Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   SDEN_RS17610 Genome accession   NC_007954
Coordinates   4046921..4047838 (+) Length   305 a.a.
NCBI ID   WP_011497809.1    Uniprot ID   Q12IQ9
Organism   Shewanella denitrificans OS217     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4041921..4052838
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SDEN_RS17595 (Sden_3388) - 4043125..4043541 (+) 417 WP_011497806.1 pilin -
  SDEN_RS17600 (Sden_3389) pilB 4043609..4045318 (+) 1710 WP_011497807.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SDEN_RS17605 (Sden_3390) pilC 4045495..4046763 (+) 1269 WP_011497808.1 type II secretion system F family protein Machinery gene
  SDEN_RS17610 (Sden_3391) pilD 4046921..4047838 (+) 918 WP_011497809.1 prepilin peptidase Machinery gene
  SDEN_RS17615 (Sden_3392) coaE 4047838..4048458 (+) 621 WP_011497810.1 dephospho-CoA kinase -
  SDEN_RS17620 (Sden_3393) zapD 4048468..4049211 (+) 744 WP_011497811.1 cell division protein ZapD -
  SDEN_RS17625 (Sden_3394) - 4049249..4049473 (+) 225 WP_011497812.1 DNA gyrase inhibitor YacG -
  SDEN_RS17630 (Sden_3395) mutT 4049482..4049877 (+) 396 WP_011497813.1 8-oxo-dGTP diphosphatase MutT -
  SDEN_RS17635 (Sden_3396) - 4050197..4052584 (+) 2388 WP_011497814.1 bifunctional diguanylate cyclase/phosphodiesterase -

Sequence

Protein


Download         Length: 305 a.a.        Molecular weight: 34048.75 Da        Isoelectric Point: 7.1802

>NTDB_id=25722 SDEN_RS17610 WP_011497809.1 4046921..4047838(+) (pilD) [Shewanella denitrificans OS217]
MSEFIALMGQYPVIFISVCFIFAATIGSFLNVVIHRLPVMMKREWQAECNQYLQEYHPDIVKDVSLKRLEKPLDSFPERY
NLVVPNSCCPKCNAAIKPWHNLPILGWCMLKGKCAQCQQAISVRYPVIELLTGLMVAVLAWHFGPTSQFLFASLLTFVLI
ALTGIDLDEMLLPDQLTMPLLWLGLLINLQGVFTSPTDAIIGAIAGYMSLWSVFWLFKLVTGKEGMGYGDFKLLAVFGAW
LGWQMLPLIILLSSLVGAVVGIALILSKKLNQGNPIPFGPYIAMAGWIALIWGNDIVNWYLGTFL

Nucleotide


Download         Length: 918 bp        

>NTDB_id=25722 SDEN_RS17610 WP_011497809.1 4046921..4047838(+) (pilD) [Shewanella denitrificans OS217]
ATGAGTGAATTTATCGCCCTTATGGGCCAATATCCTGTTATTTTTATCAGTGTTTGCTTTATTTTTGCCGCCACCATAGG
CAGCTTTCTTAACGTGGTTATCCACCGTCTACCTGTAATGATGAAGCGTGAGTGGCAAGCTGAATGTAATCAATACTTAC
AAGAGTATCACCCGGATATAGTCAAAGACGTCAGCCTGAAACGCTTAGAAAAACCGTTAGATAGTTTCCCCGAACGTTAT
AACTTGGTAGTGCCTAATTCCTGCTGCCCTAAATGCAATGCCGCCATTAAGCCTTGGCATAACTTACCTATCCTTGGCTG
GTGCATGCTAAAAGGAAAGTGTGCTCAGTGCCAACAGGCTATTTCTGTACGCTATCCCGTTATCGAACTACTCACAGGGC
TTATGGTTGCTGTCTTAGCTTGGCACTTTGGCCCTACAAGTCAGTTTTTGTTTGCCTCCCTACTGACCTTTGTCTTGATA
GCATTGACTGGCATAGATCTCGATGAAATGCTATTGCCAGACCAGCTTACTATGCCGCTGCTTTGGCTAGGCTTGTTGAT
TAATTTACAAGGCGTATTCACAAGTCCGACTGATGCCATCATAGGGGCAATTGCTGGTTATATGAGCCTATGGTCGGTGT
TTTGGCTATTTAAACTCGTTACGGGTAAGGAAGGCATGGGTTACGGTGACTTTAAACTTCTGGCGGTGTTTGGCGCCTGG
CTTGGTTGGCAAATGCTGCCATTGATAATTTTACTGTCTTCATTAGTGGGTGCAGTTGTCGGGATTGCGCTGATTTTAAG
TAAAAAACTCAATCAAGGAAATCCGATCCCATTTGGTCCTTACATCGCCATGGCTGGTTGGATAGCGCTTATTTGGGGCA
ATGACATAGTTAATTGGTATCTAGGCACCTTCTTGTGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(155-262)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(21-143)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q12IQ9

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

50.495

99.344

0.502
  pilD Acinetobacter nosocomialis M2

50.165

99.344

0.498
  pilD Vibrio campbellii strain DS40M4

50.676

97.049

0.492
  pilD Vibrio cholerae strain A1552

50.676

97.049

0.492
  pilD Neisseria gonorrhoeae MS11

45

91.803

0.413

Multiple sequence alignment