Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   R3J28_RS10820 Genome accession   NZ_CP136971
Coordinates   2324701..2325564 (-) Length   287 a.a.
NCBI ID   WP_004084594.1    Uniprot ID   B2I9Q6
Organism   Xylella fastidiosa subsp. multiplex strain Santa29b     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2319701..2330564
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  R3J28_RS10800 (R3J28_10790) rimK 2320220..2321125 (+) 906 WP_004084588.1 30S ribosomal protein S6--L-glutamate ligase -
  R3J28_RS10805 (R3J28_10795) - 2321792..2322469 (+) 678 WP_010894955.1 response regulator transcription factor -
  R3J28_RS10810 (R3J28_10800) - 2322462..2323799 (+) 1338 WP_027700147.1 HAMP domain-containing sensor histidine kinase -
  R3J28_RS10815 (R3J28_10805) coaE 2324066..2324689 (-) 624 WP_004084593.1 dephospho-CoA kinase -
  R3J28_RS10820 (R3J28_10810) pilD 2324701..2325564 (-) 864 WP_004084594.1 A24 family peptidase Machinery gene
  R3J28_RS10825 (R3J28_10815) pilC 2325571..2326773 (-) 1203 WP_010894959.1 type II secretion system F family protein Machinery gene
  R3J28_RS10830 (R3J28_10820) pilA/pilAI 2327214..2327660 (+) 447 WP_154128445.1 pilin Machinery gene
  R3J28_RS10835 (R3J28_10825) pilA/pilAI 2328968..2329408 (+) 441 WP_375732100.1 pilin Machinery gene

Sequence

Protein


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

>NTDB_id=816904 R3J28_RS10820 WP_004084594.1 2324701..2325564(-) (pilD) [Xylella fastidiosa subsp. multiplex strain Santa29b]
MAFLDQHPGLGYPLASGLGLLLGSFLNVVILRLPRRLEWQWKRDAREILEMPDIYDPPPPGIVVEPSHDPVTGDRLKWWE
NIPVLSWLLLRGRSRYSGKSISLQYPLVELLTCLLVLASVWRFGFGWHGFGAIVFSCFLVALAGIDLRTRLLPDQLTLML
MWLGLIGSADNLFMAAKPALLGAAVGYLSLWIVAALFKLIFNKEGMGHGDFKMLGALGAWCGLKGILPIILISSLAGVVL
GSVWLVVRGHNRTTMIPFGPYLAVGGWIVFFFGDQIIHAYLELLSIG

Nucleotide


Download         Length: 864 bp        

>NTDB_id=816904 R3J28_RS10820 WP_004084594.1 2324701..2325564(-) (pilD) [Xylella fastidiosa subsp. multiplex strain Santa29b]
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