Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   H9L11_RS03685 Genome accession   NZ_CP060589
Coordinates   803964..804833 (+) Length   289 a.a.
NCBI ID   WP_017635919.1    Uniprot ID   A0A2I3C9C8
Organism   Vibrio sp. sp1     
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 791213..808892 803964..804833 within 0


Gene organization within MGE regions


Location: 791213..808892
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  H9L11_RS03640 (H9L11_03640) lpdA 791213..792640 (-) 1428 WP_005379993.1 dihydrolipoyl dehydrogenase -
  H9L11_RS03645 (H9L11_03645) aceF 792908..794800 (-) 1893 WP_033905589.1 pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase -
  H9L11_RS03650 (H9L11_03650) aceE 794820..797483 (-) 2664 WP_005386612.1 pyruvate dehydrogenase (acetyl-transferring), homodimeric type -
  H9L11_RS03655 (H9L11_03655) pdhR 797532..798299 (-) 768 WP_005379989.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  H9L11_RS03660 (H9L11_03660) ampD 798705..799256 (-) 552 WP_005386614.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  H9L11_RS03665 (H9L11_03665) nadC 799349..800236 (+) 888 WP_033905590.1 carboxylating nicotinate-nucleotide diphosphorylase -
  H9L11_RS03670 (H9L11_03670) pilA 800499..800963 (+) 465 WP_033905592.1 prepilin-type N-terminal cleavage/methylation domain-containing protein Machinery gene
  H9L11_RS03675 (H9L11_03675) pilB 800967..802652 (+) 1686 WP_033905593.1 type IV-A pilus assembly ATPase PilB Machinery gene
  H9L11_RS03680 (H9L11_03680) pilC 802676..803899 (+) 1224 WP_205390996.1 type II secretion system F family protein Machinery gene
  H9L11_RS03685 (H9L11_03685) pilD 803964..804833 (+) 870 WP_017635919.1 A24 family peptidase Machinery gene
  H9L11_RS03690 (H9L11_03690) coaE 804834..805448 (+) 615 WP_017635920.1 dephospho-CoA kinase -
  H9L11_RS03695 (H9L11_03695) zapD 805476..806216 (+) 741 WP_005373086.1 cell division protein ZapD -
  H9L11_RS03700 (H9L11_03700) yacG 806375..806569 (+) 195 WP_017635922.1 DNA gyrase inhibitor YacG -
  H9L11_RS03705 (H9L11_03705) rplS 806882..807235 (-) 354 WP_005379971.1 50S ribosomal protein L19 -
  H9L11_RS03710 (H9L11_03710) trmD 807277..808038 (-) 762 WP_033905595.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  H9L11_RS03715 (H9L11_03715) rimM 808066..808614 (-) 549 WP_005379964.1 ribosome maturation factor RimM -
  H9L11_RS03720 (H9L11_03720) rpsP 808644..808892 (-) 249 WP_005379962.1 30S ribosomal protein S16 -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 32563.76 Da        Isoelectric Point: 6.8450

>NTDB_id=476752 H9L11_RS03685 WP_017635919.1 803964..804833(+) (pilD) [Vibrio sp. sp1]
MEVFQYYPWLFVVFATIFGLIVGSFLNVVIYRLPKIMELEWRRECAESFPEYKIEPPKEVLTLSVPRSSCQKCATPIRIR
DNIPVISWLLLKGKCHNCQATISARYPLIELLTAFCSGFIAYYFGFSYFTVALLFFTFILIAATFIDLDTMLLPDQLTLP
LTWAGIALALVEISPVTLQDSVIGAIAGYLCLWSVYWGFKLLTGKEGMGYGDFKLLAALGAWLGWQSLPMIILLSSVVGI
VFGIIQLRLQKQGIEKAFPFGPYLAIAGWISLIWGDQILNWYFTSVLGV

Nucleotide


Download         Length: 870 bp        

>NTDB_id=476752 H9L11_RS03685 WP_017635919.1 803964..804833(+) (pilD) [Vibrio sp. sp1]
ATGGAAGTATTCCAGTACTACCCTTGGCTATTCGTTGTGTTTGCCACCATCTTCGGTCTTATCGTGGGTAGCTTCCTCAA
TGTGGTTATTTATCGACTACCTAAAATCATGGAACTAGAATGGCGACGCGAATGTGCCGAGTCATTTCCTGAATACAAAA
TAGAACCTCCTAAAGAAGTGCTGACCTTGAGCGTCCCACGCTCCTCCTGCCAGAAATGCGCAACACCGATACGTATTCGC
GACAACATTCCTGTGATTAGCTGGCTGCTTTTAAAAGGCAAATGTCACAACTGTCAGGCAACCATTAGTGCACGCTATCC
ACTGATTGAACTGCTCACCGCGTTCTGTTCAGGCTTTATCGCTTATTACTTTGGTTTTAGTTACTTTACCGTTGCCCTAC
TCTTTTTTACTTTTATCTTAATCGCCGCAACATTTATCGATCTCGATACTATGTTGTTACCTGACCAATTAACATTACCA
TTAACTTGGGCTGGCATTGCCTTAGCATTAGTCGAAATAAGTCCTGTTACTCTACAAGATTCTGTCATTGGTGCTATTGC
TGGTTACCTATGTCTCTGGTCCGTTTACTGGGGCTTTAAGCTACTTACTGGTAAAGAAGGAATGGGGTATGGTGATTTTA
AACTACTGGCGGCACTAGGAGCTTGGCTAGGTTGGCAGTCACTGCCGATGATCATTCTACTTTCTTCTGTGGTTGGCATC
GTATTTGGCATCATTCAACTACGCTTGCAAAAGCAGGGAATTGAAAAAGCTTTCCCTTTCGGTCCTTACTTAGCAATTGC
TGGTTGGATAAGCTTAATTTGGGGCGACCAGATTTTAAACTGGTACTTTACTTCAGTTCTAGGAGTGTAA

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 A0A2I3C9C8

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

91.349

100

0.913
  pilD Vibrio cholerae strain A1552

73.264

99.654

0.73
  pilD Acinetobacter baumannii D1279779

52.222

93.426

0.488
  pilD Acinetobacter nosocomialis M2

51.852

93.426

0.484
  pilD Neisseria gonorrhoeae MS11

47.653

95.848

0.457