Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   M1V28_RS24735 Genome accession   NZ_CP096822
Coordinates   5355813..5356685 (+) Length   290 a.a.
NCBI ID   WP_019726811.1    Uniprot ID   -
Organism   Pseudomonas aeruginosa strain NY8709     
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 5334611..5355810 5355813..5356685 flank 3


Gene organization within MGE regions


Location: 5334611..5356685
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  M1V28_RS24585 (M1V28_24545) - 5334611..5335327 (-) 717 WP_073624880.1 hypothetical protein -
  M1V28_RS24590 (M1V28_24550) - 5335476..5335676 (+) 201 WP_023435053.1 helix-turn-helix domain-containing protein -
  M1V28_RS24595 (M1V28_24555) - 5335673..5336089 (+) 417 WP_023435054.1 hypothetical protein -
  M1V28_RS24600 (M1V28_24560) - 5336082..5336315 (+) 234 WP_023110507.1 hypothetical protein -
  M1V28_RS24605 (M1V28_24565) - 5336312..5336560 (+) 249 WP_023435055.1 hypothetical protein -
  M1V28_RS24610 (M1V28_24570) - 5336557..5336862 (+) 306 WP_023109345.1 hypothetical protein -
  M1V28_RS32965 - 5336865..5337302 (+) 438 WP_305954514.1 hypothetical protein -
  M1V28_RS24620 (M1V28_24580) - 5337341..5337808 (+) 468 WP_031285502.1 hypothetical protein -
  M1V28_RS24625 (M1V28_24585) - 5337815..5338768 (+) 954 WP_306279704.1 DUF3631 domain-containing protein -
  M1V28_RS24630 (M1V28_24590) - 5338768..5339061 (+) 294 WP_023435057.1 hypothetical protein -
  M1V28_RS24635 (M1V28_24595) - 5339117..5340019 (+) 903 WP_023435058.1 hypothetical protein -
  M1V28_RS24640 (M1V28_24600) - 5340943..5341107 (+) 165 WP_153519866.1 hypothetical protein -
  M1V28_RS24645 (M1V28_24605) - 5341124..5342716 (+) 1593 WP_079383750.1 anti-phage dCTP deaminase -
  M1V28_RS24650 (M1V28_24610) - 5343438..5343944 (-) 507 WP_003096122.1 GNAT family N-acetyltransferase -
  M1V28_RS24655 (M1V28_24615) - 5344404..5344646 (-) 243 WP_003096120.1 hypothetical protein -
  M1V28_RS24660 (M1V28_24620) - 5344697..5344966 (+) 270 WP_073646154.1 hypothetical protein -
  M1V28_RS24665 (M1V28_24625) - 5344966..5345202 (+) 237 WP_003096116.1 hypothetical protein -
  M1V28_RS24670 (M1V28_24630) - 5345409..5345690 (-) 282 WP_023435065.1 hypothetical protein -
  M1V28_RS24675 (M1V28_24635) - 5345887..5346585 (+) 699 WP_124014670.1 hypothetical protein -
  M1V28_RS24680 (M1V28_24640) - 5346610..5347614 (+) 1005 WP_031689993.1 pesticin C-terminus-like muramidase -
  M1V28_RS24685 (M1V28_24645) - 5347627..5348289 (+) 663 WP_033992423.1 DUF3218 family protein -
  M1V28_RS24690 (M1V28_24650) fliP 5348569..5349324 (+) 756 WP_031285507.1 flagellar type III secretion system pore protein FliP -
  M1V28_RS24695 (M1V28_24655) fliQ 5349369..5349638 (+) 270 WP_023435365.1 flagellar biosynthesis protein FliQ -
  M1V28_RS24700 (M1V28_24660) fliR 5349638..5350420 (+) 783 Protein_4893 flagellar biosynthetic protein FliR -
  M1V28_RS24705 (M1V28_24665) - 5350423..5350682 (+) 260 Protein_4894 EscU/YscU/HrcU family type III secretion system export apparatus switch protein -
  M1V28_RS24710 (M1V28_24670) - 5351712..5351954 (+) 243 WP_023082027.1 hypothetical protein -
  M1V28_RS24720 (M1V28_24680) - 5352185..5352658 (-) 474 WP_015503553.1 pilin -
  M1V28_RS24725 (M1V28_24685) pilB 5352889..5354589 (+) 1701 WP_003120945.1 type IV-A pilus assembly ATPase PilB Machinery gene
  M1V28_RS24730 (M1V28_24690) pilC 5354593..5355810 (+) 1218 WP_010792214.1 type II secretion system F family protein Machinery gene
  M1V28_RS24735 (M1V28_24695) pilD 5355813..5356685 (+) 873 WP_019726811.1 type IV prepilin peptidase/methyltransferase PilD Machinery gene

