Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   RDV63_RS05085 Genome accession   NZ_CP135084
Coordinates   1010044..1011738 (-) Length   564 a.a.
NCBI ID   WP_313908424.1    Uniprot ID   -
Organism   Rheinheimera sp. MMS21-TC3     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 1005044..1016738
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  RDV63_RS05055 (RDV63_05055) - 1005045..1005554 (-) 510 WP_313908418.1 hypothetical protein -
  RDV63_RS05060 (RDV63_05060) yacG 1006030..1006263 (-) 234 WP_313908419.1 DNA gyrase inhibitor YacG -
  RDV63_RS05065 (RDV63_05065) zapD 1006331..1007077 (-) 747 WP_313908420.1 cell division protein ZapD -
  RDV63_RS05070 (RDV63_05070) coaE 1007092..1007706 (-) 615 WP_313908421.1 dephospho-CoA kinase -
  RDV63_RS05075 (RDV63_05075) pilD 1007744..1008646 (-) 903 WP_313908422.1 A24 family peptidase Machinery gene
  RDV63_RS05080 (RDV63_05080) pilC 1008646..1009875 (-) 1230 WP_313908423.1 type II secretion system F family protein Machinery gene
  RDV63_RS05085 (RDV63_05085) pilB 1010044..1011738 (-) 1695 WP_313908424.1 type IV-A pilus assembly ATPase PilB Machinery gene
  RDV63_RS05090 (RDV63_05090) - 1012082..1012270 (-) 189 WP_313908425.1 hypothetical protein -
  RDV63_RS05095 (RDV63_05095) - 1012260..1012733 (-) 474 WP_313908426.1 hypothetical protein -
  RDV63_RS05100 (RDV63_05100) - 1012738..1013514 (-) 777 WP_313908427.1 hypothetical protein -
  RDV63_RS05105 (RDV63_05105) - 1013860..1014252 (-) 393 WP_313908428.1 hypothetical protein -
  RDV63_RS05110 (RDV63_05110) - 1014255..1014965 (-) 711 WP_313908429.1 DNA/RNA non-specific endonuclease -
  RDV63_RS05115 (RDV63_05115) - 1015297..1016241 (-) 945 WP_313908430.1 hypothetical protein -

Sequence

Protein


Download         Length: 564 a.a.        Molecular weight: 61774.91 Da        Isoelectric Point: 5.2899

>NTDB_id=884819 RDV63_RS05085 WP_313908424.1 1010044..1011738(-) (pilB) [Rheinheimera sp. MMS21-TC3]
MAVTATSTLLKRLSQLGLVDSDQTLKVITEKGSQYKNLPELLITEKLISSEMLANAAAKISLTTQFDLTHYDSSMVPEDL
RNEKLVRKTHMLPLGKRGRSMFLAVVDPTDIQTIEDCEFNTGLNAEVVVVDYSQLTKLIDTVFDNSFGQEYGHTEWDLGS
LGIEDKADDDASMVVDAEDQPIIAFINKMLHDAIRKGASDLHFEPYEKTYRIRFRIDGILNEVASPPVELATRLSARLKV
MSRLDIAEKRVPQDGRIKLKISAKKSIDFRVSTLPTIWGEKIVMRILDSDSAMLGIDVLGYEPEQKQLYLNALKQPQGMI
LVTGPTGSGKTVSLYTGLAILNTEQTNISTAEDPVEINLAGINQVQVNPRAGLTFSSALKSFLRQDPDVVMVGEVRDLET
AEIAIKAAQTGHLVLSTLHTNSAPETLTRLLNMGVPSYNVASSVSLIIAQRLARRLCSHCKIPEQLPEAELLKQGFTPEQ
LSSITIYKPVGCDNCTSGYKGRVGIYEVMPVSAKMADIIMQGGNSLDISNQAQLEGVNNLRQSGLIKAAAGLTSLAEVNR
VTQG

