Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SSED_RS02250 Genome accession   NC_009831
Coordinates   516774..518483 (-) Length   569 a.a.
NCBI ID   WP_012140775.1    Uniprot ID   -
Organism   Shewanella sediminis HAW-EB3     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 511774..523483
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SSED_RS24755 - 512033..512170 (+) 138 WP_190273185.1 hypothetical protein -
  SSED_RS02220 (Ssed_0419) mutT 512380..512769 (-) 390 WP_012140769.1 8-oxo-dGTP diphosphatase MutT -
  SSED_RS02225 (Ssed_0420) yacG 512773..512985 (-) 213 WP_012140770.1 DNA gyrase inhibitor YacG -
  SSED_RS02230 (Ssed_0421) zapD 513065..513799 (-) 735 WP_012140771.1 cell division protein ZapD -
  SSED_RS02235 (Ssed_0422) coaE 513808..514413 (-) 606 WP_012140772.1 dephospho-CoA kinase -
  SSED_RS02240 (Ssed_0423) pilD 514459..515370 (-) 912 WP_012140773.1 A24 family peptidase Machinery gene
  SSED_RS02245 (Ssed_0424) pilC 515443..516708 (-) 1266 WP_012140774.1 type II secretion system F family protein Machinery gene
  SSED_RS02250 (Ssed_0425) pilB 516774..518483 (-) 1710 WP_012140775.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SSED_RS02255 (Ssed_0426) - 518556..518966 (-) 411 WP_012140776.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  SSED_RS02260 (Ssed_0427) nadC 519719..520624 (-) 906 WP_012140777.1 carboxylating nicotinate-nucleotide diphosphorylase -
  SSED_RS02265 (Ssed_0428) ampD 520949..521566 (+) 618 WP_012140778.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  SSED_RS02270 (Ssed_0429) ampE 521706..522557 (+) 852 WP_012140779.1 beta-lactamase regulator AmpE -

Sequence

Protein


Download         Length: 569 a.a.        Molecular weight: 63081.22 Da        Isoelectric Point: 5.1178

>NTDB_id=29197 SSED_RS02250 WP_012140775.1 516774..518483(-) (pilB) [Shewanella sediminis HAW-EB3]
MPTTGLHLGLSTLFIRKQLLSEEQIASAIAKSRQSKRPLVSTIISEKLISGREIAELCYEEYGTPLLDLDEFDIASIPEN
FLNKKLIEKHKCLPLFKRGNRLYIGTSDPTNIAALEDFQFSAGLHAEAILVEDDKLTKALEKVLEEDISALDIGDIDEDS
LAGIEIEDTSKRDDDQNGDSSDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPVNLSNRISA
RLKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSTLPTIWGEKIVMRILDSSSAQLGIEKLGYEDDQRELYEEMLAKP
QGMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIR
DLETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLARRLCPECKQPEEVPKHELEKLGF
NPTHIEAGITVYKPIGCDLCSGGYKGRVGIYEVMRMSDEIARTIMEGGNSLQIANQAKEQGMRDLRGSGLLKVIQGVTSI
AEINRVTSF