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31862.88 Da        Isoelectric Point: 7.2974

>NTDB_id=684486 M1V28_RS24735 WP_019726811.1 5355813..5356685(+) (pilD) [Pseudomonas aeruginosa strain NY8709]
MELLDYLASHPLAFVLCAILLGLLVGSFLNVVVHRLPKMMERNWKAEAREALGLEPEPKQATYNLVLPNSACPRCGHEIR
PWENIPLVSYLALGGKCSSCKAAIGKRYPLVELATALLSGYVAWQFGFTWQAGAMLLLTWGLLAMSLIDADHQLLPDVLV
LPLLWLGLIANHFGLFASLDDALFGAVFGYLSLWSVFWLFKLVTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AILGVIMLRLRNAESGTPIPFGPYLAIAGWIALLWGDQITRTYLQFAGFK

Nucleotide


Download         Length: 873 bp        

>NTDB_id=684486 M1V28_RS24735 WP_019726811.1 5355813..5356685(+) (pilD) [Pseudomonas aeruginosa strain NY8709]
ATGGAACTCCTCGACTACCTGGCCAGCCATCCGCTGGCCTTTGTCTTGTGCGCTATCCTCCTTGGCCTGCTGGTCGGCAG
CTTCCTCAACGTCGTCGTGCATCGCCTGCCGAAGATGATGGAGCGCAACTGGAAGGCCGAAGCCCGCGAAGCGCTCGGGC
TGGAGCCGGAACCCAAGCAGGCGACCTACAACCTGGTGCTGCCGAATTCGGCGTGCCCGCGCTGCGGCCACGAGATCCGC
CCCTGGGAAAACATCCCGCTGGTCAGCTACCTGGCGCTGGGCGGCAAGTGCTCGTCCTGCAAGGCCGCCATCGGCAAACG
CTACCCCCTGGTGGAACTGGCCACCGCGCTGCTTTCCGGCTACGTCGCCTGGCAATTCGGCTTCACCTGGCAGGCGGGCG
CGATGCTCCTGCTGACCTGGGGTCTGCTGGCGATGAGCCTGATCGATGCCGATCACCAACTGCTGCCGGACGTGCTGGTG
CTGCCGCTGCTCTGGCTGGGCCTGATCGCCAACCATTTCGGCCTCTTCGCCAGCCTCGACGATGCGCTGTTCGGCGCGGT
GTTCGGCTACCTGAGCCTGTGGTCGGTGTTCTGGCTGTTCAAGCTGGTGACCGGCAAGGAGGGCATGGGCTACGGCGACT
TCAAGCTGCTGGCCATGCTCGGTGCCTGGGGTGGCTGGCAGATCCTGCCGCTGACCATCCTGCTGTCGTCGCTGGTCGGG
GCGATCCTCGGGGTGATCATGCTGCGCCTGCGCAACGCCGAAAGCGGCACGCCGATCCCCTTCGGTCCCTATCTGGCTAT
TGCCGGGTGGATTGCTTTGCTCTGGGGTGATCAAATAACCCGGACCTATCTGCAATTCGCCGGATTCAAATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)


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

54.671

99.655

0.545
  pilD Vibrio campbellii strain DS40M4

53.147

98.621

0.524
  pilD Acinetobacter nosocomialis M2

50.352

97.931

0.493
  pilD Acinetobacter baumannii D1279779

50.352

97.931

0.493
  pilD Neisseria gonorrhoeae MS11

49.64

95.862

0.476