Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   I596_RS11855 Genome accession   NZ_CP015249
Coordinates   2918681..2919547 (+) Length   288 a.a.
NCBI ID   WP_067648117.1    Uniprot ID   A0A160DWC4
Organism   Dokdonella koreensis DS-123     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2913681..2924547
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  I596_RS11840 (I596_2534) - 2914492..2914962 (+) 471 WP_067648111.1 pilin -
  I596_RS18110 pilA/pilAI 2915093..2915482 (+) 390 WP_083965547.1 pilin Machinery gene
  I596_RS11845 (I596_2535) pilB 2915670..2917385 (+) 1716 WP_067651867.1 type IV-A pilus assembly ATPase PilB Machinery gene
  I596_RS11850 (I596_2536) pilC 2917389..2918681 (+) 1293 WP_067648114.1 type II secretion system F family protein Machinery gene
  I596_RS11855 (I596_2537) pilD 2918681..2919547 (+) 867 WP_067648117.1 A24 family peptidase Machinery gene
  I596_RS11860 (I596_2538) - 2919678..2920829 (-) 1152 WP_083965548.1 efflux RND transporter periplasmic adaptor subunit -
  I596_RS11865 (I596_2539) - 2920826..2924023 (-) 3198 WP_067648123.1 efflux RND transporter permease subunit -

Sequence

Protein


Download         Length: 288 a.a.        Molecular weight: 31068.16 Da        Isoelectric Point: 8.3484

>NTDB_id=178047 I596_RS11855 WP_067648117.1 2918681..2919547(+) (pilD) [Dokdonella koreensis DS-123]
MGDYAWLAQPAPLIVLCGLLGLIVGSFLNVVILRLPARLEHGWRQQAHEFLGTVPTAEAAPPDLVVTASHCPHCKHRLAA
WDNIPLLGWLLLRGRCRYCKAPISIQYPLVELLTGVASAVIAWQLGFGWPLLAGLVFTWILIAASGIDFRTQLLPDQLTL
PLLWLGLLIALLPLFVDAPTAILGAAIGYLSLWSVFWLFKLLTGKEGMGYGDFKLLAALGAWMGAASLLPIILVSSLIGA
IIGGTVLAVRGKDRSTPIPFGPFIAAAGWVWFVFGDRLSVLYASLFGL

Nucleotide


Download         Length: 867 bp        

>NTDB_id=178047 I596_RS11855 WP_067648117.1 2918681..2919547(+) (pilD) [Dokdonella koreensis DS-123]
ATGGGTGACTACGCCTGGCTGGCGCAGCCTGCGCCGCTGATCGTGCTGTGCGGGCTGCTGGGCCTGATCGTCGGCAGTTT
TCTCAATGTGGTGATCCTGCGCCTGCCGGCGCGGCTGGAGCATGGCTGGCGGCAGCAGGCGCACGAGTTCCTCGGCACTG
TGCCGACCGCGGAGGCAGCGCCGCCAGACCTGGTGGTCACGGCGTCCCATTGCCCGCACTGCAAGCACCGGCTGGCCGCC
TGGGACAATATCCCGCTGCTCGGCTGGCTGTTGCTGCGCGGGCGCTGCCGCTACTGCAAGGCGCCGATCTCGATCCAGTA
CCCGCTGGTGGAACTGCTGACGGGCGTCGCCTCGGCGGTGATCGCCTGGCAGCTCGGCTTCGGCTGGCCGCTGCTGGCGG
GGTTGGTCTTCACGTGGATCCTGATTGCGGCCAGCGGCATCGATTTCCGCACCCAACTGCTGCCGGACCAGCTCACCCTG
CCCTTGCTGTGGCTGGGCCTGCTGATCGCCCTGCTGCCGCTGTTCGTCGATGCGCCGACCGCCATCCTCGGCGCGGCGAT
CGGCTACCTCAGCCTCTGGTCGGTGTTCTGGCTGTTCAAGCTGCTGACCGGCAAGGAGGGCATGGGCTACGGCGACTTCA
AGCTGCTGGCCGCACTGGGCGCCTGGATGGGCGCGGCCAGCCTGCTGCCGATCATCCTGGTCTCGTCGCTGATCGGCGCG
ATCATCGGCGGCACGGTGCTGGCGGTGCGCGGCAAGGACCGCTCGACGCCGATCCCGTTCGGCCCGTTCATCGCGGCGGC
GGGCTGGGTCTGGTTCGTCTTCGGCGATCGCCTGTCCGTTCTCTACGCGAGCCTGTTCGGGCTCTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(19-124)

Type IV leader peptidase family (Peptidase_A24)

(135-243)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A160DWC4

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

54.275

93.403

0.507
  pilD Vibrio campbellii strain DS40M4

49.485

100

0.5
  pilD Acinetobacter nosocomialis M2

49.815

94.097

0.469
  pilD Acinetobacter baumannii D1279779

49.446

94.097

0.465
  pilD Neisseria gonorrhoeae MS11

47.727

91.667

0.437

Multiple sequence alignment