Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   ND446_RS12740 Genome accession   NZ_CP098694
Coordinates   2807759..2808268 (+) Length   169 a.a.
NCBI ID   WP_267262846.1    Uniprot ID   -
Organism   Yersinia ruckeri strain NVI-8270     
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 2808327..2809477 2807759..2808268 flank 59


Gene organization within MGE regions


Location: 2807759..2809477
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ND446_RS12740 (ND446_12740) pilD 2807759..2808268 (+) 510 WP_267262846.1 prepilin peptidase Machinery gene
  ND446_RS12745 (ND446_12745) - 2808327..2809477 (+) 1151 WP_087931031.1 IS3 family transposase -

Sequence

Protein


Download         Length: 169 a.a.        Molecular weight: 19005.94 Da        Isoelectric Point: 6.7289

>NTDB_id=697091 ND446_RS12740 WP_267262846.1 2807759..2808268(+) (pilD) [Yersinia ruckeri strain NVI-8270]
MAQMIAPLWWGGLAVLGLCVGSFLNVAIYRLPLMLTRENPHDFNLCLPHSHCPQCKHSLKWRDNIPVFSWLFLQGQCRYC
RASIPVRYPLVEIMTMLMTLFIAAVIPLGSPLLAALLLSWMLIALTMIDIDHLLLPDNLTLPLLWMGLLFHLFDSQLALS
EAVIGAVAE

Nucleotide


Download         Length: 510 bp        

>NTDB_id=697091 ND446_RS12740 WP_267262846.1 2807759..2808268(+) (pilD) [Yersinia ruckeri strain NVI-8270]
ATGGCTCAAATGATAGCGCCACTGTGGTGGGGCGGGCTGGCGGTTCTTGGCCTGTGTGTCGGTAGTTTTCTCAACGTCGC
TATTTATCGGCTACCGCTGATGTTAACCCGCGAAAATCCGCATGATTTTAATCTGTGTCTACCTCATTCCCACTGTCCTC
AGTGTAAACATTCGTTGAAATGGCGAGATAATATTCCTGTATTCAGTTGGCTATTCCTGCAAGGACAATGTCGTTACTGT
CGGGCATCTATCCCAGTGCGCTACCCGCTGGTTGAAATCATGACGATGTTGATGACCTTGTTTATTGCTGCAGTCATCCC
ATTGGGCAGCCCGTTACTGGCCGCACTACTACTCAGTTGGATGCTGATCGCGTTAACCATGATCGATATTGACCACTTGC
TCTTACCGGATAATCTGACATTGCCTCTGCTATGGATGGGGCTACTTTTTCACCTGTTTGATAGTCAGTTGGCATTAAGT
GAGGCAGTGATTGGTGCTGTCGCTGAATAG

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(15-104)

Type IV leader peptidase family (Peptidase_A24)

(117-168)


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

48.837

100

0.497
  pilD Vibrio campbellii strain DS40M4

42.442

100

0.432
  pilD Neisseria gonorrhoeae MS11

42.105

100

0.426
  pilD Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

45.161

91.716

0.414
  pilD Acinetobacter baumannii D1279779

40.828

100

0.408
  pilD Acinetobacter nosocomialis M2

40.237

100

0.402