Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   H5404_RS21140 Genome accession   NZ_CP060088
Coordinates   2855402..2857087 (+) Length   561 a.a.
NCBI ID   WP_140218815.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain TJA114     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2850402..2862087
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  H5404_RS21120 (H5404_21120) pdhR 2851948..2852715 (-) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  H5404_RS21125 (H5404_21125) ampD 2853121..2853672 (-) 552 WP_025508895.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  H5404_RS21130 (H5404_21130) nadC 2853765..2854652 (+) 888 WP_015297249.1 carboxylating nicotinate-nucleotide diphosphorylase -
  H5404_RS21135 (H5404_21135) - 2854916..2855401 (+) 486 WP_069502799.1 pilin -
  H5404_RS21140 (H5404_21140) pilB 2855402..2857087 (+) 1686 WP_140218815.1 type IV-A pilus assembly ATPase PilB Machinery gene
  H5404_RS21145 (H5404_21145) pilC 2857111..2858334 (+) 1224 WP_140218813.1 type II secretion system F family protein Machinery gene
  H5404_RS21150 (H5404_21150) pilD 2858399..2859268 (+) 870 WP_074545612.1 prepilin peptidase Machinery gene
  H5404_RS21155 (H5404_21155) coaE 2859269..2859883 (+) 615 WP_005480887.1 dephospho-CoA kinase -
  H5404_RS21160 (H5404_21160) zapD 2859911..2860651 (+) 741 WP_023624252.1 cell division protein ZapD -
  H5404_RS21165 (H5404_21165) yacG 2860720..2860914 (+) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  H5404_RS21170 (H5404_21170) rplS 2861299..2861652 (-) 354 WP_005462554.1 50S ribosomal protein L19 -

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 62352.22 Da        Isoelectric Point: 5.5340

>NTDB_id=473894 H5404_RS21140 WP_140218815.1 2855402..2857087(+) (pilB) [Vibrio parahaemolyticus strain TJA114]
MLTNLSTILRQNGLLTFPQEESLFEQIKASGISMPEALLSSGLFTSSELAEHLSSLFGLSQPELSQYEYASLCQQLGLRE
LITRHNALPLQRTTSTLLLAVADPTNQQAEDDFRFATGLQIELVLADCRQLSAAIRRLYGRSLSHEKSGLKEINQEELAN
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQQPPNHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLNIDKLGYSEQQKQLYLEALRRPQGMI
LMTGPTGSGKTVSLYTGLNILNKPEINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETIIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEHTVQLQHLGIQTTDN
IFRANPDGCNECTHGYSGRTGIYEVMRFDESLSEALIKGASVHELEKLAIANGMSTLQMSGIEKLKQGITSFSELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=473894 H5404_RS21140 WP_140218815.1 2855402..2857087(+) (pilB) [Vibrio parahaemolyticus strain TJA114]
ATGCTAACCAACCTCTCAACAATTCTTCGCCAAAACGGGTTACTGACTTTTCCCCAAGAAGAATCGTTATTTGAGCAAAT
CAAAGCTTCTGGCATCTCGATGCCAGAGGCTTTACTCAGTTCTGGATTATTTACATCAAGCGAACTCGCTGAGCACTTAA
GTTCTCTCTTTGGTTTGAGTCAGCCCGAGTTATCTCAGTACGAGTACGCCTCGCTTTGTCAGCAACTTGGCCTTAGGGAA
TTAATCACACGGCATAACGCACTCCCACTCCAGCGCACGACTTCAACGTTATTACTCGCCGTTGCCGACCCCACGAACCA
ACAAGCAGAAGACGATTTCCGCTTTGCCACTGGTTTACAGATTGAATTGGTGTTGGCGGATTGTCGTCAACTCAGTGCAG
CAATTCGACGCTTATATGGTCGTTCATTGAGTCACGAGAAGTCTGGATTAAAAGAGATAAACCAAGAAGAATTAGCCAAC
CTGGTTGATGTGGGCGCAGATGAAATCGACAACATCGAAGACTTGAGCCAAGACGAGTCACCCGTTAGCCGTTACATCAA
CCAAATTCTGTTGGACGCTGTGCGTAAAGGCGCATCCGATATCCACTTTGAGCCTTATGAAAAGATGTACCGAGTTCGTC
TACGTTGCGATGGCATTTTGATCGAAACTCAGCAACCGCCAAATCACTTGAGTCGTCGCTTATCAGCTCGTATCAAAATT
CTCTCTAAACTTGATATTGCCGAGCGACGTTTACCACAAGATGGGCGAATTAAACTCAAACTGAATCAAGACACCGCGAT
TGATATGCGGGTATCCACGCTACCTACCTTGTTTGGAGAGAAAATCGTACTCCGACTGCTCGATAGCAGCTCAGCATCAC
TGAATATCGACAAGCTTGGTTATAGTGAGCAACAAAAGCAGCTGTATTTAGAGGCGCTGCGTCGTCCACAAGGTATGATT
CTGATGACAGGTCCAACAGGAAGTGGCAAAACCGTTTCGTTGTACACTGGGTTAAATATTCTCAATAAACCAGAGATCAA
CATCTCCACAGCGGAAGACCCGGTGGAAATTAACTTATCGGGTATTAACCAAGTTCAAGTCCAACCTAAGATTGGTTTTG
GCTTTGCAGAAGCACTACGCTCTTTTCTGCGTCAAGATCCCGATGTGGTCATGGTGGGTGAGATTCGAGACCTAGATACT
GCGGAAATCGCGATTAAGGCGTCCCAAACCGGTCACTTAGTGCTCTCTACTTTGCATACCAACTCTGCGGCTGAAACCAT
CATTCGTTTATCAAACATGGGCGTAGAAAGTTTTAACCTCGCCTCTTCACTTAGCTTGATTATTGCCCAACGCCTAGCTC
GCAAACTTTGTCCATATTGTAAACAACCGCAAGAGCATACCGTTCAACTTCAGCACCTCGGCATTCAAACAACTGACAAC
ATTTTTAGAGCCAATCCAGATGGTTGTAACGAATGCACCCATGGTTATTCTGGCCGAACAGGTATCTATGAAGTCATGCG
CTTTGATGAATCTCTATCCGAAGCTCTTATTAAAGGAGCCTCGGTACATGAACTGGAAAAGCTTGCCATTGCGAACGGCA
TGAGCACCTTGCAAATGTCCGGAATAGAAAAACTCAAACAAGGCATCACAAGCTTTAGTGAGTTACAACGCGTGCTCTAT
TTCTAA

Domains

Predicted by InterproScan.

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

(38-144)

Type II/IV secretion system protein (T2SSE)

(188-455)


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

97.148

100

0.971
  pilB Vibrio campbellii strain DS40M4

89.661

100

0.897
  pilB Vibrio cholerae strain A1552

73.665

100

0.738
  pilB Acinetobacter baumannii D1279779

52.199

93.226

0.487
  pilB Legionella pneumophila strain ERS1305867

49.165

96.078

0.472
  pilB Acinetobacter baylyi ADP1

50.677

92.157

0.467
  pilF Neisseria gonorrhoeae MS11

45.745

100

0.46
  pilB/pilB1 Synechocystis sp. PCC 6803

36.425

100

0.385
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.037

100

0.374
  pilF Thermus thermophilus HB27

37.158

97.861

0.364