Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   AB8808_RS06065 Genome accession   NZ_CP166101
Coordinates   1539300..1540169 (+) Length   289 a.a.
NCBI ID   WP_369930573.1    Uniprot ID   -
Organism   Xanthomonas sp. NCPPB 2632     
Function   assembly of type IV pilus (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 1523714..1539219 1539300..1540169 flank 81


Gene organization within MGE regions


Location: 1523714..1540169
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AB8808_RS06000 (AB8808_06000) - 1523714..1524148 (+) 435 WP_369930558.1 pilin -
  AB8808_RS06005 (AB8808_06005) pilE 1524452..1524898 (+) 447 WP_369930559.1 pilin Machinery gene
  AB8808_RS06010 (AB8808_06010) - 1524978..1526996 (+) 2019 WP_369930561.1 tetratricopeptide repeat protein -
  AB8808_RS06015 (AB8808_06015) - 1527049..1529028 (+) 1980 WP_369930562.1 hypothetical protein -
  AB8808_RS06020 (AB8808_06020) - 1529025..1530254 (+) 1230 WP_369930563.1 lipopolysaccharide biosynthesis protein -
  AB8808_RS06025 (AB8808_06025) - 1530260..1531132 (-) 873 WP_369930564.1 hypothetical protein -
  AB8808_RS06030 (AB8808_06030) - 1531137..1532237 (-) 1101 WP_369930565.1 class I SAM-dependent methyltransferase -
  AB8808_RS06035 (AB8808_06035) - 1532240..1533193 (-) 954 WP_369930566.1 rhamnosyltransferase -
  AB8808_RS06040 (AB8808_06040) - 1533165..1534310 (-) 1146 WP_369930568.1 glycosyltransferase family 4 protein -
  AB8808_RS06045 (AB8808_06045) - 1534317..1535048 (-) 732 WP_369930569.1 methyltransferase domain-containing protein -
  AB8808_RS06050 (AB8808_06050) - 1535045..1535911 (-) 867 WP_369930570.1 glycosyltransferase family 2 protein -
  AB8808_RS06055 (AB8808_06055) pilB 1536082..1537809 (+) 1728 WP_369930571.1 type IV-A pilus assembly ATPase PilB Machinery gene
  AB8808_RS06060 (AB8808_06060) pilC 1537954..1539219 (+) 1266 WP_369930572.1 type II secretion system F family protein Machinery gene
  AB8808_RS06065 (AB8808_06065) pilD 1539300..1540169 (+) 870 WP_369930573.1 A24 family peptidase Machinery gene

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 31313.45 Da        Isoelectric Point: 8.6125

>NTDB_id=1033415 AB8808_RS06065 WP_369930573.1 1539300..1540169(+) (pilD) [Xanthomonas sp. NCPPB 2632]
MPDMPLALWIGLAGVFGLLVGSFLNVVILRVPARMQAEWRRQAREVLELDTVDEPLPPGVVVESSHCPRCKHPLAARDNI
PLLGWLLLRGRCRYCREPISIQYPLVELLAGLASAAVVWRFGPTPGAAAGLVLTYFLIALSGIDARTQLLPDELNYPLLW
IGLALCLVPGWQPLPVAPTSAILAALLGYLSLWSVYWLFKLLTGKEGMGHGDFKLLAALGAWMGPLSLLPIVMLSSLIGA
LVGGALILLRRHGREVPIPFGPYIAAAGWVWLLLGDRLLGAYLSATGLR

Nucleotide


Download         Length: 870 bp        

>NTDB_id=1033415 AB8808_RS06065 WP_369930573.1 1539300..1540169(+) (pilD) [Xanthomonas sp. NCPPB 2632]
ATGCCCGACATGCCCCTCGCTCTCTGGATCGGCCTTGCCGGCGTCTTCGGCCTGCTGGTCGGCAGTTTCCTCAATGTGGT
GATCCTGCGCGTGCCCGCGCGCATGCAGGCCGAGTGGCGCCGGCAGGCGCGCGAGGTGCTGGAACTGGATACGGTGGACG
AGCCGCTGCCGCCCGGCGTGGTGGTGGAGTCGTCGCACTGCCCGCGCTGCAAGCATCCGCTGGCCGCGCGCGACAACATC
CCGCTGCTGGGCTGGCTGCTGCTGCGCGGGCGCTGCCGATACTGCCGCGAGCCGATCTCCATCCAGTATCCCCTGGTCGA
ACTGCTGGCCGGACTGGCCAGCGCCGCGGTGGTCTGGCGGTTCGGGCCCACGCCCGGCGCGGCAGCCGGCCTGGTACTGA
CCTACTTCCTCATCGCCTTGTCCGGCATCGACGCACGCACCCAGCTGCTGCCCGATGAGCTGAATTACCCGCTGCTGTGG
ATCGGCCTGGCCCTGTGCCTGGTGCCGGGCTGGCAGCCGCTGCCCGTCGCACCCACCTCAGCCATCCTCGCCGCCCTGCT
CGGCTACCTCAGCCTGTGGAGCGTCTACTGGCTGTTCAAGCTGCTGACCGGCAAGGAAGGCATGGGCCATGGCGACTTCA
AGTTGCTGGCTGCGCTGGGCGCGTGGATGGGTCCGTTGTCCCTCCTGCCCATCGTCATGCTGTCGTCCCTCATCGGTGCC
CTGGTGGGCGGTGCGCTGATCCTGCTGCGGCGACATGGGCGAGAGGTGCCGATCCCCTTCGGCCCCTACATCGCGGCGGC
CGGCTGGGTCTGGTTGCTGCTGGGCGACCGCTTGCTCGGAGCCTACCTGAGCGCCACGGGCCTGCGATGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(15-121)

Type IV leader peptidase family (Peptidase_A24)

(131-243)


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 Acinetobacter nosocomialis M2

50.538

96.54

0.488
  pilD Acinetobacter baumannii D1279779

49.301

98.962

0.488
  pilD Vibrio cholerae strain A1552

49.819

95.848

0.478
  pilD Vibrio campbellii strain DS40M4

48.029

96.54

0.464
  pilD Neisseria gonorrhoeae MS11

47.015

92.734

0.436

Multiple sequence alignment