Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   VCA1004_RS09630 Genome accession   NZ_AP018689
Coordinates   2121469..2122362 (+) Length   297 a.a.
NCBI ID   WP_086981570.1    Uniprot ID   -
Organism   Vibrio aphrogenes strain CA-1004     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2116469..2127362
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  VCA1004_RS09610 nadC 2116701..2117621 (+) 921 WP_086981566.1 carboxylating nicotinate-nucleotide diphosphorylase -
  VCA1004_RS09615 pilA 2118017..2118475 (+) 459 WP_086981567.1 pilin Machinery gene
  VCA1004_RS09620 pilB 2118475..2120163 (+) 1689 WP_086981568.1 type IV-A pilus assembly ATPase PilB Machinery gene
  VCA1004_RS09625 pilC 2120199..2121431 (+) 1233 WP_086981569.1 type II secretion system F family protein Machinery gene
  VCA1004_RS09630 pilD 2121469..2122362 (+) 894 WP_086981570.1 A24 family peptidase Machinery gene
  VCA1004_RS09635 coaE 2122366..2122989 (+) 624 WP_086981571.1 dephospho-CoA kinase -
  VCA1004_RS09640 zapD 2123035..2123766 (+) 732 WP_086981572.1 cell division protein ZapD -
  VCA1004_RS09645 yacG 2123806..2124006 (+) 201 WP_086981573.1 DNA gyrase inhibitor YacG -
  VCA1004_RS09650 mutT 2124450..2124848 (-) 399 WP_086981574.1 8-oxo-dGTP diphosphatase MutT -

Sequence

Protein


Download         Length: 297 a.a.        Molecular weight: 33429.00 Da        Isoelectric Point: 6.6706

>NTDB_id=70411 VCA1004_RS09630 WP_086981570.1 2121469..2122362(+) (pilD) [Vibrio aphrogenes strain CA-1004]
MLIFDYYPILFPIVAGLFGLIIGSFLNVVIHRLPIMMEREWQQECLESFPQLAQDPELKSQLAALNKPFNLNVPRSRCPK
CDTQIRAIDNIPVLSWLLLRGKCHQCANPISFRYPAIELLTAALCVVIGMYFPADWYGVALLFFTFVLVSATFIDLDTML
LPDQLTLPLMWAGIALSLFHISPVSLQDAVIGAMAGYLCLWIVFWAFKLLTGKEGMGYGDFKLLAALGAWLGWQQLPLLI
LLSSLVGLIFGIIQLRLQKRGIEKAFPFGPYLAIAGWFCLIWGNDLTSWYLTNMLGM

Nucleotide


Download         Length: 894 bp        

>NTDB_id=70411 VCA1004_RS09630 WP_086981570.1 2121469..2122362(+) (pilD) [Vibrio aphrogenes strain CA-1004]
ATGCTCATTTTTGATTATTATCCTATTCTTTTCCCAATTGTTGCCGGACTCTTTGGCTTGATTATTGGCAGTTTTTTAAA
TGTGGTCATCCACCGCTTACCCATCATGATGGAACGAGAATGGCAACAAGAATGCCTTGAAAGCTTTCCCCAATTAGCAC
AAGACCCTGAACTTAAATCGCAACTCGCAGCACTAAACAAACCGTTTAACTTAAATGTGCCACGTTCCCGCTGCCCTAAA
TGTGATACTCAAATTCGGGCTATCGATAATATTCCTGTGCTCAGTTGGCTTTTACTTCGAGGTAAATGCCATCAATGTGC
CAACCCTATCAGCTTTCGCTATCCCGCTATCGAATTGCTTACGGCGGCTTTGTGTGTGGTCATTGGCATGTATTTTCCTG
CCGATTGGTATGGCGTGGCCTTATTATTTTTTACCTTTGTTTTAGTCTCTGCCACCTTTATCGACCTTGATACCATGTTA
TTGCCCGACCAACTGACTTTACCCTTAATGTGGGCAGGCATCGCGTTATCTTTATTTCACATCAGCCCTGTTTCTTTACA
AGATGCAGTCATTGGTGCCATGGCCGGTTACTTGTGTTTGTGGATTGTCTTTTGGGCCTTTAAATTACTGACAGGTAAAG
AAGGCATGGGTTATGGCGATTTCAAACTGTTGGCCGCTCTAGGGGCTTGGCTTGGCTGGCAACAATTGCCACTGCTTATT
TTACTCTCTTCCTTAGTTGGATTAATCTTTGGCATTATTCAATTACGTTTGCAAAAACGAGGGATAGAAAAGGCATTTCC
ATTTGGCCCATATTTAGCCATTGCAGGATGGTTTTGTCTTATTTGGGGGAATGATTTAACCTCTTGGTATCTTACCAATA
TGTTAGGTATGTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(143-252)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(17-131)


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

68.35

100

0.684
  pilD Vibrio cholerae strain A1552

65.541

99.663

0.653
  pilD Acinetobacter baumannii D1279779

52.688

93.939

0.495
  pilD Acinetobacter nosocomialis M2

51.971

93.939

0.488
  pilD Neisseria gonorrhoeae MS11

46.996

95.286

0.448

Multiple sequence alignment