Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   C7M42_RS00180 Genome accession   NZ_CP028249
Coordinates   27427..27858 (-) Length   143 a.a.
NCBI ID   WP_160212174.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain SRCM102732     
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 531..37678 27427..27858 within 0


Gene organization within MGE regions


Location: 531..37678
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  C7M42_RS00010 (C7M42_00001) - 531..782 (-) 252 WP_160212150.1 DUF6275 family protein -
  C7M42_RS00015 (C7M42_00002) - 801..2054 (-) 1254 WP_160212151.1 GH25 family lysozyme -
  C7M42_RS00020 (C7M42_00003) - 2038..2292 (-) 255 WP_160212152.1 phage holin -
  C7M42_RS00025 (C7M42_00004) - 2292..2537 (-) 246 WP_144235585.1 hypothetical protein -
  C7M42_RS00030 (C7M42_00005) - 2613..4103 (-) 1491 WP_065124781.1 hypothetical protein -
  C7M42_RS00035 (C7M42_00006) - 4119..4940 (-) 822 WP_065124782.1 collagen-like protein -
  C7M42_RS00040 (C7M42_00007) - 4953..5990 (-) 1038 WP_065124783.1 BppU family phage baseplate upper protein -
  C7M42_RS00045 (C7M42_00008) - 5980..6390 (-) 411 WP_065124784.1 hypothetical protein -
  C7M42_RS00050 (C7M42_00009) - 6371..6601 (-) 231 WP_065124785.1 hypothetical protein -
  C7M42_RS00055 (C7M42_00010) - 6594..7715 (-) 1122 WP_160212153.1 prophage endopeptidase tail family protein -
  C7M42_RS00060 (C7M42_00011) - 7721..8545 (-) 825 WP_159225198.1 phage tail domain-containing protein -
  C7M42_RS00065 (C7M42_00012) - 8546..13642 (-) 5097 WP_160212154.1 tape measure protein -
  C7M42_RS00070 (C7M42_00013) - 13676..14296 (-) 621 WP_160212155.1 Gp15 family bacteriophage protein -
  C7M42_RS00075 (C7M42_00014) - 14306..14698 (-) 393 WP_160212156.1 hypothetical protein -
  C7M42_RS00080 (C7M42_00015) - 14769..15236 (-) 468 WP_160212157.1 Ig-like domain-containing protein -
  C7M42_RS00085 (C7M42_00016) - 15310..15843 (-) 534 WP_180946786.1 phage tail tube protein -
  C7M42_RS00090 (C7M42_00017) - 15856..16251 (-) 396 WP_160212158.1 minor capsid protein -
  C7M42_RS00095 (C7M42_00018) - 16251..16595 (-) 345 WP_160212159.1 minor capsid protein -
  C7M42_RS00100 (C7M42_00019) - 16595..16945 (-) 351 WP_160212160.1 putative minor capsid protein -
  C7M42_RS00105 (C7M42_00020) - 16942..17361 (-) 420 WP_160212161.1 hypothetical protein -
  C7M42_RS00110 (C7M42_00021) - 17433..18329 (-) 897 WP_160212162.1 hypothetical protein -
  C7M42_RS00115 (C7M42_00022) - 18341..18898 (-) 558 WP_236656703.1 phage scaffolding protein -
  C7M42_RS00120 (C7M42_00023) - 18995..20128 (-) 1134 WP_268894717.1 phage minor capsid protein -
  C7M42_RS00125 (C7M42_00024) - 20128..21630 (-) 1503 WP_236656699.1 phage portal protein -
  C7M42_RS00130 (C7M42_00025) - 21694..23001 (-) 1308 WP_160212166.1 PBSX family phage terminase large subunit -
  C7M42_RS00135 (C7M42_00026) - 22988..23680 (-) 693 WP_160212167.1 terminase gpP N-terminus-related DNA-binding protein -
  C7M42_RS10195 - 23680..23847 (-) 168 WP_201752460.1 hypothetical protein -
  C7M42_RS00140 (C7M42_00028) - 23964..24530 (-) 567 WP_160212168.1 hypothetical protein -
  C7M42_RS00150 (C7M42_00030) - 24904..25335 (-) 432 WP_160212169.1 ArpU family phage packaging/lysis transcriptional regulator -
  C7M42_RS00155 (C7M42_00031) - 25541..25951 (-) 411 WP_160212170.1 hypothetical protein -
  C7M42_RS00160 (C7M42_00034) - 26336..26578 (-) 243 WP_160212171.1 hypothetical protein -
  C7M42_RS00165 (C7M42_00035) - 26571..26762 (-) 192 WP_160212172.1 hypothetical protein -
  C7M42_RS00170 (C7M42_00036) - 26763..26954 (-) 192 WP_159206544.1 helix-turn-helix domain-containing protein -
  C7M42_RS00175 (C7M42_00037) - 27093..27257 (+) 165 WP_160212173.1 YjzC family protein -
  C7M42_RS00180 (C7M42_00039) ssb 27427..27858 (-) 432 WP_160212174.1 single-stranded DNA-binding protein Machinery gene
  C7M42_RS00185 (C7M42_00040) - 27861..28268 (-) 408 WP_160212175.1 hypothetical protein -
  C7M42_RS00190 (C7M42_00041) - 28213..28935 (-) 723 WP_160212176.1 putative HNHc nuclease -
  C7M42_RS00195 (C7M42_00042) - 28940..29818 (-) 879 WP_160212177.1 helix-turn-helix domain-containing protein -
  C7M42_RS00200 (C7M42_00043) - 29811..30638 (-) 828 WP_160212178.1 ERF family protein -
  C7M42_RS00205 (C7M42_00044) - 30638..31531 (-) 894 WP_160212179.1 DUF1351 domain-containing protein -
  C7M42_RS00210 (C7M42_00047) - 31718..31861 (-) 144 WP_160212180.1 hypothetical protein -
  C7M42_RS00215 (C7M42_00048) - 31875..32141 (-) 267 WP_160212181.1 hypothetical protein -
  C7M42_RS00220 (C7M42_00049) - 32123..32590 (-) 468 WP_160212182.1 helix-turn-helix domain-containing protein -
  C7M42_RS00225 (C7M42_00050) - 32673..32888 (-) 216 WP_160212183.1 hypothetical protein -
  C7M42_RS00230 (C7M42_00051) - 32885..33127 (-) 243 WP_004165747.1 helix-turn-helix transcriptional regulator -
  C7M42_RS00235 (C7M42_00052) - 33289..33660 (+) 372 WP_004165746.1 helix-turn-helix domain-containing protein -
  C7M42_RS00240 (C7M42_00053) - 33672..34079 (+) 408 WP_159225223.1 ImmA/IrrE family metallo-endopeptidase -
  C7M42_RS00245 (C7M42_00054) - 34153..34671 (+) 519 WP_160212184.1 SHOCT domain-containing protein -
  C7M42_RS00250 (C7M42_00055) - 34680..35105 (+) 426 WP_160212185.1 SHOCT domain-containing protein -
  C7M42_RS00255 (C7M42_00056) - 35206..36102 (+) 897 WP_235019069.1 Ltp family lipoprotein -
  C7M42_RS00260 (C7M42_00057) - 36191..36415 (+) 225 WP_159216930.1 hypothetical protein -
  C7M42_RS00265 (C7M42_00058) - 36503..37678 (+) 1176 WP_160212186.1 tyrosine-type recombinase/integrase -

