Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SDEN_RS17600 Genome accession   NC_007954
Coordinates   4043609..4045318 (+) Length   569 a.a.
NCBI ID   WP_011497807.1    Uniprot ID   Q12IR1
Organism   Shewanella denitrificans OS217     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 4038609..4050318
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SDEN_RS17580 (Sden_3385) ampE 4039404..4040387 (-) 984 WP_011497803.1 beta-lactamase regulator AmpE -
  SDEN_RS17585 (Sden_3386) ampD 4040468..4041037 (-) 570 WP_041405885.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  SDEN_RS17590 (Sden_3387) nadC 4041393..4042268 (+) 876 WP_011497805.1 carboxylating nicotinate-nucleotide diphosphorylase -
  SDEN_RS17595 (Sden_3388) - 4043125..4043541 (+) 417 WP_011497806.1 pilin -
  SDEN_RS17600 (Sden_3389) pilB 4043609..4045318 (+) 1710 WP_011497807.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SDEN_RS17605 (Sden_3390) pilC 4045495..4046763 (+) 1269 WP_011497808.1 type II secretion system F family protein Machinery gene
  SDEN_RS17610 (Sden_3391) pilD 4046921..4047838 (+) 918 WP_011497809.1 prepilin peptidase Machinery gene
  SDEN_RS17615 (Sden_3392) coaE 4047838..4048458 (+) 621 WP_011497810.1 dephospho-CoA kinase -
  SDEN_RS17620 (Sden_3393) zapD 4048468..4049211 (+) 744 WP_011497811.1 cell division protein ZapD -
  SDEN_RS17625 (Sden_3394) - 4049249..4049473 (+) 225 WP_011497812.1 DNA gyrase inhibitor YacG -
  SDEN_RS17630 (Sden_3395) mutT 4049482..4049877 (+) 396 WP_011497813.1 8-oxo-dGTP diphosphatase MutT -

Sequence

Protein


Download         Length: 569 a.a.        Molecular weight: 62659.05 Da        Isoelectric Point: 5.8166

>NTDB_id=25720 SDEN_RS17600 WP_011497807.1 4043609..4045318(+) (pilB) [Shewanella denitrificans OS217]
MPSTALHLGLSNLFIRKGLLSEDIMASAIADSRKNKHSLVATLINGKHLSAREIAELCHEEYATPLLDLAEFDVAAIAED
LLNKKLIAKHQCLPLFKRGNRLYIATSDPTNITALEDFQFSLGLHAEAILVEDDKLSKALEKVIEDDITGLDLNGMDEAA
LAGIEITDTDKRHEEPGGESSDDAPIVIYINKILTDAIRKGASDLHFEPYEKRYRIRFRIDGILHEVSEPPVALSGRISA
RLKVMSKLDIAERRVPQDGRIKMKLSRTKSIDFRVSTLPTIWGEKIVMRILDSSSAQLGIEKLGYEDDQRLLYEEMLAKP
QGMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINLKAGLTFASALRSFLRQDPDVVMVGEIR
DLETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLINMGVPGYNIASSVNLIIAQRLARRLCPECKHAEDIPVAELQRLGF
QQADIDKGFTVFKPVGCEFCSGGYKGRLGVYEVMKMSDDIARTIMEGGNSLQIARIAKEQGMRDLRQSGLLKVIQGLSSI
AEINRITSS

