Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   DVT08_RS10400 Genome accession   NZ_CP047134
Coordinates   2290691..2291554 (-) Length   287 a.a.
NCBI ID   WP_004084594.1    Uniprot ID   B2I9Q6
Organism   Xylella fastidiosa subsp. multiplex strain IVIA5901     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2285691..2296554
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DVT08_RS10380 (DVT08_010550) rimK 2286201..2287106 (+) 906 WP_004084588.1 30S ribosomal protein S6--L-glutamate ligase -
  DVT08_RS10385 (DVT08_010555) - 2287782..2288459 (+) 678 WP_010894955.1 response regulator transcription factor -
  DVT08_RS10390 (DVT08_010560) - 2288452..2289789 (+) 1338 WP_027700147.1 HAMP domain-containing sensor histidine kinase -
  DVT08_RS10395 (DVT08_010565) coaE 2290056..2290679 (-) 624 WP_004084593.1 dephospho-CoA kinase -
  DVT08_RS10400 (DVT08_010570) pilD 2290691..2291554 (-) 864 WP_004084594.1 A24 family peptidase Machinery gene
  DVT08_RS10405 (DVT08_010575) pilC 2291561..2292763 (-) 1203 WP_010894959.1 type II secretion system F family protein Machinery gene
  DVT08_RS10410 (DVT08_010580) pilA 2293204..2293650 (+) 447 WP_128283976.1 pilin Machinery gene
  DVT08_RS10415 (DVT08_010585) - 2293895..2294122 (-) 228 WP_012338102.1 hypothetical protein -
  DVT08_RS10420 (DVT08_010590) pilA/pilAI 2294967..2295407 (+) 441 WP_012338104.1 pilin Machinery gene

Sequence

Protein


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

>NTDB_id=357491 DVT08_RS10400 WP_004084594.1 2290691..2291554(-) (pilD) [Xylella fastidiosa subsp. multiplex strain IVIA5901]
MAFLDQHPGLGYPLASGLGLLLGSFLNVVILRLPRRLEWQWKRDAREILEMPDIYDPPPPGIVVEPSHDPVTGDRLKWWE
NIPVLSWLLLRGRSRYSGKSISLQYPLVELLTCLLVLASVWRFGFGWHGFGAIVFSCFLVALAGIDLRTRLLPDQLTLML
MWLGLIGSADNLFMAAKPALLGAAVGYLSLWIVAALFKLIFNKEGMGHGDFKMLGALGAWCGLKGILPIILISSLAGVVL
GSVWLVVRGHNRTTMIPFGPYLAVGGWIVFFFGDQIIHAYLELLSIG

Nucleotide


Download         Length: 864 bp        

>NTDB_id=357491 DVT08_RS10400 WP_004084594.1 2290691..2291554(-) (pilD) [Xylella fastidiosa subsp. multiplex strain IVIA5901]
ATGGCATTTCTTGATCAGCACCCCGGACTCGGCTATCCCCTTGCGTCCGGTTTGGGGTTGTTGCTTGGTAGTTTTCTCAA
TGTGGTGATCCTGCGTTTGCCGCGCCGTTTGGAATGGCAATGGAAGCGCGATGCGCGCGAAATCCTGGAGATGCCGGACA
TTTATGATCCGCCACCACCGGGAATTGTGGTCGAGCCTTCCCACGATCCAGTGACTGGTGATCGGTTGAAGTGGTGGGAA
AACATTCCGGTGCTTAGTTGGTTGTTGCTACGTGGACGCTCGCGTTACAGCGGCAAGTCAATCTCGTTGCAGTATCCGTT
GGTCGAATTGCTGACTTGCCTGCTGGTGCTGGCCAGTGTTTGGCGTTTTGGATTCGGTTGGCATGGCTTTGGGGCAATTG
TGTTCAGTTGTTTCCTGGTTGCGTTGGCTGGGATTGATTTGCGTACTCGGCTCTTACCTGACCAGTTAACTTTAATGCTT
ATGTGGCTGGGTTTGATTGGATCTGCGGATAACTTGTTTATGGCAGCCAAACCTGCGTTATTGGGGGCTGCAGTTGGTTA
TTTATCTCTGTGGATTGTGGCGGCGTTGTTCAAACTGATCTTTAACAAGGAAGGGATGGGCCATGGTGACTTCAAAATGC
TGGGCGCGCTTGGGGCATGGTGTGGGTTGAAGGGTATTCTCCCGATCATTTTGATTTCATCACTGGCTGGAGTGGTATTG
GGCTCCGTTTGGCTTGTTGTGCGTGGTCATAACCGTACGACGATGATTCCGTTTGGACCTTATCTGGCAGTTGGTGGATG
GATTGTGTTCTTTTTCGGCGATCAGATCATCCATGCTTATCTGGAGCTATTAAGTATCGGGTGA

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