Detailed information    

experimental Experimentally validated

Overview

Name   pilD   Type   Machinery gene
Locus tag   DSB67_RS12675 Genome accession   NZ_CP030788
Coordinates   2644056..2644925 (+) Length   289 a.a.
NCBI ID   WP_010643256.1    Uniprot ID   -
Organism   Vibrio campbellii strain DS40M4     
Function   type IV pilus biogenesis and function   
DNA binding and uptake

Function

Induction of TfoX expression resulted in upregulation of the genes required for DNA uptake and integration (comEC, comEA, comM, comF, and dprA) and pilus structure (pilABCD, pilMNOPQ, and minor pilins VC0857 to -0861) in DS40M4


Genomic Context

Location: 2639056..2649925
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DSB67_RS12650 (DSB67_12655) nadC 2639424..2640311 (+) 888 WP_010643264.1 carboxylating nicotinate-nucleotide diphosphorylase -
  DSB67_RS12660 (DSB67_12665) pilA 2640576..2641040 (+) 465 WP_010643261.1 pilin Machinery gene
  DSB67_RS12665 (DSB67_12670) pilB 2641040..2642725 (+) 1686 WP_010643259.1 type IV-A pilus assembly ATPase PilB Machinery gene
  DSB67_RS12670 (DSB67_12675) pilC 2642760..2643983 (+) 1224 WP_010643257.1 type II secretion system F family protein Machinery gene
  DSB67_RS12675 (DSB67_12680) pilD 2644056..2644925 (+) 870 WP_010643256.1 prepilin peptidase Machinery gene
  DSB67_RS12680 (DSB67_12685) coaE 2644926..2645540 (+) 615 WP_010643253.1 dephospho-CoA kinase -
  DSB67_RS12685 (DSB67_12690) zapD 2645568..2646308 (+) 741 WP_010643252.1 cell division protein ZapD -
  DSB67_RS12690 (DSB67_12695) yacG 2646371..2646565 (+) 195 WP_010643249.1 DNA gyrase inhibitor YacG -
  DSB67_RS12695 (DSB67_12700) rplS 2646902..2647255 (-) 354 WP_005379971.1 50S ribosomal protein L19 -
  DSB67_RS12700 (DSB67_12705) trmD 2647297..2648040 (-) 744 WP_005534054.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  DSB67_RS12705 (DSB67_12710) rimM 2648068..2648616 (-) 549 WP_005534055.1 ribosome maturation factor RimM -
  DSB67_RS12710 (DSB67_12715) rpsP 2648644..2648892 (-) 249 WP_004410028.1 30S ribosomal protein S16 -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  tfoX pilD positive effect
  tfoX pilB positive effect
  tfoX dprA positive effect
  tfoX pilC positive effect
  tfoX pilM positive effect
  tfoX pilO positive effect
  tfoX comM positive effect
  tfoX pilA positive effect
  tfoX pilQ positive effect
  tfoX comEC positive effect
  tfoX comEA positive effect
  tfoX pilP positive effect
  tfoX comF positive effect
  tfoX pilN positive effect

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 32619.83 Da        Isoelectric Point: 7.5424

>NTDB_id=1403 DSB67_RS12675 WP_010643256.1 2644056..2644925(+) (pilD) [Vibrio campbellii strain DS40M4]
MEVFQYYPWLFVVFATIFGLIVGSFLNVVIYRLPKIMELEWRRECAESFPEYKIEPPKETLTLSVPRSSCQQCGTQIRIR
DNIPVISWLLLRGKCHNCQAPINARYPLIELLTAFCSGFIAFHFGFSYFTVALVFFTFVLIAATFIDLDTMLLPDQLTLP
LMWTGIALALAGISPVSLQDSIIGAMAGYLCLWSVYWLFKLLTGKEGMGYGDFKLLAALGAWLGWQSLPMIILLSSVVGV
IFGLIQLRLQKQGIEKAFPFGPYLAIAGWVSLIWGHQILNWYFTSILGV

Nucleotide


Download         Length: 870 bp        

>NTDB_id=1403 DSB67_RS12675 WP_010643256.1 2644056..2644925(+) (pilD) [Vibrio campbellii strain DS40M4]
ATGGAAGTATTCCAGTACTACCCATGGCTATTCGTGGTGTTTGCCACAATTTTCGGTTTGATTGTGGGTAGTTTCCTCAA
CGTGGTTATTTACCGTTTACCCAAGATCATGGAACTAGAATGGCGACGTGAGTGCGCTGAATCCTTCCCTGAATATAAGA
TTGAACCACCCAAAGAGACGCTGACGTTAAGCGTACCGCGCTCATCTTGTCAGCAATGCGGCACGCAAATTCGCATTCGT
GACAATATCCCAGTGATTAGTTGGCTTCTTCTGCGCGGTAAATGCCACAACTGCCAAGCGCCCATCAATGCACGCTACCC
TCTTATCGAACTGCTTACTGCCTTTTGTTCGGGTTTTATCGCTTTTCACTTCGGTTTTAGCTACTTCACTGTAGCGCTGG
TTTTCTTTACCTTTGTATTGATTGCTGCCACGTTTATCGATCTCGATACCATGTTGTTGCCAGACCAACTGACTCTACCA
TTGATGTGGACAGGTATCGCACTTGCTCTTGCTGGTATCAGTCCTGTCAGCCTACAAGATTCTATCATTGGTGCAATGGC
AGGCTATCTGTGTCTTTGGAGTGTTTACTGGCTGTTTAAACTTCTAACAGGCAAAGAAGGCATGGGCTATGGTGACTTTA
AACTCCTTGCGGCATTGGGCGCTTGGCTGGGTTGGCAATCTCTACCGATGATCATTTTGCTCTCTTCGGTGGTTGGCGTC
ATCTTTGGTCTTATCCAACTGCGCTTGCAAAAACAAGGTATCGAGAAAGCCTTTCCTTTCGGCCCCTACCTTGCGATTGC
TGGCTGGGTGAGCCTAATTTGGGGCCATCAAATCCTCAACTGGTACTTTACGTCGATTCTAGGAGTGTAA

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

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

75.347

99.654

0.751
  pilD Acinetobacter baumannii D1279779

52.399

94.755

0.497
  pilD Acinetobacter nosocomialis M2

52.03

94.755

0.493
  pilD Neisseria gonorrhoeae MS11

45.652

96.503

0.441

Multiple sequence alignment    



References

[1] Chelsea A Simpson et al. (2019) Diversity in Natural Transformation Frequencies and Regulation across Vibrio Species. MBio 10(6):e02788-19. [PMID: 31848285]