Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   QMY06_RS03860 Genome accession   NZ_CP126697
Coordinates   776094..776519 (+) Length   141 a.a.
NCBI ID   WP_285089659.1    Uniprot ID   -
Organism   Pediococcus acidilactici strain F1493     
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 768644..807606 776094..776519 within 0


Gene organization within MGE regions


Location: 768644..807606
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  QMY06_RS03790 (QMY06_03790) - 768644..769759 (-) 1116 WP_138492811.1 site-specific integrase -
  QMY06_RS03795 (QMY06_03795) - 769984..770181 (-) 198 WP_005917307.1 hypothetical protein -
  QMY06_RS03800 (QMY06_03800) - 770413..770802 (-) 390 WP_171030855.1 transporter -
  QMY06_RS03805 (QMY06_03805) - 770868..771278 (-) 411 WP_119179165.1 hypothetical protein -
  QMY06_RS03810 (QMY06_03810) - 771282..771620 (-) 339 WP_138492812.1 XRE family transcriptional regulator -
  QMY06_RS03815 (QMY06_03815) - 771904..772107 (+) 204 WP_235016614.1 hypothetical protein -
  QMY06_RS03820 (QMY06_03820) - 772299..772625 (-) 327 WP_138492813.1 hypothetical protein -
  QMY06_RS03825 (QMY06_03825) - 772684..773418 (+) 735 WP_159214252.1 Rha family transcriptional regulator -
  QMY06_RS03830 (QMY06_03830) - 773432..773761 (+) 330 WP_285089655.1 DUF771 domain-containing protein -
  QMY06_RS03835 (QMY06_03835) - 773862..774116 (+) 255 WP_285089656.1 hypothetical protein -
  QMY06_RS03840 (QMY06_03840) - 774226..774888 (-) 663 WP_201197732.1 hypothetical protein -
  QMY06_RS03845 (QMY06_03845) - 775035..775247 (+) 213 WP_285089657.1 hypothetical protein -
  QMY06_RS03850 (QMY06_03850) - 775257..775892 (+) 636 WP_285089658.1 ERF family protein -
  QMY06_RS03855 (QMY06_03855) - 775895..776101 (+) 207 WP_152688945.1 hypothetical protein -
  QMY06_RS03860 (QMY06_03860) ssb 776094..776519 (+) 426 WP_285089659.1 single-stranded DNA-binding protein Machinery gene
  QMY06_RS03865 (QMY06_03865) - 776539..777459 (+) 921 WP_285089660.1 conserved phage C-terminal domain-containing protein -
  QMY06_RS03870 (QMY06_03870) - 777449..778681 (+) 1233 WP_065124218.1 DnaB-like helicase C-terminal domain-containing protein -
  QMY06_RS03875 (QMY06_03875) - 778690..779097 (+) 408 WP_232457171.1 hypothetical protein -
  QMY06_RS03880 (QMY06_03880) - 779094..779525 (+) 432 WP_065124216.1 RusA family crossover junction endodeoxyribonuclease -
  QMY06_RS03885 (QMY06_03885) - 779525..779752 (+) 228 WP_285089661.1 hypothetical protein -
  QMY06_RS03890 (QMY06_03890) - 779752..780387 (+) 636 WP_065124214.1 RNA polymerase subunit sigma-70 -
  QMY06_RS03895 (QMY06_03895) - 780430..780579 (+) 150 WP_173645129.1 hypothetical protein -
  QMY06_RS03900 (QMY06_03900) - 780566..780937 (+) 372 WP_002830736.1 hypothetical protein -
  QMY06_RS03905 (QMY06_03905) - 781104..781397 (+) 294 WP_058121180.1 hypothetical protein -
  QMY06_RS03910 (QMY06_03910) - 781398..781643 (+) 246 WP_036672515.1 hypothetical protein -
  QMY06_RS03915 (QMY06_03915) - 782030..782278 (+) 249 WP_065124213.1 hypothetical protein -
  QMY06_RS03920 (QMY06_03920) - 782465..782653 (+) 189 WP_036672512.1 hypothetical protein -
  QMY06_RS03925 (QMY06_03925) - 782854..783297 (+) 444 WP_065124212.1 hypothetical protein -
  QMY06_RS03930 (QMY06_03930) - 783804..784271 (+) 468 WP_081276383.1 HNH endonuclease -
  QMY06_RS03935 (QMY06_03935) - 784476..784925 (+) 450 WP_065124210.1 phage terminase small subunit P27 family -
  QMY06_RS03940 (QMY06_03940) - 784928..786826 (+) 1899 WP_065124209.1 terminase TerL endonuclease subunit -
  QMY06_RS03945 (QMY06_03945) - 786816..787010 (+) 195 WP_065124208.1 DUF1056 family protein -
  QMY06_RS03950 (QMY06_03950) - 787013..788176 (+) 1164 WP_065124207.1 phage portal protein -
  QMY06_RS03955 (QMY06_03955) - 788154..788897 (+) 744 WP_159215944.1 head maturation protease, ClpP-related -
  QMY06_RS03960 (QMY06_03960) - 788897..790129 (+) 1233 WP_002831808.1 phage major capsid protein -
  QMY06_RS03965 (QMY06_03965) - 790202..790534 (+) 333 WP_002831807.1 head-tail connector protein -
  QMY06_RS03970 (QMY06_03970) - 790524..790871 (+) 348 WP_002831805.1 phage head closure protein -
  QMY06_RS03975 (QMY06_03975) - 790874..791281 (+) 408 WP_002831803.1 HK97-gp10 family putative phage morphogenesis protein -
  QMY06_RS03980 (QMY06_03980) - 791281..791661 (+) 381 WP_065124205.1 DUF806 family protein -
  QMY06_RS03985 (QMY06_03985) - 791675..792364 (+) 690 WP_285089662.1 phage tail protein -
  QMY06_RS03990 (QMY06_03990) - 792441..792815 (+) 375 WP_285089663.1 phage tail assembly chaperone -
  QMY06_RS03995 (QMY06_03995) - 792860..793045 (+) 186 WP_002831798.1 hypothetical protein -
  QMY06_RS04000 (QMY06_04000) - 793074..797924 (+) 4851 WP_285089664.1 NlpC/P60 family protein -
  QMY06_RS04005 (QMY06_04005) - 798001..799770 (+) 1770 WP_159214256.1 phage tail domain-containing protein -
  QMY06_RS04010 (QMY06_04010) - 799834..802203 (+) 2370 WP_285089665.1 phage tail spike protein -
  QMY06_RS04015 (QMY06_04015) - 802221..804740 (+) 2520 WP_285089666.1 phage tail protein -
  QMY06_RS04020 (QMY06_04020) - 804733..804972 (+) 240 WP_138492839.1 hypothetical protein -
  QMY06_RS04025 (QMY06_04025) - 804976..805137 (+) 162 WP_171030852.1 hypothetical protein -
  QMY06_RS04030 (QMY06_04030) - 805121..805495 (+) 375 WP_138492840.1 hypothetical protein -
  QMY06_RS04035 (QMY06_04035) - 805492..806655 (+) 1164 WP_171030853.1 GH25 family lysozyme -
  QMY06_RS04040 (QMY06_04040) - 806655..806918 (+) 264 WP_138492841.1 hemolysin XhlA family protein -
  QMY06_RS04045 (QMY06_04045) - 806928..807293 (+) 366 WP_138492842.1 phage holin -

