Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   STH12_RS20225 Genome accession   NZ_CP020373
Coordinates   4603043..4604749 (-) Length   568 a.a.
NCBI ID   WP_126169206.1    Uniprot ID   -
Organism   Shewanella khirikhana strain TH2012     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4598043..4609749
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  STH12_RS20195 (STH12_04061) mutT 4598750..4599145 (-) 396 WP_126169200.1 8-oxo-dGTP diphosphatase MutT -
  STH12_RS20200 (STH12_04062) yacG 4599187..4599402 (-) 216 WP_126169201.1 DNA gyrase inhibitor YacG -
  STH12_RS20205 (STH12_04063) zapD 4599464..4600198 (-) 735 WP_126169202.1 cell division protein ZapD -
  STH12_RS20210 (STH12_04064) coaE 4600191..4600808 (-) 618 WP_126169203.1 dephospho-CoA kinase -
  STH12_RS20215 (STH12_04065) pilD 4600808..4601722 (-) 915 WP_126169204.1 prepilin peptidase Machinery gene
  STH12_RS20220 (STH12_04066) pilC 4601749..4603008 (-) 1260 WP_126169205.1 type II secretion system F family protein Machinery gene
  STH12_RS20225 (STH12_04067) pilB 4603043..4604749 (-) 1707 WP_126169206.1 type IV-A pilus assembly ATPase PilB Machinery gene
  STH12_RS20230 (STH12_04068) - 4604806..4605303 (-) 498 WP_126169207.1 pilin -
  STH12_RS20235 (STH12_04069) nadC 4606617..4607474 (-) 858 WP_126169208.1 carboxylating nicotinate-nucleotide diphosphorylase -
  STH12_RS20240 (STH12_04070) ampD 4607721..4608293 (+) 573 WP_126169209.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  STH12_RS20245 (STH12_04071) ampE 4608295..4609173 (+) 879 WP_126169210.1 beta-lactamase regulator AmpE -
  STH12_RS21475 - 4609166..4609306 (-) 141 WP_164551263.1 hypothetical protein -

Sequence

Protein


Download         Length: 568 a.a.        Molecular weight: 62970.31 Da        Isoelectric Point: 5.3571

>NTDB_id=221868 STH12_RS20225 WP_126169206.1 4603043..4604749(-) (pilB) [Shewanella khirikhana strain TH2012]
MPTTGLHLGLSTLFIRKKLLTEEQLSEAVALSRKNRHSLVTTLVASKLLSAREIAELCYEEYGTPLLDLVEFDIKSIPEE
FLNRKLIEKHRCLPLFKRGNRLYIGTSDPTNIAALEDFQFSAGLHAEAILVEDDKLVAALEKILEEDISALDLSGIDEDS
LAGIEVADTDKRPENDNEGADDAPIVIYINKILTDAIRRGASDLHFEPYEKRYRIRFRIDGILHEVSEPPINLSGRISAR
LKVMSKLDIAERRLPQDGRIKMKLSRTKSIDFRVSTLPTLWGEKIVMRILDSSSAQLGIEKLGYEPDQKQLYLDNLAKPQ
GMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINNKAGLTFASALRSFLRQDPDVVMVGEIRD
LETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLLNMGVPGYNIASSVNLIIAQRLARRLCPECKQPEEIPQHELERLGFS
PEQISEGFTVFKPCGCDLCSGGYKGRVGIYEVMPMSDEIARVIMEGGNSLEIARMAKTQGIRDLRQSGLLKVVQGVTSIT
EVNRVTSF