Nucleotide


Download         Length: 1710 bp        

>NTDB_id=25720 SDEN_RS17600 WP_011497807.1 4043609..4045318(+) (pilB) [Shewanella denitrificans OS217]
ATGCCCTCAACTGCGCTTCATCTAGGCCTCTCCAATTTGTTTATTCGCAAGGGTCTCCTTAGCGAAGACATCATGGCCTC
CGCCATCGCCGATTCACGTAAAAATAAACACTCGCTAGTAGCAACCCTGATTAACGGCAAGCACTTATCCGCTCGTGAAA
TTGCCGAGCTGTGCCATGAAGAATATGCCACCCCGCTATTAGACTTAGCAGAATTCGATGTTGCCGCCATCGCGGAAGAC
TTATTAAATAAAAAACTTATCGCCAAACATCAGTGCTTACCGCTATTTAAGCGCGGTAATCGCCTCTATATTGCTACCTC
TGACCCCACCAATATTACCGCATTGGAAGATTTTCAATTTAGCTTAGGCCTGCACGCCGAAGCCATTTTGGTGGAAGACG
ATAAGCTCAGCAAGGCCCTAGAGAAGGTCATCGAAGATGATATTACTGGGTTAGATCTAAACGGCATGGATGAAGCCGCC
CTCGCTGGCATTGAAATCACCGACACAGACAAGCGTCATGAAGAGCCAGGCGGTGAAAGCAGTGACGATGCACCCATCGT
TATTTACATTAATAAAATCCTCACCGATGCCATACGTAAAGGCGCCTCAGATTTGCATTTTGAGCCCTATGAGAAGCGCT
ATCGCATTCGTTTTCGCATCGATGGCATACTCCATGAAGTCTCAGAGCCGCCAGTGGCACTTTCCGGGCGTATTTCGGCC
CGCTTAAAGGTGATGTCAAAACTTGATATTGCCGAGCGCCGCGTGCCACAAGATGGCCGCATCAAGATGAAGCTATCCCG
CACTAAATCTATCGACTTTCGTGTTAGCACCTTGCCCACCATCTGGGGTGAGAAAATCGTAATGCGTATTTTGGACTCTT
CATCGGCGCAGTTAGGTATTGAAAAACTTGGCTATGAAGACGATCAACGCTTGCTCTATGAAGAAATGCTCGCCAAGCCT
CAGGGGATGATTTTAGTCACAGGCCCCACGGGCTCAGGTAAAACCGTGTCCTTGTACACAGGTCTTAATATTCTCAATAC
CGAAGAGCGTAATATTTCCACCGCAGAAGACCCAGTTGAAATTAACCTCGAAGGGGTGAATCAGGTCCATATCAATTTAA
AAGCCGGCCTGACGTTTGCGTCAGCCCTGCGCTCATTTTTGCGCCAAGATCCGGATGTGGTCATGGTGGGTGAAATACGT
GACTTGGAAACTGCAGAAATCGCTATTAAGGCGGCGCAAACCGGCCACTTAGTGCTATCGACACTGCATACTAACTCGGC
GGCGGAAACCCTAACCCGCCTCATTAACATGGGTGTGCCTGGTTATAACATTGCAAGTTCGGTGAATTTAATTATCGCTC
AGCGTTTGGCAAGGCGCCTGTGTCCCGAGTGCAAACATGCCGAAGATATTCCTGTGGCCGAGCTGCAGCGCTTAGGCTTT
CAACAAGCTGATATCGACAAAGGTTTCACTGTGTTTAAGCCCGTTGGCTGTGAGTTTTGCTCCGGTGGCTATAAGGGCCG
TTTAGGCGTATATGAAGTGATGAAGATGTCTGATGATATTGCCCGCACCATAATGGAAGGCGGTAACTCATTGCAAATTG
CCCGCATCGCCAAAGAGCAAGGCATGCGGGATTTACGCCAATCGGGTCTGTTAAAAGTAATCCAAGGCCTAAGTAGCATC
GCCGAGATCAATCGTATCACCAGCTCTTAG

Domains

Predicted by InterproScan.

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

(43-143)

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
  AlphaFold DB Q12IR1

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 baumannii D1279779

56.743

100

0.569
  pilB Acinetobacter baylyi ADP1

56.762

98.77

0.561
  pilB Legionella pneumophila strain ERS1305867

57.57

94.025

0.541
  pilB Vibrio parahaemolyticus RIMD 2210633

51.056

99.824

0.51
  pilB Vibrio cholerae strain A1552

55.106

91.213

0.503
  pilB Vibrio campbellii strain DS40M4

50.267

98.594

0.496
  pilF Neisseria gonorrhoeae MS11

46.82

99.473

0.466
  pilF Thermus thermophilus HB27

38.721

98.946

0.383
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.137

100

0.381

Multiple sequence alignment