Sequence

Protein


Download         Length: 141 a.a.        Molecular weight: 15648.40 Da        Isoelectric Point: 7.1662

>NTDB_id=839621 QMY06_RS03860 WP_285089659.1 776094..776519(+) (ssb) [Pediococcus acidilactici strain F1493]
MINRTVLIGRLTKDVELRHTAKGDAVASFTVAVNRQFTNSQGEREVDFINCVMWRKAAENFAKYTHKGSLVGIDGRIQTR
SYENQQGQRVYVTEIVADNFSLLDSKPKGNQQNNARPASTPGDPFANGGQSIDISDDDLPF

Nucleotide


Download         Length: 426 bp        

>NTDB_id=839621 QMY06_RS03860 WP_285089659.1 776094..776519(+) (ssb) [Pediococcus acidilactici strain F1493]
ATGATTAATCGAACAGTACTAATAGGACGCCTAACTAAAGATGTTGAGCTTCGCCACACAGCTAAAGGCGATGCGGTAGC
TAGTTTTACCGTGGCAGTTAACCGACAGTTTACCAACTCACAGGGTGAACGTGAAGTGGATTTCATCAACTGTGTAATGT
GGCGTAAGGCAGCAGAAAACTTTGCTAAGTATACACACAAAGGTTCGTTGGTAGGTATTGACGGACGGATCCAAACTCGT
TCGTACGAAAACCAACAAGGACAACGAGTTTATGTTACTGAAATTGTGGCGGATAACTTCTCGTTGCTAGATTCGAAGCC
AAAAGGCAACCAACAAAATAACGCACGGCCAGCATCAACGCCGGGAGATCCATTCGCTAACGGTGGTCAATCAATTGATA
TTTCAGATGATGATTTACCATTCTAA

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

59.412

100

0.716
  ssbA Bacillus subtilis subsp. subtilis str. 168

54.07

100

0.66
  ssbB Bacillus subtilis subsp. subtilis str. 168

59.259

76.596

0.454
  ssbB Streptococcus sobrinus strain NIDR 6715-7

41.549

100

0.418
  ssbB/cilA Streptococcus mitis NCTC 12261

40.845

100

0.411
  ssbB/cilA Streptococcus pneumoniae TIGR4

40.845

100

0.411
  ssbB/cilA Streptococcus pneumoniae Rx1

40.141

100

0.404
  ssbB/cilA Streptococcus pneumoniae D39

40.141

100

0.404
  ssbB/cilA Streptococcus pneumoniae R6

40.141

100

0.404
  ssbB/cilA Streptococcus mitis SK321

40.141

100

0.404
  ssbA Streptococcus mutans UA159

36.62

100

0.369