Detailed information    

insolico Bioinformatically predicted

Overview

Name   ssb   Type   Machinery gene
Locus tag   V4T04_RS02080 Genome accession   NZ_JAZICS010000001
Coordinates   418067..418357 (-) Length   96 a.a.
NCBI ID   WP_349651626.1    Uniprot ID   -
Organism   Lactococcus lactis subsp. lactis strain DGCC12653     
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 406190..418312 418067..418357 flank -245


Gene organization within MGE regions


Location: 406190..418357
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  V4T04_RS01985 - 406190..406720 (-) 531 WP_075070535.1 hypothetical protein -
  V4T04_RS01990 - 406803..407582 (-) 780 WP_251899735.1 peptidoglycan amidohydrolase family protein -
  V4T04_RS01995 - 407582..407857 (-) 276 WP_139917173.1 holin -
  V4T04_RS02000 - 407870..408091 (-) 222 WP_012897995.1 hemolysin XhlA family protein -
  V4T04_RS02005 - 408193..409206 (-) 1014 WP_349651623.1 pyocin knob domain-containing protein -
  V4T04_RS02010 - 409206..409343 (-) 138 WP_195229120.1 hypothetical protein -
  V4T04_RS02015 - 409534..410052 (-) 519 Protein_399 phage tail protein -
  V4T04_RS02020 - 410051..410641 (-) 591 Protein_400 phage portal protein -
  V4T04_RS02025 - 410651..411933 (-) 1283 Protein_401 PBSX family phage terminase large subunit -
  V4T04_RS02030 - 411926..412435 (-) 510 WP_311317841.1 terminase small subunit -
  V4T04_RS02035 - 412511..413701 (-) 1191 WP_349651624.1 glycoside hydrolase family protein -
  V4T04_RS02040 - 413978..414367 (-) 390 WP_139917180.1 DUF722 domain-containing protein -
  V4T04_RS02045 - 414484..414753 (+) 270 WP_161935088.1 DUF3892 domain-containing protein -
  V4T04_RS02050 - 414874..415029 (+) 156 WP_014572174.1 hypothetical protein -
  V4T04_RS02055 - 415249..415635 (+) 387 WP_195229125.1 DUF805 domain-containing protein -
  V4T04_RS02060 - 415833..416501 (+) 669 WP_139917187.1 type 1 glutamine amidotransferase -
  V4T04_RS02065 - 416603..416824 (-) 222 WP_139917189.1 hypothetical protein -
  V4T04_RS02070 - 416805..417608 (-) 804 WP_139917191.1 helix-turn-helix domain-containing protein -
  V4T04_RS02075 - 417608..417934 (-) 327 WP_349651625.1 endonuclease -
  V4T04_RS02080 ssb 418067..418357 (-) 291 WP_349651626.1 single-stranded DNA-binding protein Machinery gene

Sequence

Protein


Download         Length: 96 a.a.        Molecular weight: 10615.65 Da        Isoelectric Point: 4.3297

>NTDB_id=1113269 V4T04_RS02080 WP_349651626.1 418067..418357(-) (ssb) [Lactococcus lactis subsp. lactis strain DGCC12653]
ADFINCVIWGKSAENLANWTHKGQLIGVTGSIQTRNYENQQGQRVYIMEVVASNFQVLEKSNQANGERVGNPAAKPQNND
SFGSDPMEISDDDLPF

Nucleotide


Download         Length: 291 bp        

>NTDB_id=1113269 V4T04_RS02080 WP_349651626.1 418067..418357(-) (ssb) [Lactococcus lactis subsp. lactis strain DGCC12653]
GCTGACTTTATCAATTGTGTTATTTGGGGTAAATCAGCCGAAAACTTGGCCAATTGGACTCATAAAGGTCAATTAATTGG
AGTTACTGGTAGTATTCAAACTCGCAACTATGAGAATCAACAAGGGCAACGAGTTTATATTATGGAGGTTGTCGCAAGTA
ATTTCCAAGTACTTGAAAAAAGTAATCAAGCAAATGGTGAACGAGTTGGTAATCCAGCTGCAAAACCACAAAATAATGAT
TCTTTTGGAAGTGATCCAATGGAAATTTCAGATGATGACCTACCATTTTAA

Domains

Predicted by InterproScan.

Single-strand binding protein family (SSB)

(1-58)


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

51.2

100

0.667
  ssbA Bacillus subtilis subsp. subtilis str. 168

44.882

100

0.594
  ssbB/cilA Streptococcus mitis NCTC 12261

38.542

100

0.385
  ssbB/cilA Streptococcus pneumoniae Rx1

37.5

100

0.375
  ssbB/cilA Streptococcus pneumoniae D39

37.5

100

0.375
  ssbB/cilA Streptococcus pneumoniae R6

37.5

100

0.375
  ssbB/cilA Streptococcus mitis SK321

37.5

100

0.375
  ssbB Streptococcus sobrinus strain NIDR 6715-7

37.5

100

0.375
  ssbB/cilA Streptococcus pneumoniae TIGR4

37.5

100

0.375

Multiple sequence alignment