Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   QQA13_RS12235 Genome accession   NZ_CP127409
Coordinates   2632135..2632992 (+) Length   285 a.a.
NCBI ID   WP_108470816.1    Uniprot ID   -
Organism   Rhodanobacter thiooxydans strain C33     
Function   assembly of type IV pilus (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 2618899..2632116 2632135..2632992 flank 19


Gene organization within MGE regions


Location: 2618899..2632992
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  QQA13_RS12170 - 2618899..2620872 (+) 1974 WP_108470967.1 hypothetical protein -
  QQA13_RS12175 - 2620869..2622119 (+) 1251 WP_108470806.1 oligosaccharide flippase family protein -
  QQA13_RS12180 - 2622116..2623087 (-) 972 WP_286042671.1 glycosyltransferase -
  QQA13_RS12185 - 2622972..2623778 (-) 807 WP_199909804.1 TylF/MycF family methyltransferase -
  QQA13_RS12190 - 2623908..2624948 (-) 1041 WP_108470809.1 glycosyltransferase family 4 protein -
  QQA13_RS12195 - 2624945..2626141 (-) 1197 WP_108470810.1 glycosyltransferase family 4 protein -
  QQA13_RS12200 - 2626134..2626847 (-) 714 WP_108470811.1 class I SAM-dependent methyltransferase -
  QQA13_RS12205 - 2626859..2627719 (-) 861 WP_108470812.1 glycosyltransferase family 2 protein -
  QQA13_RS12210 - 2627748..2627903 (-) 156 WP_234411269.1 hypothetical protein -
  QQA13_RS12215 - 2628021..2628080 (-) 60 WP_234411286.1 hypothetical protein -
  QQA13_RS12220 pilB 2628490..2630214 (+) 1725 WP_108470813.1 type IV-A pilus assembly ATPase PilB Machinery gene
  QQA13_RS12225 pilC 2630360..2631631 (+) 1272 WP_108470814.1 type II secretion system F family protein Machinery gene
  QQA13_RS12230 - 2631724..2632116 (+) 393 WP_108470815.1 endonuclease domain-containing protein -
  QQA13_RS12235 pilD 2632135..2632992 (+) 858 WP_108470816.1 A24 family peptidase Machinery gene

Sequence

Protein


Download         Length: 285 a.a.        Molecular weight: 31011.20 Da        Isoelectric Point: 8.4990

>NTDB_id=844171 QQA13_RS12235 WP_108470816.1 2632135..2632992(+) (pilD) [Rhodanobacter thiooxydans strain C33]
MPELPLVLWIALAGVLGLLVGSFLNVVILRLPERMAAAWRQEAREVLELQADATPLPPGIVREPSHCPHCKHPLSARDNI
PLFGWLLLRGHCRYCQAKISIQYPLVELLSGVLSAVVVWKFGPSWAALAGLALTWTLIALSGVDFRTQLLPDQLTLPLLW
LGLLLSLLPMFVTAPASILAAAIGYLSLWSVYWAFKLLTGKEGMGHGDFKLLAALGAWMGPVSLLPIILLSSLIGALVGG
ILIALRRHEREIPMPFGPFLAAAGWVWFVAGADLLQGYMQLTGLR

Nucleotide


Download         Length: 858 bp        

>NTDB_id=844171 QQA13_RS12235 WP_108470816.1 2632135..2632992(+) (pilD) [Rhodanobacter thiooxydans strain C33]
ATGCCCGAACTTCCCCTTGTCCTGTGGATCGCCCTGGCCGGCGTGCTCGGCCTGCTGGTGGGCAGCTTTCTCAACGTGGT
GATCCTGCGGCTGCCCGAGCGGATGGCCGCGGCATGGCGGCAGGAGGCACGGGAGGTGCTGGAGCTGCAGGCTGATGCCA
CGCCGCTGCCGCCGGGCATCGTGCGCGAGCCGTCGCACTGTCCGCACTGCAAGCATCCGCTGTCGGCGCGGGACAACATC
CCGCTGTTCGGCTGGCTGCTGCTGCGCGGGCACTGCCGTTACTGCCAGGCGAAGATCTCGATCCAGTACCCGCTGGTGGA
ACTGCTCAGCGGCGTGCTGAGCGCGGTGGTCGTGTGGAAGTTCGGCCCGTCGTGGGCTGCGCTGGCCGGGCTGGCGCTGA
CCTGGACCTTGATCGCGCTGTCCGGCGTCGACTTCCGCACCCAGCTGCTGCCCGACCAGCTCACCCTGCCGCTGCTGTGG
CTGGGCCTGCTGCTGTCGCTGCTGCCGATGTTCGTCACCGCGCCAGCGTCGATCCTGGCCGCGGCGATCGGCTACCTGAG
CCTGTGGAGCGTGTACTGGGCATTCAAGCTGCTCACCGGCAAGGAGGGCATGGGCCACGGCGATTTCAAGCTGCTCGCCG
CACTGGGCGCATGGATGGGGCCGGTATCGCTGTTGCCGATCATCCTGCTGTCGTCACTGATCGGCGCGCTGGTCGGTGGC
ATCCTGATCGCGCTGCGCCGGCACGAGCGCGAGATCCCGATGCCGTTCGGCCCGTTCCTCGCCGCCGCCGGCTGGGTCTG
GTTCGTAGCCGGCGCGGATCTGCTGCAGGGTTACATGCAGCTGACTGGCCTGCGGTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(15-121)

Type IV leader peptidase family (Peptidase_A24)

(132-239)


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

50.183

95.789

0.481
  pilD Acinetobacter nosocomialis M2

49.817

95.789

0.477
  pilD Vibrio campbellii strain DS40M4

49.635

96.14

0.477
  pilD Acinetobacter baumannii D1279779

49.451

95.789

0.474
  pilD Neisseria gonorrhoeae MS11

49.81

92.281

0.46