Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   SJ2017_RS02075 Genome accession   NZ_CP020472
Coordinates   460528..461457 (-) Length   309 a.a.
NCBI ID   WP_080914718.1    Uniprot ID   -
Organism   Shewanella japonica strain KCTC 22435     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 455528..466457
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SJ2017_RS02055 (SJ2017_0400) mutT 458501..458938 (-) 438 WP_244899755.1 8-oxo-dGTP diphosphatase MutT -
  SJ2017_RS02060 (SJ2017_0401) yacG 458913..459122 (-) 210 WP_055022953.1 DNA gyrase inhibitor YacG -
  SJ2017_RS02065 (SJ2017_0402) zapD 459163..459900 (-) 738 WP_080914716.1 cell division protein ZapD -
  SJ2017_RS02070 (SJ2017_0403) coaE 459910..460515 (-) 606 WP_080914717.1 dephospho-CoA kinase -
  SJ2017_RS02075 (SJ2017_0404) pilD 460528..461457 (-) 930 WP_080914718.1 prepilin peptidase Machinery gene
  SJ2017_RS02080 (SJ2017_0405) pilC 461488..462750 (-) 1263 WP_065109604.1 type II secretion system F family protein Machinery gene
  SJ2017_RS02085 (SJ2017_0406) pilB 462811..464517 (-) 1707 WP_080914719.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SJ2017_RS02090 (SJ2017_0407) - 464844..466208 (+) 1365 WP_080914720.1 O-antigen ligase family protein -

Sequence

Protein


Download         Length: 309 a.a.        Molecular weight: 34644.30 Da        Isoelectric Point: 8.5690

>NTDB_id=223554 SJ2017_RS02075 WP_080914718.1 460528..461457(-) (pilD) [Shewanella japonica strain KCTC 22435]
MNEFVSSFITSMSQSPWLFMTISFIFAATIGSSLNVVIHRFPVMMKREWQSECNFYLSEYHPDIVKEVGEKRLNKPIDKY
PLKYNLVVPGSACPKCKSNIKPWHNLPILGWILLKGKCANCKAAISARYPLFELITGILVAVLAWHFGPTWQFLFASILT
FILIALTGIDLDEMLLPDQLTLPLLWLGLLINLKGIYASPTDAIVGAAAGYLSLWSVFWLFKLVTGKEGMGYGDFKLLAV
FGAWLGWQFLPLIILLSSLVGAIVGITMMLLKNLSRENPIPFGPYIAVAGWIALVWGQDIINWYLGTLY

Nucleotide


Download         Length: 930 bp        

>NTDB_id=223554 SJ2017_RS02075 WP_080914718.1 460528..461457(-) (pilD) [Shewanella japonica strain KCTC 22435]
ATGAATGAATTTGTATCTAGCTTCATAACATCAATGAGCCAATCACCTTGGCTCTTTATGACAATTAGCTTTATCTTCGC
TGCCACTATTGGCAGCTCTTTAAACGTCGTCATCCACCGCTTTCCAGTGATGATGAAACGTGAATGGCAAAGTGAATGTA
ACTTTTATTTATCAGAATACCACCCAGACATCGTCAAAGAAGTCGGTGAAAAACGTTTAAATAAGCCAATAGACAAATAC
CCCCTAAAATATAACTTAGTTGTACCTGGCTCAGCCTGCCCGAAATGCAAAAGTAATATCAAACCTTGGCATAATTTACC
TATCTTAGGTTGGATTTTACTAAAAGGTAAATGCGCTAATTGTAAAGCAGCAATTAGCGCTAGATACCCTCTATTTGAAT
TAATAACAGGCATTTTAGTTGCGGTGCTTGCTTGGCACTTTGGACCTACCTGGCAGTTTCTATTTGCATCAATACTGACG
TTTATACTGATAGCATTAACAGGTATTGACCTAGATGAAATGCTATTACCGGATCAGTTAACCTTACCTTTATTGTGGCT
TGGCTTGCTTATTAATCTTAAAGGTATCTATGCAAGCCCTACTGATGCCATTGTAGGTGCAGCTGCTGGTTATTTAAGCC
TTTGGTCTGTGTTTTGGTTGTTCAAGCTAGTTACAGGCAAAGAAGGCATGGGTTATGGCGATTTCAAATTGTTAGCCGTG
TTTGGTGCTTGGTTAGGCTGGCAATTTTTACCGCTTATCATCCTCCTATCTTCGTTAGTAGGAGCCATTGTCGGTATTAC
GATGATGTTATTGAAAAATTTATCGAGAGAAAACCCGATTCCATTTGGCCCATACATAGCGGTAGCAGGCTGGATTGCAT
TAGTCTGGGGACAAGATATTATCAATTGGTACCTTGGAACCTTATATTAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(25-147)

Type IV leader peptidase family (Peptidase_A24)

(158-266)


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 campbellii strain DS40M4

51.361

95.146

0.489
  pilD Vibrio cholerae strain A1552

50.68

95.146

0.482
  pilD Acinetobacter baumannii D1279779

48.039

99.029

0.476
  pilD Acinetobacter nosocomialis M2

47.712

99.029

0.472
  pilD Neisseria gonorrhoeae MS11

44.643

90.615

0.405

Multiple sequence alignment