Detailed information    

experimental Experimentally validated

Overview

Name   pilD   Type   Machinery gene
Locus tag   A1552VC_RS11080 Genome accession   NZ_CP028894
Coordinates   2376782..2377657 (+) Length   291 a.a.
NCBI ID   WP_000418747.1    Uniprot ID   H9L4S3
Organism   Vibrio cholerae strain A1552     
Function   assembly of type IV pilus   
DNA binding and uptake

Function

Prepilins are processed by the peptidase PilD and are incorporated into the growing pilus, which is driven energetically by the traffic ATPase PilB.


Genomic Context

Location: 2371782..2382657
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  A1552VC_RS11060 (A1552VC_02185) nadC 2372171..2373061 (+) 891 WP_000665274.1 carboxylating nicotinate-nucleotide diphosphorylase -
  A1552VC_RS11065 (A1552VC_02186) pilA 2373306..2373767 (+) 462 WP_000649326.1 pilin Machinery gene
  A1552VC_RS11070 (A1552VC_02187) pilB 2373767..2375455 (+) 1689 WP_000957200.1 type IV-A pilus assembly ATPase PilB Machinery gene
  A1552VC_RS11075 (A1552VC_02188) pilC 2375498..2376724 (+) 1227 WP_000648511.1 type II secretion system F family protein Machinery gene
  A1552VC_RS11080 (A1552VC_02189) pilD 2376782..2377657 (+) 876 WP_000418747.1 A24 family peptidase Machinery gene
  A1552VC_RS11085 (A1552VC_02190) coaE 2377654..2378262 (+) 609 WP_000011557.1 dephospho-CoA kinase -
  A1552VC_RS11090 (A1552VC_02191) zapD 2378294..2379034 (+) 741 WP_000207198.1 cell division protein ZapD -
  A1552VC_RS11095 (A1552VC_02192) yacG 2379176..2379373 (+) 198 WP_000162868.1 DNA gyrase inhibitor YacG -
  A1552VC_RS11100 (A1552VC_02193) parC 2379422..2381707 (-) 2286 WP_000102510.1 DNA topoisomerase IV subunit A -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  tfoX pilD positive effect
  tfoX pilO positive effect
  tfoX pilB positive effect
  tfoX pilP positive effect
  tfoX pilA positive effect
  tfoX dprA positive effect
  tfoX pilM positive effect
  tfoX pilN positive effect
  tfoX comEA positive effect
  hapR comEA positive effect
  crp comEA positive effect
  qstR comEA positive effect
  tfoX pilQ positive effect
  tfoX qstR positive effect
  qstR comEC positive effect
  qstR comF positive effect
  qstR comM positive effect
  crp qstR positive effect
  hapR qstR positive effect
  tfoX comEC positive effect
  hapR comEC positive effect
  tfoX pilC positive effect
  chiS tfoX positive effect
  hapR dns negative effect

Sequence

Protein


Download         Length: 291 a.a.        Molecular weight: 32433.69 Da        Isoelectric Point: 7.1618

>NTDB_id=1170 A1552VC_RS11080 WP_000418747.1 2376782..2377657(+) (pilD) [Vibrio cholerae strain A1552]
MELFYFYPWLFPVLATLFGLIVGSFLNVVIYRLPKIMEREWRAECAASFPEYGITPPEGKLTLSLPRSTCPHCQTPIRVI
DNIPLLSWLALRGQCSHCKAPISARYPLIELLTALMSLVIATHFPFGVFAVALLFFSYVLIAATFIDFDTLLLPDQLTLP
LLWGGIALALLGFSPVSLSDAVIGAMAGYLSLWSIYWLFKLLTGKEGMGYGDFKLLAALGAWLGWQQLPVIVLLSSVVGV
IFGLIQLRQQKKGIDMAFPFGPYLAIAGWFALLWGDKVIDWYFTTWVGQPL

Nucleotide


Download         Length: 876 bp        

>NTDB_id=1170 A1552VC_RS11080 WP_000418747.1 2376782..2377657(+) (pilD) [Vibrio cholerae strain A1552]
ATGGAACTGTTTTACTTCTACCCTTGGCTGTTTCCGGTGCTCGCCACGCTGTTTGGCTTGATTGTCGGTAGCTTTCTCAA
TGTGGTGATCTATCGCTTACCCAAAATCATGGAGCGTGAATGGCGCGCGGAATGTGCGGCGAGTTTTCCTGAATATGGCA
TCACGCCACCAGAGGGTAAACTGACCCTCAGTTTGCCGCGTTCCACTTGCCCACACTGTCAAACGCCGATTCGCGTCATT
GATAATATCCCGCTACTGAGTTGGCTAGCGCTGCGCGGTCAATGCTCACACTGTAAAGCGCCGATCAGCGCTCGCTATCC
CTTGATTGAGCTACTCACTGCCCTCATGAGCTTAGTGATTGCCACTCACTTTCCGTTCGGAGTTTTTGCCGTGGCGCTGC
TGTTTTTCAGCTATGTGTTGATTGCGGCAACCTTCATCGACTTCGATACCCTGTTGTTGCCCGACCAATTAACGCTACCT
TTACTGTGGGGCGGTATTGCACTGGCACTGCTTGGTTTTTCTCCTGTTTCACTCAGTGATGCGGTGATCGGAGCCATGGC
GGGTTATCTCTCGCTGTGGTCGATTTACTGGCTATTTAAACTGCTGACAGGTAAAGAAGGCATGGGTTATGGCGATTTCA
AATTGCTCGCCGCTCTCGGCGCTTGGCTGGGTTGGCAGCAGTTGCCTGTCATCGTACTGCTCTCATCGGTGGTTGGGGTG
ATTTTCGGTTTAATCCAACTGCGCCAGCAGAAAAAAGGTATCGATATGGCCTTTCCGTTTGGCCCTTATCTCGCCATCGC
GGGATGGTTTGCCTTGCTGTGGGGCGATAAGGTAATTGATTGGTACTTCACCACTTGGGTAGGACAACCGTTATGA

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 H9L4S3

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

75.347

99.654

0.751
  pilD Acinetobacter nosocomialis M2

53.676

95.105

0.51
  pilD Acinetobacter baumannii D1279779

53.309

95.105

0.507
  pilD Neisseria gonorrhoeae MS11

44.792

100

0.451

Multiple sequence alignment    



References

[1] Patrick Seitz et al. (2013) DNA-uptake machinery of naturally competent Vibrio cholerae. Proceedings of The National Academy of Sciences of The United States of America 110(44):17987-92. [PMID: 24127573]
[2] Mirella Lo Scrudato et al. (2012) The regulatory network of natural competence and transformation of Vibrio cholerae. PLoS Genetics 8(6):e1002778. [PMID: 22737089]
[3] K J Fullner et al. (1999) Genetic characterization of a new type IV-A pilus gene cluster found in both classical and El Tor biotypes of Vibrio cholerae. Infection And Immunity 67(3):1393-404. [PMID: 10024587]