Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   VAPA_RS21635 Genome accession   NC_022247
Coordinates   4634871..4636604 (+) Length   577 a.a.
NCBI ID   WP_021008897.1    Uniprot ID   T1XFX2
Organism   Variovorax paradoxus B4     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4629871..4641604
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  VAPA_RS21600 (VAPA_1c43710) - 4629972..4630496 (+) 525 WP_021008893.1 CNP1-like family protein -
  VAPA_RS21605 (VAPA_1c43720) proB 4630528..4631667 (-) 1140 WP_021008894.1 glutamate 5-kinase -
  VAPA_RS21610 (VAPA_1c43730) cgtA 4631710..4632798 (-) 1089 WP_021008895.1 Obg family GTPase CgtA -
  VAPA_RS21615 (VAPA_1c43740) rpmA 4632869..4633126 (-) 258 WP_015866991.1 50S ribosomal protein L27 -
  VAPA_RS21620 (VAPA_1c43750) rplU 4633139..4633450 (-) 312 WP_015866992.1 50S ribosomal protein L21 -
  VAPA_RS21625 (VAPA_1c43760) - 4633639..4634631 (+) 993 WP_021008896.1 polyprenyl synthetase family protein -
  VAPA_RS21635 (VAPA_1c43780) pilB 4634871..4636604 (+) 1734 WP_021008897.1 type IV-A pilus assembly ATPase PilB Machinery gene
  VAPA_RS21640 (VAPA_1c43790) pilC 4636634..4637863 (+) 1230 WP_021008898.1 type II secretion system F family protein Machinery gene
  VAPA_RS21645 (VAPA_1c43800) - 4637863..4638828 (+) 966 WP_021008899.1 prepilin peptidase -
  VAPA_RS21650 (VAPA_1c43810) coaE 4638839..4639444 (+) 606 WP_021008900.1 dephospho-CoA kinase -
  VAPA_RS21655 (VAPA_1c43820) - 4639523..4641016 (+) 1494 WP_021008901.1 MBOAT family O-acyltransferase -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62784.96 Da        Isoelectric Point: 6.2069

>NTDB_id=61933 VAPA_RS21635 WP_021008897.1 4634871..4636604(+) (pilB) [Variovorax paradoxus B4]
MAAAELPVKENTQIALPGLARALVSAGKLPAKTAEDIYQKSLNGRTSFIAELTGSGAVSAADLAHTLSSAFGAPLLDLDA
IDHQRLPKDLLDPKLCHAYRIVVLSKRNNRLIVATADPSDQQAVEKIKFASQMGVDWVIAEYDKLSRMIEAAAVSAAETI
NSIVGAEFEFDDVTADTSGDANEQAIAEVEDAPVVRFLHKMLLDGVSMRASDIHFEPYEHNYRVRFRIDGELREIASPPT
LIKDKLASRIKVISRLDISEKRVPQDGRMKLKIGPDRVIDFRVSTLPTLFGEKIVIRILDPSSARLGIDALGYDADEKER
LLHAIGRPYGMVLVTGPTGSGKTVSLYTCLNLLNQPGVNIATAEDPSEINLPGVNQVNVNERAGLTFATALRAFLRQDPD
IIMVGEIRDLETADISIKAAQTGHLVLSTLHTNDAPTTLTRMRNMGIAPFNIASSVILITAQRLARRLCHMCRAPADVPR
QALLDAGFREEQLDGTWKPYRPVGCAACSNGYKGRVGIYQVMPISDAIQTIILRDGSAQDIARQSEAEGVRSLRQSGLRK
VMQGLTSLEEVVAVTNE

