Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   IF561_RS00190 Genome accession   NZ_CP062150
Coordinates   29054..30739 (-) Length   561 a.a.
NCBI ID   WP_133280437.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain 19-VB00998     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 24054..35739
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  IF561_RS00160 (IF561_00160) rplS 24545..24898 (+) 354 WP_005462554.1 50S ribosomal protein L19 -
  IF561_RS00165 (IF561_00165) yacG 25227..25421 (-) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  IF561_RS00170 (IF561_00170) zapD 25490..26230 (-) 741 WP_023624252.1 cell division protein ZapD -
  IF561_RS00175 (IF561_00175) coaE 26258..26872 (-) 615 WP_005480887.1 dephospho-CoA kinase -
  IF561_RS00180 (IF561_00180) pilD 26873..27742 (-) 870 WP_025533026.1 A24 family peptidase Machinery gene
  IF561_RS00185 (IF561_00185) pilC 27807..29030 (-) 1224 WP_029804706.1 type II secretion system F family protein Machinery gene
  IF561_RS00190 (IF561_00190) pilB 29054..30739 (-) 1686 WP_133280437.1 type IV-A pilus assembly ATPase PilB Machinery gene
  IF561_RS00195 (IF561_00195) pilA 30739..31197 (-) 459 WP_025536236.1 pilin Machinery gene
  IF561_RS00200 (IF561_00200) nadC 31460..32347 (-) 888 WP_005479699.1 carboxylating nicotinate-nucleotide diphosphorylase -
  IF561_RS00205 (IF561_00205) ampD 32440..32991 (+) 552 WP_005479703.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  IF561_RS00210 (IF561_00210) pdhR 33397..34164 (+) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 62313.21 Da        Isoelectric Point: 5.5424

>NTDB_id=486440 IF561_RS00190 WP_133280437.1 29054..30739(-) (pilB) [Vibrio parahaemolyticus strain 19-VB00998]
MITNLSAVLRQKGVLTFSQEESLIEQVKASGISMPEALLSSGFFTSSELTEHLSSIFGLSQPELSQYEYASLCQQLGLRE
LITRHNALPLHRTPSTLLLAVADPTNQQAEDDFRFATGLQVELVLADFRELSAAIRRLYGRALGKERSQIKEINQEELAS
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQQPPNHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLDIDKLGYSEQQKQLYLEALRRPQGMI
LMTGPTGSGKTVSLYTGLSILNKPEINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETIIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEHTVQLQHLGIQTTDN
IFKANPDGCNECTHGYSGRTGIYEVMRFDESLSEALIKGASVHELEKLAIANGMSTLQMSGIEKLKQGITSFSELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=486440 IF561_RS00190 WP_133280437.1 29054..30739(-) (pilB) [Vibrio parahaemolyticus strain 19-VB00998]
ATGATCACCAACCTCTCCGCGGTTCTTCGCCAAAAAGGGGTACTGACCTTTTCCCAAGAAGAATCGTTAATAGAGCAAGT
CAAAGCTTCTGGCATTTCGATGCCGGAAGCTTTACTCAGTTCTGGATTCTTCACGTCAAGCGAACTGACCGAGCACTTAA
GTTCTATTTTTGGCTTAAGTCAGCCCGAGTTATCTCAATATGAATATGCTTCGCTTTGCCAACAACTCGGCCTACGTGAA
TTAATCACACGACATAATGCACTCCCGCTCCACCGCACGCCTTCAACGTTATTATTAGCGGTTGCCGACCCCACTAATCA
ACAAGCTGAAGATGATTTCCGCTTTGCCACTGGTTTACAGGTTGAATTGGTGTTGGCGGATTTTCGCGAACTCAGTGCAG
CAATACGCCGTCTTTATGGTCGCGCGCTTGGTAAAGAACGATCCCAGATCAAAGAGATCAACCAAGAAGAGCTAGCGAGT
CTGGTGGATGTCGGTGCAGATGAAATCGACAATATCGAAGACTTGAGCCAAGACGAATCTCCTGTTAGCCGTTACATCAA
CCAAATTCTGTTGGACGCTGTACGCAAAGGCGCATCCGATATCCACTTTGAACCTTATGAAAAGATGTACCGAGTTCGTC
TACGTTGCGATGGCATTTTGATCGAAACTCAGCAACCGCCAAATCACTTGAGTCGTCGCTTATCAGCTCGTATAAAAATT
CTCTCTAAACTTGATATTGCCGAGCGACGTTTACCACAAGATGGGCGAATTAAACTCAAACTGAATCAAGACACCGCGAT
TGATATGCGGGTATCCACTCTACCTACCTTGTTTGGAGAGAAGATCGTACTACGACTGCTCGATAGCAGCTCCGCATCAC
TGGATATCGACAAGCTTGGTTATAGTGAGCAACAAAAACAGCTGTATTTAGAGGCTCTGCGTCGTCCACAAGGCATGATT
CTGATGACAGGCCCAACAGGAAGCGGTAAGACCGTTTCGTTGTACACTGGGCTAAGTATCCTCAATAAGCCAGAGATCAA
CATCTCCACAGCGGAAGACCCGGTGGAAATTAACTTATCGGGTATTAACCAAGTTCAAGTCCAACCTAAGATTGGTTTTG
GCTTTGCAGAAGCTCTACGTTCTTTTCTGCGTCAAGATCCCGATGTGGTCATGGTGGGGGAGATTCGAGACCTAGATACT
GCGGAAATCGCGATTAAGGCGTCCCAAACCGGTCACTTAGTGCTCTCTACTTTGCATACCAACTCTGCGGCTGAAACCAT
CATTCGTTTATCAAACATGGGCGTAGAAAGTTTTAACCTCGCCTCTTCTCTTAGCTTGATTATTGCCCAACGCCTAGCTC
GCAAACTTTGTCCATATTGTAAACAACCGCAAGAGCATACCGTTCAACTTCAGCACCTCGGCATCCAAACAACTGACAAC
ATCTTTAAAGCCAATCCAGATGGTTGCAACGAATGTACCCATGGTTATTCTGGCCGAACGGGTATCTATGAAGTCATGCG
CTTTGATGAATCTCTATCCGAAGCTCTTATTAAAGGAGCCTCAGTACATGAACTGGAAAAGCTTGCCATTGCGAACGGCA
TGAGCACCTTGCAAATGTCCGGAATAGAAAAACTCAAACAAGGCATCACAAGCTTTAGTGAGTTACAACGCGTGCTCTAT
TTCTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(188-455)

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

(38-142)


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 Vibrio parahaemolyticus RIMD 2210633

97.326

100

0.973
  pilB Vibrio campbellii strain DS40M4

90.553

100

0.906
  pilB Vibrio cholerae strain A1552

74.021

100

0.742
  pilB Acinetobacter baumannii D1279779

50.94

94.831

0.483
  pilB Acinetobacter baylyi ADP1

50.573

93.405

0.472
  pilB Legionella pneumophila strain ERS1305867

48.614

96.435

0.469
  pilF Neisseria gonorrhoeae MS11

44.504

100

0.447
  pilB/pilB1 Synechocystis sp. PCC 6803

37.5

100

0.396
  pilF Thermus thermophilus HB27

37.66

97.504

0.367
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

35.965

100

0.365