Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SVI_RS01235 Genome accession   NC_014012
Coordinates   302689..304398 (-) Length   569 a.a.
NCBI ID   WP_013049543.1    Uniprot ID   D4ZEJ8
Organism   Shewanella violacea DSS12     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 297689..309398
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SVI_RS01205 (SVI_0251) mutT 298297..298713 (-) 417 WP_013049537.1 8-oxo-dGTP diphosphatase MutT -
  SVI_RS01210 (SVI_0252) yacG 298719..298931 (-) 213 WP_013049538.1 DNA gyrase inhibitor YacG -
  SVI_RS01215 (SVI_0253) zapD 299029..299763 (-) 735 WP_013049539.1 cell division protein ZapD -
  SVI_RS01220 (SVI_0254) coaE 299772..300377 (-) 606 WP_013049540.1 dephospho-CoA kinase -
  SVI_RS01225 (SVI_0255) pilD 300410..301327 (-) 918 WP_013049541.1 A24 family peptidase Machinery gene
  SVI_RS01230 (SVI_0256) pilC 301388..302659 (-) 1272 WP_013049542.1 type II secretion system F family protein Machinery gene
  SVI_RS01235 (SVI_0257) pilB 302689..304398 (-) 1710 WP_013049543.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SVI_RS01240 (SVI_0258) - 304497..304943 (-) 447 WP_013049544.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  SVI_RS01245 (SVI_0259) nadC 305970..306887 (-) 918 WP_013049545.1 carboxylating nicotinate-nucleotide diphosphorylase -
  SVI_RS01250 (SVI_0261) ampD 307235..307813 (+) 579 WP_013049547.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  SVI_RS01255 (SVI_0262) ampE 307912..308763 (+) 852 WP_013049548.1 beta-lactamase regulator AmpE -

Sequence

Protein


Download         Length: 569 a.a.        Molecular weight: 63176.36 Da        Isoelectric Point: 4.9594

>NTDB_id=36851 SVI_RS01235 WP_013049543.1 302689..304398(-) (pilB) [Shewanella violacea DSS12]
MPTTGLHLGLSTLFIRKQLLSEEQIASAIAKSRQNKQSLVSTIVSEKLISAREIAELCYEEYGTPLLDLDEFDVASIPED
FLNKKLIEKHKCLPLFKRGNRLYIGTSDPTNITALEDFQFSAGLHAEAILVEDDKLTKAIEKILEDDISALDISGIDESA
LADIEVDDPSKREEEQKSESGDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPVNLSARISA
RLKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSTLPTIWGEKIVMRILDSSSAQLGIEKLGYEDDQRELYEEMLEKP
QGMILVTGPTGSGKTVSLYTGLNILNTEARNISTVEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIR
DLETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLSRRLCPECKQAEDIPEHELQRLGF
KQANIDEGITTYKPVGCDLCSGGYKGRVGIYEVMKISDEIARIIMEGGNSLQIATMAKEEGMRDLRESGLLKVIHGVTSI
AEINRVTSF

