Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   VARPA_RS24105 Genome accession   NC_014931
Coordinates   5247887..5249620 (+) Length   577 a.a.
NCBI ID   WP_013543201.1    Uniprot ID   -
Organism   Variovorax paradoxus EPS     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 5242887..5254620
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  VARPA_RS24075 (Varpa_4827) proB 5243509..5244648 (-) 1140 WP_041943027.1 glutamate 5-kinase -
  VARPA_RS24080 (Varpa_4828) cgtA 5244728..5245804 (-) 1077 WP_013543197.1 Obg family GTPase CgtA -
  VARPA_RS24085 (Varpa_4829) rpmA 5245876..5246136 (-) 261 WP_013543198.1 50S ribosomal protein L27 -
  VARPA_RS24090 (Varpa_4830) rplU 5246158..5246469 (-) 312 WP_013543199.1 50S ribosomal protein L21 -
  VARPA_RS24095 (Varpa_4831) - 5246653..5247645 (+) 993 WP_013543200.1 polyprenyl synthetase family protein -
  VARPA_RS24105 (Varpa_4832) pilB 5247887..5249620 (+) 1734 WP_013543201.1 type IV-A pilus assembly ATPase PilB Machinery gene
  VARPA_RS24110 (Varpa_4833) pilC 5249645..5250877 (+) 1233 WP_013543202.1 type II secretion system F family protein Machinery gene
  VARPA_RS24115 (Varpa_4834) - 5250877..5251842 (+) 966 WP_013543203.1 prepilin peptidase -
  VARPA_RS24120 (Varpa_4835) coaE 5251853..5252461 (+) 609 WP_013543204.1 dephospho-CoA kinase -
  VARPA_RS24125 (Varpa_4836) - 5252535..5254028 (+) 1494 WP_013543205.1 MBOAT family O-acyltransferase -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62534.90 Da        Isoelectric Point: 5.5901

>NTDB_id=39548 VARPA_RS24105 WP_013543201.1 5247887..5249620(+) (pilB) [Variovorax paradoxus EPS]
MAAAELPVKELSQIALPGLARALVSAGKLPAKIAEDIYQKSLSGRTSFIAELTGTGAVSAADLAHTLSTAFGAPLLDLDA
IDHQRLPKDLLDPKLCLAYRIVVLSKRNNRLIVATADPSDQQAAEKIKFASQMGVDWVIAEYDKLSRMIEAAAATAAESI
NSIVGSEFEFDDVSADTSGDVSEQAVAEVEDAPVVRFLHKMLLDAVSMRASDIHFEPYEHHYRVRFRVDGELREIASPPT
VIKEKLASRIKVISRLDISEKRVPQDGRMKLKIGPDRVIDFRVSTLPTLFGEKIVVRILDPSSARMGIDALGYDAVEKER
LLYAIGRPYGMVLVTGPTGSGKTVSLYTCLNLLNQPGVNIATAEDPSEINLPGVNQVNVNERAGLTFAAALRAFLRQDPD
IIMVGEIRDLETADISIKAAQTGHLVLSTLHTNDAPTTLTRMRNMGIAPFNIASSVILITAQRLARRLCTVCRVPIDIPR
EALLDAGFKEADLDGTWKPYRPVGCSACSSGYKGRVGIYQVMPITEAIQEIILRDGSALDIAQQSEAEGVRSLRQSGLAK
VKQGLTSLEEVVACTNE

