Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilA   Type   Machinery gene
Locus tag   VAPA_RS26480 Genome accession   NC_022247
Coordinates   5673352..5673813 (-) Length   153 a.a.
NCBI ID   WP_021013069.1    Uniprot ID   T1XJY3
Organism   Variovorax paradoxus B4     
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 5646868..5673813 5673352..5673813 within 0


Gene organization within MGE regions


Location: 5646868..5673813
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  VAPA_RS26395 (VAPA_1c53700) - 5646868..5647347 (+) 480 WP_021013047.1 type IV pilin protein -
  VAPA_RS26400 (VAPA_1c53710) - 5647355..5647966 (+) 612 WP_021013048.1 GspH/FimT family pseudopilin -
  VAPA_RS26405 (VAPA_1c53720) - 5648062..5648427 (+) 366 WP_230559046.1 pilus assembly protein PilV -
  VAPA_RS26410 (VAPA_1c53730) - 5648441..5649664 (-) 1224 WP_021003967.1 IS110 family transposase -
  VAPA_RS26415 (VAPA_1c53740) - 5649903..5651042 (+) 1140 WP_041946261.1 PilW family protein -
  VAPA_RS26420 (VAPA_1c53750) - 5651052..5651750 (+) 699 WP_021013051.1 hypothetical protein -
  VAPA_RS34100 (VAPA_1c53760) - 5651793..5655689 (+) 3897 WP_021013052.1 pilus assembly protein -
  VAPA_RS34940 (VAPA_1c53770) - 5656092..5656349 (+) 258 WP_021013053.1 energy transducer TonB -
  VAPA_RS26435 (VAPA_1c53780) - 5656496..5657092 (-) 597 WP_021013054.1 sugar transferase -
  VAPA_RS26440 (VAPA_1c53790) - 5657102..5658265 (-) 1164 WP_021013055.1 DegT/DnrJ/EryC1/StrS family aminotransferase -
  VAPA_RS26445 (VAPA_1c53800) - 5658278..5658856 (-) 579 WP_230558936.1 class I SAM-dependent methyltransferase -
  VAPA_RS26450 (VAPA_1c53810) - 5658985..5660169 (-) 1185 WP_329604091.1 glycosyltransferase family 4 protein -
  VAPA_RS34105 (VAPA_1c53820) - 5660321..5661487 (-) 1167 WP_329604092.1 glycosyltransferase -
  VAPA_RS34110 (VAPA_1c53830) - 5661415..5662104 (-) 690 WP_021013059.1 class I SAM-dependent methyltransferase -
  VAPA_RS34115 (VAPA_1c53840) - 5662091..5663101 (-) 1011 WP_196232533.1 glycosyltransferase -
  VAPA_RS34120 (VAPA_1c53850) - 5663446..5664120 (-) 675 WP_021013061.1 class I SAM-dependent methyltransferase -
  VAPA_RS34125 (VAPA_1c53860) - 5664140..5665594 (-) 1455 WP_021013062.1 lipopolysaccharide biosynthesis protein -
  VAPA_RS26460 (VAPA_1c53870) - 5665658..5666755 (-) 1098 WP_041946263.1 DegT/DnrJ/EryC1/StrS family aminotransferase -
  VAPA_RS34130 (VAPA_1c53880) - 5666764..5667339 (-) 576 WP_021013064.1 acyltransferase -
  VAPA_RS26465 (VAPA_1c53890) - 5667336..5668283 (-) 948 WP_021013065.1 Gfo/Idh/MocA family protein -
  VAPA_RS26470 (VAPA_1c53900) - 5668291..5669595 (-) 1305 WP_021013066.1 nucleotide sugar dehydrogenase -
  VAPA_RS26475 (VAPA_1c53910) - 5669588..5671522 (-) 1935 WP_021013067.1 polysaccharide biosynthesis protein -
  VAPA_RS34135 (VAPA_1c53920) - 5671573..5673054 (-) 1482 WP_155248097.1 PglL family O-oligosaccharyltransferase -
  VAPA_RS26480 (VAPA_1c53930) pilA 5673352..5673813 (-) 462 WP_021013069.1 pilin Machinery gene

Sequence

Protein


Download         Length: 153 a.a.        Molecular weight: 15609.17 Da        Isoelectric Point: 9.9702

>NTDB_id=61942 VAPA_RS26480 WP_021013069.1 5673352..5673813(-) (pilA) [Variovorax paradoxus B4]
MNRRLIARNVQKGFTLIELMIVVAIIGILAAVALPAYQDYTVRARVTEALVIASGAKANIAENAANGASLDAGVEPIAAA
SGLKNLSTMSTATASGVITLVTTAAAKSLTLTLTPTSNGAALVNGTLPAGPIKWTCTVTGQANNKYVPTECRI

Nucleotide


Download         Length: 462 bp        

>NTDB_id=61942 VAPA_RS26480 WP_021013069.1 5673352..5673813(-) (pilA) [Variovorax paradoxus B4]
ATGAACCGTCGTTTGATTGCGCGTAACGTGCAAAAGGGTTTCACCCTTATCGAATTGATGATCGTTGTGGCGATCATTGG
TATTTTGGCTGCTGTAGCTCTGCCCGCCTATCAAGACTATACCGTTCGTGCACGCGTTACCGAAGCACTGGTGATTGCAT
CTGGCGCCAAGGCAAACATCGCTGAAAATGCCGCCAATGGCGCGTCGCTCGATGCTGGCGTTGAGCCGATCGCTGCTGCT
TCTGGCCTGAAAAACCTTTCGACGATGTCCACGGCAACGGCTAGTGGCGTGATCACTTTGGTGACCACTGCTGCCGCAAA
GAGCTTGACTCTCACCCTCACTCCAACGTCGAACGGCGCGGCGTTAGTTAACGGCACATTGCCGGCCGGCCCGATTAAAT
GGACCTGCACGGTCACGGGGCAGGCGAATAACAAATACGTGCCGACCGAGTGCCGTATCTAA

Domains

Predicted by InterproScan.

Prokaryotic N-terminal methylation motif (N_methyl)

(8-34)

Pilin (bacterial filament) (Pilin)

(42-152)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB T1XJY3

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
  pilA Ralstonia pseudosolanacearum GMI1000

50

100

0.536
  comP Acinetobacter baylyi ADP1

45.223

100

0.464
  pilA2 Legionella pneumophila str. Paris

47.973

96.732

0.464
  pilA2 Legionella pneumophila strain ERS1305867

47.973

96.732

0.464
  pilA/pilA1 Eikenella corrodens VA1

40.625

100

0.425
  pilE Neisseria gonorrhoeae strain FA1090

38.922

100

0.425
  pilA Vibrio campbellii strain DS40M4

40

100

0.405
  pilE Neisseria gonorrhoeae MS11

37.195

100

0.399
  pilA/pilAI Pseudomonas stutzeri DSM 10701

38

98.039

0.373

Multiple sequence alignment