Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   GPY34_RS20175 Genome accession   NZ_CP046778
Coordinates   2311037..2312722 (-) Length   561 a.a.
NCBI ID   WP_005493983.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain 2014V-1125     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 2306037..2317722
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GPY34_RS20145 rplS 2306441..2306794 (+) 354 WP_005462554.1 50S ribosomal protein L19 -
  GPY34_RS20150 yacG 2307210..2307404 (-) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  GPY34_RS20155 zapD 2307473..2308213 (-) 741 WP_005480890.1 cell division protein ZapD -
  GPY34_RS20160 coaE 2308241..2308855 (-) 615 WP_005493969.1 dephospho-CoA kinase -
  GPY34_RS20165 pilD 2308856..2309725 (-) 870 WP_005493974.1 A24 family peptidase Machinery gene
  GPY34_RS20170 pilC 2309790..2311013 (-) 1224 WP_005493981.1 type II secretion system F family protein Machinery gene
  GPY34_RS20175 pilB 2311037..2312722 (-) 1686 WP_005493983.1 type IV-A pilus assembly ATPase PilB Machinery gene
  GPY34_RS20180 - 2312724..2313176 (-) 453 WP_005493986.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  GPY34_RS20185 nadC 2313440..2314327 (-) 888 WP_005493988.1 carboxylating nicotinate-nucleotide diphosphorylase -
  GPY34_RS20190 ampD 2314420..2314971 (+) 552 WP_005484832.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  GPY34_RS20195 pdhR 2315377..2316144 (+) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 62455.37 Da        Isoelectric Point: 5.5375

>NTDB_id=407575 GPY34_RS20175 WP_005493983.1 2311037..2312722(-) (pilB) [Vibrio parahaemolyticus strain 2014V-1125]
MLTNLSTILRQNGLLTFPQEESLFEQIKASGISMPEALLSSGFFTSSELAEHLSSIFGLSQPELSQYEYASLCQQLGLRE
LITRHNALPLHRTPSTLLLAVADPTNQQAEDDFRFATGLQVELVLADFRQLSAAIRRLYGRAIGQERSQLKEINQEELAS
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQRPPNHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLDIDKLGYSEQQKQLYLEALRRPQGMI
LMTGPTGSGKTVSLYTGLNILNKPEINISTAEDPVEINLSGINQVQVQLKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETIIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEHTVQLQHLGIQTTDN
IFKANPDGCNECTHGYSGRTGIYEVMRFDESLSEALIKGASVHELEKLAIANGMSTLQMSGIEKLKQGITSFSELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=407575 GPY34_RS20175 WP_005493983.1 2311037..2312722(-) (pilB) [Vibrio parahaemolyticus strain 2014V-1125]
ATGCTAACCAACCTCTCGACAATTCTTCGCCAAAACGGGTTACTGACTTTTCCCCAAGAAGAATCGTTATTTGAGCAAAT
CAAAGCTTCTGGCATCTCGATGCCGGAGGCTTTACTTAGTTCTGGATTCTTCACGTCAAGCGAACTGGCCGAGCACTTAA
GTTCTATTTTTGGCTTAAGTCAGCCCGAGTTATCTCAATATGAATATGCTTCGCTTTGCCAACAACTCGGCCTGCGTGAA
CTAATCACACGACATAATGCACTCCCACTCCACCGTACTCCTTCAACTTTATTATTAGCGGTTGCCGACCCCACGAATCA
ACAAGCTGAAGATGATTTCCGCTTTGCCACTGGGTTACAGGTTGAACTGGTCTTGGCGGATTTTCGTCAACTCAGCGCGG
CAATTCGTCGCTTGTACGGGCGTGCCATCGGTCAGGAACGCTCCCAACTCAAAGAGATCAACCAAGAAGAGCTAGCGAGT
CTGGTGGATGTCGGTGCAGATGAAATCGATAATATCGAAGACTTGAGCCAAGACGAGTCGCCCGTTAGCCGCTACATCAA
CCAAATTCTGTTGGACGCGGTGCGTAAAGGTGCATCCGATATCCACTTTGAGCCTTATGAAAAGATGTACCGAGTTCGCC
TACGTTGTGATGGCATTTTGATCGAAACTCAGCGACCGCCAAATCACTTGAGTCGTCGCTTATCAGCTCGTATCAAAATT
CTCTCTAAACTTGATATTGCAGAGCGACGTTTACCACAAGATGGGCGAATTAAGCTCAAACTGAATCAAGACACCGCGAT
TGATATGCGGGTATCCACGCTACCTACCTTGTTTGGAGAGAAAATCGTACTCCGACTGCTCGATAGCAGTTCTGCATCAC
TGGATATCGACAAGCTTGGTTATAGTGAGCAACAAAAACAGCTGTATTTAGAAGCTCTGCGTCGCCCACAAGGCATGATT
CTGATGACAGGCCCAACCGGGAGCGGAAAAACCGTTTCGTTGTACACTGGGTTAAATATTCTCAATAAACCAGAGATCAA
CATCTCCACAGCGGAAGACCCGGTGGAAATTAACTTATCGGGCATTAACCAAGTTCAAGTCCAACTTAAGATTGGTTTTG
GCTTTGCAGAGGCTCTACGTTCTTTTCTGCGTCAAGACCCAGATGTAGTCATGGTGGGTGAGATTCGAGACCTAGATACT
GCGGAAATCGCGATTAAGGCGTCCCAAACCGGTCACTTAGTGCTCTCTACTTTGCATACCAACTCTGCGGCTGAAACCAT
CATTCGTTTATCAAACATGGGCGTAGAAAGTTTTAACCTCGCCTCTTCGCTTAGTTTGATTATTGCCCAACGCCTAGCTC
GCAAACTTTGTCCATATTGTAAACAACCGCAAGAGCATACCGTTCAACTTCAGCACCTCGGCATTCAAACAACTGACAAC
ATCTTTAAAGCCAATCCAGATGGTTGCAACGAATGCACCCATGGTTATTCTGGCCGAACGGGTATCTATGAAGTCATGCG
CTTTGATGAATCTCTATCCGAAGCTCTTATTAAAGGAGCCTCGGTACATGAACTGGAAAAGCTTGCTATTGCGAACGGCA
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)

(38-141)


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

96.97

100

0.97
  pilB Vibrio campbellii strain DS40M4

89.661

100

0.897
  pilB Vibrio cholerae strain A1552

73.843

100

0.74
  pilB Acinetobacter baumannii D1279779

51.128

94.831

0.485
  pilB Legionella pneumophila strain ERS1305867

48.98

96.078

0.471
  pilB Acinetobacter baylyi ADP1

50.677

92.157

0.467
  pilF Neisseria gonorrhoeae MS11

45.035

100

0.453
  pilB/pilB1 Synechocystis sp. PCC 6803

37.5

100

0.396
  pilF Thermus thermophilus HB27

36.525

100

0.367
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

36.155

100

0.365

Multiple sequence alignment