Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   SSED_RS02240 Genome accession   NC_009831
Coordinates   514459..515370 (-) Length   303 a.a.
NCBI ID   WP_012140773.1    Uniprot ID   -
Organism   Shewanella sediminis HAW-EB3     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 509459..520370
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SSED_RS24755 - 512033..512170 (+) 138 WP_190273185.1 hypothetical protein -
  SSED_RS02220 (Ssed_0419) mutT 512380..512769 (-) 390 WP_012140769.1 8-oxo-dGTP diphosphatase MutT -
  SSED_RS02225 (Ssed_0420) yacG 512773..512985 (-) 213 WP_012140770.1 DNA gyrase inhibitor YacG -
  SSED_RS02230 (Ssed_0421) zapD 513065..513799 (-) 735 WP_012140771.1 cell division protein ZapD -
  SSED_RS02235 (Ssed_0422) coaE 513808..514413 (-) 606 WP_012140772.1 dephospho-CoA kinase -
  SSED_RS02240 (Ssed_0423) pilD 514459..515370 (-) 912 WP_012140773.1 A24 family peptidase Machinery gene
  SSED_RS02245 (Ssed_0424) pilC 515443..516708 (-) 1266 WP_012140774.1 type II secretion system F family protein Machinery gene
  SSED_RS02250 (Ssed_0425) pilB 516774..518483 (-) 1710 WP_012140775.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SSED_RS02255 (Ssed_0426) - 518556..518966 (-) 411 WP_012140776.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -

Sequence

Protein


Download         Length: 303 a.a.        Molecular weight: 33705.93 Da        Isoelectric Point: 6.4714

>NTDB_id=29195 SSED_RS02240 WP_012140773.1 514459..515370(-) (pilD) [Shewanella sediminis HAW-EB3]
MSEFISILSQNLWLFSIISFIFSAVIGSFLNVVIHRFPVMLKREWQQECNQYLNEYHEKLIAPISEQLNNPIDDYPERYN
LVVPASACPKCKTNIKPWHNLPIVGWLMLKGKCAACGTSISPRYPIIELLTGLAVALLAYHFGPGWEFIFATVLTFVLIA
LTGIDLDEMLLPDQLTLPLLWLGLLINLNGTFASPTDAMIGAAAGYLSLWSVFWAFKLLTGKEGMGYGDFKLLAVFGAWF
GWQMLPLIILLSSLVGAIVGIGLIVTKKINKTNPIPFGPYIAAAGWIAMIWGSDITNWYLSTL

Nucleotide


Download         Length: 912 bp        

>NTDB_id=29195 SSED_RS02240 WP_012140773.1 514459..515370(-) (pilD) [Shewanella sediminis HAW-EB3]
ATGTCAGAATTTATCTCCATATTGAGCCAGAACCTTTGGCTCTTCAGTATTATCAGTTTTATTTTTTCGGCTGTCATAGG
CAGTTTTCTTAATGTGGTAATACACCGCTTCCCCGTCATGTTAAAGCGTGAATGGCAGCAAGAGTGTAATCAGTATTTGA
ACGAATACCACGAAAAGCTGATAGCGCCCATTTCGGAGCAACTTAACAATCCCATCGATGACTACCCCGAGAGATACAAT
TTAGTCGTTCCTGCTTCTGCATGCCCGAAGTGTAAAACAAACATCAAACCATGGCACAACCTACCGATTGTCGGTTGGCT
GATGCTGAAAGGAAAATGTGCGGCGTGTGGTACCAGTATTTCGCCCAGATATCCAATTATCGAGCTCCTCACCGGGCTGG
CTGTAGCATTGCTTGCATATCATTTCGGGCCTGGCTGGGAATTCATTTTTGCGACGGTACTGACATTTGTTTTAATAGCC
CTAACAGGTATTGATCTGGATGAAATGTTACTGCCAGATCAGCTCACCCTTCCTCTACTCTGGCTTGGCTTACTGATAAA
TCTGAATGGTACCTTTGCGTCACCGACCGATGCAATGATCGGTGCTGCGGCTGGCTATTTAAGCCTCTGGAGTGTCTTCT
GGGCCTTTAAGCTTTTAACGGGTAAGGAAGGCATGGGATATGGTGATTTTAAACTATTAGCCGTTTTCGGAGCCTGGTTT
GGTTGGCAGATGTTACCACTCATTATTTTATTATCATCGCTGGTTGGCGCAATAGTCGGTATAGGCTTGATAGTAACCAA
GAAGATAAATAAAACTAACCCAATTCCTTTCGGCCCATATATAGCAGCAGCAGGTTGGATCGCCATGATCTGGGGCTCCG
ATATTACAAACTGGTACCTTTCTACACTGTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(153-261)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-142)


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 Acinetobacter baumannii D1279779

50.667

99.01

0.502
  pilD Acinetobacter nosocomialis M2

50.333

99.01

0.498
  pilD Vibrio cholerae strain A1552

50.847

97.36

0.495
  pilD Vibrio campbellii strain DS40M4

51.027

96.37

0.492
  pilD Neisseria gonorrhoeae MS11

43.902

94.719

0.416

Multiple sequence alignment