Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   D5S12_RS04520 Genome accession   NZ_CP032459
Coordinates   987062..988756 (-) Length   564 a.a.
NCBI ID   WP_058397524.1    Uniprot ID   -
Organism   Pseudomonas syringae strain CAS02     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 982062..993756
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  D5S12_RS26395 - 982147..982383 (-) 237 WP_316933231.1 DUF3094 family protein -
  D5S12_RS04485 (D5S12_04805) - 982268..982801 (-) 534 WP_003430737.1 MOSC domain-containing protein -
  D5S12_RS04490 (D5S12_04810) - 982798..983427 (-) 630 WP_003345130.1 DUF1780 domain-containing protein -
  D5S12_RS04495 (D5S12_04815) - 983555..984016 (+) 462 WP_058397529.1 hypothetical protein -
  D5S12_RS04500 (D5S12_04820) yacG 984142..984351 (-) 210 WP_002552020.1 DNA gyrase inhibitor YacG -
  D5S12_RS04505 (D5S12_04825) coaE 984348..984971 (-) 624 WP_058397527.1 dephospho-CoA kinase -
  D5S12_RS04510 (D5S12_04830) pilD 984968..985840 (-) 873 WP_187600008.1 prepilin peptidase Machinery gene
  D5S12_RS04515 (D5S12_04835) pilC 985842..987059 (-) 1218 WP_058397525.1 type II secretion system F family protein Machinery gene
  D5S12_RS04520 (D5S12_04840) pilB 987062..988756 (-) 1695 WP_058397524.1 type IV-A pilus assembly ATPase PilB Machinery gene
  D5S12_RS04525 (D5S12_04845) pilA2 988982..989407 (+) 426 WP_044323946.1 pilin Machinery gene
  D5S12_RS04535 (D5S12_04855) - 989767..990312 (-) 546 WP_003371273.1 DUF1523 family protein -
  D5S12_RS04540 (D5S12_04860) - 990432..991430 (+) 999 WP_187600010.1 ATP-grasp domain-containing protein -
  D5S12_RS04545 (D5S12_04865) - 991485..992624 (+) 1140 WP_060708665.1 trypsin-like peptidase domain-containing protein -

Sequence

Protein


Download         Length: 564 a.a.        Molecular weight: 62421.63 Da        Isoelectric Point: 5.9786

>NTDB_id=316021 D5S12_RS04520 WP_058397524.1 987062..988756(-) (pilB) [Pseudomonas syringae strain CAS02]
MTDAVLTGLAKQLVLAELLTEPAALQAYQQARRDKISLVSYLVQNGLVKSLTLAEMASDQFGVPFMDLASLDKESQPKGL
VSEKLVRQHHALPLWRRGNKLFIGISDPTNHQAVTDIQFSTGLNTEAILVEDDKLTTAIDRFFDSDSGLGNLEDVDLGLD
IEPADGKETSLATQNDADDAPVVRFVNKMLMDAIRLGSSDLHFEPYEKIFRVRLRTDGILHEVARPPIHLANRIAARLKV
MASLDISERRKPQDGRVKLRVSKTKAIDFRMNTLPTLWGEKIVMRILDPTSAQMGIDALGYEPEQKALYLEALKQPQGMI
LVTGPTGSGKTVSLYTGLNILNTVDINISTAEDPVEINLEGINQVNVNPRQGLDFSQALRAFLRQDPDVIMVGEIRDLET
AEIAIKASQTGHMVLSTLHTNSAAETLTRLHHMGVAAFNIATAINLIIAQRLARKLCSHCKKELDIPRETLIQEGFPEEK
IGTFKIYGPVGCEHCNGGYRGRVGIYEVVKKTPELERIIMEEGNSLEISRQMRKDGFNDLRTSGLSKAMQGITSLEEVNR
VTKD

