Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ITG08_RS03195 Genome accession   NZ_CP065206
Coordinates   730098..730967 (+) Length   289 a.a.
NCBI ID   WP_016768203.1    Uniprot ID   A0AAN0LNW9
Organism   Vibrio cyclitrophicus strain ED653     
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 718952..734923 730098..730967 within 0


Gene organization within MGE regions


Location: 718952..734923
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ITG08_RS03155 (ITG08_03145) aceF 718952..720844 (-) 1893 WP_248370540.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  ITG08_RS03160 (ITG08_03150) aceE 720875..723538 (-) 2664 WP_016787824.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  ITG08_RS03165 (ITG08_03155) pdhR 723601..724362 (-) 762 WP_016768209.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  ITG08_RS03170 (ITG08_03160) ampD 724844..725443 (-) 600 WP_016796130.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  ITG08_RS03175 (ITG08_03165) nadC 725527..726417 (+) 891 WP_004738163.1 carboxylating nicotinate-nucleotide diphosphorylase -
  ITG08_RS03180 (ITG08_03170) pilA 726672..727097 (+) 426 WP_016796129.1 pilin Machinery gene
  ITG08_RS03185 (ITG08_03175) pilB 727102..728787 (+) 1686 WP_029189239.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ITG08_RS03190 (ITG08_03180) pilC 728802..730031 (+) 1230 WP_016768204.1 type II secretion system F family protein Machinery gene
  ITG08_RS03195 (ITG08_03185) pilD 730098..730967 (+) 870 WP_016768203.1 A24 family peptidase Machinery gene
  ITG08_RS03200 (ITG08_03190) coaE 730970..731584 (+) 615 WP_010435920.1 dephospho-CoA kinase -
  ITG08_RS03205 (ITG08_03195) zapD 731611..732351 (+) 741 WP_010435917.1 cell division protein ZapD -
  ITG08_RS03210 (ITG08_03200) yacG 732433..732630 (+) 198 WP_010435916.1 DNA gyrase inhibitor YacG -
  ITG08_RS03215 (ITG08_03205) rplS 732916..733269 (-) 354 WP_004735514.1 50S ribosomal protein L19 -
  ITG08_RS03220 (ITG08_03210) trmD 733329..734069 (-) 741 WP_010435912.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  ITG08_RS03225 (ITG08_03215) rimM 734096..734650 (-) 555 WP_016768202.1 ribosome maturation factor RimM -
  ITG08_RS03230 (ITG08_03220) rpsP 734675..734923 (-) 249 WP_004410028.1 30S ribosomal protein S16 -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 32578.79 Da        Isoelectric Point: 7.9444

>NTDB_id=507999 ITG08_RS03195 WP_016768203.1 730098..730967(+) (pilD) [Vibrio cyclitrophicus strain ED653]
MEVFHYYPWLFPVLAFIFSLLIGSFLNVVIHRLPIMMEREWQQECSEYFSQYKIPAPEGKFNLSIPRSTCPKCKTQLRAI
DNIPVLSWLFLKGKCRSCTNPISARYPLVELLTAILCTVVASHFGFSYYAIALIFFTFALITATFIDLDTMLLPDQITLP
LVWSGIALALFNISPVSLQDSVVGAMAGYLALWSVYWLFKLLTGKEGMGYGDFKLLAALGAWLGWQHLPMIILLSSLVGL
VFGLIQLRLKQQGIDKAFPFGPYLAIAGWVSLMWGNDIMGWYFTSVLGI

Nucleotide


Download         Length: 870 bp        

>NTDB_id=507999 ITG08_RS03195 WP_016768203.1 730098..730967(+) (pilD) [Vibrio cyclitrophicus strain ED653]
ATGGAAGTATTTCACTACTATCCTTGGCTATTCCCCGTATTAGCTTTCATTTTTAGCCTCCTTATCGGTAGCTTCCTCAA
TGTGGTCATACATCGTTTACCGATTATGATGGAGCGAGAGTGGCAACAAGAGTGCTCGGAATATTTCTCTCAATATAAAA
TTCCAGCACCAGAAGGAAAGTTTAATCTCAGCATTCCTCGCTCTACTTGCCCTAAGTGTAAAACCCAACTGAGAGCAATC
GACAACATCCCTGTATTAAGCTGGTTATTCCTAAAAGGTAAGTGCCGCAGTTGTACTAACCCCATCAGCGCCCGTTATCC
CTTGGTCGAACTGCTTACAGCGATACTTTGTACCGTAGTCGCTAGCCACTTTGGTTTCAGTTATTACGCGATTGCTCTGA
TATTTTTCACCTTTGCTTTGATTACCGCGACCTTTATCGATCTCGATACTATGTTACTGCCGGATCAAATTACCTTACCT
TTAGTTTGGTCTGGTATCGCTTTGGCCTTATTTAATATCAGCCCGGTATCACTGCAAGATTCCGTCGTTGGAGCGATGGC
TGGTTACCTAGCACTTTGGTCTGTTTACTGGCTGTTCAAGCTGCTCACTGGCAAAGAAGGGATGGGGTACGGTGATTTTA
AATTGCTAGCGGCATTAGGGGCATGGCTTGGTTGGCAACATCTACCAATGATCATCCTTCTGTCATCGCTAGTGGGCCTT
GTGTTCGGATTGATTCAACTGCGACTGAAGCAACAAGGCATAGACAAAGCTTTCCCATTTGGGCCCTATCTAGCGATTGC
TGGTTGGGTAAGTCTGATGTGGGGTAACGACATCATGGGTTGGTATTTCACTTCTGTACTAGGAATTTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(135-244)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(17-124)


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

73.702

100

0.737
  pilD Vibrio cholerae strain A1552

69.097

99.654

0.689
  pilD Acinetobacter nosocomialis M2

51.311

92.388

0.474
  pilD Acinetobacter baumannii D1279779

50.936

92.388

0.471
  pilD Neisseria gonorrhoeae MS11

46.739

95.502

0.446