Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   Vp2S01_RS03180 Genome accession   NZ_CP020034
Coordinates   600951..602636 (-) Length   561 a.a.
NCBI ID   WP_031855538.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain 20130629002S01     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 595951..607636
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  Vp2S01_RS03150 (Vp2S01_0541) rplS 596391..596744 (+) 354 WP_005462554.1 50S ribosomal protein L19 -
  Vp2S01_RS03155 (Vp2S01_0542) yacG 597123..597317 (-) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  Vp2S01_RS03160 (Vp2S01_0543) zapD 597386..598126 (-) 741 WP_023624252.1 cell division protein ZapD -
  Vp2S01_RS03165 (Vp2S01_0544) coaE 598154..598768 (-) 615 WP_005480887.1 dephospho-CoA kinase -
  Vp2S01_RS03170 (Vp2S01_0545) pilD 598769..599638 (-) 870 WP_031855539.1 A24 family peptidase Machinery gene
  Vp2S01_RS03175 (Vp2S01_0546) pilC 599703..600926 (-) 1224 WP_023585959.1 type II secretion system F family protein Machinery gene
  Vp2S01_RS03180 (Vp2S01_0547) pilB 600951..602636 (-) 1686 WP_031855538.1 type IV-A pilus assembly ATPase PilB Machinery gene
  Vp2S01_RS03185 (Vp2S01_0548) pilA 602636..603064 (-) 429 WP_009698754.1 pilin Machinery gene
  Vp2S01_RS03195 (Vp2S01_0549) nadC 603329..604216 (-) 888 WP_015297249.1 carboxylating nicotinate-nucleotide diphosphorylase -
  Vp2S01_RS03200 (Vp2S01_0550) ampD 604309..604860 (+) 552 WP_025637088.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  Vp2S01_RS03205 (Vp2S01_0551) pdhR 605266..606033 (+) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 62469.43 Da        Isoelectric Point: 5.6709

>NTDB_id=220578 Vp2S01_RS03180 WP_031855538.1 600951..602636(-) (pilB) [Vibrio parahaemolyticus strain 20130629002S01]
MLTNLSTILRQKGLLTFFQEESLIEQVKASGISMPEALLSSGFFTSSELAEHLSSIFGLSQPELSQYEYASLCQQLGLRE
LITRHNALPLHRTPSTLLLAVADPTNQQAEDDFRFATGLQVELVLADFRELSAVIRRLYGRSLSHEKSGLKEINQEELAS
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQQPPNHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLDIDKLGYSEQQKQLYLKALRRPQGMI
LMTGPTGSGKTVSLYTGLNILNKPEINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETIIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEHTVQLQHLDIQTTDN
IFKANPDGCNECTHGYSGRTGIYEVMRFDESLSEALIKGASVHELEKLAIANGMSTLQMSGIEKLKQGITSFSELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=220578 Vp2S01_RS03180 WP_031855538.1 600951..602636(-) (pilB) [Vibrio parahaemolyticus strain 20130629002S01]
ATGCTAACCAACCTCTCCACGATTCTTCGTCAAAAAGGATTACTGACGTTTTTCCAAGAAGAATCGTTAATAGAGCAAGT
TAAAGCTTCTGGCATCTCGATGCCGGAAGCTTTACTCAGTTCTGGATTCTTCACGTCAAGCGAACTGGCCGAGCACTTAA
GTTCTATTTTTGGCTTAAGTCAGCCCGAGTTATCTCAATATGAATATGCTTCTCTTTGCCAACAGCTCGGCCTACGTGAA
TTAATCACACGACATAATGCACTCCCGCTCCACCGTACTCCTTCAACGTTATTGTTAGCGGTTGCCGATCCCACTAATCA
ACAAGCTGAAGATGATTTCCGCTTTGCCACTGGTTTACAGGTTGAATTGGTGTTGGCGGATTTTCGCGAACTCAGTGCAG
TAATTCGACGCTTATATGGTCGTTCATTGAGTCATGAAAAGTCTGGGTTAAAAGAGATCAACCAAGAAGAGCTAGCGAGT
CTGGTGGATGTCGGTGCAGATGAAATCGACAACATCGAAGACTTGAGCCAAGACGAGTCACCCGTTAGCCGTTACATCAA
CCAAATTCTGTTGGATGCTGTGCGTAAAGGCGCATCCGATATCCACTTTGAGCCTTATGAAAAGATGTACCGAGTTCGTC
TACGTTGCGATGGCATTTTGATCGAAACTCAGCAACCGCCAAATCACTTGAGTCGTCGCTTATCAGCTCGTATCAAAATT
CTCTCTAAACTTGATATTGCAGAGCGACGTTTACCACAAGATGGGCGAATTAAACTCAAACTGAATCAAGACACTGCGAT
TGATATGCGGGTATCTACGCTACCAACCTTGTTTGGAGAGAAAATCGTACTCCGACTGCTCGATAGCAGCTCTGCATCAC
TAGATATCGACAAGCTTGGTTATAGTGAGCAACAAAAACAACTGTATTTAAAGGCTCTGCGTCGTCCACAAGGTATGATT
CTGATGACAGGCCCAACAGGAAGCGGCAAAACCGTTTCGTTGTACACTGGGCTAAATATTCTCAATAAACCAGAGATCAA
CATCTCCACAGCGGAAGACCCGGTGGAAATTAACTTATCGGGCATTAACCAAGTTCAAGTCCAGCCTAAAATTGGTTTTG
GCTTTGCAGAAGCACTACGCTCTTTCCTGCGTCAAGATCCCGACGTGGTCATGGTGGGTGAGATTCGAGACCTAGATACT
GCGGAAATCGCCATCAAGGCGTCCCAAACAGGTCACTTAGTGCTCTCTACTTTGCATACCAACTCTGCAGCTGAAACCAT
CATTCGCTTATCAAACATGGGCGTGGAAAGTTTTAACCTCGCCTCTTCGCTTAGTTTGATTATTGCCCAACGCCTAGCTC
GCAAACTTTGTCCATATTGTAAACAACCGCAAGAGCATACCGTTCAACTTCAGCACCTCGACATCCAAACAACTGACAAC
ATCTTTAAAGCAAACCCAGATGGTTGCAACGAATGTACCCATGGTTATTCTGGCCGAACAGGTATCTATGAAGTCATGCG
CTTTGATGAATCTCTATCCGAAGCTCTTATTAAAGGAGCCTCGGTACATGAACTGGAAAAGCTTGCCATTGCGAATGGCA
TGAGTACCTTGCAAATGTCCGGAATAGAAAAACTCAAGCAAGGCATCACAAGCTTTAGTGAGTTACAACGCGTGCTCTAT
TTCTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(188-455)

Type II secretion system (T2SS), protein E, N-terminal domain (MshEN)

(38-144)


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
  pilB Vibrio parahaemolyticus RIMD 2210633

98.574

100

0.986
  pilB Vibrio campbellii strain DS40M4

90.374

100

0.904
  pilB Vibrio cholerae strain A1552

74.021

100

0.742
  pilB Acinetobacter baumannii D1279779

50.933

95.544

0.487
  pilB Legionella pneumophila strain ERS1305867

49.168

96.435

0.474
  pilB Acinetobacter baylyi ADP1

50.484

92.157

0.465
  pilF Neisseria gonorrhoeae MS11

44.858

100

0.451
  pilB/pilB1 Synechocystis sp. PCC 6803

36.379

100

0.383
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

36.332

100

0.367
  pilF Thermus thermophilus HB27

36.46

100

0.367

Multiple sequence alignment