Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SDE_RS04550 Genome accession   NC_007912
Coordinates   1119009..1120730 (-) Length   573 a.a.
NCBI ID   WP_011467346.1    Uniprot ID   Q21MF4
Organism   Saccharophagus degradans 2-40     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1114009..1125730
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SDE_RS04525 (Sde_0858) - 1115075..1116064 (+) 990 WP_041324216.1 Nudix family hydrolase -
  SDE_RS04530 (Sde_0859) - 1116061..1116273 (-) 213 WP_011467342.1 DNA gyrase inhibitor YacG -
  SDE_RS04535 (Sde_0860) coaE 1116278..1116889 (-) 612 WP_011467343.1 dephospho-CoA kinase -
  SDE_RS04540 (Sde_0861) pilD 1116889..1117785 (-) 897 WP_011467344.1 prepilin peptidase Machinery gene
  SDE_RS04545 (Sde_0862) pilC 1117788..1119005 (-) 1218 WP_011467345.1 type II secretion system F family protein Machinery gene
  SDE_RS04550 (Sde_0863) pilB 1119009..1120730 (-) 1722 WP_011467346.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SDE_RS04555 (Sde_0864) pilA2 1121089..1121508 (+) 420 WP_011467347.1 pilin Machinery gene
  SDE_RS04560 (Sde_0865) - 1121579..1123504 (+) 1926 WP_041324223.1 hypothetical protein -
  SDE_RS04565 (Sde_0866) - 1123481..1124425 (-) 945 WP_158303854.1 lysylphosphatidylglycerol synthase domain-containing protein -
  SDE_RS04570 (Sde_0867) - 1124331..1124870 (-) 540 WP_011467350.1 acyltransferase -

Sequence

Protein


Download         Length: 573 a.a.        Molecular weight: 62692.80 Da        Isoelectric Point: 5.2551

>NTDB_id=25564 SDE_RS04550 WP_011467346.1 1119009..1120730(-) (pilB) [Saccharophagus degradans 2-40]
MGSQAIVLSGLARRLVRDSVLNEEEARLALEEATKAKLPLPIYLSQKSGISALTIATAASEEFGTPLCDLRAVRKDSIPV
GLVDKKLISKHHALPLFKRGNRLFVALTDPTNLHAIDEIKFNTGLTTEAVLAEADILNTYIEAYLNAEEESLSDSLGGLD
GDGLDIEAVDEEGRTPGEDTSEIDETPIVRFVNKVLLDAIKIGASDIHFEPYEKTYRVRYRTDGILKEVARPPTNLAPRI
SARLKVMSQMDISERRVPQDGRIKMKLSKTRAIDFRVNTLPTLFGEKVVLRILDPSSAKLGIDALGYEDFQKKLFMDALH
QPQGMILVTGPTGSGKTVSLYTGLNILNTPERNISTAEDPVEINLEGINQVNVSNKVGLTFAEALRSFLRQDPDIVMVGE
IRDLETAEIGIKAAQTGHLVLSTLHTNSAAETLTRLMNMGVPTFNVATTVSLIIAQRLARRLCSECKIPADDITNEVLTE
EGFDDIGIDRKDFQLFHPKGCDKCNNGYKGRVGIYEVVRITPQISRIIMSGGSAIDIADAAKEAGFFNLRVAALRKAATG
LTSLEEANRVTKD

