Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   JYB85_RS16885 Genome accession   NZ_CP071502
Coordinates   3781461..3783170 (+) Length   569 a.a.
NCBI ID   WP_207380211.1    Uniprot ID   -
Organism   Shewanella sedimentimangrovi strain FJAT-52962     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 3776461..3788170
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JYB85_RS16860 (JYB85_16860) pdhR 3776605..3777357 (-) 753 WP_207321093.1 pyruvate dehydrogenase complex transcriptional repressor PdhR -
  JYB85_RS16865 (JYB85_16865) ampE 3777538..3778413 (-) 876 WP_207380207.1 beta-lactamase regulator AmpE -
  JYB85_RS16870 (JYB85_16870) ampD 3778448..3779002 (-) 555 WP_207380208.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  JYB85_RS16875 (JYB85_16875) nadC 3779215..3780072 (+) 858 WP_207380209.1 carboxylating nicotinate-nucleotide diphosphorylase -
  JYB85_RS16880 (JYB85_16880) - 3780977..3781375 (+) 399 WP_207380210.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  JYB85_RS16885 (JYB85_16885) pilB 3781461..3783170 (+) 1710 WP_207380211.1 type IV-A pilus assembly ATPase PilB Machinery gene
  JYB85_RS16890 (JYB85_16890) pilC 3783209..3784477 (+) 1269 WP_207380212.1 type II secretion system F family protein Machinery gene
  JYB85_RS16895 (JYB85_16895) pilD 3784503..3785417 (+) 915 WP_207380213.1 A24 family peptidase Machinery gene
  JYB85_RS16900 (JYB85_16900) coaE 3785426..3786031 (+) 606 WP_207380214.1 dephospho-CoA kinase -
  JYB85_RS16905 (JYB85_16905) zapD 3786038..3786772 (+) 735 WP_207321102.1 cell division protein ZapD -
  JYB85_RS16910 (JYB85_16910) yacG 3786819..3787028 (+) 210 WP_207321103.1 DNA gyrase inhibitor YacG -
  JYB85_RS16915 (JYB85_16915) mutT 3787035..3787430 (+) 396 WP_207321104.1 8-oxo-dGTP diphosphatase MutT -

Sequence

Protein


Download         Length: 569 a.a.        Molecular weight: 63039.32 Da        Isoelectric Point: 5.3482

>NTDB_id=545727 JYB85_RS16885 WP_207380211.1 3781461..3783170(+) (pilB) [Shewanella sedimentimangrovi strain FJAT-52962]
MPTSGLHLGLATLFIRKRFLTEEQMATAISKSRQSKQTLVSTLISDSIMSAREIAEMCYEEYGTPLLDLAEFDIPSIPEE
HLNKKLIEKHRCLPLFRRGNRLYIATSDPTNISALEDFQFSAGLHAEAILVEDDKLGKALEKILEEDISALDLGGLDEDS
LAGIEVTDTDRRHEDQQGDSSDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPINLAGRISA
RLKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSTLPTLWGEKIVMRILDSSSAQLGIEKLGYEEDQKAAYLEMLAKP
QGMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIR
DLETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLARRLCPECKEPEEIPEHELLRLGF
SQEQITQGVTLYKPCGCDLCSGGYKGRVGIYEVMKMSDEIARTIMEGGNSLQIASMAKSQGMRDLRQSGLLKVIQGVTSI
AEVNRVTSF