Sequence

Protein


Download         Length: 143 a.a.        Molecular weight: 16095.73 Da        Isoelectric Point: 5.1660

>NTDB_id=283691 C7M42_RS00180 WP_160212174.1 27427..27858(-) (ssb) [Pediococcus acidilactici strain SRCM102732]
MINRTVLVGRLTKDPEIRYTQSGMAVANFTVAVNRQFTNANGEREADFISCIIWRKAAENFCNFTHKGSLVGIDGRIQTS
SYEKEGQRVYSTQVVVDSFSLLEPKQQSQQRGQQSDASDALHNNFGQPTNNNDFDIDDNNLPF

Nucleotide


Download         Length: 432 bp        

>NTDB_id=283691 C7M42_RS00180 WP_160212174.1 27427..27858(-) (ssb) [Pediococcus acidilactici strain SRCM102732]
ATGATTAATCGAACCGTATTAGTTGGCCGGCTTACCAAAGATCCAGAAATCCGCTACACCCAATCAGGGATGGCGGTGGC
CAACTTTACTGTAGCTGTGAATCGGCAGTTTACCAATGCTAACGGCGAAAGAGAAGCGGACTTTATCAGTTGCATAATTT
GGCGCAAAGCGGCCGAAAATTTCTGTAATTTTACGCACAAAGGTTCATTGGTCGGGATTGACGGTCGGATTCAGACGAGT
TCATACGAGAAGGAAGGCCAGCGTGTTTACTCAACACAGGTGGTTGTAGATAGCTTTTCGCTGTTGGAACCGAAACAGCA
AAGCCAACAGCGTGGCCAGCAATCCGACGCTAGCGATGCTTTGCATAACAATTTCGGCCAACCTACTAACAATAACGATT
TTGATATTGATGACAACAATCTGCCATTTTAG

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(2-101)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  ssb Latilactobacillus sakei subsp. sakei 23K

54.118

100

0.643
  ssbA Bacillus subtilis subsp. subtilis str. 168

46.893

100

0.58
  ssbB Bacillus subtilis subsp. subtilis str. 168

55.455

76.923

0.427
  ssbB Streptococcus sobrinus strain NIDR 6715-7

40.559

100

0.406
  ssbB/cilA Streptococcus mitis NCTC 12261

39.86

100

0.399
  ssbB/cilA Streptococcus pneumoniae TIGR4

39.86

100

0.399
  ssbB/cilA Streptococcus mitis SK321

39.161

100

0.392
  ssbB/cilA Streptococcus pneumoniae Rx1

39.161

100

0.392
  ssbB/cilA Streptococcus pneumoniae D39

39.161

100

0.392
  ssbB/cilA Streptococcus pneumoniae R6

39.161

100

0.392

Multiple sequence alignment