Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   FDV78_RS03830 Genome accession   NZ_CP040101
Coordinates   785453..787138 (-) Length   561 a.a.
NCBI ID   WP_179000451.1    Uniprot ID   -
Organism   Vibrio parahaemolyticus strain LVP2     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 780453..792138
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  FDV78_RS03800 (FDV78_04110) rplS 780872..781225 (+) 354 WP_005462554.1 50S ribosomal protein L19 -
  FDV78_RS03805 (FDV78_04115) yacG 781625..781819 (-) 195 WP_005462546.1 DNA gyrase inhibitor YacG -
  FDV78_RS03810 (FDV78_04120) zapD 781888..782628 (-) 741 WP_179000449.1 cell division protein ZapD -
  FDV78_RS03815 (FDV78_04125) coaE 782656..783270 (-) 615 WP_179000450.1 dephospho-CoA kinase -
  FDV78_RS03820 (FDV78_04130) pilD 783271..784140 (-) 870 WP_025501249.1 A24 family peptidase Machinery gene
  FDV78_RS03825 (FDV78_04135) pilC 784205..785428 (-) 1224 WP_005462561.1 type II secretion system F family protein Machinery gene
  FDV78_RS03830 (FDV78_04140) pilB 785453..787138 (-) 1686 WP_179000451.1 type IV-A pilus assembly ATPase PilB Machinery gene
  FDV78_RS03835 (FDV78_04145) - 787143..787571 (-) 429 WP_179000452.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  FDV78_RS03840 (FDV78_04150) nadC 787835..788722 (-) 888 WP_025523107.1 carboxylating nicotinate-nucleotide diphosphorylase -
  FDV78_RS03845 (FDV78_04155) ampD 788815..789366 (+) 552 WP_005479703.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  FDV78_RS03850 (FDV78_04160) pdhR 789772..790539 (+) 768 WP_005462576.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -

Sequence

Protein


Download         Length: 561 a.a.        Molecular weight: 62412.30 Da        Isoelectric Point: 5.6724

>NTDB_id=362141 FDV78_RS03830 WP_179000451.1 785453..787138(-) (pilB) [Vibrio parahaemolyticus strain LVP2]
MQTNLSTVLRQKGLLTFSQEESLIEHVKASGISMPEALLSSGLLTSSELTEHLSSLFGLSQPELSQYEYASLCQQLGLRE
LITRHNALPLHRTPSTLLLAVADPTNQQAEDDFRFATGLQVELVLADFRELSTAIRRLYGRAIGQERSQLKEINQEELAS
LVDVGADEIDNIEDLSQDESPVSRYINQILLDAVRKGASDIHFEPYEKMYRVRLRCDGILIETQQPPNHLSRRLSARIKI
LSKLDIAERRLPQDGRIKLKLNQDTAIDMRVSTLPTLFGEKIVLRLLDSSSASLDIDKLGYSEQQKQLYLEALRRPQGMI
LMTGPTGSGKTVSLYTGLNILNKPEINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLDT
AEIAIKASQTGHLVLSTLHTNSAAETIIRLSNMGVESFNLASSLSLIIAQRLARKLCPYCKQPQEHTVQLQHLGIQTTDK
IFRANPDGCNECTHGYSGRTGIYEVMRFDESLSEALIKGASVHELEKLAIANGMSTLQMSGIEKLKQGITSFSELQRVLY
F

