Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SFRI_RS19425 Genome accession   NC_008345
Coordinates   4504003..4505709 (+) Length   568 a.a.
NCBI ID   WP_011639197.1    Uniprot ID   -
Organism   Shewanella frigidimarina NCIMB 400     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4499003..4510709
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SFRI_RS19405 (Sfri_3779) ampE 4499635..4500486 (-) 852 WP_011639193.1 beta-lactamase regulator AmpE -
  SFRI_RS19410 (Sfri_3780) ampD 4500612..4501166 (-) 555 WP_011639194.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  SFRI_RS19415 (Sfri_3781) nadC 4501586..4502464 (+) 879 WP_011639195.1 carboxylating nicotinate-nucleotide diphosphorylase -
  SFRI_RS21815 (Sfri_3782) pilE 4503482..4503910 (+) 429 WP_049763611.1 pilin Machinery gene
  SFRI_RS19425 (Sfri_3783) pilB 4504003..4505709 (+) 1707 WP_011639197.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SFRI_RS19430 (Sfri_3784) pilC 4505817..4507076 (+) 1260 WP_011639198.1 type II secretion system F family protein Machinery gene
  SFRI_RS19435 (Sfri_3785) pilD 4507106..4508032 (+) 927 WP_011639199.1 A24 family peptidase Machinery gene
  SFRI_RS19440 (Sfri_3786) coaE 4508029..4508658 (+) 630 WP_011639200.1 dephospho-CoA kinase -
  SFRI_RS19445 (Sfri_3787) zapD 4508651..4509385 (+) 735 WP_011639201.1 cell division protein ZapD -
  SFRI_RS19450 (Sfri_3788) yacG 4509428..4509640 (+) 213 WP_041413247.1 DNA gyrase inhibitor YacG -
  SFRI_RS19455 (Sfri_3789) mutT 4509664..4510059 (+) 396 WP_011639203.1 8-oxo-dGTP diphosphatase MutT -

Sequence

Protein


Download         Length: 568 a.a.        Molecular weight: 62820.16 Da        Isoelectric Point: 5.5820

>NTDB_id=26350 SFRI_RS19425 WP_011639197.1 4504003..4505709(+) (pilB) [Shewanella frigidimarina NCIMB 400]
MSSAAVHLGLSTLFIRKGLLNEEQISTSISESRKHKQSLVTTLVNSKFLSAREIAELCYEEYGTPLLDLNEFDVTGIADE
LLNKKLIEKHKCLPLFKRGNRLYIATSDPTNIAALEDFQFSLGLHAEAILVEDDKLLKALEKIIEDDISGLDLAGADEEA
LANMEVADTERRDEPSGDSSDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPVNLSNRISAR
LKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSSLPTIWGEKIVMRILDSSSAQLGIEKLGYEDDQRLLYEEMLAKPQ
GMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIRD
LETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLARRLCPACKHEEEIPVAEMQRLGFS
EANIAKGFTVFKPIGCELCSGGYKGRVGIYEVMKMSDEIARTIMEGGNSLQIATLAKQQGMRDLRQSGLLKVIHGVTSIA
EINRVTSF

