Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   N5O87_RS04210 Genome accession   NZ_CP104582
Coordinates   874821..875690 (-) Length   289 a.a.
NCBI ID   WP_279532181.1    Uniprot ID   -
Organism   Pseudomonas sp. GD03919     
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)
IScluster/Tn 872279..874525 874821..875690 flank 296


Gene organization within MGE regions


Location: 872279..875690
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  N5O87_RS04195 (N5O87_04195) - 872279..872596 (+) 318 WP_279532179.1 IS66-like element accessory protein TnpA -
  N5O87_RS04200 (N5O87_04200) tnpB 872602..872928 (+) 327 WP_279531102.1 IS66 family insertion sequence element accessory protein TnpB -
  N5O87_RS04205 (N5O87_04205) - 872990..874525 (+) 1536 WP_279532180.1 IS66 family transposase -
  N5O87_RS04210 (N5O87_04210) pilD 874821..875690 (-) 870 WP_279532181.1 prepilin peptidase Machinery gene

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 31914.04 Da        Isoelectric Point: 6.8190

>NTDB_id=730701 N5O87_RS04210 WP_279532181.1 874821..875690(-) (pilD) [Pseudomonas sp. GD03919]
MLVIDFLASHALAFVLCALLLGLLIGSFLNVVIYRLPVMLQRDWQNQAREVLELPSAPTAQTFNLILPNSCCPQCGHEIR
PWENIPVISYLFLRGKCSNCKTPISKRYPIVELTCGLLSAYVAWHFGFTWQAGAMLVLAWGLLAMSLIDADHQILPDVLV
LPLLWLGLIVNYFGLFTSLEDALWGAIAGYLSLWSVYWLFKLITGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AVLGVIMLRMRGSDSGTPIPFGPYLAIAGWIALLWGDVITSSYLKFAGF

Nucleotide


Download         Length: 870 bp        

>NTDB_id=730701 N5O87_RS04210 WP_279532181.1 874821..875690(-) (pilD) [Pseudomonas sp. GD03919]
ATGCTCGTAATCGACTTCCTGGCCAGCCATGCGCTGGCCTTTGTTTTGTGTGCTCTGCTACTGGGCCTGCTGATTGGCAG
CTTCCTCAATGTAGTGATCTATCGACTACCCGTGATGCTGCAACGCGACTGGCAGAACCAGGCGCGCGAGGTGCTGGAAT
TGCCGTCGGCACCAACCGCTCAGACCTTCAACCTGATCCTGCCCAATTCCTGCTGCCCGCAATGCGGCCATGAGATTCGC
CCCTGGGAGAACATCCCGGTCATCAGCTATTTGTTCCTGCGCGGCAAGTGTTCGAACTGCAAGACGCCGATCAGCAAGCG
CTACCCCATCGTCGAACTAACCTGCGGGCTACTTTCCGCTTACGTCGCCTGGCACTTCGGCTTTACCTGGCAGGCCGGGG
CGATGCTGGTGCTGGCCTGGGGGCTGCTGGCGATGAGCCTGATCGATGCCGATCACCAGATTCTGCCGGATGTGCTGGTG
CTGCCGTTGCTCTGGCTGGGCTTGATCGTCAATTACTTCGGGCTTTTCACCAGCCTGGAGGATGCCCTGTGGGGGGCGAT
TGCCGGTTACCTGAGCTTGTGGTCGGTGTACTGGCTGTTCAAGCTGATCACCGGCAAGGAAGGCATGGGTTATGGCGACT
TCAAGCTGCTGGCCATGCTCGGCGCCTGGGGTGGCTGGCAGATTCTGCCGCTGACCATTCTGCTGTCGTCGCTGGTCGGG
GCGGTGCTCGGGGTCATTATGCTGCGTATGCGTGGCAGCGATTCCGGCACGCCGATTCCATTCGGCCCTTATCTGGCGAT
TGCCGGGTGGATCGCCCTGCTGTGGGGCGATGTGATTACCAGCAGTTATCTGAAGTTCGCTGGGTTTTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(136-245)

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

54.015

94.81

0.512
  pilD Acinetobacter baumannii D1279779

52.113

98.27

0.512
  pilD Acinetobacter nosocomialis M2

51.761

98.27

0.509
  pilD Vibrio campbellii strain DS40M4

52.747

94.464

0.498
  pilD Neisseria gonorrhoeae MS11

50.951

91.003

0.464