Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   GPY13_RS12190 Genome accession   NZ_CP046823
Coordinates   2662016..2662891 (+) Length   291 a.a.
NCBI ID   WP_000418513.1    Uniprot ID   A0A2J9UYJ7
Organism   Vibrio mimicus strain 06-2455     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2657016..2667891
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GPY13_RS12170 nadC 2657418..2658308 (+) 891 WP_032470672.1 carboxylating nicotinate-nucleotide diphosphorylase -
  GPY13_RS12175 - 2658553..2658990 (+) 438 WP_000649324.1 type IV pilin protein -
  GPY13_RS12180 pilB 2659000..2660688 (+) 1689 WP_000957197.1 type IV-A pilus assembly ATPase PilB Machinery gene
  GPY13_RS12185 pilC 2660727..2661953 (+) 1227 WP_000648444.1 type II secretion system F family protein Machinery gene
  GPY13_RS12190 pilD 2662016..2662891 (+) 876 WP_000418513.1 A24 family peptidase Machinery gene
  GPY13_RS12195 coaE 2662888..2663496 (+) 609 WP_000011562.1 dephospho-CoA kinase -
  GPY13_RS12200 zapD 2663528..2664268 (+) 741 WP_000207199.1 cell division protein ZapD -
  GPY13_RS12205 yacG 2664519..2664716 (+) 198 WP_000162865.1 DNA gyrase inhibitor YacG -
  GPY13_RS12210 parC 2664761..2667046 (-) 2286 WP_000102527.1 DNA topoisomerase IV subunit A -

Sequence

Protein


Download         Length: 291 a.a.        Molecular weight: 32265.50 Da        Isoelectric Point: 7.1615

>NTDB_id=408463 GPY13_RS12190 WP_000418513.1 2662016..2662891(+) (pilD) [Vibrio mimicus strain 06-2455]
MELFFYYPWLFPVLATLFGLIVGSFLNVVIYRLPKIMEREWRADCAASFPEYGISPPEGQLTLSLPRSTCPHCQTPIRVI
DNIPVVSWLALRGKCSHCKAPISARYPLIELLTALMSLVIATHFPFGVFAVALLFFSYVLIAATFIDFDTMLLPDQLTLP
LLWGGIALALFGLSPVSLTDAVIGAMAGYLSLWSIYWLFKLLTGKEGMGYGDFKLLAALGAWLGWQQLPVIVLLSSVVGL
LFGLIQLRLQKQGIDKAFPFGPYLAIAGWIALLWGNTVIDWYLASWVGQPL

Nucleotide


Download         Length: 876 bp        

>NTDB_id=408463 GPY13_RS12190 WP_000418513.1 2662016..2662891(+) (pilD) [Vibrio mimicus strain 06-2455]
ATGGAACTGTTTTTCTACTACCCTTGGCTGTTTCCCGTTTTAGCTACCTTATTTGGGCTTATAGTCGGCAGCTTTCTTAA
TGTGGTGATTTATCGCTTACCGAAAATCATGGAGCGTGAGTGGCGCGCTGACTGTGCGGCCAGCTTTCCGGAGTACGGAA
TAAGCCCACCAGAAGGGCAACTTACGCTCAGTTTGCCACGCTCAACCTGCCCACATTGCCAAACACCCATTCGAGTGATT
GATAATATTCCGGTAGTCAGTTGGCTTGCTCTGCGAGGAAAATGCTCACACTGCAAAGCACCGATCAGTGCCCGCTATCC
CTTAATTGAGCTACTCACTGCCCTCATGAGCTTAGTGATTGCCACTCACTTTCCATTCGGTGTATTTGCCGTGGCGTTGC
TGTTTTTCAGCTATGTGTTGATTGCGGCAACCTTCATCGACTTCGATACTATGCTGTTGCCTGACCAGCTCACATTGCCT
CTGCTGTGGGGTGGCATTGCACTAGCCCTGTTTGGACTGTCCCCGGTGTCTCTCACCGATGCAGTGATTGGTGCAATGGC
CGGTTACCTCTCTCTTTGGTCGATTTACTGGTTATTTAAATTATTGACTGGCAAAGAAGGCATGGGTTATGGGGATTTCA
AATTGCTCGCTGCTCTTGGAGCTTGGCTGGGTTGGCAACAGTTGCCAGTCATCGTGCTGCTATCGTCTGTGGTTGGTCTT
CTCTTCGGTTTAATTCAGTTACGCCTACAGAAACAAGGCATAGATAAAGCTTTCCCATTTGGCCCATATTTAGCCATTGC
TGGGTGGATTGCCTTACTATGGGGCAATACGGTGATTGACTGGTACTTAGCCTCTTGGGTAGGACAACCGCTATGA

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
  AlphaFold DB A0A2J9UYJ7

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 cholerae strain A1552

92.096

100

0.921
  pilD Vibrio campbellii strain DS40M4

76.389

98.969

0.756
  pilD Acinetobacter baumannii D1279779

53.846

93.814

0.505
  pilD Acinetobacter nosocomialis M2

53.114

93.814

0.498
  pilD Neisseria gonorrhoeae MS11

46.35

94.158

0.436

Multiple sequence alignment