Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   AYJ58_RS04880 Genome accession   NZ_CP015194
Coordinates   1091924..1092850 (-) Length   308 a.a.
NCBI ID   WP_106649215.1    Uniprot ID   -
Organism   Shewanella sp. Pdp11     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1086924..1097850
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AYJ58_RS04850 (AYJ58_04765) - 1088023..1088949 (+) 927 WP_106649211.1 exopolyphosphatase -
  AYJ58_RS04855 (AYJ58_04770) - 1089018..1089554 (-) 537 WP_106649212.1 thioredoxin family protein -
  AYJ58_RS04860 (AYJ58_04775) mutT 1089785..1090177 (-) 393 WP_106649213.1 8-oxo-dGTP diphosphatase MutT -
  AYJ58_RS04865 (AYJ58_04780) yacG 1090257..1090466 (-) 210 WP_006083355.1 DNA gyrase inhibitor YacG -
  AYJ58_RS04870 (AYJ58_04785) zapD 1090540..1091274 (-) 735 WP_106649214.1 cell division protein ZapD -
  AYJ58_RS04875 (AYJ58_04790) coaE 1091267..1091884 (-) 618 WP_063884698.1 dephospho-CoA kinase -
  AYJ58_RS04880 (AYJ58_04795) pilD 1091924..1092850 (-) 927 WP_106649215.1 A24 family peptidase Machinery gene
  AYJ58_RS04885 (AYJ58_04800) pilC 1092890..1094161 (-) 1272 WP_106649216.1 type II secretion system F family protein Machinery gene
  AYJ58_RS04890 (AYJ58_04805) pilB 1094312..1096024 (-) 1713 WP_106649217.1 type IV-A pilus assembly ATPase PilB Machinery gene

Sequence

Protein


Download         Length: 308 a.a.        Molecular weight: 34331.72 Da        Isoelectric Point: 7.0177

>NTDB_id=177386 AYJ58_RS04880 WP_106649215.1 1091924..1092850(-) (pilD) [Shewanella sp. Pdp11]
MSEFISLLGQSLDQSPWLFIALSFIFAATIGSFLNVVIHRFPVMMKREWQQECNQYLQEYHEDTVKKIGIDQLNRPIDAF
PEKYNLVVPGSACPKCKTAIKPWHNLPVLGWLMLKGNCAACHAPISARYPIIEFITGLLIATLAWHFGPSWQFVFASILT
FVLVALTGIDLDEMLLPDQMTLPLLWLGLIINLNHTFASPTDAIIGAAAGYLSLWSIFWLFKILTGKEGMGYGDFKLLAV
FGAWLGWQMLPLVILLSSLVGAVVGITMIVSKRLKQGNPIPFGPYIAAAGWIALLFGQQIVDWYLSTL

Nucleotide


Download         Length: 927 bp        

>NTDB_id=177386 AYJ58_RS04880 WP_106649215.1 1091924..1092850(-) (pilD) [Shewanella sp. Pdp11]
ATGTCAGAATTCATCTCCCTTTTAGGCCAGTCTCTAGATCAGAGTCCTTGGCTGTTTATTGCGTTAAGCTTTATTTTTGC
CGCTACCATAGGTAGTTTTTTAAACGTAGTGATCCACAGATTTCCTGTGATGATGAAACGGGAGTGGCAGCAAGAATGTA
ATCAGTATTTGCAGGAATACCACGAAGACACAGTCAAAAAAATAGGGATAGACCAACTCAATAGACCTATTGATGCCTTC
CCTGAAAAGTACAATCTTGTTGTGCCTGGTTCAGCCTGCCCTAAATGTAAAACCGCGATTAAACCTTGGCATAATTTGCC
TGTATTAGGCTGGTTAATGCTCAAAGGCAATTGCGCCGCCTGTCACGCCCCTATTTCTGCTCGCTACCCTATTATTGAAT
TCATCACAGGGCTACTTATCGCGACTTTAGCTTGGCATTTTGGTCCAAGCTGGCAGTTTGTTTTTGCGAGCATACTCACC
TTTGTGCTTGTAGCACTGACGGGTATCGATCTTGATGAGATGTTGCTCCCCGACCAAATGACGCTACCGTTGCTTTGGCT
CGGCTTGATAATCAATCTAAATCATACCTTTGCGAGCCCAACCGATGCCATTATCGGTGCGGCGGCAGGCTATTTAAGCC
TGTGGTCCATTTTTTGGCTATTTAAGATCCTCACCGGCAAGGAAGGCATGGGTTATGGTGACTTTAAACTGCTAGCCGTA
TTCGGTGCTTGGCTTGGCTGGCAAATGCTGCCGCTGGTGATTTTACTTTCGTCCCTCGTTGGCGCAGTCGTTGGCATCAC
TATGATTGTCAGTAAACGCCTGAAACAAGGGAATCCAATCCCATTTGGCCCTTATATTGCCGCAGCTGGCTGGATAGCCT
TGCTATTTGGACAACAGATTGTCGATTGGTATCTATCAACACTGTAA

Domains

Predicted by InterproScan.

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(25-147)

Type IV leader peptidase family (Peptidase_A24)

(158-266)


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

51.525

95.779

0.494
  pilD Acinetobacter nosocomialis M2

47.869

99.026

0.474
  pilD Vibrio campbellii strain DS40M4

49.66

95.455

0.474
  pilD Acinetobacter baumannii D1279779

47.712

99.351

0.474
  pilD Neisseria gonorrhoeae MS11

43.643

94.481

0.412

Multiple sequence alignment