Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   BSG32_RS16260 Genome accession   NZ_CP022552
Coordinates   3223348..3224217 (+) Length   289 a.a.
NCBI ID   WP_021450018.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain MAVP-R     
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 3210602..3228248 3223348..3224217 within 0


Gene organization within MGE regions


Location: 3210602..3228248
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  BSG32_RS16215 (BSG32_16225) lpdA 3210602..3212029 (-) 1428 WP_005479684.1 dihydrolipoyl dehydrogenase -
  BSG32_RS16220 (BSG32_16230) aceF 3212298..3214187 (-) 1890 WP_089190213.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  BSG32_RS16225 (BSG32_16235) aceE 3214207..3216870 (-) 2664 WP_021450014.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  BSG32_RS16230 (BSG32_16240) pdhR 3216919..3217686 (-) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  BSG32_RS16235 (BSG32_16245) ampD 3218092..3218643 (-) 552 WP_005462574.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  BSG32_RS16240 (BSG32_16250) nadC 3218736..3219623 (+) 888 WP_021450015.1 carboxylating nicotinate-nucleotide diphosphorylase -
  BSG32_RS16245 (BSG32_16255) - 3219887..3220351 (+) 465 WP_021450016.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  BSG32_RS16250 (BSG32_16260) pilB 3220351..3222036 (+) 1686 WP_021450017.1 type IV-A pilus assembly ATPase PilB Machinery gene
  BSG32_RS16255 (BSG32_16265) pilC 3222060..3223283 (+) 1224 WP_005479682.1 type II secretion system F family protein Machinery gene
  BSG32_RS16260 (BSG32_16270) pilD 3223348..3224217 (+) 870 WP_021450018.1 A24 family peptidase Machinery gene
  BSG32_RS16265 (BSG32_16275) coaE 3224218..3224832 (+) 615 WP_021450019.1 dephospho-CoA kinase -
  BSG32_RS16270 (BSG32_16280) zapD 3224860..3225600 (+) 741 WP_021450020.1 cell division protein ZapD -
  BSG32_RS16275 (BSG32_16285) yacG 3225669..3225863 (+) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  BSG32_RS16280 (BSG32_16290) rplS 3226257..3226610 (-) 354 WP_005462554.1 50S ribosomal protein L19 -
  BSG32_RS16285 (BSG32_16295) trmD 3226652..3227395 (-) 744 WP_005462562.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  BSG32_RS16290 (BSG32_16300) rimM 3227423..3227971 (-) 549 WP_005462552.1 ribosome maturation factor RimM -
  BSG32_RS16295 (BSG32_16305) rpsP 3228000..3228248 (-) 249 WP_005379962.1 30S ribosomal protein S16 -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 32409.53 Da        Isoelectric Point: 7.1970

>NTDB_id=240673 BSG32_RS16260 WP_021450018.1 3223348..3224217(+) (pilD) [Vibrio parahaemolyticus strain MAVP-R]
MEVFQYYPWLFVVFASIFGLIVGSFLNVVIYRLPKIMELEWRRECAESFPEYKIKPPQEVLTLSMPRSSCQNCATPIRIR
DNIPVISWLLLKGKCHHCHTAISPRYPLIELLTAACAGFVAYHFGFSYFTVALIFFTFVLIAATFIDLDTMLLPDQLTLP
LTWAGIALALTEISPVSLQDAVIGAIAGYLCLWSVYWGFKLLTGKEGMGYGDFKLLAALGAWLGWQSLPMIILLSSVVGV
IFGLVQLRLQKQGIEKAFPFGPYLAIAGWVSLIWGDQILSWYFTSILGV

Nucleotide


Download         Length: 870 bp        

>NTDB_id=240673 BSG32_RS16260 WP_021450018.1 3223348..3224217(+) (pilD) [Vibrio parahaemolyticus strain MAVP-R]
ATGGAAGTGTTCCAGTACTACCCTTGGCTATTCGTTGTGTTTGCCAGTATCTTCGGTTTAATTGTGGGTAGTTTTCTTAA
TGTGGTCATTTATCGGCTACCTAAAATCATGGAATTAGAATGGCGCCGTGAATGCGCCGAATCATTCCCTGAATATAAGA
TTAAGCCACCTCAAGAAGTTTTGACATTGAGCATGCCTCGCTCTTCGTGCCAAAACTGCGCGACGCCAATTCGTATTCGA
GACAATATTCCAGTAATCAGCTGGCTATTGTTAAAAGGAAAATGCCATCATTGTCATACCGCAATTAGTCCTCGCTATCC
GCTGATAGAATTACTCACTGCAGCGTGCGCTGGTTTTGTGGCTTATCATTTCGGCTTTAGCTACTTTACGGTTGCGTTAA
TCTTTTTCACATTTGTCTTAATAGCCGCGACTTTTATCGATCTCGATACTATGCTGCTACCGGACCAATTAACATTACCA
TTAACTTGGGCTGGCATTGCGTTAGCATTAACAGAAATAAGCCCTGTTAGTCTACAAGACGCCGTAATTGGTGCGATTGC
CGGTTATTTATGTCTTTGGTCAGTATATTGGGGTTTCAAACTGCTTACTGGTAAAGAAGGCATGGGTTACGGTGATTTTA
AATTGCTGGCTGCCCTTGGCGCTTGGCTAGGATGGCAATCATTACCAATGATCATCCTACTTTCTTCCGTCGTCGGTGTG
ATATTCGGGCTCGTTCAGTTACGACTACAAAAACAAGGTATAGAGAAAGCTTTCCCTTTCGGCCCATATTTAGCGATTGC
AGGATGGGTAAGCTTAATCTGGGGCGATCAAATTCTAAGTTGGTACTTCACGTCAATTTTAGGGGTGTAA

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 campbellii strain DS40M4

89.273

100

0.893
  pilD Vibrio cholerae strain A1552

73.611

99.654

0.734
  pilD Acinetobacter baumannii D1279779

52.612

92.734

0.488
  pilD Acinetobacter nosocomialis M2

52.239

92.734

0.484
  pilD Neisseria gonorrhoeae MS11

46.739

95.502

0.446

Multiple sequence alignment