Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   D0871_RS03450 Genome accession   NZ_CP033141
Coordinates   651919..653604 (-) Length   561 a.a.
NCBI ID   WP_023624254.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain 160807     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 646919..658604
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  D0871_RS03420 (D0871_03420) rplS 647352..647705 (+) 354 WP_005462554.1 50S ribosomal protein L19 -
  D0871_RS03425 (D0871_03425) yacG 648092..648286 (-) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  D0871_RS03430 (D0871_03430) zapD 648355..649095 (-) 741 WP_023624252.1 cell division protein ZapD -
  D0871_RS03435 (D0871_03435) coaE 649123..649737 (-) 615 WP_023624253.1 dephospho-CoA kinase -
  D0871_RS03440 (D0871_03440) pilD 649738..650607 (-) 870 WP_069514824.1 A24 family peptidase Machinery gene
  D0871_RS03445 (D0871_03445) pilC 650672..651895 (-) 1224 WP_005479682.1 type II secretion system F family protein Machinery gene
  D0871_RS03450 (D0871_03450) pilB 651919..653604 (-) 1686 WP_023624254.1 type IV-A pilus assembly ATPase PilB Machinery gene
  D0871_RS03455 (D0871_03455) pilA 653614..654033 (-) 420 WP_069514826.1 pilin Machinery gene
  D0871_RS03460 (D0871_03460) nadC 654297..655184 (-) 888 WP_015297249.1 carboxylating nicotinate-nucleotide diphosphorylase -
  D0871_RS03465 (D0871_03465) ampD 655277..655828 (+) 552 WP_005479703.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  D0871_RS03470 (D0871_03470) pdhR 656234..657001 (+) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 62391.24 Da        Isoelectric Point: 5.9393

>NTDB_id=321787 D0871_RS03450 WP_023624254.1 651919..653604(-) (pilB) [Vibrio parahaemolyticus strain 160807]
MHSNLSTILRQKGLLTFSQEESLIEQVKASGISMPEALLSSGFFTSSELAKHLSSIFGLSQPELSQYEYASLCQQLGLRE
LITRHNALPLHRTPSTLLLAVADPTNQQAEDDFRFATGLQVELVLADFRELSTAIRRLYGRSLSHEKSGLKEINQEELAS
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQQPPNHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLDIDKLGYSEQQKQLYLEALRRPQGMI
LMTGPTGSGKTVSLYTGLNILNKPEINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETIIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEHTVQLQHLGIQTTDN
IFRANPDGCNECTHGYSGRTGIYEVMRFDESLSEALIKGASVHELEKLAIANGMSTLQMSGIEKLKQGITSFSELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=321787 D0871_RS03450 WP_023624254.1 651919..653604(-) (pilB) [Vibrio parahaemolyticus strain 160807]
ATGCACTCCAACCTCTCCACGATTCTTCGTCAAAAAGGATTACTGACGTTTTCCCAAGAAGAATCGTTAATAGAGCAAGT
TAAAGCTTCTGGCATCTCGATGCCGGAAGCTTTACTCAGTTCTGGATTCTTCACATCAAGCGAACTGGCCAAGCACTTAA
GTTCTATTTTTGGCCTAAGTCAGCCCGAGTTATCTCAATATGAATATGCTTCGCTTTGCCAACAGCTCGGCCTACGTGAA
TTAATCACACGACATAATGCACTCCCACTCCACCGTACTCCTTCAACTTTATTATTAGCGGTTGCCGACCCCACGAATCA
ACAAGCTGAAGATGATTTCCGCTTTGCCACTGGTTTACAGGTTGAGTTGGTGTTGGCGGATTTTCGCGAACTCAGTACAG
CAATTCGACGCTTATATGGTCGTTCATTGAGTCATGAAAAGTCTGGGTTAAAAGAGATCAACCAAGAAGAACTAGCGAGT
CTGGTGGATGTCGGTGCAGATGAAATCGACAATATCGAAGACTTGAGCCAAGACGAATCTCCTGTTAGCCGTTACATCAA
CCAAATTCTGTTGGACGCTGTACGCAAAGGCGCATCCGATATCCACTTTGAACCTTATGAAAAGATGTACCGAGTTCGTC
TACGTTGCGATGGCATTTTGATCGAAACTCAGCAACCGCCAAATCACTTGAGTCGTCGCTTATCAGCTCGTATAAAAATT
CTCTCTAAACTTGATATTGCCGAGCGACGTTTACCACAAGATGGGCGAATTAAACTCAAACTGAATCAAGACACCGCGAT
TGATATGCGGGTATCCACTCTACCTACCTTGTTTGGAGAGAAGATCGTACTACGACTGCTCGATAGCAGCTCTGCATCAC
TGGATATCGACAAGCTTGGTTATAGTGAGCAACAAAAACAGCTGTATTTAGAGGCTCTGCGTCGTCCACAAGGTATGATT
CTGATGACAGGCCCAACAGGAAGCGGCAAGACCGTTTCGTTGTACACTGGGTTAAATATTCTCAATAAACCAGAGATCAA
CATCTCTACAGCGGAAGACCCGGTGGAAATTAACTTATCGGGCATTAACCAAGTTCAAGTCCAACCTAAAATTGGTTTTG
GCTTTGCAGAAGCACTACGCTCTTTCCTGCGTCAAGATCCCGATGTGGTCATGGTTGGTGAGATTCGAGACCTAGATACT
GCGGAAATCGCGATTAAGGCGTCCCAAACCGGTCACTTAGTGCTCTCTACTTTGCATACCAACTCTGCGGCTGAAACAAT
CATTCGTTTATCAAACATGGGCGTAGAAAGTTTTAACCTCGCCTCTTCTCTTAGTTTGATTATTGCCCAACGCCTAGCTC
GCAAACTTTGTCCATATTGTAAACAACCGCAAGAGCATACCGTTCAACTTCAGCACCTAGGCATTCAAACAACTGACAAC
ATTTTTAGAGCCAATCCAGATGGTTGCAACGAATGCACCCATGGTTATTCTGGCCGAACAGGTATCTATGAAGTCATGCG
CTTTGATGAATCTCTATCCGAAGCTCTTATTAAAGGAGCCTCGGTACATGAACTGGAAAAGCTTGCCATTGCGAACGGCA
TGAGCACCTTGCAAATGTCCGGAATAGAAAAACTCAAGCAAGGCATCACAAGCTTTAGTGAGTTACAACGCGTGCTCTAT
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)

(38-144)


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

99.822

100

0.998
  pilB Vibrio campbellii strain DS40M4

90.196

100

0.902
  pilB Vibrio cholerae strain A1552

73.488

100

0.736
  pilB Acinetobacter baumannii D1279779

51.509

94.474

0.487
  pilB Acinetobacter baylyi ADP1

47.935

99.287

0.476
  pilB Legionella pneumophila strain ERS1305867

48.98

96.078

0.471
  pilF Neisseria gonorrhoeae MS11

45.39

100

0.456
  pilB/pilB1 Synechocystis sp. PCC 6803

37.099

100

0.392
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

36.861

100

0.373
  pilF Thermus thermophilus HB27

36.396

100

0.367

Multiple sequence alignment