Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   JOS67_RS03475 Genome accession   NZ_CP069195
Coordinates   609821..610690 (-) Length   289 a.a.
NCBI ID   WP_012841418.1    Uniprot ID   -
Organism   Vibrio diabolicus strain SLV18     
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 605426..623422 609821..610690 within 0


Gene organization within MGE regions


Location: 605426..623422
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JOS67_RS03440 (JOS67_03435) rpsP 605426..605674 (+) 249 WP_005379962.1 30S ribosomal protein S16 -
  JOS67_RS03445 (JOS67_03440) rimM 605704..606252 (+) 549 WP_005379964.1 ribosome maturation factor RimM -
  JOS67_RS03450 (JOS67_03445) trmD 606280..607023 (+) 744 WP_203346927.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  JOS67_RS03455 (JOS67_03450) rplS 607065..607418 (+) 354 WP_005379971.1 50S ribosomal protein L19 -
  JOS67_RS03460 (JOS67_03455) yacG 608084..608278 (-) 195 WP_005396692.1 DNA gyrase inhibitor YacG -
  JOS67_RS03465 (JOS67_03460) zapD 608438..609178 (-) 741 WP_005396691.1 cell division protein ZapD -
  JOS67_RS03470 (JOS67_03465) coaE 609206..609820 (-) 615 WP_047008979.1 dephospho-CoA kinase -
  JOS67_RS03475 (JOS67_03470) pilD 609821..610690 (-) 870 WP_012841418.1 prepilin peptidase Machinery gene
  JOS67_RS03480 (JOS67_03475) pilC 610755..611978 (-) 1224 WP_074191781.1 type II secretion system F family protein Machinery gene
  JOS67_RS03485 (JOS67_03480) pilB 612002..613687 (-) 1686 WP_203346928.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JOS67_RS03490 (JOS67_03485) pilA 613699..614136 (-) 438 WP_203346929.1 pilin Machinery gene
  JOS67_RS03495 (JOS67_03490) nadC 614399..615286 (-) 888 WP_047102656.1 carboxylating nicotinate-nucleotide diphosphorylase -
  JOS67_RS03500 (JOS67_03495) ampD 615379..615930 (+) 552 WP_012841421.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  JOS67_RS03505 (JOS67_03500) pdhR 616336..617103 (+) 768 WP_005396680.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  JOS67_RS03510 (JOS67_03505) aceE 617152..619815 (+) 2664 WP_005396679.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  JOS67_RS03515 (JOS67_03510) aceF 619835..621727 (+) 1893 WP_203346930.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  JOS67_RS03520 (JOS67_03515) lpdA 621995..623422 (+) 1428 WP_005379993.1 dihydrolipoyl dehydrogenase -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 32523.70 Da        Isoelectric Point: 7.0195

>NTDB_id=532821 JOS67_RS03475 WP_012841418.1 609821..610690(-) (pilD) [Vibrio diabolicus strain SLV18]
MEVFQYYPWLFVVFATIFGLIVGSFLNVVIYRLPKIMELEWRRECAESFPEYKIEPPKEVLTLSVPRSSCQKCATPIRIR
DNIPVISWLLLKGKCHNCQTAISARYPLIELLTAFCSGFVAYHFGFSYFTVALLFFTFILIAATFIDLDTMLLPDQLTLP
LTWAGIALALVEISPVTLQDSVIGAIAGYLCLWSVYWGFKLLTGKEGMGYGDFKLLAALGAWLGWQSLPMIILLSSVVGI
VFGIIQLRLQKQGIEKAFPFGPYLAIAGWISLIWGDQILNWYFTSVLGV

Nucleotide


Download         Length: 870 bp        

>NTDB_id=532821 JOS67_RS03475 WP_012841418.1 609821..610690(-) (pilD) [Vibrio diabolicus strain SLV18]
ATGGAAGTATTCCAGTACTACCCTTGGCTATTCGTTGTGTTTGCCACCATCTTCGGTCTGATCGTGGGTAGCTTCCTCAA
TGTGGTTATTTATCGACTACCTAAAATCATGGAACTAGAATGGCGACGCGAATGTGCCGAGTCATTTCCTGAATACAAAA
TAGAACCTCCTAAAGAAGTGCTGACGTTGAGCGTCCCACGCTCCTCCTGTCAGAAGTGCGCAACGCCGATACGTATTCGA
GACAACATCCCTGTGATTAGCTGGCTGCTTTTAAAAGGCAAATGCCACAACTGTCAGACAGCCATTAGCGCACGCTATCC
ACTGATTGAACTGCTCACTGCGTTCTGCTCAGGCTTTGTCGCTTACCACTTTGGTTTTAGTTACTTTACCGTTGCCCTAC
TCTTTTTCACTTTTATCTTAATCGCCGCAACATTTATCGATCTCGATACTATGTTGTTACCTGACCAATTAACATTACCA
TTAACTTGGGCTGGCATTGCCTTAGCATTAGTCGAAATAAGTCCTGTTACTCTACAAGATTCTGTCATTGGTGCTATTGC
TGGTTACCTATGTCTCTGGTCCGTTTACTGGGGCTTTAAGCTACTTACTGGTAAAGAAGGAATGGGATATGGTGATTTTA
AACTACTAGCAGCACTAGGGGCTTGGCTGGGCTGGCAGTCACTGCCGATGATCATTCTACTTTCTTCTGTGGTTGGCATC
GTATTTGGCATCATTCAACTACGCTTGCAAAAACAGGGAATTGAAAAAGCTTTTCCTTTCGGTCCTTACTTAGCAATTGC
TGGTTGGATAAGCTTAATTTGGGGCGACCAGATTTTAAACTGGTACTTTACTTCAGTTCTAGGAGTGTAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(17-124)

Type IV leader peptidase family (Peptidase_A24)

(135-244)


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

91.003

100

0.91
  pilD Vibrio cholerae strain A1552

72.917

99.654

0.727
  pilD Acinetobacter baumannii D1279779

52.593

93.426

0.491
  pilD Acinetobacter nosocomialis M2

52.222

93.426

0.488
  pilD Neisseria gonorrhoeae MS11

48.551

95.502

0.464