Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   vm_RS02860 Genome accession   NZ_CP016383
Coordinates   557517..559205 (-) Length   562 a.a.
NCBI ID   WP_070381370.1    Uniprot ID   -
Organism   Vibrio mimicus strain SCCF01     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 552517..564205
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  vm_RS02835 (VM_02835) yacG 553489..553686 (-) 198 WP_000162865.1 DNA gyrase inhibitor YacG -
  vm_RS02840 (VM_02840) zapD 553937..554677 (-) 741 WP_070381366.1 cell division protein ZapD -
  vm_RS02845 (VM_02845) coaE 554709..555317 (-) 609 WP_070381367.1 dephospho-CoA kinase -
  vm_RS02850 (VM_02850) pilD 555314..556189 (-) 876 WP_070381368.1 prepilin peptidase Machinery gene
  vm_RS02855 (VM_02855) pilC 556252..557478 (-) 1227 WP_070381369.1 type II secretion system F family protein Machinery gene
  vm_RS02860 (VM_02860) pilB 557517..559205 (-) 1689 WP_070381370.1 type IV-A pilus assembly ATPase PilB Machinery gene
  vm_RS02865 (VM_02865) pilA 559209..559658 (-) 450 WP_070381371.1 pilin Machinery gene
  vm_RS02870 (VM_02870) nadC 559903..560793 (-) 891 WP_070382548.1 carboxylating nicotinate-nucleotide diphosphorylase -
  vm_RS02875 (VM_02875) ampD 560958..561506 (+) 549 WP_070381372.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  vm_RS02880 (VM_02880) fldB 561564..562082 (-) 519 WP_000690114.1 flavodoxin FldB -
  vm_RS02885 (VM_02885) xerD 562250..563128 (+) 879 WP_196770036.1 site-specific tyrosine recombinase XerD -
  vm_RS02890 (VM_02890) dsbC 563145..563897 (+) 753 WP_061051575.1 bifunctional protein-disulfide isomerase/oxidoreductase DsbC -

Sequence

Protein


Download         Length: 562 a.a.        Molecular weight: 62145.00 Da        Isoelectric Point: 5.5276

>NTDB_id=187678 vm_RS02860 WP_070381370.1 557517..559205(-) (pilB) [Vibrio mimicus strain SCCF01]
MLTNLVAILRQAELISSTQEQAVVEQVSASGTSVPEALLELSIFHAQELTEQLSHIFGLPETDLSHYDYPNLCQQLGLRE
LITRYEALPIAKQGNLLQLAVSDPTLLQAEEEFRFATGLQVELALADHRALQAAIRRLYGRSIQGGANQGKEISQDELAN
LVKVSDDELQSIEDLSQDDSPVSRFINQVLLDAVRKGASDIHFEPYEAQYRIRLRCDGILVETQQPASHLSRRLAARIKI
LSKLDIAERRLPQDGRIKLRLNSDTAIDMRVSTLPTLWGEKIVLRLLDSSAANLDIDKLGYNPQQKQLYLNALKRPQGMI
LMTGPTGSGKTVSLYTGLRILNTSQINISTAEDPVEINLSGINQVQVQPKIGFGFAEALRSFLRQDPDVVMVGEIRDLET
AEIAVKAAQTGHLVLSTLHTNSAAETVIRLANMGVEPFNLASSLSLIIAQRLARRLCKHCKVAVHPSAILQNQFAFQSQE
ILYEANAAGCNECTGGYSGRVGIYEVMAFNTELAEAIMRRATIHQIESLAKNNGMQTLQESGLEKLREGITSFAELQRVL
YF

