Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   RMET_RS15575 Genome accession   NC_007973
Coordinates   3370268..3371137 (+) Length   289 a.a.
NCBI ID   WP_011517606.1    Uniprot ID   Q1LIP4
Organism   Cupriavidus metallidurans CH34     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 3365268..3376137
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RMET_RS33620 - 3365537..3365677 (-) 141 WP_155877846.1 hypothetical protein -
  RMET_RS15555 (Rmet_3107) ispB 3365831..3366760 (+) 930 WP_049799754.1 octaprenyl diphosphate synthase -
  RMET_RS15565 (Rmet_3108) pilB 3367233..3368954 (+) 1722 WP_011517604.1 type IV-A pilus assembly ATPase PilB Machinery gene
  RMET_RS15570 (Rmet_3109) - 3368984..3370249 (+) 1266 WP_011517605.1 type II secretion system F family protein -
  RMET_RS15575 (Rmet_3110) pilD 3370268..3371137 (+) 870 WP_011517606.1 A24 family peptidase Machinery gene
  RMET_RS15580 (Rmet_3111) coaE 3371208..3371852 (+) 645 WP_011517607.1 dephospho-CoA kinase -
  RMET_RS15585 (Rmet_3112) zapD 3372075..3372833 (+) 759 WP_008650332.1 cell division protein ZapD -
  RMET_RS15590 (Rmet_3113) - 3372842..3373033 (+) 192 WP_011517608.1 DNA gyrase inhibitor YacG -
  RMET_RS15595 (Rmet_3114) - 3373119..3375149 (-) 2031 WP_011517609.1 OPT family oligopeptide transporter -
  RMET_RS15600 (Rmet_3115) - 3375205..3375648 (-) 444 WP_011517610.1 NUDIX domain-containing protein -

Sequence

Protein


Download         Length: 289 a.a.        Molecular weight: 31268.40 Da        Isoelectric Point: 8.1375

>NTDB_id=25794 RMET_RS15575 WP_011517606.1 3370268..3371137(+) (pilD) [Cupriavidus metallidurans CH34]
MQAVLSSLAALPPAFLIVAAGVVGLMVGSFLNVVIHRLPKMMEYDEANYIAEIRGEPLPHPERYNLMVPRSACPKCGHQI
APWENIPVISYLFLRGRCKACKTPIGIRYPLVELITAALSALAMWHFGPTAQALAAIVMTWSLVALFMIDADTQLLPDQI
TLPLLWLGLLLNLQGLFAPLADAVIGAAAGYLLLWSVYWLYKLVRGREGMGHGDFKLMAALGAWFGWQALPALILMSSVV
GAVLGGAMLVFRRKSSDTTFPFGPYIVGAGLIVLFFGADVLPLTLVAGH

Nucleotide


Download         Length: 870 bp        

>NTDB_id=25794 RMET_RS15575 WP_011517606.1 3370268..3371137(+) (pilD) [Cupriavidus metallidurans CH34]
ATGCAAGCTGTCCTGTCATCGCTGGCGGCGTTGCCGCCAGCTTTCCTTATTGTCGCGGCAGGGGTGGTTGGCCTGATGGT
CGGCAGTTTCCTCAACGTGGTGATCCATCGTCTGCCGAAGATGATGGAGTACGACGAGGCCAACTACATCGCGGAAATCC
GTGGCGAACCGTTGCCGCACCCCGAGCGCTATAACCTGATGGTGCCGCGATCCGCGTGCCCGAAGTGCGGCCACCAGATC
GCCCCCTGGGAGAACATCCCCGTCATCAGCTACCTGTTCCTGCGTGGCCGCTGCAAGGCCTGCAAGACGCCGATCGGCAT
CCGCTATCCGCTCGTCGAGCTGATCACGGCGGCGCTCAGCGCCCTGGCGATGTGGCACTTCGGTCCGACGGCGCAGGCGC
TGGCCGCGATCGTGATGACCTGGTCGCTGGTCGCGTTGTTCATGATCGATGCCGACACCCAGCTTCTGCCAGACCAGATC
ACGCTGCCGCTGCTATGGCTGGGCCTGCTGCTGAACCTGCAGGGCTTGTTCGCGCCGCTGGCGGATGCCGTCATCGGCGC
TGCGGCGGGCTACCTGCTGCTGTGGAGCGTCTACTGGCTCTACAAGCTCGTGCGGGGCCGCGAGGGCATGGGCCACGGCG
ATTTCAAGTTGATGGCGGCGCTTGGCGCATGGTTCGGCTGGCAGGCACTGCCCGCGCTGATCCTGATGTCGTCGGTGGTC
GGTGCCGTGCTTGGCGGCGCGATGCTGGTCTTCCGCCGCAAGAGTAGTGACACGACCTTCCCGTTTGGCCCGTACATCGT
CGGTGCCGGGCTGATCGTGCTGTTCTTTGGCGCAGACGTATTACCGCTGACGCTGGTGGCCGGACACTAG

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(138-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(22-127)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q1LIP4

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

52.015

94.464

0.491
  pilD Vibrio campbellii strain DS40M4

52.206

94.118

0.491
  pilD Neisseria gonorrhoeae MS11

49.632

94.118

0.467
  pilD Acinetobacter baumannii D1279779

45.956

94.118

0.433
  pilD Acinetobacter nosocomialis M2

44.853

94.118

0.422

Multiple sequence alignment