Nucleotide


Download         Length: 1722 bp        

>NTDB_id=25564 SDE_RS04550 WP_011467346.1 1119009..1120730(-) (pilB) [Saccharophagus degradans 2-40]
ATGGGTAGCCAAGCAATAGTACTTAGCGGTCTAGCAAGGCGATTGGTAAGAGACAGCGTTTTAAACGAAGAAGAAGCGAG
GCTAGCCCTTGAAGAAGCAACAAAAGCCAAGTTACCACTCCCTATTTACCTTTCTCAAAAAAGTGGCATTAGCGCCCTCA
CTATAGCCACAGCAGCCTCGGAAGAGTTCGGCACCCCCCTATGCGATTTACGAGCAGTTAGGAAAGACTCCATACCGGTT
GGCCTCGTCGACAAAAAGCTAATAAGTAAACATCACGCCCTTCCCCTTTTTAAACGTGGGAACCGGCTATTTGTAGCCCT
AACAGATCCAACCAATCTACATGCTATCGATGAGATTAAATTCAATACAGGATTAACTACAGAAGCAGTACTTGCCGAAG
CAGATATCTTAAACACCTATATTGAAGCATATTTAAATGCAGAGGAAGAAAGCCTTAGCGATTCATTAGGAGGCTTAGAC
GGTGACGGCTTGGACATTGAGGCCGTCGACGAGGAAGGAAGAACACCAGGCGAAGACACCTCTGAAATAGATGAAACCCC
TATTGTTCGGTTTGTAAACAAAGTGCTACTAGATGCCATTAAAATAGGTGCTTCAGATATTCACTTTGAGCCTTACGAGA
AAACCTATCGGGTTCGATATAGAACAGACGGCATTCTCAAAGAAGTAGCCAGACCCCCAACAAACCTAGCACCAAGAATA
TCTGCACGACTTAAAGTTATGTCGCAAATGGACATATCTGAACGGCGGGTACCCCAAGATGGCCGCATTAAAATGAAGCT
CTCTAAAACGCGCGCCATCGATTTTCGTGTAAACACTCTCCCAACGCTTTTTGGCGAGAAAGTGGTGTTGCGGATCTTAG
ACCCATCCAGTGCAAAGCTCGGTATTGACGCTTTAGGCTACGAAGATTTTCAGAAAAAGCTATTTATGGATGCCCTCCAT
CAACCACAGGGCATGATTCTTGTTACTGGCCCAACCGGTTCAGGTAAAACAGTATCTCTTTATACGGGACTGAATATACT
AAACACCCCGGAACGAAACATTTCTACCGCGGAAGACCCAGTAGAAATCAACCTTGAGGGTATTAACCAAGTAAACGTTA
GTAATAAAGTTGGGCTAACATTTGCCGAAGCTTTACGCTCCTTTCTTCGTCAAGACCCTGATATTGTGATGGTGGGCGAG
ATACGCGACCTAGAAACAGCGGAAATTGGCATTAAAGCAGCGCAAACAGGTCACTTAGTGCTATCCACGCTTCACACCAA
CAGTGCCGCTGAAACTTTAACGCGCCTAATGAACATGGGGGTTCCTACGTTTAACGTGGCAACAACCGTAAGCCTGATTA
TTGCCCAGCGTCTTGCTCGGCGATTATGCTCTGAATGTAAGATACCCGCCGACGATATAACTAACGAGGTATTAACAGAA
GAAGGCTTCGACGATATAGGTATAGATAGAAAAGATTTTCAACTTTTTCACCCCAAAGGGTGCGACAAATGTAATAACGG
CTATAAAGGCCGCGTAGGTATTTATGAAGTTGTTCGCATTACCCCACAGATATCTCGCATTATAATGAGCGGTGGCAGCG
CAATCGACATAGCCGACGCAGCAAAAGAAGCCGGCTTTTTTAACTTACGGGTTGCGGCACTGCGCAAAGCGGCAACAGGC
CTAACCAGCTTAGAAGAAGCAAACCGAGTAACCAAGGACTAA

Domains

Predicted by InterproScan.

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

(50-150)

Type II/IV secretion system protein (T2SSE)

(194-461)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB Q21MF4

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

60.633

99.302

0.602
  pilB Acinetobacter baylyi ADP1

59.894

98.778

0.592
  pilB Legionella pneumophila strain ERS1305867

55.634

99.127

0.551
  pilB Vibrio parahaemolyticus RIMD 2210633

50.963

99.651

0.508
  pilB Vibrio campbellii strain DS40M4

50.435

100

0.506
  pilB Vibrio cholerae strain A1552

49.485

100

0.503
  pilF Neisseria gonorrhoeae MS11

48.763

98.778

0.482
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

40.374

93.368

0.377
  pilB/pilB1 Synechocystis sp. PCC 6803

41.7

88.307

0.368

Multiple sequence alignment