Nucleotide


Download         Length: 1695 bp        

>NTDB_id=884819 RDV63_RS05085 WP_313908424.1 1010044..1011738(-) (pilB) [Rheinheimera sp. MMS21-TC3]
ATGGCAGTTACAGCAACCTCTACTTTATTAAAACGCTTAAGTCAACTTGGCTTGGTTGATTCTGATCAGACCCTAAAAGT
GATTACTGAAAAAGGCAGTCAATATAAAAACTTGCCCGAGCTGCTAATTACCGAAAAGCTAATTAGTAGTGAGATGCTAG
CCAATGCTGCGGCTAAAATAAGTTTAACTACTCAGTTTGATTTAACCCATTATGACAGCAGCATGGTGCCAGAAGATTTG
CGCAACGAAAAGCTAGTGCGCAAAACCCATATGTTACCGCTAGGTAAACGCGGTCGCAGTATGTTTTTAGCTGTAGTAGA
CCCTACTGATATTCAAACCATTGAAGATTGCGAATTTAATACTGGCCTAAACGCTGAAGTGGTTGTAGTAGATTACAGCC
AATTAACTAAATTAATTGATACCGTTTTTGATAACAGTTTTGGCCAAGAGTATGGCCATACCGAGTGGGATTTAGGCTCT
TTAGGCATTGAAGATAAAGCAGACGATGATGCCAGCATGGTAGTGGACGCTGAAGATCAGCCCATTATTGCTTTTATTAA
TAAAATGCTCCATGACGCTATTCGCAAGGGCGCCTCGGATTTACACTTTGAACCTTATGAAAAAACCTACCGCATTCGGT
TTCGTATAGACGGTATTTTAAATGAAGTGGCCAGCCCACCTGTTGAACTAGCCACTAGGCTATCGGCACGGTTAAAGGTA
ATGTCGCGCTTAGATATTGCCGAAAAAAGGGTACCGCAAGATGGCCGCATAAAGTTAAAAATTTCTGCTAAAAAATCCAT
AGACTTTCGGGTTAGTACCTTGCCTACTATTTGGGGTGAAAAAATAGTAATGCGGATCCTCGACTCCGACAGCGCTATGT
TAGGCATAGATGTGTTAGGCTACGAGCCAGAGCAAAAACAGCTGTACTTAAATGCTTTAAAGCAACCGCAAGGCATGATT
TTAGTAACAGGCCCTACTGGCTCGGGTAAAACGGTATCACTTTATACCGGCTTGGCCATTTTAAATACTGAGCAAACTAA
TATTTCTACTGCTGAAGATCCTGTAGAGATTAACTTAGCTGGCATTAACCAAGTGCAAGTTAACCCACGCGCAGGTTTAA
CCTTTTCATCGGCTTTAAAATCTTTTTTACGCCAAGACCCCGACGTAGTTATGGTGGGTGAGGTGCGAGACTTAGAAACC
GCCGAAATAGCCATTAAAGCGGCGCAAACCGGTCACTTGGTATTGTCTACTTTGCACACTAATTCGGCACCAGAAACCTT
AACCAGACTGCTTAATATGGGCGTACCCTCTTATAACGTGGCCAGTTCAGTATCCCTAATTATTGCCCAGCGCTTAGCGC
GCCGGCTATGCAGCCATTGTAAAATTCCCGAGCAACTGCCAGAGGCAGAATTATTAAAGCAAGGTTTTACCCCAGAGCAA
CTAAGTAGTATAACTATTTATAAACCTGTTGGTTGTGATAACTGCACTAGTGGCTATAAAGGCCGAGTCGGTATTTATGA
AGTTATGCCAGTTAGCGCTAAAATGGCCGACATTATAATGCAAGGCGGTAATTCGTTAGATATTAGCAACCAAGCCCAAC
TAGAAGGCGTTAACAATTTACGCCAGTCGGGCTTAATTAAAGCCGCTGCTGGCTTAACTAGCTTAGCGGAAGTAAACCGA
GTGACTCAAGGCTAA

Domains

Predicted by InterproScan.

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

(42-145)

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 Acinetobacter baylyi ADP1

55.674

100

0.557
  pilB Acinetobacter baumannii D1279779

58.891

92.73

0.546
  pilB Legionella pneumophila strain ERS1305867

52.787

100

0.537
  pilB Vibrio cholerae strain A1552

52.65

100

0.528
  pilF Neisseria gonorrhoeae MS11

51.805

98.227

0.509
  pilB Vibrio parahaemolyticus RIMD 2210633

50.995

98.05

0.5
  pilB Vibrio campbellii strain DS40M4

49.911

99.823

0.498
  pilB/pilB1 Synechocystis sp. PCC 6803

37.213

100

0.402
  pilF Thermus thermophilus HB27

36.673

99.113

0.363