.1 | hypothetical protein | - |
| AB3223_RS04660 | - | 897987..898226 (-) | 240 | WP_367365887.1 | hypothetical protein | - |
| AB3223_RS04665 | - | 898239..898952 (-) | 714 | WP_367365888.1 | phage antirepressor KilAC domain-containing protein | - |
| AB3223_RS04670 | - | 898954..899163 (-) | 210 | WP_367365889.1 | XRE family transcriptional regulator | - |
| AB3223_RS04675 | - | 899220..899402 (-) | 183 | WP_367365890.1 | helix-turn-helix domain-containing protein | - |
| AB3223_RS04680 | - | 899445..899660 (-) | 216 | WP_367365891.1 | hypothetical protein | - |
| AB3223_RS04685 | - | 899942..900262 (+) | 321 | WP_367365892.1 | helix-turn-helix domain-containing protein | - |
| AB3223_RS04690 | - | 900249..900701 (+) | 453 | WP_367365893.1 | ImmA/IrrE family metallo-endopeptidase | - |
| AB3223_RS04695 | - | 900751..901077 (+) | 327 | WP_367365894.1 | hypothetical protein | - |
| AB3223_RS04700 | - | 901139..901807 (+) | 669 | WP_367365895.1 | Ltp family lipoprotein | - |
| AB3223_RS04705 | - | 902222..902674 (+) | 453 | WP_367365896.1 | hypothetical protein | - |
| AB3223_RS04710 | - | 902664..903047 (+) | 384 | WP_367365897.1 | hypothetical protein | - |
| AB3223_RS04715 | - | 903111..904013 (+) | 903 | WP_367371030.1 | Abi family protein | - |
| AB3223_RS04720 | - | 904312..905334 (+) | 1023 | WP_367365899.1 | tyrosine-type recombinase/integrase | - |
| AB3223_RS04725 | - | 905922..906515 (+) | 594 | WP_057784939.1 | type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein | - |
| AB3223_RS04730 | - | 906512..907372 (+) | 861 | WP_367365900.1 | nucleotidyl transferase AbiEii/AbiGii toxin family protein | - |
| AB3223_RS04735 | - | 907619..907840 (-) | 222 | WP_367365901.1 | hypothetical protein | - |
| AB3223_RS04740 | - | 907949..908179 (-) | 231 | WP_057784943.1 | helix-turn-helix domain-containing protein | - |
| AB3223_RS04745 | - | 908207..909073 (-) | 867 | WP_367365902.1 | DegV family protein | - |
Sequence
Protein
Download Length: 146 a.a. Molecular weight: 16300.95 Da Isoelectric Point: 4.9497
>NTDB_id=1166072 AB3223_RS04615 WP_367365880.1 894327..894767(-) (ssb) [Pediococcus parvulus isolate Pediococcus parvulus IOEB-8801]
MINRTVLIGRLTKEPDLRYTNSGTAVASFTLAVNRQFTNSDGEREADFINCVIWRKAAENFANFTHKGSLVGIDGRIQTR
SYENQQGNKVYVTEVVVENFSLLEPKSHSDSDRQSNNKTPSINKQASSDPFAGSNPIDIDEDDLPF
MINRTVLIGRLTKEPDLRYTNSGTAVASFTLAVNRQFTNSDGEREADFINCVIWRKAAENFANFTHKGSLVGIDGRIQTR
SYENQQGNKVYVTEVVVENFSLLEPKSHSDSDRQSNNKTPSINKQASSDPFAGSNPIDIDEDDLPF
Nucleotide
Download Length: 441 bp
>NTDB_id=1166072 AB3223_RS04615 WP_367365880.1 894327..894767(-) (ssb) [Pediococcus parvulus isolate Pediococcus parvulus IOEB-8801]
ATGATAAATCGAACAGTTCTTATTGGACGCTTAACCAAGGAGCCAGATTTACGGTACACCAATAGTGGTACTGCAGTTGC
TAGTTTTACATTGGCAGTCAATCGCCAATTCACTAACTCTGATGGTGAACGTGAAGCTGATTTCATTAACTGCGTGATCT
GGCGAAAGGCAGCCGAGAACTTTGCTAACTTTACCCATAAAGGTTCATTGGTTGGAATTGATGGACGGATTCAAACCCGT
TCTTACGAAAACCAACAAGGCAACAAAGTTTATGTAACGGAGGTTGTCGTTGAAAACTTCTCGTTGCTGGAACCCAAGTC
GCATTCTGATTCTGACCGGCAAAGCAATAACAAGACACCGTCAATAAACAAACAAGCATCTTCAGACCCGTTTGCCGGCA
GCAATCCAATTGATATTGATGAAGACGACTTGCCATTCTAA
ATGATAAATCGAACAGTTCTTATTGGACGCTTAACCAAGGAGCCAGATTTACGGTACACCAATAGTGGTACTGCAGTTGC
TAGTTTTACATTGGCAGTCAATCGCCAATTCACTAACTCTGATGGTGAACGTGAAGCTGATTTCATTAACTGCGTGATCT
GGCGAAAGGCAGCCGAGAACTTTGCTAACTTTACCCATAAAGGTTCATTGGTTGGAATTGATGGACGGATTCAAACCCGT
TCTTACGAAAACCAACAAGGCAACAAAGTTTATGTAACGGAGGTTGTCGTTGAAAACTTCTCGTTGCTGGAACCCAAGTC
GCATTCTGATTCTGACCGGCAAAGCAATAACAAGACACCGTCAATAAACAAACAAGCATCTTCAGACCCGTTTGCCGGCA
GCAATCCAATTGATATTGATGAAGACGACTTGCCATTCTAA
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 |
58.14 |
100 |
0.685 |
| ssbA | Bacillus subtilis subsp. subtilis str. 168 |
52.907 |
100 |
0.623 |
| ssbB | Bacillus subtilis subsp. subtilis str. 168 |
61.321 |
72.603 |
0.445 |
| ssbB | Streptococcus sobrinus strain NIDR 6715-7 |
41.781 |
100 |
0.418 |
| ssbB/cilA | Streptococcus mitis NCTC 12261 |
40.541 |
100 |
0.411 |
| ssbB/cilA | Streptococcus pneumoniae TIGR4 |
40.541 |
100 |
0.411 |
| ssbB/cilA | Streptococcus pneumoniae D39 |
39.865 |
100 |
0.404 |
| ssbB/cilA | Streptococcus pneumoniae Rx1 |
39.865 |
100 |
0.404 |
| ssbB/cilA | Streptococcus pneumoniae R6 |
39.865 |
100 |
0.404 |
| ssbB/cilA | Streptococcus mitis SK321 |
39.865 |
100 |
0.404 |
| ssbA | Streptococcus mutans UA159 |
36.986 |
100 |
0.37 |
| ssbB | Lactococcus lactis subsp. cremoris KW2 |
40.769 |
89.041 |
0.363 |