Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   L1F06_RS04015 Genome accession   NZ_CP099397
Coordinates   879381..880250 (-) Length   289 a.a.
NCBI ID   WP_129482850.1    Uniprot ID   -
Organism   Pseudomonas hydrolytica strain DSWY01     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 874381..885250
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  L1F06_RS03975 (L1F06_003975) - 874486..875787 (-) 1302 WP_129482848.1 NAD(P)/FAD-dependent oxidoreductase -
  L1F06_RS03980 (L1F06_003980) - 875851..876024 (-) 174 WP_003242714.1 DUF3094 domain-containing protein -
  L1F06_RS03985 (L1F06_003985) - 876049..876597 (-) 549 WP_011920932.1 MOSC domain-containing protein -
  L1F06_RS03990 (L1F06_003990) - 876594..877223 (-) 630 WP_003242718.1 DUF1780 domain-containing protein -
  L1F06_RS03995 (L1F06_003995) - 877350..878039 (+) 690 WP_011920933.1 energy-coupling factor ABC transporter permease -
  L1F06_RS04000 (L1F06_004000) - 878146..878361 (+) 216 WP_003242722.1 hypothetical protein -
  L1F06_RS04005 (L1F06_004005) yacG 878414..878608 (-) 195 WP_003242724.1 DNA gyrase inhibitor YacG -
  L1F06_RS04010 (L1F06_004010) coaE 878605..879213 (-) 609 WP_129482849.1 dephospho-CoA kinase -
  L1F06_RS04015 (L1F06_004015) pilD 879381..880250 (-) 870 WP_129482850.1 A24 family peptidase Machinery gene
  L1F06_RS04020 (L1F06_004020) - 880257..881482 (-) 1226 Protein_797 type II secretion system F family protein -
  L1F06_RS04025 (L1F06_004025) pilB 881487..883190 (-) 1704 WP_129482851.1 type IV-A pilus assembly ATPase PilB Machinery gene
  L1F06_RS24905 - 883419..883760 (+) 342 WP_129482852.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  L1F06_RS24910 - 883889..884221 (+) 333 WP_129482853.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  L1F06_RS04040 (L1F06_004040) nadC 884223..885071 (-) 849 WP_129482854.1 carboxylating nicotinate-nucleotide diphosphorylase -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 31792.86 Da        Isoelectric Point: 7.1414

>NTDB_id=699472 L1F06_RS04015 WP_129482850.1 879381..880250(-) (pilD) [Pseudomonas hydrolytica strain DSWY01]
MSVFNVMASNPLAFVLCALLLGLLVGSFLNVVIYRLPLMLQRDWQSQAREVLELPAAPPAQTFNLILPNSSCPQCGHEIR
PWENIPVISYLFLRGKCSNCKTPISKRYPIVELVCGLLSGYIAWHFGFTWQAGAMLVLAWGLLAMSLIDADHQILPDVLV
LPLLWLGLIVNYFGLFTSLEDALWGAIAGYLSLWSVYWLFKLITGKEGMGYGDFKLLAMLGAWGGWQILPLTILLSSLVG
AVLGVILLRLRGSDSSTPIPFGPYLAIAGWIALLWGDVITGSYLKFAGF

Nucleotide


Download         Length: 870 bp        

>NTDB_id=699472 L1F06_RS04015 WP_129482850.1 879381..880250(-) (pilD) [Pseudomonas hydrolytica strain DSWY01]
ATGTCCGTTTTTAATGTCATGGCCAGCAACCCGCTGGCCTTTGTTTTATGCGCCCTGCTGCTGGGCCTGCTGGTCGGCAG
CTTCCTTAATGTTGTGATCTATCGATTGCCCCTGATGTTGCAACGTGACTGGCAGAGCCAGGCGCGAGAGGTACTGGAGT
TACCGGCGGCGCCCCCTGCACAGACTTTCAATCTGATCCTCCCCAACTCATCCTGCCCACAATGCGGTCATGAGATTCGC
CCTTGGGAGAACATCCCGGTCATCAGCTACCTCTTCCTGCGCGGTAAGTGCTCGAACTGCAAGACCCCGATCAGCAAGCG
TTACCCCATCGTCGAGCTGGTCTGCGGACTGCTTTCCGGCTACATCGCCTGGCATTTCGGTTTTACCTGGCAGGCCGGGG
CCATGCTGGTGCTGGCCTGGGGGCTGCTGGCGATGAGTCTGATAGATGCCGATCATCAGATTCTGCCGGACGTACTGGTG
CTGCCGCTGTTATGGCTGGGCTTGATCGTCAATTACTTCGGACTGTTCACCAGCCTGGAGGACGCGCTGTGGGGGGCGAT
TGCGGGCTATCTGAGCCTATGGTCGGTGTATTGGCTGTTCAAGCTGATCACCGGCAAGGAAGGCATGGGTTACGGTGATT
TCAAGCTGCTGGCCATGCTCGGCGCCTGGGGCGGCTGGCAGATCCTGCCTTTGACCATCCTGCTGTCCTCGCTGGTCGGG
GCGGTGCTTGGGGTGATTCTGCTGCGCCTGCGTGGTAGCGACTCCAGTACGCCGATCCCCTTCGGACCTTATCTGGCCAT
TGCCGGCTGGATCGCCCTGCTCTGGGGTGACGTGATTACCGGTAGCTATCTGAAGTTTGCCGGGTTCTGA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)

Type IV leader peptidase family (Peptidase_A24)

(136-245)


Secondary structure

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



3D structure

Source ID Structure

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 cholerae strain A1552

54.874

95.848

0.526
  pilD Vibrio campbellii strain DS40M4

53.71

97.924

0.526
  pilD Acinetobacter baumannii D1279779

53.237

96.194

0.512
  pilD Acinetobacter nosocomialis M2

52.878

96.194

0.509
  pilD Neisseria gonorrhoeae MS11

49.815

93.772

0.467