Nucleotide


Download         Length: 1686 bp        

>NTDB_id=362141 FDV78_RS03830 WP_179000451.1 785453..787138(-) (pilB) [Vibrio parahaemolyticus strain LVP2]
GTGCAAACTAACCTATCAACAGTTCTTCGTCAAAAAGGATTACTGACGTTTTCCCAAGAAGAATCGTTAATAGAGCACGT
CAAAGCTTCTGGCATTTCGATGCCGGAAGCTTTACTCAGTTCTGGATTATTGACATCAAGCGAACTCACTGAGCACTTAA
GTTCTCTCTTTGGTTTGAGTCAGCCCGAGTTATCTCAATATGAATATGCTTCGCTTTGCCAACAGCTCGGCCTACGTGAA
TTAATCACACGACATAATGCACTCCCACTCCACCGTACTCCTTCAACTTTATTATTAGCGGTTGCCGACCCCACGAATCA
ACAAGCTGAAGATGATTTCCGCTTTGCCACTGGTTTACAGGTTGAGTTGGTGTTGGCGGATTTTCGCGAACTCAGTACAG
CAATTCGACGCTTGTACGGGCGTGCCATCGGTCAGGAACGCTCCCAACTCAAAGAGATCAACCAAGAAGAGCTAGCGAGT
CTGGTGGATGTCGGTGCAGATGAAATCGACAATATCGAAGACTTGAGCCAAGACGAGTCGCCCGTTAGCCGCTACATCAA
CCAAATTCTGTTGGACGCGGTGCGTAAAGGCGCATCCGATATCCACTTTGAACCTTATGAAAAGATGTACCGAGTTCGTC
TACGTTGCGATGGCATTTTGATCGAAACTCAGCAACCGCCAAATCACTTGAGTCGTCGCTTATCAGCTCGTATAAAAATT
CTCTCTAAACTTGATATTGCCGAGCGACGTTTACCACAAGATGGGCGAATTAAACTCAAACTGAATCAAGACACCGCGAT
TGATATGCGGGTATCCACTCTACCTACCTTGTTTGGAGAGAAGATCGTACTACGACTGCTCGATAGCAGCTCCGCATCAC
TGGATATCGACAAGCTTGGTTATAGTGAGCAACAAAAACAGCTGTATTTAGAGGCTCTGCGTCGTCCACAAGGTATGATT
CTGATGACAGGCCCAACAGGAAGCGGCAAGACTGTTTCATTGTACACTGGGTTAAATATTCTCAATAAACCAGAGATCAA
TATATCCACAGCAGAGGATCCTGTGGAAATTAACTTATCGGGCATTAACCAAGTTCAAGTCCAACCTAAGATTGGTTTTG
GCTTTGCAGAAGCTCTACGTTCTTTTCTACGTCAAGATCCCGATGTGGTCATGGTGGGTGAGATTCGAGACCTAGATACT
GCGGAAATCGCGATTAAGGCGTCCCAAACCGGTCACTTAGTGCTCTCTACTTTGCATACCAACTCTGCAGCTGAAACCAT
CATTCGCTTATCAAACATGGGCGTAGAAAGTTTTAACCTCGCCTCTTCTCTTAGTTTGATTATTGCCCAACGCCTAGCTC
GCAAACTTTGTCCATATTGTAAACAACCGCAAGAGCATACCGTTCAACTTCAGCACCTAGGCATTCAAACAACTGACAAA
ATTTTTAGAGCCAATCCAGATGGTTGCAACGAATGCACCCATGGTTATTCTGGCCGAACGGGTATCTATGAAGTCATGCG
CTTTGATGAATCTTTATCCGAAGCTCTTATTAAAGGAGCCTCGGTACATGAACTGGAAAAGCTTGCTATTGCGAACGGCA
TGAGCACCTTGCAAATGTCCGGAATAGAAAAACTCAAGCAAGGCATCACAAGCTTTAGTGAGTTACAACGCGTGCTCTAT
TTCTAA

Domains

Predicted by InterproScan.

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

(38-141)

Type II/IV secretion system protein (T2SSE)

(188-455)


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

90.018

100

0.9
  pilB Vibrio cholerae strain A1552

73.488

100

0.736
  pilB Acinetobacter baumannii D1279779

51.711

93.761

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

44.858

100

0.451
  pilB/pilB1 Synechocystis sp. PCC 6803

37.5

100

0.396
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

36.749

100

0.371
  pilF Thermus thermophilus HB27

36.525

100

0.367
  pilB Haemophilus influenzae 86-028NP

38.593

93.761

0.362

Multiple sequence alignment