Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   EXZ61_RS16310 Genome accession   NZ_CP036282
Coordinates   3541811..3542653 (+) Length   280 a.a.
NCBI ID   WP_142814282.1    Uniprot ID   -
Organism   Rhodoferax aquaticus strain Gr-4     
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 3534630..3553286 3541811..3542653 within 0


Gene organization within MGE regions


Location: 3534630..3553286
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  EXZ61_RS16275 (EXZ61_16285) proB 3534630..3535766 (-) 1137 WP_142812761.1 glutamate 5-kinase -
  EXZ61_RS16280 (EXZ61_16290) cgtA 3535821..3536903 (-) 1083 WP_142812762.1 Obg family GTPase CgtA -
  EXZ61_RS16285 (EXZ61_16295) rpmA 3536975..3537232 (-) 258 WP_142812763.1 50S ribosomal protein L27 -
  EXZ61_RS16290 (EXZ61_16300) rplU 3537245..3537556 (-) 312 WP_142812764.1 50S ribosomal protein L21 -
  EXZ61_RS16295 (EXZ61_16305) - 3537769..3538698 (+) 930 WP_142814281.1 polyprenyl synthetase family protein -
  EXZ61_RS16300 (EXZ61_16310) pilB 3538842..3540575 (+) 1734 WP_142812765.1 type IV-A pilus assembly ATPase PilB Machinery gene
  EXZ61_RS16305 (EXZ61_16315) pilC 3540594..3541811 (+) 1218 WP_142812766.1 type II secretion system F family protein Machinery gene
  EXZ61_RS16310 (EXZ61_16320) pilD 3541811..3542653 (+) 843 WP_142814282.1 A24 family peptidase Machinery gene
  EXZ61_RS16315 (EXZ61_16325) coaE 3542654..3543268 (+) 615 WP_142812767.1 dephospho-CoA kinase -
  EXZ61_RS16320 (EXZ61_16330) zapD 3543291..3544046 (+) 756 WP_142814283.1 cell division protein ZapD -
  EXZ61_RS16325 (EXZ61_16335) - 3544043..3544252 (+) 210 WP_142812768.1 DNA gyrase inhibitor YacG -
  EXZ61_RS16330 (EXZ61_16340) - 3544333..3544794 (-) 462 WP_142812769.1 NUDIX domain-containing protein -
  EXZ61_RS16335 (EXZ61_16345) - 3544799..3545680 (-) 882 WP_142812770.1 ATP-binding protein -
  EXZ61_RS16340 (EXZ61_16350) argJ 3545694..3546923 (-) 1230 WP_142812771.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -
  EXZ61_RS16345 (EXZ61_16355) secA 3546933..3549698 (-) 2766 WP_142812772.1 preprotein translocase subunit SecA -
  EXZ61_RS16350 (EXZ61_16360) - 3549901..3550836 (-) 936 WP_142812773.1 M23 family metallopeptidase -
  EXZ61_RS22200 (EXZ61_16365) - 3550861..3551175 (+) 315 WP_142812774.1 hypothetical protein -
  EXZ61_RS16365 (EXZ61_16375) - 3551327..3551803 (-) 477 WP_142812775.1 ClpXP protease specificity-enhancing factor -
  EXZ61_RS16370 (EXZ61_16380) - 3551812..3552423 (-) 612 WP_142812776.1 glutathione S-transferase N-terminal domain-containing protein -
  EXZ61_RS16375 (EXZ61_16385) - 3552528..3553286 (-) 759 WP_142812777.1 cytochrome c1 -

Sequence

Protein


Download         Length: 280 a.a.        Molecular weight: 30678.20 Da        Isoelectric Point: 6.2122

>NTDB_id=347855 EXZ61_RS16310 WP_142814282.1 3541811..3542653(+) (pilD) [Rhodoferax aquaticus strain Gr-4]
MLESADIYLVLAAILGLLIGSFLNVVIYRLPKMLEIEWAADCEPNSDMGRGKADTFNLVVPRSSCPHCGHQITWYENIPL
FSYLALRGRCSQCQAKISVRYPLIEVTAAALFYHCADTWGMTYSAMAWASFASILLALACIDWDTTLLPDVLTLPLLWLG
LVAASLQWTQVSLFSSLWGAVAGYLSLWIVYWVFKIVTGKEGMGYGDFKLFAALGAWFGWQGLIPIILLSSVIGAIIGIG
MKYSSGLREGGYIPFGPFLAGAGFAMLVLGPYQISRFLGI

Nucleotide


Download         Length: 843 bp        

>NTDB_id=347855 EXZ61_RS16310 WP_142814282.1 3541811..3542653(+) (pilD) [Rhodoferax aquaticus strain Gr-4]
ATGCTTGAATCTGCGGATATCTATCTAGTACTGGCGGCAATATTGGGATTGTTAATCGGCAGCTTCTTGAATGTGGTGAT
TTACAGATTGCCAAAGATGCTTGAGATTGAATGGGCGGCGGACTGCGAACCAAATAGCGACATGGGGCGAGGAAAAGCAG
ATACCTTCAATCTGGTAGTACCCCGCTCAAGCTGCCCTCATTGTGGACACCAGATCACTTGGTATGAAAACATCCCTTTA
TTCAGTTACTTGGCATTGAGAGGAAGATGCAGTCAATGCCAAGCAAAAATAAGTGTTCGTTACCCCCTGATTGAAGTTAC
AGCCGCAGCACTGTTCTATCATTGTGCCGATACGTGGGGCATGACTTACTCCGCAATGGCATGGGCATCGTTTGCTTCTA
TTTTGCTAGCTCTCGCATGTATTGACTGGGACACAACTTTACTGCCTGATGTGTTGACGCTACCGCTGCTTTGGCTTGGG
CTCGTTGCAGCAAGCTTGCAATGGACTCAGGTGAGCCTGTTCTCCTCTCTTTGGGGCGCGGTTGCGGGTTACTTGTCGCT
ATGGATCGTCTATTGGGTGTTCAAAATCGTGACTGGTAAGGAGGGCATGGGGTACGGTGATTTCAAGCTTTTTGCGGCGC
TTGGAGCTTGGTTTGGCTGGCAAGGTTTGATACCGATAATTCTCTTGTCCTCCGTTATTGGGGCAATCATTGGAATTGGC
ATGAAGTACAGCTCGGGTCTGCGGGAGGGTGGCTACATCCCTTTCGGCCCATTTTTGGCCGGCGCGGGTTTCGCAATGCT
AGTACTTGGCCCATATCAAATTTCTAGATTCCTGGGGATTTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(131-239)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(14-116)


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

52.612

95.714

0.504
  pilD Vibrio cholerae strain A1552

52.652

94.286

0.496
  pilD Acinetobacter nosocomialis M2

44.853

97.143

0.436
  pilD Acinetobacter baumannii D1279779

44.853

97.143

0.436
  pilD Neisseria gonorrhoeae MS11

47.843

91.071

0.436

Multiple sequence alignment