Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilA   Type   Machinery gene
Locus tag   GSR97_RS12510 Genome accession   NZ_CP047990
Coordinates   2701956..2702393 (+) Length   145 a.a.
NCBI ID   WP_021453050.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain 20140723005     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

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)
Genomic island 2692675..2710283 2701956..2702393 within 0


Gene organization within MGE regions


Location: 2692675..2710283
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GSR97_RS12480 (GSR97_13110) lpdA 2692675..2694102 (-) 1428 WP_005479684.1 dihydrolipoyl dehydrogenase -
  GSR97_RS12485 (GSR97_13115) aceF 2694371..2696257 (-) 1887 WP_021453621.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  GSR97_RS12490 (GSR97_13120) aceE 2696277..2698940 (-) 2664 WP_140391276.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  GSR97_RS12495 (GSR97_13125) pdhR 2698989..2699756 (-) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  GSR97_RS12500 (GSR97_13130) ampD 2700162..2700713 (-) 552 WP_005484832.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  GSR97_RS12505 (GSR97_13135) nadC 2700806..2701693 (+) 888 WP_015297249.1 carboxylating nicotinate-nucleotide diphosphorylase -
  GSR97_RS12510 (GSR97_13140) pilA 2701956..2702393 (+) 438 WP_021453050.1 pilin Machinery gene
  GSR97_RS12515 (GSR97_13145) pilB 2702405..2704090 (+) 1686 WP_031845921.1 type IV-A pilus assembly ATPase PilB Machinery gene
  GSR97_RS12520 (GSR97_13150) pilC 2704115..2705338 (+) 1224 WP_005462561.1 type II secretion system F family protein Machinery gene
  GSR97_RS12525 (GSR97_13155) pilD 2705403..2706272 (+) 870 WP_025524821.1 prepilin peptidase Machinery gene
  GSR97_RS12530 (GSR97_13160) coaE 2706273..2706887 (+) 615 WP_005480887.1 dephospho-CoA kinase -
  GSR97_RS12535 (GSR97_13165) zapD 2706915..2707655 (+) 741 WP_023624252.1 cell division protein ZapD -
  GSR97_RS12540 (GSR97_13170) yacG 2707724..2707918 (+) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  GSR97_RS12545 (GSR97_13175) rplS 2708292..2708645 (-) 354 WP_005462554.1 50S ribosomal protein L19 -
  GSR97_RS12550 (GSR97_13180) trmD 2708687..2709430 (-) 744 WP_005462562.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  GSR97_RS12555 (GSR97_13185) rimM 2709458..2710006 (-) 549 WP_005462552.1 ribosome maturation factor RimM -
  GSR97_RS12560 (GSR97_13190) rpsP 2710035..2710283 (-) 249 WP_005379962.1 30S ribosomal protein S16 -

Sequence

Protein


Download         Length: 145 a.a.        Molecular weight: 14854.00 Da        Isoelectric Point: 9.7639

>NTDB_id=419092 GSR97_RS12510 WP_021453050.1 2701956..2702393(+) (pilA) [Vibrio parahaemolyticus strain 20140723005]
MKQSKQKKQQGFTLIELMIVVAVIGVLAAIAVPQYQKYVAKSEAASALASITGHRINVETYVVENGSFPTTAQLPVPTSP
LGVVSYTASASGAGASSGAIKFTFNSTGVSPDVISKDVTLGRDGTGQWSCTSGITATGVKPKACS

Nucleotide


Download         Length: 438 bp        

>NTDB_id=419092 GSR97_RS12510 WP_021453050.1 2701956..2702393(+) (pilA) [Vibrio parahaemolyticus strain 20140723005]
ATGAAACAGAGTAAACAGAAAAAACAGCAAGGTTTTACCTTGATTGAACTGATGATTGTGGTAGCGGTAATTGGTGTTTT
AGCTGCAATTGCAGTTCCACAATACCAAAAATATGTAGCTAAAAGTGAGGCAGCGTCTGCACTAGCCTCCATCACTGGGC
ATAGAATAAATGTTGAGACTTATGTTGTTGAAAATGGCTCATTTCCAACAACGGCCCAGCTGCCAGTTCCGACTTCTCCA
CTTGGTGTAGTTAGCTATACAGCTTCAGCTTCAGGAGCAGGTGCATCGTCAGGTGCAATAAAATTCACATTTAATAGCAC
AGGTGTAAGTCCAGACGTTATAAGTAAGGACGTGACTCTAGGGCGTGATGGAACAGGTCAATGGAGCTGTACCTCTGGTA
TTACTGCTACAGGTGTAAAACCTAAAGCATGCTCTTAA

Domains

Predicted by InterproScan.

Prokaryotic N-terminal methylation motif (N_methyl)

(7-31)

Pilin (bacterial filament) (Pilin)

(40-144)


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
  pilA Vibrio cholerae O1 biovar El Tor strain E7946

46.711

100

0.49
  pilA Vibrio cholerae strain A1552

46.711

100

0.49
  pilA Vibrio cholerae C6706

46.711

100

0.49
  pilA Vibrio parahaemolyticus RIMD 2210633

42.953

100

0.441
  pilA Pseudomonas aeruginosa PAK

41.447

100

0.434
  pilA/pilAI Pseudomonas stutzeri DSM 10701

41.781

100

0.421
  pilA Acinetobacter baumannii strain A118

42.336

94.483

0.4
  pilA/pilAII Pseudomonas stutzeri DSM 10701

37.671

100

0.379

Multiple sequence alignment