Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   PD_RS10185 Genome accession   NC_004556
Coordinates   2254242..2255105 (-) Length   287 a.a.
NCBI ID   WP_004084594.1    Uniprot ID   B2I9Q6
Organism   Xylella fastidiosa Temecula1     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2249242..2260105
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  PD_RS10165 (PD1918) rimK 2249743..2250648 (+) 906 WP_004090391.1 30S ribosomal protein S6--L-glutamate ligase -
  PD_RS10170 (PD1919) - 2251333..2252010 (+) 678 WP_010894955.1 response regulator transcription factor -
  PD_RS10175 (PD1920) - 2252003..2253340 (+) 1338 WP_004090387.1 sensor histidine kinase -
  PD_RS10180 (PD1921) coaE 2253607..2254230 (-) 624 WP_004090385.1 dephospho-CoA kinase -
  PD_RS10185 (PD1922) pilD 2254242..2255105 (-) 864 WP_004084594.1 prepilin peptidase Machinery gene
  PD_RS10190 (PD1923) pilC 2255112..2256314 (-) 1203 WP_011098309.1 type II secretion system F family protein Machinery gene
  PD_RS10195 (PD1924) pilA 2256755..2257201 (+) 447 WP_004090380.1 pilin Machinery gene
  PD_RS10200 (PD1925) - 2257447..2257674 (-) 228 WP_011098310.1 hypothetical protein -
  PD_RS10205 (PD1926) pilA/pilAI 2258510..2258950 (+) 441 WP_004090375.1 pilin Machinery gene

Sequence

Protein


Download         Length: 287 a.a.        Molecular weight: 31704.79 Da        Isoelectric Point: 8.6709

>NTDB_id=23337 PD_RS10185 WP_004084594.1 2254242..2255105(-) (pilD) [Xylella fastidiosa Temecula1]
MAFLDQHPGLGYPLASGLGLLLGSFLNVVILRLPRRLEWQWKRDAREILEMPDIYDPPPPGIVVEPSHDPVTGDRLKWWE
NIPVLSWLLLRGRSRYSGKSISLQYPLVELLTCLLVLASVWRFGFGWHGFGAIVFSCFLVALAGIDLRTRLLPDQLTLML
MWLGLIGSADNLFMAAKPALLGAAVGYLSLWIVAALFKLIFNKEGMGHGDFKMLGALGAWCGLKGILPIILISSLAGVVL
GSVWLVVRGHNRTTMIPFGPYLAVGGWIVFFFGDQIIHAYLELLSIG

Nucleotide


Download         Length: 864 bp        

>NTDB_id=23337 PD_RS10185 WP_004084594.1 2254242..2255105(-) (pilD) [Xylella fastidiosa Temecula1]
ATGGCATTTCTTGATCAGCACCCCGGACTCGGCTATCCCCTTGCGTCCGGTTTGGGGTTGTTGCTTGGTAGTTTTCTCAA
TGTGGTGATCCTGCGTTTGCCGCGCCGTTTGGAATGGCAATGGAAGCGCGATGCGCGCGAAATCCTGGAAATGCCGGACA
TTTATGATCCGCCACCGCCGGGAATTGTGGTCGAGCCTTCCCACGATCCAGTGACTGGTGATCGGTTGAAGTGGTGGGAA
AACATTCCGGTGCTTAGCTGGTTGTTGCTACGTGGACGTTCGCGTTACAGCGGCAAGTCAATCTCGTTGCAGTATCCGTT
GGTCGAATTGCTGACTTGCCTGCTGGTGCTGGCCAGTGTTTGGCGTTTTGGATTCGGTTGGCATGGTTTTGGGGCAATTG
TGTTCAGTTGTTTCCTGGTTGCGTTGGCTGGGATTGATTTGCGTACTCGGCTCTTACCTGACCAGTTAACTTTAATGCTC
ATGTGGCTGGGTTTGATTGGATCGGCGGATAACTTGTTTATGGCAGCCAAACCTGCGTTATTGGGGGCTGCAGTTGGTTA
TTTATCTCTGTGGATTGTGGCGGCGTTGTTCAAACTGATCTTTAACAAGGAAGGGATGGGCCATGGTGACTTCAAAATGC
TGGGCGCGCTTGGGGCATGGTGTGGGTTAAAGGGTATTCTCCCGATCATTTTGATTTCATCACTGGCTGGAGTGGTATTG
GGCTCTGTTTGGCTTGTTGTGCGTGGTCATAACCGTACGACGATGATTCCGTTTGGACCTTATCTGGCAGTTGGTGGATG
GATCGTGTTCTTTTTCGGCGATCAGATCATCCATGCTTATCTGGAGCTATTAAGTATCGGGTGA

Domains

Predicted by InterProScan.

Type IV leader peptidase family (Peptidase_A24)

(133-241)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(18-123)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB B2I9Q6

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

41.754

99.303

0.415
  pilD Vibrio cholerae strain A1552

42.049

98.606

0.415
  pilD Acinetobacter nosocomialis M2

41.343

98.606

0.408
  pilD Acinetobacter baumannii D1279779

41.343

98.606

0.408
  pilD Neisseria gonorrhoeae MS11

43.284

93.38

0.404

Multiple sequence alignment