Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ELR50_RS12670 Genome accession   NZ_CP034688
Coordinates   2869387..2870259 (+) Length   290 a.a.
NCBI ID   WP_269964082.1    Uniprot ID   -
Organism   Pseudomonas citronellolis strain WXP-4     
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 2850394..2870259 2869387..2870259 within 0


Gene organization within MGE regions


Location: 2850394..2870259
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ELR50_RS12550 (ELR50_12475) - 2850394..2851590 (+) 1197 WP_269964071.1 type II toxin-antitoxin system HipA family toxin -
  ELR50_RS12555 (ELR50_12480) - 2851778..2851927 (-) 150 WP_237770692.1 DUF433 domain-containing protein -
  ELR50_RS12560 (ELR50_12485) - 2852075..2852416 (-) 342 WP_043318088.1 type II toxin-antitoxin system HicB family antitoxin -
  ELR50_RS12565 (ELR50_12490) - 2852413..2852664 (-) 252 WP_269964072.1 type II toxin-antitoxin system HicA family toxin -
  ELR50_RS12570 (ELR50_12500) - 2852911..2853984 (-) 1074 WP_269964073.1 diguanylate cyclase -
  ELR50_RS12575 (ELR50_12505) - 2854304..2855518 (+) 1215 WP_269964074.1 site-specific integrase -
  ELR50_RS12580 (ELR50_12510) - 2855515..2856210 (-) 696 WP_156060094.1 hypothetical protein -
  ELR50_RS12585 (ELR50_12515) - 2856209..2856409 (+) 201 WP_043272284.1 helix-turn-helix domain-containing protein -
  ELR50_RS12590 - 2856406..2856534 (+) 129 WP_256204891.1 hypothetical protein -
  ELR50_RS12595 (ELR50_12520) - 2856531..2856800 (+) 270 WP_269964075.1 hypothetical protein -
  ELR50_RS12600 (ELR50_12525) - 2856797..2857099 (+) 303 WP_269964076.1 hypothetical protein -
  ELR50_RS12605 (ELR50_12530) - 2857223..2857423 (+) 201 WP_043272281.1 helix-turn-helix domain-containing protein -
  ELR50_RS12610 (ELR50_12535) - 2857477..2857869 (+) 393 WP_218187152.1 hypothetical protein -
  ELR50_RS12615 (ELR50_12540) - 2858763..2859989 (+) 1227 WP_269964077.1 phage major capsid protein -
  ELR50_RS12620 (ELR50_12545) - 2860148..2860348 (+) 201 WP_043272279.1 hypothetical protein -
  ELR50_RS12625 (ELR50_12550) - 2860358..2860699 (+) 342 WP_269964078.1 HNH endonuclease -
  ELR50_RS12630 (ELR50_12555) - 2860770..2861252 (+) 483 WP_043272278.1 HK97-gp10 family putative phage morphogenesis protein -
  ELR50_RS12635 (ELR50_12560) - 2861262..2863616 (+) 2355 WP_269964079.1 phage tail tape measure protein -
  ELR50_RS12645 (ELR50_12570) - 2863997..2864650 (-) 654 WP_082656963.1 methyltransferase family protein -
  ELR50_RS12650 (ELR50_12575) - 2864659..2865630 (-) 972 WP_152989201.1 hypothetical protein -
  ELR50_RS12655 (ELR50_12580) comP 2865784..2866230 (-) 447 WP_082656964.1 pilin Machinery gene
  ELR50_RS12660 (ELR50_12585) pilB 2866460..2868163 (+) 1704 WP_269964080.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ELR50_RS12665 (ELR50_12590) pilC 2868167..2869384 (+) 1218 WP_269964081.1 type II secretion system F family protein Machinery gene
  ELR50_RS12670 (ELR50_12595) pilD 2869387..2870259 (+) 873 WP_269964082.1 prepilin peptidase Machinery gene

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31946.85 Da        Isoelectric Point: 6.4778

>NTDB_id=332539 ELR50_RS12670 WP_269964082.1 2869387..2870259(+) (pilD) [Pseudomonas citronellolis strain WXP-4]
MPVLDFLASHALAFVLCAALLGLLVGSFLNVVIHRLPKMMELEWQQQARDALSLPQPEQEPTYNLVLPNSACPHCGHEIR
AWENIPVISYLALRGKCSACKAPISARYPLVELATALLSGFVAWHFGFTWQAGAMLLLTWGLLAMSLIDVDHQLLPDALV
LPLLWLGLIVNYFGLFTSLGDALWGAVFGYLSLWSVYWLFKLLTGKEGMGYGDFKLLAMLGAWGGWQVLPLTILFSSLVG
AVLGVILLRLRNAETSTPIPFGPYLAIAGWIALLWGDQITTTYLQFAGFR

Nucleotide


Download         Length: 873 bp        

>NTDB_id=332539 ELR50_RS12670 WP_269964082.1 2869387..2870259(+) (pilD) [Pseudomonas citronellolis strain WXP-4]
ATGCCTGTACTCGACTTCCTGGCCAGCCACGCGCTGGCCTTTGTTTTATGCGCGGCCTTGCTCGGCCTTCTGGTCGGTAG
CTTCCTCAACGTGGTCATCCATCGCCTGCCGAAGATGATGGAACTGGAGTGGCAGCAACAAGCGCGTGACGCTCTTTCCC
TGCCTCAGCCTGAGCAGGAGCCCACCTACAACCTGGTCCTACCCAACTCGGCGTGCCCGCACTGCGGCCATGAGATTCGC
GCCTGGGAGAACATCCCCGTCATCAGCTACCTGGCCCTGCGCGGCAAGTGCTCGGCCTGTAAGGCGCCGATCAGTGCGCG
CTATCCGCTGGTCGAGCTGGCCACCGCCCTGCTTTCCGGTTTCGTTGCCTGGCACTTCGGTTTTACCTGGCAGGCAGGGG
CCATGCTGTTGCTGACCTGGGGGCTGTTGGCCATGAGCCTGATCGACGTCGACCACCAGTTGTTGCCGGATGCGCTGGTT
CTACCGCTGCTCTGGCTGGGGTTGATTGTCAATTATTTCGGGCTTTTCACCAGCCTGGGCGATGCGCTCTGGGGTGCGGT
GTTCGGTTACCTGAGCCTGTGGTCGGTGTACTGGCTGTTCAAGCTGCTGACCGGCAAGGAAGGCATGGGTTATGGCGACT
TCAAGCTGCTGGCCATGCTCGGCGCCTGGGGTGGCTGGCAGGTGTTGCCGCTGACCATTCTGTTCTCGTCCCTGGTCGGG
GCCGTGCTGGGTGTCATTCTGCTGCGTCTGCGCAATGCCGAGACCAGCACGCCGATCCCCTTCGGGCCCTATCTGGCCAT
CGCCGGCTGGATTGCGCTGCTCTGGGGTGATCAAATAACCACTACCTATCTGCAGTTCGCCGGTTTCCGGTAG

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)

Type IV leader peptidase family (Peptidase_A24)

(137-245)


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

58.182

94.828

0.552
  pilD Vibrio campbellii strain DS40M4

57.455

94.828

0.545
  pilD Acinetobacter baumannii D1279779

53.71

97.586

0.524
  pilD Acinetobacter nosocomialis M2

53.004

97.586

0.517
  pilD Neisseria gonorrhoeae MS11

50.951

90.69

0.462

Multiple sequence alignment