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=61933 VAPA_RS21635 WP_021008897.1 4634871..4636604(+) (pilB) [Variovorax paradoxus B4]
ATGGCTGCTGCCGAACTTCCTGTTAAAGAAAACACGCAAATCGCCCTCCCGGGCCTTGCGCGCGCCTTGGTTTCGGCCGG
CAAGCTTCCCGCGAAGACTGCGGAAGACATCTACCAGAAGTCGCTCAACGGCCGCACCAGCTTCATTGCCGAGCTGACCG
GCAGCGGCGCCGTCTCGGCCGCCGACCTCGCCCATACGCTTTCCAGCGCCTTCGGCGCGCCGCTGCTGGACCTGGACGCC
ATCGACCACCAGCGCCTGCCCAAGGACCTGCTTGACCCGAAGCTGTGCCACGCCTACCGGATCGTGGTTCTCAGCAAGCG
CAACAACCGTCTCATTGTTGCAACGGCCGACCCCTCGGACCAGCAGGCGGTGGAAAAGATCAAGTTCGCGTCCCAGATGG
GCGTGGACTGGGTCATTGCCGAATACGACAAGCTGTCGCGCATGATCGAAGCCGCCGCGGTCAGCGCGGCGGAAACCATC
AACAGCATCGTCGGCGCCGAGTTCGAGTTCGACGACGTCACGGCGGACACCTCGGGCGACGCCAACGAACAGGCGATTGC
CGAAGTCGAGGACGCGCCGGTCGTGCGCTTCCTGCACAAGATGCTGCTCGACGGCGTCAGCATGCGGGCCTCGGACATCC
ACTTCGAGCCCTACGAGCACAACTACCGCGTGCGCTTTCGCATCGACGGCGAGCTGCGCGAGATCGCGAGCCCGCCCACG
CTCATCAAGGACAAGCTGGCCTCGCGGATCAAGGTCATTTCACGGCTCGACATTTCCGAGAAGCGCGTGCCGCAGGACGG
CCGCATGAAGCTCAAGATCGGTCCCGACCGGGTCATCGACTTCCGCGTCAGCACGCTGCCCACGCTGTTCGGCGAGAAGA
TCGTGATCCGTATTCTCGACCCGAGCAGCGCGCGCCTGGGCATCGACGCCCTGGGCTACGACGCCGACGAAAAGGAGCGC
CTGCTGCATGCGATCGGGCGGCCCTACGGCATGGTGCTGGTGACGGGCCCCACCGGTTCGGGCAAGACGGTTTCGCTCTA
CACCTGCCTGAACCTGCTGAACCAGCCGGGCGTCAACATCGCAACGGCGGAAGATCCTTCCGAAATCAACCTGCCGGGCG
TGAACCAGGTGAACGTCAACGAGCGTGCCGGACTCACCTTCGCCACGGCGCTGCGCGCCTTCCTGCGGCAGGATCCCGAC
ATCATCATGGTCGGCGAAATCCGGGACCTCGAAACCGCCGACATCTCGATCAAGGCCGCGCAAACGGGCCACCTGGTCCT
CTCGACGCTGCACACCAACGACGCGCCGACCACGCTCACGCGCATGCGGAACATGGGCATTGCGCCGTTCAACATTGCCT
CCAGCGTGATCCTCATCACCGCGCAGCGGCTCGCGCGGCGCCTGTGCCACATGTGCCGCGCGCCGGCCGACGTGCCGCGC
CAGGCGCTGCTCGATGCGGGCTTCAGGGAAGAACAGCTCGACGGTACCTGGAAGCCCTATCGGCCGGTCGGCTGCGCGGC
GTGCAGCAACGGCTACAAGGGCCGGGTCGGCATCTACCAGGTGATGCCGATCTCGGACGCCATCCAGACCATCATCCTGC
GCGACGGCAGCGCACAGGACATCGCGCGACAGTCCGAGGCCGAGGGCGTGCGCTCGCTGCGGCAGTCCGGGCTGCGAAAA
GTCATGCAAGGGCTCACCTCACTCGAAGAAGTGGTGGCGGTCACCAACGAATAA

Domains

Predicted by InterproScan.

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

(54-153)

Type II/IV secretion system protein (T2SSE)

(200-467)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB T1XFX2

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 Acinetobacter baumannii D1279779

53.345

98.44

0.525
  pilB Acinetobacter baylyi ADP1

53.476

97.227

0.52
  pilF Neisseria gonorrhoeae MS11

51.865

97.574

0.506
  pilB Legionella pneumophila strain ERS1305867

48.227

97.747

0.471
  pilB Vibrio campbellii strain DS40M4

45.23

98.094

0.444
  pilB Vibrio parahaemolyticus RIMD 2210633

45.455

97.227

0.442
  pilB Vibrio cholerae strain A1552

48.077

90.121

0.433
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

40.566

91.854

0.373
  pilF Thermus thermophilus HB27

37.653

98.96

0.373

Multiple sequence alignment