Nucleotide


Download         Length: 1710 bp        

>NTDB_id=545727 JYB85_RS16885 WP_207380211.1 3781461..3783170(+) (pilB) [Shewanella sedimentimangrovi strain FJAT-52962]
ATGCCGACATCTGGATTGCACTTGGGCCTCGCAACCTTGTTTATCCGTAAGAGATTTCTTACGGAAGAGCAAATGGCCAC
TGCAATATCCAAGTCACGGCAAAGCAAACAAACCTTAGTTTCAACACTGATTTCCGACAGCATTATGTCTGCACGGGAAA
TAGCTGAGATGTGCTATGAGGAATATGGCACCCCACTGCTGGACCTGGCCGAATTTGATATTCCCAGCATTCCCGAAGAA
CATCTCAACAAAAAACTGATTGAAAAGCACCGCTGCCTGCCACTTTTCCGCCGCGGTAACCGTCTTTATATCGCCACCTC
AGATCCCACCAATATATCCGCACTGGAAGACTTCCAGTTTTCGGCCGGTTTACATGCCGAAGCCATCCTGGTGGAAGACG
ATAAGCTGGGCAAGGCTCTGGAGAAGATCCTCGAAGAAGATATCAGTGCCTTGGATCTGGGTGGTCTTGATGAGGATTCA
CTTGCCGGCATTGAAGTTACTGATACAGATAGGCGTCATGAAGATCAACAGGGTGACAGCAGCGATGACGCGCCAATCGT
TATCTATATCAATAAAATTCTGACCGATGCCATCCGCAAGGGAGCGTCGGATTTGCACTTTGAGCCCTACGAAAAGCGTT
ATCGCATCCGTTTTCGTATTGATGGCATCTTACACGAAGTCTCTGAACCGCCGATTAATCTCGCCGGCCGTATTTCGGCT
CGCTTAAAGGTGATGTCCAAGCTGGATATTGCTGAGCGTAGGGTTCCCCAGGACGGTCGCATCAAAATGAAACTGTCGCG
GACCAAGTCAATAGACTTCCGTGTCAGCACACTGCCCACATTGTGGGGCGAAAAGATTGTAATGCGTATATTGGATTCTT
CCTCCGCGCAGCTTGGTATCGAAAAGCTGGGCTACGAAGAAGACCAAAAGGCCGCCTATCTGGAAATGCTAGCCAAGCCC
CAGGGCATGATACTGGTTACAGGCCCCACAGGTTCGGGTAAGACGGTATCCCTGTACACCGGCCTTAATATACTTAATAC
CGAAGAGCGCAATATCAGCACCGCCGAAGATCCGGTGGAAATAAACCTGGAAGGGGTAAACCAGGTTCACATTAACCTCA
AGGCAGGACTAACCTTTGCCTCGGCACTGCGCTCTTTTCTACGTCAGGATCCCGATGTAGTTATGGTGGGTGAGATTCGT
GACCTGGAAACGGCGGAAATTGCCATTAAGGCCGCACAAACGGGTCACTTGGTATTATCCACCCTGCACACCAATTCTGC
CGCAGAGACCCTCACCCGACTGATTAACATGGGCGTCCCCGGCTACAACATAGCCAGCTCGGTGAATCTGATTATTGCGC
AGCGCCTCGCCAGAAGACTTTGCCCTGAATGCAAAGAGCCCGAAGAGATTCCCGAGCATGAGTTGTTACGGCTGGGATTC
TCACAGGAGCAAATAACCCAAGGTGTCACCCTATACAAGCCTTGCGGATGCGATCTCTGCTCCGGCGGCTATAAAGGCCG
TGTGGGTATCTATGAAGTGATGAAAATGTCAGACGAGATAGCCCGAACTATTATGGAAGGAGGCAACTCGTTGCAAATTG
CGTCCATGGCCAAGAGCCAGGGAATGCGTGATTTGCGCCAGTCGGGTCTGCTTAAAGTCATTCAAGGTGTGACCAGCATA
GCAGAGGTCAACCGGGTGACCAGTTTTTAG

Domains

Predicted by InterproScan.

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

(16-144)

Type II/IV secretion system protein (T2SSE)

(192-459)


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

59.715

98.594

0.589
  pilB Acinetobacter baumannii D1279779

57.672

99.649

0.575
  pilB Legionella pneumophila strain ERS1305867

55.36

100

0.554
  pilB Vibrio parahaemolyticus RIMD 2210633

52.197

100

0.522
  pilB Vibrio cholerae strain A1552

51.761

99.824

0.517
  pilB Vibrio campbellii strain DS40M4

51.332

98.946

0.508
  pilF Neisseria gonorrhoeae MS11

48.763

99.473

0.485
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

39.497

97.891

0.387
  pilF Thermus thermophilus HB27

39.099

97.54

0.381
  pilB/pilB1 Synechocystis sp. PCC 6803

41.082

87.698

0.36