Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   D934_RS12485 Genome accession   NZ_CP006696
Coordinates   2695355..2696218 (-) Length   287 a.a.
NCBI ID   WP_004084594.1    Uniprot ID   B2I9Q6
Organism   Xylella fastidiosa subsp. sandyi Ann-1     
Function   type IV pilus biogenesis and function (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2690355..2701218
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  D934_RS12465 (D934_13440) rimK 2690871..2691776 (+) 906 WP_020851233.1 30S ribosomal protein S6--L-glutamate ligase -
  D934_RS12470 (D934_13445) - 2692442..2693119 (+) 678 WP_010894955.1 response regulator transcription factor -
  D934_RS12475 (D934_13450) - 2693112..2694449 (+) 1338 WP_004090387.1 HAMP domain-containing sensor histidine kinase -
  D934_RS12480 (D934_13455) coaE 2694720..2695343 (-) 624 WP_020851236.1 dephospho-CoA kinase -
  D934_RS12485 (D934_13460) pilD 2695355..2696218 (-) 864 WP_004084594.1 A24 family peptidase Machinery gene
  D934_RS12490 (D934_13465) pilC 2696225..2697427 (-) 1203 WP_010894959.1 type II secretion system F family protein Machinery gene
  D934_RS12495 (D934_13470) pilA/pilAI 2697869..2698315 (+) 447 WP_020851238.1 pilin Machinery gene
  D934_RS12500 (D934_13475) - 2698554..2698781 (-) 228 WP_020851239.1 hypothetical protein -
  D934_RS12510 (D934_13485) pilA 2699620..2700072 (+) 453 WP_020851240.1 pilin Machinery gene

Sequence

Protein


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

>NTDB_id=100964 D934_RS12485 WP_004084594.1 2695355..2696218(-) (pilD) [Xylella fastidiosa subsp. sandyi Ann-1]
MAFLDQHPGLGYPLASGLGLLLGSFLNVVILRLPRRLEWQWKRDAREILEMPDIYDPPPPGIVVEPSHDPVTGDRLKWWE
NIPVLSWLLLRGRSRYSGKSISLQYPLVELLTCLLVLASVWRFGFGWHGFGAIVFSCFLVALAGIDLRTRLLPDQLTLML
MWLGLIGSADNLFMAAKPALLGAAVGYLSLWIVAALFKLIFNKEGMGHGDFKMLGALGAWCGLKGILPIILISSLAGVVL
GSVWLVVRGHNRTTMIPFGPYLAVGGWIVFFFGDQIIHAYLELLSIG

Nucleotide


Download         Length: 864 bp        

>NTDB_id=100964 D934_RS12485 WP_004084594.1 2695355..2696218(-) (pilD) [Xylella fastidiosa subsp. sandyi Ann-1]
ATGGCATTTCTTGACCAGCACCCCGGACTCGGCTATCCCCTTGCGTCCGGTTTGGGGTTGTTGCTTGGTAGTTTTCTCAA
TGTGGTGATCCTGCGTTTGCCGCGCCGTTTGGAATGGCAATGGAAGCGCGATGCGCGCGAAATCCTGGAGATGCCGGACA
TTTATGATCCGCCACCACCGGGAATTGTGGTCGAGCCTTCCCACGATCCAGTGACTGGTGATCGGTTGAAGTGGTGGGAA
AACATTCCGGTGCTTAGCTGGTTGTTGCTACGTGGACGCTCGCGTTACAGCGGCAAGTCAATCTCGTTGCAGTATCCGTT
GGTCGAATTGCTGACTTGCCTGCTGGTGCTGGCCAGTGTTTGGCGTTTTGGATTCGGTTGGCATGGTTTTGGGGCAATTG
TGTTCAGTTGTTTCCTGGTTGCGTTGGCTGGGATTGATTTGCGTACTCGGCTCTTACCTGACCAGTTAACTTTAATGCTT
ATGTGGCTGGGTTTGATTGGATCGGCGGATAACTTGTTTATGGCAGCCAAACCTGCGTTATTGGGAGCTGCAGTTGGTTA
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