Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   A4V11_RS04355 Genome accession   NZ_CP015206
Coordinates   898020..898445 (-) Length   141 a.a.
NCBI ID   WP_070366333.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain ZPA017     
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 866973..905121 898020..898445 within 0


Gene organization within MGE regions


Location: 866973..905121
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  A4V11_RS04160 (A4V11_04155) - 866973..867836 (-) 864 WP_065124661.1 energy-coupling factor ABC transporter ATP-binding protein -
  A4V11_RS04165 (A4V11_04160) - 867812..868654 (-) 843 WP_070366308.1 energy-coupling factor transporter ATPase -
  A4V11_RS04170 (A4V11_04165) - 869586..870272 (-) 687 WP_070366309.1 DUF3800 domain-containing protein -
  A4V11_RS04175 (A4V11_04170) - 870388..871509 (-) 1122 WP_081335293.1 peptidoglycan recognition family protein -
  A4V11_RS04180 (A4V11_04175) - 871493..871735 (-) 243 WP_070366310.1 phage holin -
  A4V11_RS04185 (A4V11_04180) - 871735..871962 (-) 228 WP_070366790.1 hypothetical protein -
  A4V11_RS04190 (A4V11_04185) - 872126..874531 (-) 2406 WP_070366311.1 BppU family phage baseplate upper protein -
  A4V11_RS04195 (A4V11_04190) - 874535..874948 (-) 414 WP_070366312.1 hypothetical protein -
  A4V11_RS04200 (A4V11_04195) - 874948..877893 (-) 2946 WP_070366313.1 peptidoglycan amidohydrolase family protein -
  A4V11_RS04205 (A4V11_04200) - 877893..878657 (-) 765 WP_070366314.1 phage tail protein -
  A4V11_RS04210 (A4V11_04205) - 878657..881494 (-) 2838 WP_070366315.1 tape measure protein -
  A4V11_RS04215 (A4V11_04210) - 881478..881756 (-) 279 WP_237028531.1 hypothetical protein -
  A4V11_RS04220 (A4V11_04215) - 881903..882244 (-) 342 WP_070366317.1 tail assembly chaperone -
  A4V11_RS04225 (A4V11_04220) - 882317..882973 (-) 657 WP_070366318.1 phage major tail protein, TP901-1 family -
  A4V11_RS04230 (A4V11_04225) - 882985..883368 (-) 384 WP_070366319.1 hypothetical protein -
  A4V11_RS04235 (A4V11_04230) - 883393..883734 (-) 342 WP_070366320.1 HK97-gp10 family putative phage morphogenesis protein -
  A4V11_RS04240 (A4V11_04235) - 883727..884035 (-) 309 WP_070366321.1 hypothetical protein -
  A4V11_RS04245 (A4V11_04240) - 884040..884405 (-) 366 WP_070366322.1 phage head-tail connector protein -
  A4V11_RS04250 (A4V11_04245) - 884416..884682 (-) 267 WP_081335296.1 Ig-like domain-containing protein -
  A4V11_RS04255 (A4V11_04250) - 884700..885518 (-) 819 WP_070366324.1 N4-gp56 family major capsid protein -
  A4V11_RS04260 (A4V11_04255) - 885518..886234 (-) 717 WP_002830727.1 capsid assembly scaffolding protein Gp46 family protein -
  A4V11_RS04265 (A4V11_04260) - 886339..887322 (-) 984 WP_002830728.1 minor capsid protein -
  A4V11_RS04270 (A4V11_04265) - 887291..888625 (-) 1335 WP_002830730.1 phage portal protein -
  A4V11_RS04275 (A4V11_04270) - 888707..890053 (-) 1347 WP_070366325.1 PBSX family phage terminase large subunit -
  A4V11_RS04280 (A4V11_04275) - 890046..890537 (-) 492 WP_070366326.1 terminase small subunit -
  A4V11_RS04285 (A4V11_04280) - 890616..891215 (-) 600 WP_070366327.1 hypothetical protein -
  A4V11_RS04295 (A4V11_04290) - 891775..892218 (-) 444 WP_002830733.1 hypothetical protein -
  A4V11_RS04300 (A4V11_04295) - 892418..892606 (-) 189 WP_036672512.1 hypothetical protein -
  A4V11_RS04305 (A4V11_04300) - 892793..893041 (-) 249 WP_002830734.1 hypothetical protein -
  A4V11_RS04310 (A4V11_04305) - 893223..893435 (-) 213 WP_036672514.1 hypothetical protein -
  A4V11_RS04315 (A4V11_04310) - 893428..893673 (-) 246 WP_036672515.1 hypothetical protein -
  A4V11_RS04320 (A4V11_04315) - 893674..893967 (-) 294 WP_002830735.1 hypothetical protein -
  A4V11_RS04325 (A4V11_04320) - 894134..894505 (-) 372 WP_002830736.1 hypothetical protein -
  A4V11_RS10460 - 894492..894641 (-) 150 WP_167626491.1 hypothetical protein -
  A4V11_RS04330 (A4V11_04325) - 894638..895039 (-) 402 WP_070366328.1 RusA family crossover junction endodeoxyribonuclease -
  A4V11_RS04335 (A4V11_04330) - 895032..895652 (-) 621 WP_070366329.1 RNA polymerase subunit sigma-70 -
  A4V11_RS04340 (A4V11_04335) - 895770..896585 (-) 816 WP_070366330.1 ATP-binding protein -
  A4V11_RS04345 (A4V11_04340) - 896566..897330 (-) 765 WP_070366331.1 conserved phage C-terminal domain-containing protein -
  A4V11_RS04350 (A4V11_04345) - 897308..898009 (-) 702 WP_070366332.1 putative HNHc nuclease -
  A4V11_RS04355 (A4V11_04350) ssb 898020..898445 (-) 426 WP_070366333.1 single-stranded DNA-binding protein Machinery gene
  A4V11_RS04360 (A4V11_04355) - 898438..899130 (-) 693 WP_070366334.1 ERF family protein -
  A4V11_RS04365 (A4V11_04360) - 899131..899586 (-) 456 WP_237028533.1 chromosome segregation protein SMC -
  A4V11_RS10415 (A4V11_04365) - 899707..900024 (-) 318 WP_070366336.1 hypothetical protein -
  A4V11_RS04375 (A4V11_04370) - 900121..900327 (-) 207 WP_070366337.1 helix-turn-helix transcriptional regulator -
  A4V11_RS04380 (A4V11_04375) - 900396..901130 (-) 735 WP_070366338.1 Rha family transcriptional regulator -
  A4V11_RS04385 (A4V11_04380) - 901144..901353 (-) 210 WP_065124225.1 helix-turn-helix domain-containing protein -
  A4V11_RS04390 (A4V11_04385) - 901610..901951 (+) 342 WP_002831842.1 helix-turn-helix domain-containing protein -
  A4V11_RS04395 (A4V11_04390) - 901960..902406 (+) 447 WP_002830701.1 ImmA/IrrE family metallo-endopeptidase -
  A4V11_RS04400 (A4V11_04395) - 902431..902991 (+) 561 WP_002830700.1 hypothetical protein -
  A4V11_RS04405 - 903010..903900 (+) 891 WP_070366339.1 DUF5067 domain-containing protein -
  A4V11_RS04410 (A4V11_04405) - 904042..905121 (+) 1080 WP_070366340.1 tyrosine-type recombinase/integrase -