Nucleotide


Download         Length: 1710 bp        

>NTDB_id=29197 SSED_RS02250 WP_012140775.1 516774..518483(-) (pilB) [Shewanella sediminis HAW-EB3]
GTGCCAACGACTGGGTTACACTTAGGATTATCAACCCTTTTCATTCGCAAACAACTGCTCAGCGAAGAGCAGATAGCATC
GGCGATAGCCAAATCTCGTCAATCGAAGCGACCTCTAGTTTCAACCATAATCTCAGAAAAGCTTATCTCAGGGCGAGAAA
TTGCCGAGTTATGCTATGAAGAGTACGGTACTCCACTGCTGGATCTCGATGAATTTGATATTGCCAGTATCCCGGAAAAC
TTTCTCAACAAAAAGCTAATTGAAAAACACAAGTGCCTGCCACTTTTTAAGCGTGGCAACCGCCTCTATATTGGCACCTC
AGATCCGACCAATATCGCAGCACTGGAGGATTTTCAATTTAGCGCAGGCCTGCACGCCGAAGCCATTTTGGTTGAAGACG
ACAAGTTAACCAAGGCTCTGGAAAAGGTACTCGAAGAGGACATTTCGGCCCTCGATATCGGCGACATAGATGAAGACTCT
TTAGCTGGCATAGAGATAGAGGACACCAGTAAACGCGATGACGATCAGAATGGTGACAGCTCCGATGATGCCCCGATCGT
TATCTATATCAATAAAATTTTGACCGATGCGATACGAAAAGGCGCATCGGATCTTCATTTCGAGCCCTATGAGAAACGAT
ATCGAATTCGCTTTCGCATCGATGGCATCTTACACGAAGTATCAGAGCCTCCGGTAAATCTCTCTAACCGTATTTCGGCT
CGCCTCAAGGTGATGTCAAAGCTGGATATCGCCGAGCGCCGCGTCCCCCAAGATGGCCGCATAAAGATGAAGCTATCTCG
CACCAAATCAATCGATTTTCGTGTCAGTACGCTGCCAACAATTTGGGGGGAGAAGATCGTAATGCGTATCCTGGACTCAT
CCTCTGCTCAACTAGGCATCGAGAAGCTGGGTTACGAGGATGATCAGCGAGAGCTTTACGAGGAGATGCTGGCAAAACCA
CAAGGCATGATCTTAGTGACTGGCCCAACGGGTTCGGGTAAGACGGTATCTCTCTACACCGGACTCAACATCCTTAACAC
CGAAGAGCGTAATATCTCAACGGCAGAGGATCCGGTAGAGATAAACTTAGAAGGTGTCAATCAGGTACATATCAATCTAA
AAGCCGGACTCACCTTCGCATCGGCCCTGCGTTCGTTCCTCCGTCAAGATCCCGATGTCGTCATGGTGGGTGAGATCCGA
GACTTAGAGACAGCCGAAATAGCCATTAAGGCGGCACAAACCGGTCACTTAGTGCTCTCGACACTGCATACTAACTCGGC
GGCAGAGACTCTCACTCGTCTCATTAATATGGGCGTGCCCGGGTACAATATTGCCAGCTCGGTCAACCTGATTATCGCCC
AACGTCTGGCTCGTCGTTTATGTCCAGAGTGTAAACAACCTGAAGAGGTGCCCAAACACGAATTGGAAAAACTGGGGTTT
AATCCAACTCATATCGAAGCTGGCATCACAGTCTATAAGCCAATAGGCTGCGATCTCTGCTCAGGTGGTTATAAAGGCCG
TGTCGGTATCTATGAAGTGATGAGAATGTCAGATGAGATAGCCCGTACTATTATGGAGGGAGGTAACTCCTTACAAATAG
CCAACCAGGCAAAAGAGCAGGGGATGAGAGATCTCAGGGGTTCCGGGTTATTAAAAGTCATTCAAGGTGTTACCAGCATT
GCAGAGATAAATCGTGTAACCAGTTTTTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(192-459)

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

(15-144)


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

58.289

98.594

0.575
  pilB Acinetobacter baumannii D1279779

56.684

98.594

0.559
  pilB Legionella pneumophila strain ERS1305867

55.654

99.473

0.554
  pilB Vibrio parahaemolyticus RIMD 2210633

52.12

99.473

0.518
  pilB Vibrio cholerae strain A1552

51.858

99.297

0.515
  pilB Vibrio campbellii strain DS40M4

51.418

99.121

0.51
  pilF Neisseria gonorrhoeae MS11

47.35

99.473

0.471
  pilB/pilB1 Synechocystis sp. PCC 6803

37

100

0.39
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

37.882

97.891

0.371
  pilF Thermus thermophilus HB27

36.702

99.121

0.364

Multiple sequence alignment