Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   H9K44_RS03130 Genome accession   NZ_CP064035
Coordinates   643513..644382 (-) Length   289 a.a.
NCBI ID   WP_169608825.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain DLM1799     
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 639553..657115 643513..644382 within 0


Gene organization within MGE regions


Location: 639553..657115
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  H9K44_RS03095 (H9K44_03100) rpsP 639553..639801 (+) 249 WP_005379962.1 30S ribosomal protein S16 -
  H9K44_RS03100 (H9K44_03105) rimM 639830..640378 (+) 549 WP_005462552.1 ribosome maturation factor RimM -
  H9K44_RS03105 (H9K44_03110) trmD 640406..641149 (+) 744 WP_005462562.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  H9K44_RS03110 (H9K44_03115) rplS 641191..641544 (+) 354 WP_005462554.1 50S ribosomal protein L19 -
  H9K44_RS03115 (H9K44_03120) yacG 641867..642061 (-) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  H9K44_RS03120 (H9K44_03125) zapD 642130..642870 (-) 741 WP_023624252.1 cell division protein ZapD -
  H9K44_RS03125 (H9K44_03130) coaE 642898..643512 (-) 615 WP_005480887.1 dephospho-CoA kinase -
  H9K44_RS03130 (H9K44_03135) pilD 643513..644382 (-) 870 WP_169608825.1 A24 family peptidase Machinery gene
  H9K44_RS03135 (H9K44_03140) pilC 644447..645670 (-) 1224 WP_005479682.1 type II secretion system F family protein Machinery gene
  H9K44_RS03140 (H9K44_03145) pilB 645694..647379 (-) 1686 WP_169608822.1 type IV-A pilus assembly ATPase PilB Machinery gene
  H9K44_RS03145 (H9K44_03150) - 647376..647834 (-) 459 WP_169608820.1 pilin -
  H9K44_RS03150 (H9K44_03155) nadC 648097..648984 (-) 888 WP_015297249.1 carboxylating nicotinate-nucleotide diphosphorylase -
  H9K44_RS03155 (H9K44_03160) ampD 649077..649628 (+) 552 WP_020841256.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  H9K44_RS03160 (H9K44_03165) pdhR 650034..650801 (+) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  H9K44_RS03165 (H9K44_03170) aceE 650850..653513 (+) 2664 WP_005462566.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  H9K44_RS03170 (H9K44_03175) aceF 653533..655419 (+) 1887 WP_031830968.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  H9K44_RS03175 (H9K44_03180) lpdA 655688..657115 (+) 1428 WP_005479684.1 dihydrolipoyl dehydrogenase -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 32451.54 Da        Isoelectric Point: 7.2155

>NTDB_id=498600 H9K44_RS03130 WP_169608825.1 643513..644382(-) (pilD) [Vibrio parahaemolyticus strain DLM1799]
MEVFQYYPWLFVVFASIFGLIVGSFLNVVIYRLPKIMELEWRREYAESFPEYKIKPPQEVLTLSVPRSSCQNCATPIRIR
DNIPVISWLLLKGKCHHCHTAISPRYPLIELLTAACAGFVAYHFGFSYFTVALIFFTFILIAATFIDLDTMLLPDQLTLP
LTWAGIALALTEISPVSLQDAVIGAIAGYLCLWSVYWGFKLLTGKEGMGYGDFKLLAALGAWLGWQSLPMIILLSSVVGV
IFGLVQLRLQKQGIEKAFPFGPYLAIAGWVSLIWGDQILSWYFTSILGV

Nucleotide


Download         Length: 870 bp        

>NTDB_id=498600 H9K44_RS03130 WP_169608825.1 643513..644382(-) (pilD) [Vibrio parahaemolyticus strain DLM1799]
ATGGAAGTGTTCCAGTACTACCCTTGGCTATTCGTTGTGTTTGCCAGTATCTTCGGTTTAATTGTGGGTAGTTTTCTTAA
TGTGGTCATTTATCGGCTACCTAAAATCATGGAATTAGAATGGCGCCGTGAATACGCCGAATCATTCCCTGAATATAAGA
TTAAGCCACCTCAAGAAGTTTTGACATTGAGCGTGCCTCGCTCTTCGTGCCAAAACTGCGCGACGCCAATTCGTATTCGA
GACAATATTCCAGTAATCAGCTGGCTATTGTTAAAAGGAAAATGCCATCATTGTCATACCGCAATTAGTCCTCGCTATCC
GCTGATAGAATTACTCACTGCAGCGTGCGCTGGTTTTGTGGCTTATCATTTCGGCTTTAGCTACTTTACGGTTGCGTTAA
TCTTTTTCACATTTATCTTAATAGCCGCGACTTTTATCGATCTCGATACTATGCTGCTACCGGACCAATTAACATTACCA
TTAACTTGGGCTGGCATTGCGTTAGCATTAACAGAAATAAGCCCTGTTAGTCTACAAGACGCCGTAATTGGTGCGATTGC
CGGTTATTTATGTCTTTGGTCAGTATATTGGGGTTTCAAACTGCTTACTGGTAAAGAAGGCATGGGTTACGGTGATTTTA
AATTGCTGGCCGCCCTTGGCGCTTGGCTAGGATGGCAATCATTACCAATGATCATCCTACTTTCTTCCGTCGTCGGTGTG
ATATTCGGGCTCGTTCAGTTACGACTACAAAAACAAGGTATAGAGAAAGCTTTCCCTTTCGGCCCATATTTAGCGATTGC
AGGATGGGTAAGCTTAATCTGGGGCGATCAAATTCTAAGTTGGTACTTCACGTCAATTTTAGGGGTGTAA

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

72.917

99.654

0.727
  pilD Acinetobacter baumannii D1279779

51.866

92.734

0.481
  pilD Acinetobacter nosocomialis M2

51.493

92.734

0.478
  pilD Neisseria gonorrhoeae MS11

46.739

95.502

0.446