Sequence

Protein


Download         Length: 141 a.a.        Molecular weight: 15596.28 Da        Isoelectric Point: 6.9831

>NTDB_id=177508 A4V11_RS04355 WP_070366333.1 898020..898445(-) (ssb) [Pediococcus acidilactici strain ZPA017]
MINRTILIGRLTKDAELRHTAKGDAVASFTVAVNRQFTNSQGEREADFINCVMWRKAAENFANFTRKGSLVGIEGRIQTR
SYENQQGQRVYVTEVVADNFSLLDSKPKGNQQNNARQASTPGDPFANGGQSIDIGDDDLPF

Nucleotide


Download         Length: 426 bp        

>NTDB_id=177508 A4V11_RS04355 WP_070366333.1 898020..898445(-) (ssb) [Pediococcus acidilactici strain ZPA017]
ATGATTAATCGAACAATACTAATAGGACGCTTAACTAAAGATGCTGAGCTTCGCCACACAGCGAAAGGTGATGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACTAACTCACAGGGTGAACGTGAAGCGGATTTCATTAACTGTGTAATGT
GGCGGAAAGCGGCGGAAAACTTTGCCAACTTCACGCGTAAAGGTTCTCTAGTAGGCATTGAAGGGCGGATTCAAACCCGT
TCGTACGAAAACCAACAAGGACAACGAGTTTATGTAACTGAGGTTGTAGCTGATAACTTCTCGTTGCTAGATTCGAAACC
AAAAGGCAACCAGCAAAATAATGCACGGCAAGCATCAACGCCAGGAGATCCATTCGCTAATGGTGGGCAGTCAATTGATA
TTGGTGACGACGATTTACCGTTCTAG

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(2-102)


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

58.824

100

0.709
  ssbA Bacillus subtilis subsp. subtilis str. 168

54.651

100

0.667
  ssbB Bacillus subtilis subsp. subtilis str. 168

60.185

76.596

0.461
  ssbB/cilA Streptococcus mitis NCTC 12261

41.549

100

0.418
  ssbB/cilA Streptococcus pneumoniae TIGR4

41.549

100

0.418
  ssbB/cilA Streptococcus pneumoniae Rx1

40.845

100

0.411
  ssbB/cilA Streptococcus pneumoniae D39

40.845

100

0.411
  ssbB/cilA Streptococcus pneumoniae R6

40.845

100

0.411
  ssbB Streptococcus sobrinus strain NIDR 6715-7

40.845

100

0.411
  ssbB/cilA Streptococcus mitis SK321

40.845

100

0.411
  ssbA Streptococcus mutans UA159

37.324

100

0.376

Multiple sequence alignment