Nucleotide


Download         Length: 1710 bp        

>NTDB_id=36851 SVI_RS01235 WP_013049543.1 302689..304398(-) (pilB) [Shewanella violacea DSS12]
ATGCCGACAACGGGTCTTCATTTAGGTTTATCTACACTCTTTATTCGTAAGCAGTTGCTCAGCGAAGAGCAGATAGCTTC
CGCTATAGCAAAGTCTCGCCAAAATAAGCAATCTCTAGTCTCTACCATAGTCTCAGAAAAGCTCATTTCTGCACGAGAAA
TAGCCGAGCTTTGTTACGAAGAATACGGCACTCCCTTGCTAGATCTCGACGAATTCGATGTCGCCAGCATTCCCGAAGAC
TTCCTCAATAAGAAGCTGATAGAGAAACATAAATGCCTGCCACTGTTTAAGCGGGGCAACCGCCTCTATATCGGCACCTC
AGACCCAACTAACATTACCGCCCTGGAAGACTTTCAGTTTAGCGCTGGCCTACATGCCGAAGCCATATTGGTCGAGGATG
ATAAGCTTACTAAGGCCATAGAGAAGATTCTCGAGGATGACATCTCGGCGCTGGATATCAGCGGCATAGATGAGTCGGCT
CTTGCCGATATCGAAGTCGATGACCCCAGTAAGCGTGAGGAAGAGCAAAAAAGCGAAAGCGGTGATGATGCGCCGATCGT
CATCTATATCAACAAAATATTGACCGACGCTATACGCAAAGGGGCATCGGATCTGCATTTCGAACCCTATGAGAAACGTT
ACCGTATACGTTTTCGTATTGACGGTATCTTGCATGAAGTCTCTGAGCCCCCAGTCAATCTTTCAGCCCGAATTTCCGCC
CGCCTCAAGGTGATGTCTAAGCTAGATATAGCCGAACGTCGTGTGCCCCAAGACGGCCGCATCAAGATGAAGCTATCGCG
CACTAAGTCCATAGACTTTCGTGTCAGTACCTTGCCTACTATCTGGGGCGAGAAGATAGTGATGCGTATTCTGGACTCCT
CTTCGGCGCAACTAGGCATCGAGAAGCTGGGTTATGAAGACGATCAGCGCGAGCTGTACGAGGAGATGCTGGAAAAACCT
CAGGGTATGATCCTGGTCACTGGCCCTACTGGCTCGGGAAAAACAGTCTCTCTCTATACTGGTCTCAACATACTCAATAC
CGAAGCTAGAAACATCTCTACCGTCGAAGACCCGGTGGAGATAAACCTCGAAGGGGTCAATCAGGTTCATATCAATCTCA
AGGCGGGGCTGACATTTGCCTCTGCATTGCGCTCATTTCTGCGCCAAGATCCCGATGTGGTCATGGTCGGTGAGATTCGA
GACTTAGAGACCGCCGAAATTGCTATCAAGGCGGCGCAAACAGGCCACCTGGTATTGTCGACGCTGCACACTAACTCGGC
CGCCGAAACACTGACTCGACTCATCAATATGGGCGTTCCTGGATACAACATAGCTAGTTCGGTAAACCTAATCATAGCTC
AGCGCCTGTCTCGACGCCTCTGCCCCGAATGTAAGCAAGCAGAAGATATCCCTGAACACGAACTGCAGAGGTTAGGCTTT
AAGCAAGCAAACATAGATGAAGGCATCACCACCTATAAACCAGTGGGCTGCGATCTCTGCTCCGGCGGTTACAAGGGCCG
GGTCGGCATCTATGAGGTGATGAAGATATCAGATGAGATAGCCCGCATCATCATGGAAGGAGGCAACTCCTTACAGATAG
CCACCATGGCCAAAGAAGAAGGCATGCGAGATTTACGAGAGTCGGGGCTACTCAAGGTCATCCATGGTGTCACCAGCATC
GCCGAGATCAATCGAGTCACTAGTTTCTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(192-459)

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

(17-145)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB D4ZEJ8

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

57.754

98.594

0.569
  pilB Acinetobacter baumannii D1279779

57.041

98.594

0.562
  pilB Legionella pneumophila strain ERS1305867

55.477

99.473

0.552
  pilB Vibrio cholerae strain A1552

52.575

98.946

0.52
  pilB Vibrio parahaemolyticus RIMD 2210633

51.224

100

0.515
  pilB Vibrio campbellii strain DS40M4

51.15

99.297

0.508
  pilF Neisseria gonorrhoeae MS11

47.007

99.824

0.469
  pilF Thermus thermophilus HB27

39.362

99.121

0.39
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.882

97.891

0.371

Multiple sequence alignment