Nucleotide


Download         Length: 1707 bp        

>NTDB_id=26350 SFRI_RS19425 WP_011639197.1 4504003..4505709(+) (pilB) [Shewanella frigidimarina NCIMB 400]
ATGTCATCAGCTGCCGTTCATTTAGGACTATCAACTTTATTTATCCGTAAAGGCCTCCTAAACGAAGAGCAAATATCAAC
TTCCATTTCCGAATCTCGAAAGCACAAACAATCCTTAGTCACGACATTAGTAAACTCCAAGTTCCTTTCTGCTCGCGAAA
TAGCTGAACTGTGCTATGAAGAGTATGGCACCCCATTACTTGATTTAAATGAATTTGATGTAACTGGTATCGCAGATGAG
CTACTCAATAAAAAGCTCATAGAGAAACATAAATGCTTACCTCTCTTCAAGCGTGGTAATCGTCTTTACATCGCCACATC
AGATCCAACCAATATTGCTGCTCTTGAGGATTTTCAATTTAGTCTAGGTCTCCATGCCGAAGCTATTTTGGTTGAAGATG
ACAAATTGCTAAAAGCGCTAGAAAAAATCATCGAAGATGATATCTCTGGTTTGGACTTAGCTGGCGCAGATGAAGAAGCC
TTAGCCAATATGGAAGTGGCTGATACAGAAAGACGTGACGAACCAAGCGGAGATAGCAGTGACGATGCACCTATTGTAAT
CTATATTAATAAAATTCTCACCGATGCTATTCGTAAAGGCGCCTCTGATTTACATTTTGAGCCTTACGAAAAACGCTATC
GTATCCGCTTTCGAATTGATGGTATCTTGCATGAAGTATCTGAACCACCAGTCAATCTATCCAACCGTATTTCAGCCCGC
TTAAAAGTGATGTCGAAACTCGATATTGCTGAGCGTCGAGTTCCGCAAGATGGCCGCATTAAAATGAAGCTGTCGCGCAC
CAAATCAATCGATTTCCGTGTCAGTAGCTTGCCGACCATTTGGGGCGAGAAGATCGTGATGCGTATTTTGGATTCATCTT
CCGCTCAGTTGGGGATTGAAAAGCTCGGTTATGAAGATGATCAACGCTTATTATACGAAGAAATGCTCGCTAAACCTCAA
GGGATGATATTAGTCACTGGCCCTACGGGTTCAGGTAAAACAGTCTCCTTGTATACTGGCCTCAATATTCTTAATACCGA
AGAGCGTAATATATCTACCGCAGAAGATCCGGTCGAAATTAACCTCGAAGGCGTTAACCAAGTACACATTAATTTAAAAG
CTGGCCTAACTTTCGCTTCAGCGCTACGATCATTTTTACGTCAAGATCCTGATGTGGTGATGGTTGGTGAAATCCGCGAT
TTAGAAACTGCAGAGATCGCCATTAAAGCCGCCCAAACGGGTCACTTAGTGTTATCAACATTACATACCAATTCAGCCGC
CGAAACCTTAACCCGTTTAATCAATATGGGTGTGCCAGGTTATAACATTGCTAGCTCAGTCAATTTAATTATAGCCCAAC
GACTTGCCAGGCGCCTATGCCCAGCATGTAAACATGAAGAAGAAATTCCTGTTGCTGAGATGCAGCGCTTAGGCTTCAGT
GAAGCTAATATCGCCAAAGGTTTTACCGTATTCAAACCAATTGGTTGTGAGCTATGCTCAGGTGGTTATAAAGGCCGAGT
GGGTATATACGAAGTGATGAAAATGAGCGATGAAATAGCGCGTACAATTATGGAAGGCGGTAACTCACTCCAAATTGCCA
CCCTTGCCAAGCAGCAAGGTATGCGCGATTTACGTCAATCAGGATTGCTCAAAGTCATTCACGGCGTGACTAGCATCGCG
GAAATTAACCGTGTAACCAGCTTTTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(191-458)

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

(43-143)


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

58.289

98.768

0.576
  pilB Acinetobacter baumannii D1279779

58.007

98.944

0.574
  pilB Legionella pneumophila strain ERS1305867

56.584

98.944

0.56
  pilB Vibrio cholerae strain A1552

53.321

98.063

0.523
  pilB Vibrio parahaemolyticus RIMD 2210633

51.67

100

0.518
  pilB Vibrio campbellii strain DS40M4

50.697

100

0.512
  pilF Neisseria gonorrhoeae MS11

47.163

99.296

0.468
  pilF Thermus thermophilus HB27

39.037

98.768

0.386
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.297

97.711

0.364

Multiple sequence alignment