Nucleotide


Download         Length: 1689 bp        

>NTDB_id=187678 vm_RS02860 WP_070381370.1 557517..559205(-) (pilB) [Vibrio mimicus strain SCCF01]
ATGCTCACCAACCTTGTTGCTATCTTGCGTCAAGCCGAGTTAATCAGCTCGACGCAAGAACAAGCTGTGGTCGAACAGGT
TAGCGCTTCAGGTACTTCTGTGCCGGAAGCGCTGCTAGAGTTAAGTATTTTCCACGCTCAAGAACTGACTGAACAACTCA
GCCATATTTTCGGCTTACCGGAAACCGATTTAAGCCACTACGATTACCCAAATCTCTGCCAACAGCTTGGTTTACGTGAG
CTGATTACCCGTTATGAAGCTCTTCCCATTGCCAAACAAGGCAATCTGCTTCAACTCGCCGTCTCTGACCCCACTTTACT
GCAAGCCGAAGAAGAGTTTCGCTTTGCCACTGGATTACAAGTGGAGTTGGCACTCGCAGATCATCGTGCACTACAAGCGG
CGATTCGCCGTTTGTATGGCCGCTCGATTCAAGGGGGAGCCAACCAAGGTAAAGAGATCAGCCAAGATGAGCTCGCCAAT
CTAGTTAAAGTCAGTGATGACGAGCTGCAATCCATCGAAGACCTCAGCCAAGATGACTCTCCAGTCAGCCGCTTTATCAA
CCAAGTATTGCTGGATGCGGTACGTAAAGGCGCATCCGACATTCATTTTGAGCCTTATGAAGCGCAATACCGCATTCGCC
TGCGCTGCGATGGTATTTTGGTGGAAACCCAACAACCAGCCAGCCATTTAAGCCGTCGCTTAGCCGCCCGAATTAAGATT
CTCTCTAAACTGGACATTGCTGAACGCCGCTTGCCACAAGATGGCCGAATAAAGCTGCGCCTTAATAGTGATACTGCGAT
TGATATGCGCGTATCAACTTTACCCACCTTGTGGGGTGAAAAAATTGTATTGCGCCTGCTCGATAGCAGCGCTGCAAATC
TGGATATTGATAAGCTCGGTTACAATCCGCAGCAGAAGCAACTTTATCTCAATGCACTCAAAAGACCGCAAGGAATGATA
TTGATGACGGGCCCAACCGGTAGCGGAAAAACCGTCTCACTCTATACTGGGCTGCGCATTCTCAATACCTCACAAATTAA
TATTTCCACCGCCGAAGATCCGGTTGAAATTAACCTCTCTGGCATTAACCAAGTCCAGGTGCAACCGAAAATTGGTTTTG
GTTTTGCCGAAGCTCTACGTTCATTTCTACGCCAAGACCCTGATGTAGTGATGGTGGGCGAAATTCGCGATTTGGAAACT
GCTGAAATTGCGGTCAAGGCGGCGCAAACGGGCCACTTGGTGCTTTCAACTCTGCATACCAACTCAGCAGCCGAAACCGT
CATTCGCTTAGCCAACATGGGGGTTGAACCCTTTAACCTCGCTTCATCACTTAGTTTAATTATCGCCCAGCGCCTTGCTC
GCCGTTTATGTAAACACTGCAAAGTGGCGGTACATCCGTCAGCCATACTGCAAAATCAGTTTGCCTTTCAATCTCAAGAA
ATTTTGTATGAAGCGAATGCGGCAGGCTGCAACGAATGCACCGGTGGTTATTCAGGGCGAGTCGGGATCTATGAAGTCAT
GGCATTTAATACTGAACTGGCAGAGGCCATTATGCGTCGTGCCACCATTCACCAAATTGAAAGTTTAGCCAAAAACAATG
GTATGCAAACCCTGCAAGAGTCCGGCCTTGAAAAGCTGCGTGAAGGCATCACCAGTTTTGCCGAGCTGCAACGTGTGCTT
TATTTTTAA

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 cholerae strain A1552

96.441

100

0.964
  pilB Vibrio parahaemolyticus RIMD 2210633

73.31

100

0.733
  pilB Vibrio campbellii strain DS40M4

73.132

100

0.731
  pilB Legionella pneumophila strain ERS1305867

49.55

98.754

0.489
  pilB Acinetobacter baylyi ADP1

50

92.171

0.461
  pilB Acinetobacter baumannii D1279779

49.614

92.171

0.457
  pilF Neisseria gonorrhoeae MS11

45.552

100

0.456
  pilB/pilB1 Synechocystis sp. PCC 6803

37.105

100

0.397
  pilF Thermus thermophilus HB27

40.111

96.263

0.386
  pilB Haemophilus influenzae 86-028NP

39.205

93.95

0.368
  pilB Haemophilus influenzae Rd KW20

38.826

93.95

0.365

Multiple sequence alignment