Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   GSR97_RS12525 Genome accession   NZ_CP047990
Coordinates   2705403..2706272 (+) Length   289 a.a.
NCBI ID   WP_025524821.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain 20140723005     
Function   type IV pilus biogenesis and function (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 2705403..2706272 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: 289 a.a.        Molecular weight: 32419.51 Da        Isoelectric Point: 7.1971

>NTDB_id=419095 GSR97_RS12525 WP_025524821.1 2705403..2706272(+) (pilD) [Vibrio parahaemolyticus strain 20140723005]
MEVFQYYPWLFVVFASIFGLIVGSFLNVVIYRLPKIMELEWRRECAESFPEYKIKPPQEVLTLSVPRSSCQNCATPIRIR
DNIPVISWLLLKGKCHHCHTAISPRYPLIELLTAACAGFVAYHFGFSYFTVALIFFTFVLIAATFIDLDTMLLPDQLTLP
LTWAGIALALTEISPVSLQDAVIGAIAGYLCLWSVYWGFKLLTGKEGMGYGDFKLLAALGAWLGWQSLPMIILLSSVVGV
IFGLVQLRLQKQGIERAFPFGPYLAIAGWISLIWGDQILSWYFTSILGV

Nucleotide


Download         Length: 870 bp        

>NTDB_id=419095 GSR97_RS12525 WP_025524821.1 2705403..2706272(+) (pilD) [Vibrio parahaemolyticus strain 20140723005]
ATGGAAGTGTTCCAGTACTACCCTTGGCTATTCGTTGTGTTTGCCAGTATCTTCGGTTTAATTGTGGGTAGTTTTCTTAA
TGTGGTCATTTATCGGCTACCTAAAATCATGGAATTAGAATGGCGCCGTGAATGCGCCGAATCATTCCCTGAATATAAGA
TTAAGCCACCTCAAGAAGTTTTGACATTGAGCGTGCCTCGCTCTTCGTGCCAAAACTGCGCGACGCCAATTCGTATTCGA
GACAATATTCCAGTAATCAGCTGGCTATTGTTAAAAGGAAAATGCCATCATTGTCATACCGCAATTAGTCCTCGCTATCC
GCTGATAGAATTACTCACTGCAGCGTGCGCTGGTTTTGTGGCTTATCATTTCGGCTTTAGCTACTTTACGGTTGCGTTAA
TCTTTTTCACATTTGTCTTAATAGCCGCGACTTTTATCGATCTCGATACTATGCTGCTACCGGACCAATTAACATTACCA
TTAACTTGGGCTGGCATTGCGTTAGCATTAACAGAAATAAGCCCTGTTAGTCTACAAGACGCCGTAATTGGTGCGATTGC
CGGTTATTTGTGTCTTTGGTCAGTATATTGGGGGTTCAAACTGCTTACTGGTAAAGAAGGCATGGGTTACGGTGATTTTA
AATTGCTGGCTGCCCTTGGCGCTTGGCTAGGATGGCAATCATTACCAATGATCATCCTACTTTCTTCCGTCGTCGGTGTG
ATATTCGGGCTAGTCCAGTTACGACTACAAAAACAAGGTATAGAGAGAGCTTTCCCTTTCGGCCCATATTTAGCGATTGC
AGGATGGATAAGCTTAATCTGGGGCGATCAAATTCTAAGTTGGTACTTCACGTCAATTTTAGGGGTGTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(135-244)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(17-124)


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
  pilD Vibrio campbellii strain DS40M4

88.927

100

0.889
  pilD Vibrio cholerae strain A1552

73.611

99.654

0.734
  pilD Acinetobacter baumannii D1279779

52.239

92.734

0.484
  pilD Acinetobacter nosocomialis M2

51.866

92.734

0.481
  pilD Neisseria gonorrhoeae MS11

47.464

95.502

0.453

Multiple sequence alignment