Nucleotide


Download         Length: 1695 bp        

>NTDB_id=316021 D5S12_RS04520 WP_058397524.1 987062..988756(-) (pilB) [Pseudomonas syringae strain CAS02]
ATGACTGATGCTGTTCTCACTGGCTTGGCCAAACAATTGGTCTTAGCCGAGCTGCTTACTGAACCTGCTGCGCTGCAAGC
GTATCAACAAGCGCGTCGTGACAAAATTTCGTTAGTGAGCTATTTGGTTCAGAACGGACTAGTCAAAAGCCTGACGCTGG
CAGAAATGGCTTCCGATCAGTTTGGCGTCCCCTTCATGGACCTAGCCAGCCTGGACAAAGAAAGCCAGCCTAAAGGCCTG
GTAAGTGAAAAGCTGGTTCGACAACATCACGCGCTGCCGCTGTGGCGACGCGGCAATAAACTGTTTATAGGGATTTCGGA
CCCTACGAATCATCAGGCGGTCACCGATATTCAGTTCAGTACTGGCCTGAATACCGAAGCGATTCTGGTAGAAGATGACA
AGCTAACCACTGCCATAGATCGTTTTTTTGACAGTGATAGCGGTCTAGGTAATCTGGAAGATGTCGATCTGGGTCTGGAT
ATCGAACCGGCTGATGGCAAGGAAACTTCCCTCGCTACGCAGAATGACGCAGACGATGCCCCGGTGGTACGCTTCGTCAA
CAAGATGCTGATGGACGCTATTCGGTTAGGATCGTCCGATCTGCATTTTGAGCCTTACGAAAAGATCTTCCGCGTGCGGT
TGCGTACCGATGGCATCTTGCATGAAGTCGCTAGACCACCAATTCATTTGGCAAACCGTATTGCCGCGCGCTTGAAAGTC
ATGGCCAGCCTGGATATCTCGGAACGGCGCAAACCGCAGGACGGACGGGTCAAGTTACGCGTGTCCAAAACAAAAGCCAT
CGATTTTCGTATGAACACCTTGCCCACATTATGGGGCGAGAAGATCGTGATGCGGATCCTTGATCCGACCAGTGCGCAGA
TGGGCATTGACGCCTTGGGATACGAGCCAGAACAAAAAGCGCTGTATCTGGAGGCGCTTAAACAACCGCAAGGCATGATT
CTTGTCACTGGCCCGACAGGGTCCGGCAAGACCGTATCACTGTATACCGGTCTGAATATCCTCAATACTGTGGACATTAA
CATTTCCACAGCTGAAGACCCGGTAGAGATCAACCTGGAAGGTATCAATCAGGTTAACGTCAACCCGCGTCAGGGGCTGG
ACTTTTCTCAGGCTTTGCGCGCATTTCTGCGTCAAGATCCCGACGTAATCATGGTCGGCGAGATACGGGACTTGGAAACG
GCAGAAATTGCCATCAAAGCCTCGCAGACCGGACACATGGTGTTATCTACTCTGCATACTAATAGTGCCGCAGAAACCCT
GACCCGCCTGCATCATATGGGTGTCGCAGCGTTCAACATCGCCACAGCAATCAACCTCATCATTGCTCAGCGGCTGGCGC
GCAAGCTATGCAGCCATTGTAAGAAAGAACTCGATATCCCCCGGGAAACGCTCATCCAGGAGGGTTTTCCAGAGGAGAAG
ATCGGTACGTTTAAAATCTATGGCCCAGTAGGTTGTGAGCATTGCAACGGCGGCTACAGAGGCAGGGTCGGCATTTACGA
AGTAGTCAAGAAAACACCAGAACTGGAGCGCATCATCATGGAAGAAGGCAACTCGCTGGAGATCTCCAGACAGATGCGCA
AGGACGGTTTCAATGACCTTCGCACATCTGGGCTTTCGAAAGCCATGCAAGGCATCACCAGCCTTGAAGAAGTCAACCGC
GTGACCAAGGATTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(188-455)

Type II secretion system (T2SS), protein E, N-terminal domain (MshEN)

(42-147)


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
  pilB Acinetobacter baumannii D1279779

57.672

100

0.58
  pilB Acinetobacter baylyi ADP1

56.94

99.645

0.567
  pilB Legionella pneumophila strain ERS1305867

55.044

100

0.551
  pilB Vibrio cholerae strain A1552

50.712

99.645

0.505
  pilB Vibrio parahaemolyticus RIMD 2210633

51.184

97.34

0.498
  pilB Vibrio campbellii strain DS40M4

49.47

100

0.496
  pilF Neisseria gonorrhoeae MS11

48.399

99.645

0.482
  pilF Thermus thermophilus HB27

39.046

100

0.392
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.973

93.262

0.363

Multiple sequence alignment