Nucleotide


Download         Length: 1707 bp        

>NTDB_id=221868 STH12_RS20225 WP_126169206.1 4603043..4604749(-) (pilB) [Shewanella khirikhana strain TH2012]
ATGCCAACTACTGGTCTCCACTTAGGATTATCGACGCTATTTATCCGTAAGAAGCTACTCACAGAGGAGCAACTGTCGGA
GGCCGTCGCACTTTCGCGTAAAAACAGGCATTCGCTGGTCACCACCTTGGTGGCCAGCAAATTACTGTCGGCGAGGGAAA
TTGCTGAACTGTGCTACGAGGAGTATGGAACTCCACTACTGGATTTAGTCGAATTTGATATTAAGAGCATCCCTGAGGAA
TTCCTTAATCGCAAATTAATCGAAAAACACCGTTGCTTACCACTGTTTAAGCGTGGTAATAGGCTGTATATAGGCACATC
TGACCCAACCAATATTGCCGCCCTCGAAGACTTTCAGTTTTCCGCAGGCCTGCATGCTGAAGCAATATTGGTGGAAGATG
ACAAACTAGTTGCAGCCCTTGAGAAAATCCTCGAAGAGGACATTAGTGCGCTGGACTTAAGTGGGATTGACGAGGACTCA
CTAGCTGGCATTGAGGTTGCTGATACTGATAAACGCCCCGAGAATGACAACGAAGGTGCAGATGATGCCCCTATCGTAAT
TTACATTAATAAAATCCTAACAGATGCCATTAGGCGTGGTGCATCAGATTTGCACTTTGAGCCCTATGAAAAGCGCTATC
GCATTCGCTTTCGTATTGATGGGATCCTTCATGAAGTTTCTGAGCCACCGATAAACCTTTCGGGTCGTATATCCGCCCGA
CTAAAGGTAATGTCAAAACTGGATATTGCTGAGAGACGGCTGCCTCAGGACGGCCGTATCAAGATGAAACTCAGTCGTAC
CAAGAGCATCGATTTCCGTGTAAGCACCCTACCTACGCTCTGGGGCGAAAAAATTGTAATGCGTATTCTGGACTCATCCT
CTGCCCAACTCGGCATTGAGAAGCTGGGGTATGAGCCAGACCAAAAGCAACTCTATCTGGACAATCTAGCCAAACCTCAG
GGTATGATTTTGGTAACCGGCCCCACCGGCTCGGGTAAAACCGTATCCCTCTACACGGGTCTTAATATCCTCAATACCGA
AGAGCGCAATATTTCCACCGCCGAAGACCCGGTGGAAATTAACTTGGAAGGTGTTAACCAAGTTCATATTAATAATAAAG
CGGGTCTCACATTCGCTTCAGCCCTTCGTTCCTTCCTGCGTCAAGATCCTGATGTGGTGATGGTCGGGGAAATCCGTGAT
CTAGAAACTGCTGAAATCGCCATCAAAGCAGCACAAACCGGCCACTTGGTGCTTTCAACTCTGCACACGAATTCAGCGGC
AGAAACATTAACACGTCTTCTGAACATGGGTGTTCCAGGCTACAACATAGCAAGCTCCGTGAATCTCATCATTGCCCAGC
GTCTTGCCCGTAGACTATGTCCGGAGTGTAAGCAACCAGAAGAGATCCCACAGCATGAGCTTGAACGACTAGGATTCTCG
CCGGAGCAGATTTCAGAAGGTTTTACTGTATTCAAGCCCTGCGGCTGCGACCTCTGCTCTGGTGGTTACAAAGGCCGCGT
AGGTATTTATGAAGTGATGCCCATGTCTGACGAGATTGCCCGGGTTATTATGGAGGGTGGCAACTCACTGGAGATTGCCA
GAATGGCCAAAACGCAGGGCATTAGGGACCTCAGGCAATCGGGCCTTTTAAAAGTCGTCCAAGGCGTTACCAGCATCACA
GAAGTGAACCGGGTAACCAGTTTCTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(191-458)

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

(43-144)


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

58.645

98.768

0.579
  pilB Legionella pneumophila strain ERS1305867

56.838

99.12

0.563
  pilB Acinetobacter baumannii D1279779

56.964

98.592

0.562
  pilB Vibrio cholerae strain A1552

53.214

98.592

0.525
  pilB Vibrio parahaemolyticus RIMD 2210633

52.205

99.824

0.521
  pilB Vibrio campbellii strain DS40M4

51.957

98.944

0.514
  pilF Neisseria gonorrhoeae MS11

48.85

99.472

0.486
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

40.219

96.303

0.387
  pilF Thermus thermophilus HB27

38.571

98.592

0.38

Multiple sequence alignment