Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   P4B31_RS25560 Genome accession   NZ_CP120857
Coordinates   5450759..5451631 (+) Length   290 a.a.
NCBI ID   WP_003116251.1    Uniprot ID   -
Organism   Pseudomonas aeruginosa strain NY7570     
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 5431003..5450756 5450759..5451631 flank 3


Gene organization within MGE regions


Location: 5431003..5451631
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  P4B31_RS25450 (P4B31_25455) - 5431003..5432562 (-) 1560 WP_256825318.1 PAS domain-containing methyl-accepting chemotaxis protein -
  P4B31_RS25455 (P4B31_25460) - 5432630..5433394 (-) 765 WP_001389365.1 IS6-like element IS6100 family transposase -
  P4B31_RS25465 (P4B31_25470) - 5433901..5434401 (-) 501 WP_000376623.1 GNAT family N-acetyltransferase -
  P4B31_RS25470 (P4B31_25475) sul1 5434529..5435368 (-) 840 WP_000259031.1 sulfonamide-resistant dihydropteroate synthase Sul1 -
  P4B31_RS25475 (P4B31_25480) - 5435362..5435709 (-) 348 WP_000679427.1 quaternary ammonium compound efflux SMR transporter QacE delta 1 -
  P4B31_RS25480 (P4B31_25485) aadA1 5435826..5436664 (-) 839 Protein_5037 ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1 -
  P4B31_RS25485 (P4B31_25490) aadB 5436722..5437255 (-) 534 WP_000381802.1 aminoglycoside nucleotidyltransferase ANT(2'')-Ia -
  P4B31_RS25490 (P4B31_25495) aadB 5437313..5437846 (-) 534 WP_000381802.1 aminoglycoside nucleotidyltransferase ANT(2'')-Ia -
  P4B31_RS25495 (P4B31_25500) intI1 5437992..5439005 (+) 1014 WP_309253346.1 class 1 integron integrase IntI1 -
  P4B31_RS25500 (P4B31_25505) - 5439296..5440147 (+) 852 WP_010792468.1 recombinase family protein -
  P4B31_RS25505 (P4B31_25510) - 5440175..5440609 (-) 435 WP_000414383.1 mercury resistance transcriptional regulator MerR -
  P4B31_RS25510 (P4B31_25515) - 5440681..5441031 (+) 351 WP_001294666.1 mercuric transport protein MerT -
  P4B31_RS25515 (P4B31_25520) merP 5441047..5441322 (+) 276 WP_000732290.1 mercury resistance system periplasmic binding protein MerP -
  P4B31_RS25520 (P4B31_25525) merA 5441394..5443079 (+) 1686 WP_003090700.1 mercury(II) reductase -
  P4B31_RS25525 (P4B31_25530) merD 5443097..5443462 (+) 366 WP_003090698.1 mercury resistance co-regulator MerD -
  P4B31_RS25530 (P4B31_25535) merE 5443459..5443695 (+) 237 WP_003090697.1 broad-spectrum mercury transporter MerE -
  P4B31_RS25535 (P4B31_25540) - 5443692..5444680 (+) 989 Protein_5048 DUF3330 domain-containing protein -
  P4B31_RS25540 (P4B31_25545) - 5444856..5445416 (+) 561 WP_033943780.1 recombinase family protein -
  P4B31_RS25545 (P4B31_25550) - 5445420..5448386 (+) 2967 WP_033991895.1 Tn3-like element TnAs1 family transposase -
  P4B31_RS25550 (P4B31_25555) pilB 5448420..5449535 (+) 1116 Protein_5051 type IV-A pilus assembly ATPase PilB -
  P4B31_RS25555 (P4B31_25560) pilC 5449539..5450756 (+) 1218 WP_010792214.1 type II secretion system F family protein Machinery gene
  P4B31_RS25560 (P4B31_25565) pilD 5450759..5451631 (+) 873 WP_003116251.1 type IV prepilin peptidase/methyltransferase PilD Machinery gene

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 31871.89 Da        Isoelectric Point: 7.3454

>NTDB_id=808945 P4B31_RS25560 WP_003116251.1 5450759..5451631(+) (pilD) [Pseudomonas aeruginosa strain NY7570]
MELLDYLASHPLAFVLCAILLGLLVGSFLNVVVHRLPKMMERNWKAEAREALGLEPEPKQATYNLVLPNSACPRCGHEIR
PWENIPLVSYLALGGKCSSCKAAIGKRYPLVELATALLSGYVAWHFGFTWQAGAMLLLTWGLLAMSLIDADHQLLPDVLV
LPLLWLGLIANHFGLFASLDDALFGAVFGYLSLWSVFWLFKLVTGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AILGVIMLRLRNAESGTPIPFGPYLAIAGWIALLWGDQITRTYLQFAGFK

Nucleotide


Download         Length: 873 bp        

>NTDB_id=808945 P4B31_RS25560 WP_003116251.1 5450759..5451631(+) (pilD) [Pseudomonas aeruginosa strain NY7570]
ATGGAACTCCTCGACTACCTGGCCAGCCATCCGCTGGCCTTTGTCTTGTGCGCTATCCTCCTTGGCCTGCTGGTCGGCAG
CTTCCTCAACGTCGTCGTGCATCGCCTGCCGAAGATGATGGAGCGCAACTGGAAGGCCGAAGCCCGCGAAGCGCTCGGGC
TGGAGCCGGAACCCAAGCAGGCGACCTACAACCTGGTGCTGCCGAATTCGGCGTGCCCGCGCTGCGGCCACGAGATCCGC
CCCTGGGAAAACATCCCGCTGGTCAGCTACCTGGCGCTGGGCGGCAAGTGCTCGTCCTGCAAGGCCGCCATCGGCAAACG
CTACCCCCTGGTGGAACTGGCCACCGCGCTGCTTTCCGGCTACGTCGCCTGGCATTTCGGCTTCACCTGGCAGGCGGGCG
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

55.017

99.655

0.548
  pilD Vibrio campbellii strain DS40M4

53.497

98.621

0.528
  pilD Acinetobacter nosocomialis M2

50.352

97.931

0.493
  pilD Acinetobacter baumannii D1279779

50.352

97.931

0.493
  pilD Neisseria gonorrhoeae MS11

49.281

95.862

0.472