Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   HF888_RS13010 Genome accession   NZ_CP051183
Coordinates   2794116..2794976 (+) Length   286 a.a.
NCBI ID   WP_007016583.1    Uniprot ID   Q1MZP7
Organism   Bermanella marisrubri strain RED65     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2789116..2799976
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  HF888_RS16675 (HF888_12995) - 2790556..2791020 (+) 465 WP_007016580.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  HF888_RS13000 (HF888_13000) pilB 2791159..2792838 (+) 1680 WP_007016581.1 type IV-A pilus assembly ATPase PilB Machinery gene
  HF888_RS13005 (HF888_13005) pilC 2792851..2794077 (+) 1227 WP_007016582.1 type II secretion system F family protein Machinery gene
  HF888_RS13010 (HF888_13010) pilD 2794116..2794976 (+) 861 WP_007016583.1 A24 family peptidase Machinery gene
  HF888_RS13015 (HF888_13015) coaE 2794978..2795583 (+) 606 WP_007016584.1 dephospho-CoA kinase -
  HF888_RS13020 (HF888_13020) yacG 2795594..2795794 (+) 201 WP_007016585.1 DNA gyrase inhibitor YacG -
  HF888_RS13025 (HF888_13025) mutT 2795817..2796233 (-) 417 WP_007016586.1 8-oxo-dGTP diphosphatase MutT -
  HF888_RS13030 (HF888_13030) argJ 2796246..2797463 (-) 1218 WP_007016587.1 bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ -

Sequence

Protein


Download         Length: 286 a.a.        Molecular weight: 31739.04 Da        Isoelectric Point: 5.2380

>NTDB_id=436704 HF888_RS13010 WP_007016583.1 2794116..2794976(+) (pilD) [Bermanella marisrubri strain RED65]
MFDFLFQDTLGFYLGVFFVSLCVGSFLNVVIYRLPVMMKSQLQLEHDELIGKEVNQPEPFNLMVPSSTCPKCNSKIKPWQ
NIPVLSYLWLKGKCANCKTSISVRYPIIELITGFIPLGIAILLGPTLEAYALILMSYFFIALTMIDLDEFLLPDQLTLPL
IWIGLLFNLHGAIVPLEDAVLGAVFGYMSLWSIFWLFKLATGKEGMGYGDFKLLAAIGAFIGWQLLPVVVLLSSFVGAIV
GISMMIVLGRDKNIPIPFGPYLAAAGLLAALWGEEILNHYLRFAGL

Nucleotide


Download         Length: 861 bp        

>NTDB_id=436704 HF888_RS13010 WP_007016583.1 2794116..2794976(+) (pilD) [Bermanella marisrubri strain RED65]
ATGTTTGATTTCCTATTCCAAGATACCCTAGGTTTCTACCTAGGTGTATTTTTTGTCAGCCTATGTGTAGGCAGTTTTCT
CAACGTCGTTATTTACCGTTTACCGGTAATGATGAAGTCTCAATTACAATTGGAGCATGATGAATTAATTGGCAAAGAGG
TGAATCAACCCGAGCCTTTTAATCTAATGGTTCCATCTTCTACTTGCCCTAAATGCAATTCTAAAATCAAACCTTGGCAA
AACATTCCAGTACTCAGCTATCTGTGGTTGAAAGGGAAATGCGCGAATTGCAAAACATCTATAAGCGTACGCTATCCGAT
TATCGAATTAATCACTGGGTTCATTCCATTAGGCATTGCCATACTATTGGGTCCTACATTAGAGGCCTATGCGCTCATAT
TAATGAGTTACTTTTTCATCGCCTTAACCATGATTGATTTGGATGAATTTTTATTACCCGATCAACTTACCTTACCTTTG
ATTTGGATTGGGTTATTGTTTAATTTACATGGCGCTATTGTGCCGCTGGAAGATGCAGTATTAGGTGCTGTATTTGGCTA
CATGTCACTGTGGAGTATTTTCTGGTTATTCAAATTGGCCACTGGCAAAGAGGGTATGGGCTACGGTGACTTTAAATTAC
TCGCCGCTATTGGCGCATTTATAGGATGGCAGCTATTACCTGTGGTGGTTCTACTTTCTAGTTTTGTTGGTGCGATTGTT
GGTATCAGTATGATGATTGTACTAGGTAGAGATAAAAATATTCCTATTCCATTTGGACCTTACTTAGCAGCTGCTGGTTT
ACTAGCGGCACTTTGGGGTGAAGAAATATTAAATCATTATTTACGTTTCGCTGGACTCTAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(19-120)

Type IV leader peptidase family (Peptidase_A24)

(135-242)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q1MZP7

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

53.232

91.958

0.49
  pilD Vibrio campbellii strain DS40M4

50.951

91.958

0.469
  pilD Acinetobacter baumannii D1279779

47.163

98.601

0.465
  pilD Acinetobacter nosocomialis M2

46.809

98.601

0.462
  pilD Neisseria gonorrhoeae MS11

50.403

86.713

0.437