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=39548 VARPA_RS24105 WP_013543201.1 5247887..5249620(+) (pilB) [Variovorax paradoxus EPS]
ATGGCCGCTGCCGAACTTCCAGTTAAAGAACTCTCGCAAATCGCTCTTCCGGGCTTGGCGCGTGCTCTCGTTTCGGCCGG
CAAACTGCCCGCAAAAATCGCAGAGGACATTTACCAAAAGTCCCTGAGCGGCCGCACGAGTTTCATCGCCGAACTGACCG
GCACCGGCGCCGTCTCGGCTGCGGACCTCGCCCACACGCTTTCCACAGCATTCGGTGCTCCGCTGCTCGATCTCGATGCG
ATCGATCACCAGCGCCTGCCCAAGGACCTGCTAGATCCGAAGCTGTGCCTCGCATACCGGATCGTCGTCCTCAGCAAACG
CAATAACCGTCTCATTGTTGCGACGGCAGATCCGTCGGACCAACAAGCGGCCGAAAAGATCAAGTTCGCCTCCCAGATGG
GGGTCGACTGGGTCATCGCTGAGTACGACAAGCTTTCGCGAATGATCGAAGCCGCTGCGGCAACTGCGGCGGAGAGCATC
AACAGCATCGTCGGCAGCGAATTCGAATTCGACGACGTCAGTGCGGATACATCAGGCGATGTCAGCGAGCAGGCCGTCGC
AGAAGTCGAAGATGCGCCGGTCGTGCGCTTTCTGCACAAGATGCTGCTCGACGCAGTCAGCATGCGCGCCTCGGACATTC
ACTTCGAGCCCTACGAGCATCACTACCGCGTTCGTTTTCGGGTCGACGGCGAGTTGCGCGAAATTGCCAGCCCGCCCACG
GTCATCAAGGAAAAGCTGGCATCCCGCATCAAGGTCATCTCCCGGCTCGACATCTCCGAAAAGCGCGTGCCGCAAGACGG
CCGCATGAAGCTCAAGATCGGGCCGGACCGCGTCATCGACTTTCGCGTGAGCACGTTGCCCACTCTGTTCGGCGAGAAGA
TCGTGGTTCGTATTCTTGACCCGAGCAGCGCGCGGATGGGCATCGATGCGTTGGGTTACGACGCCGTCGAAAAGGAACGG
CTCCTCTATGCGATTGGCCGTCCCTACGGCATGGTGCTCGTGACCGGTCCCACGGGCTCGGGCAAGACGGTGTCGCTCTA
TACCTGCCTGAATCTGTTGAATCAACCGGGCGTCAACATCGCAACGGCCGAAGACCCGTCCGAAATCAACCTGCCGGGCG
TCAACCAGGTCAACGTCAATGAACGGGCCGGACTGACCTTCGCCGCAGCGCTACGCGCCTTCCTACGCCAGGATCCCGAC
ATCATCATGGTCGGCGAAATCCGCGACCTGGAAACAGCCGACATCTCGATCAAGGCCGCGCAGACCGGCCACTTGGTGCT
CTCGACGCTGCACACCAACGACGCGCCGACCACGCTCACGCGCATGCGCAACATGGGCATCGCGCCGTTCAACATCGCAT
CGAGCGTGATTCTCATCACTGCACAGCGATTGGCACGGCGGCTGTGCACCGTGTGCCGCGTGCCGATCGACATTCCGCGT
GAAGCGCTGCTCGATGCCGGCTTCAAGGAAGCGGACCTGGACGGCACCTGGAAGCCTTACCGCCCAGTGGGCTGCTCTGC
GTGCAGCAGCGGCTACAAGGGCCGGGTCGGCATCTATCAGGTGATGCCGATCACCGAGGCCATCCAGGAAATCATCCTGC
GCGATGGCAGCGCGCTCGACATCGCGCAGCAATCCGAAGCCGAGGGCGTGCGTTCGCTGCGCCAGTCGGGCCTCGCAAAA
GTCAAGCAGGGCCTCACTTCACTCGAAGAAGTGGTGGCCTGCACCAATGAATAA

Domains

Predicted by InterproScan.

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

(55-156)

Type II/IV secretion system protein (T2SSE)

(200-467)


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 baumannii D1279779

54.448

97.4

0.53
  pilB Acinetobacter baylyi ADP1

53.169

98.44

0.523
  pilF Neisseria gonorrhoeae MS11

51.858

97.92

0.508
  pilB Legionella pneumophila strain ERS1305867

49.821

97.054

0.484
  pilB Vibrio campbellii strain DS40M4

45.455

97.227

0.442
  pilB Vibrio cholerae strain A1552

46.961

94.107

0.442
  pilB Vibrio parahaemolyticus RIMD 2210633

45.438

96.88

0.44
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

40.619

95.147

0.386
  pilF Thermus thermophilus HB27

37.696

99.307

0.374

Multiple sequence alignment