Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   GPX85_RS15890 Genome accession   NZ_CP046822
Coordinates   2643437..2644303 (+) Length   288 a.a.
NCBI ID   WP_158138884.1    Uniprot ID   -
Organism   Vibrio metschnikovii strain 07-2421     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2638437..2649303
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GPX85_RS15870 nadC 2638663..2639553 (+) 891 WP_158138881.1 carboxylating nicotinate-nucleotide diphosphorylase -
  GPX85_RS15875 - 2639837..2640289 (+) 453 WP_158138882.1 pilin -
  GPX85_RS15880 pilB 2640328..2642016 (+) 1689 WP_158138883.1 type IV-A pilus assembly ATPase PilB Machinery gene
  GPX85_RS15885 pilC 2642035..2643261 (+) 1227 WP_154170154.1 type II secretion system F family protein Machinery gene
  GPX85_RS15890 pilD 2643437..2644303 (+) 867 WP_158138884.1 prepilin peptidase Machinery gene
  GPX85_RS15895 coaE 2644309..2644917 (+) 609 WP_158138885.1 dephospho-CoA kinase -
  GPX85_RS15900 zapD 2644949..2645689 (+) 741 WP_004394266.1 cell division protein ZapD -
  GPX85_RS15905 yacG 2645731..2645928 (+) 198 WP_158138886.1 DNA gyrase inhibitor YacG -
  GPX85_RS15910 parC 2646025..2648298 (-) 2274 WP_158138887.1 DNA topoisomerase IV subunit A -

Sequence

Protein


Download         Length: 288 a.a.        Molecular weight: 31889.16 Da        Isoelectric Point: 7.8853

>NTDB_id=408425 GPX85_RS15890 WP_158138884.1 2643437..2644303(+) (pilD) [Vibrio metschnikovii strain 07-2421]
MDIFYYIPWLFPALATLLGLIIGSFLNVVIYRLPTMMQREWRQECADAFPDYGITPPDGKLTLSTPRSTCPKCHTPLRIR
DNIPLISWLCLQGKCAHCSAPISARYPAIELLTAVSSLIIALHFGFSPYSVALLLFTYVLIAATFIDLDSMLLPDQLTLP
LLWAGISLALLNISPLSLNDAVIGAIAGYLCLWSIYWLFKLLTGKEGMGYGDFKLLAALGAWLGWQLLPLIVLLSSLVGL
VFGLIQLRLQKQGINKAFPFGPYLAIAGWLAMLWGDKLIAWYLHSLVG

Nucleotide


Download         Length: 867 bp        

>NTDB_id=408425 GPX85_RS15890 WP_158138884.1 2643437..2644303(+) (pilD) [Vibrio metschnikovii strain 07-2421]
ATGGACATTTTTTACTATATACCTTGGCTATTTCCCGCCTTAGCAACGCTATTAGGGTTAATCATTGGTAGTTTTTTGAA
TGTGGTGATTTACCGCTTACCAACGATGATGCAACGAGAATGGCGTCAAGAATGTGCCGACGCTTTTCCTGACTATGGCA
TCACACCCCCTGATGGCAAGCTCACGCTCAGTACACCTCGTTCAACTTGCCCTAAATGTCATACGCCTTTGCGCATAAGA
GATAATATTCCACTTATCAGTTGGCTCTGCTTGCAAGGCAAATGCGCGCACTGTTCAGCACCGATCAGCGCTCGCTATCC
GGCGATTGAGCTATTAACTGCCGTGAGCAGTTTGATCATTGCTCTGCACTTTGGCTTTAGCCCTTATAGTGTGGCACTGC
TGCTGTTTACTTATGTGTTAATTGCCGCCACCTTCATTGATTTGGATAGCATGTTGCTGCCAGACCAATTGACTCTGCCT
TTACTGTGGGCAGGGATCAGCCTAGCACTGTTGAATATTAGCCCACTCTCACTCAATGACGCCGTGATTGGAGCGATAGC
AGGCTATCTTTGCTTATGGTCGATTTATTGGCTATTTAAGCTACTGACCGGTAAAGAAGGTATGGGCTATGGTGACTTTA
AGTTGCTTGCCGCGCTCGGAGCTTGGTTAGGTTGGCAATTATTACCGTTAATCGTATTACTCTCTTCACTGGTCGGTTTG
GTGTTTGGATTGATTCAATTGCGTTTGCAAAAACAAGGCATTAATAAAGCTTTCCCGTTTGGTCCTTACTTGGCGATTGC
TGGTTGGCTGGCGATGTTGTGGGGCGATAAACTGATCGCTTGGTATCTACATTCATTGGTAGGATAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(135-244)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(17-124)


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

76.736

100

0.767
  pilD Vibrio campbellii strain DS40M4

71.875

100

0.719
  pilD Acinetobacter nosocomialis M2

57.037

93.75

0.535
  pilD Acinetobacter baumannii D1279779

55.556

93.75

0.521
  pilD Neisseria gonorrhoeae MS11

45.105

99.306

0.448

Multiple sequence alignment