Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   vm_RS02850 Genome accession   NZ_CP016383
Coordinates   555314..556189 (-) Length   291 a.a.
NCBI ID   WP_070381368.1    Uniprot ID   -
Organism   Vibrio mimicus strain SCCF01     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 550314..561189
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  vm_RS02830 (VM_02830) parC 551155..553440 (+) 2286 WP_070381365.1 DNA topoisomerase IV subunit A -
  vm_RS02835 (VM_02835) yacG 553489..553686 (-) 198 WP_000162865.1 DNA gyrase inhibitor YacG -
  vm_RS02840 (VM_02840) zapD 553937..554677 (-) 741 WP_070381366.1 cell division protein ZapD -
  vm_RS02845 (VM_02845) coaE 554709..555317 (-) 609 WP_070381367.1 dephospho-CoA kinase -
  vm_RS02850 (VM_02850) pilD 555314..556189 (-) 876 WP_070381368.1 prepilin peptidase Machinery gene
  vm_RS02855 (VM_02855) pilC 556252..557478 (-) 1227 WP_070381369.1 type II secretion system F family protein Machinery gene
  vm_RS02860 (VM_02860) pilB 557517..559205 (-) 1689 WP_070381370.1 type IV-A pilus assembly ATPase PilB Machinery gene
  vm_RS02865 (VM_02865) pilA 559209..559658 (-) 450 WP_070381371.1 pilin Machinery gene
  vm_RS02870 (VM_02870) nadC 559903..560793 (-) 891 WP_070382548.1 carboxylating nicotinate-nucleotide diphosphorylase -

Sequence

Protein


Download         Length: 291 a.a.        Molecular weight: 32212.34 Da        Isoelectric Point: 7.0559

>NTDB_id=187676 vm_RS02850 WP_070381368.1 555314..556189(-) (pilD) [Vibrio mimicus strain SCCF01]
MELFFYYPWLFPVLATLFGLIVGSFLNVVIYRLPKIMEREWRADCAASFPEYGISPPEGQLTLSLPRSTCPHCQTPIRVI
DNIPVVSWLALRGKCSHCKSPISARYPLIELFTALVSLMVSTQLGFSPFAVAALLFSYVLIAATFIDLDTMLLPDQLTLP
LLWSGIALALFGLSPVSLTDAVIGAMAGYLSLWSIYWLFKLLTGKEGMGYGDFKLLAALGAWLGWQQLPVIVLLSSVVGL
LFGLIQLRLQKQGIDKAFPFGPYLAIAGWIALLWGNTVIDWYLTSWVGQPL

Nucleotide


Download         Length: 876 bp        

>NTDB_id=187676 vm_RS02850 WP_070381368.1 555314..556189(-) (pilD) [Vibrio mimicus strain SCCF01]
ATGGAACTGTTTTTCTACTACCCTTGGCTGTTTCCGGTTTTGGCTACCTTATTTGGGCTTATCGTCGGCAGCTTTCTTAA
TGTGGTGATTTATCGCTTACCGAAAATTATGGAGCGTGAATGGCGCGCTGACTGTGCGGCCAGCTTTCCGGAATACGGAA
TAAGCCCACCAGAAGGGCAACTTACGCTCAGTTTGCCACGCTCAACCTGCCCACATTGCCAAACACCCATTCGAGTGATT
GATAATATTCCGGTAGTCAGTTGGCTTGCACTGCGAGGAAAATGCTCACACTGCAAATCACCAATCAGTGCCCGCTATCC
TTTAATTGAATTATTCACCGCTTTAGTGAGTTTAATGGTTTCTACTCAGCTCGGTTTTAGCCCTTTTGCGGTTGCTGCAC
TCCTGTTTAGCTATGTACTGATTGCTGCTACGTTTATCGACCTCGATACTATGCTGTTGCCTGACCAGCTCACTTTGCCT
CTGCTGTGGAGTGGTATTGCGCTAGCCCTGTTTGGACTGTCCCCGGTGTCGCTCACCGATGCAGTGATTGGTGCAATGGC
GGGTTATCTTTCACTGTGGTCGATTTATTGGCTGTTTAAACTGCTGACCGGCAAAGAAGGCATGGGTTATGGGGATTTCA
AATTGCTCGCCGCCCTTGGAGCTTGGCTGGGTTGGCAACAGTTGCCAGTCATCGTGCTGCTCTCGTCTGTGGTTGGTCTT
CTCTTCGGTTTAATTCAGTTACGCCTACAGAAACAAGGCATAGATAAAGCTTTTCCATTTGGCCCATATTTAGCCATTGC
TGGGTGGATTGCCTTACTATGGGGCAATACGGTGATTGACTGGTACTTAACCTCTTGGGTAGGGCAACCATTATGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(17-122)

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 cholerae strain A1552

87.285

100

0.873
  pilD Vibrio campbellii strain DS40M4

75

98.969

0.742
  pilD Acinetobacter baumannii D1279779

53.309

93.471

0.498
  pilD Acinetobacter nosocomialis M2

52.574

93.471

0.491
  pilD Neisseria gonorrhoeae MS11

47.445

94.158

0.447

Multiple sequence alignment