Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SAMA_RS02010 Genome accession   NC_008700
Coordinates   446213..447919 (-) Length   568 a.a.
NCBI ID   WP_011758490.1    Uniprot ID   A1S2H4
Organism   Shewanella amazonensis SB2B     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 441213..452919
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SAMA_RS01980 (Sama_0363) mutT 441876..442271 (-) 396 WP_011758484.1 8-oxo-dGTP diphosphatase MutT -
  SAMA_RS01985 (Sama_0364) yacG 442313..442528 (-) 216 WP_011758485.1 DNA gyrase inhibitor YacG -
  SAMA_RS01990 (Sama_0365) zapD 442590..443324 (-) 735 WP_011758486.1 cell division protein ZapD -
  SAMA_RS01995 (Sama_0366) coaE 443317..443934 (-) 618 WP_011758487.1 dephospho-CoA kinase -
  SAMA_RS02000 (Sama_0367) pilD 443934..444848 (-) 915 WP_011758488.1 A24 family peptidase Machinery gene
  SAMA_RS02005 (Sama_0368) pilC 444884..446143 (-) 1260 WP_011758489.1 type II secretion system F family protein Machinery gene
  SAMA_RS02010 (Sama_0369) pilB 446213..447919 (-) 1707 WP_011758490.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SAMA_RS02015 (Sama_0370) - 447973..448446 (-) 474 WP_011758491.1 prepilin-type N-terminal cleavage/methylation domain-containing protein -
  SAMA_RS02020 (Sama_0371) nadC 450088..450945 (-) 858 WP_011758492.1 carboxylating nicotinate-nucleotide diphosphorylase -
  SAMA_RS02025 (Sama_0372) ampD 451281..451853 (+) 573 WP_011758493.1 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD -
  SAMA_RS02030 (Sama_0373) ampE 451931..452791 (+) 861 WP_011758494.1 beta-lactamase regulator AmpE -

Sequence

Protein


Download         Length: 568 a.a.        Molecular weight: 62783.02 Da        Isoelectric Point: 5.3515

>NTDB_id=27059 SAMA_RS02010 WP_011758490.1 446213..447919(-) (pilB) [Shewanella amazonensis SB2B]
MPTTGLHLGLSTLFLRKGLLTEEQLSEAVSQSRKNRHSLVTTLVISKLISAREIAELCYEEYGTPLLDLAEFDVSSIPED
FLNKKLIEKHRCLPLFKRGNRLYIGTSDPTNIPALEDFQFSAGLHAEAILVEDDKLAKALEKILEEDISALDLGGLDEEA
LAGIEVTDTDKRPENDNEGADDAPIVIYINKILTDAIRRGASDLHFEPYEKRYRIRFRIDGILHEVSEPPINLSGRISAR
LKVMSKLDIAERRLPQDGRIKMKLSRTKSIDFRVSTLPTLWGEKIVMRILDSSSAQLGIEKLGYEPDQKQLYLDNLAKPQ
GMILVTGPTGSGKTVSLYTGLNILNTEERNISTAEDPVEINLEGVNQVHINNKAGLTFASALRSFLRQDPDVVMVGEIRD
LETAEIAIKAAQTGHLVLSTLHTNSAAETLTRLLNMGVPGYNIASSVNLIIAQRLARRLCPECKQPEEIPNHELERLGFN
QAQIAEGFTAFKPCGCDLCSGGYKGRVGIYEVMPMSDEIARVIMEGGNSLEIARMAKSQGVRDLRLSGLLKVIQGVTSIA
EVNRVTSF

Nucleotide


Download         Length: 1707 bp        

>NTDB_id=27059 SAMA_RS02010 WP_011758490.1 446213..447919(-) (pilB) [Shewanella amazonensis SB2B]
ATGCCAACAACCGGCTTGCACTTAGGATTGTCGACGCTGTTTTTACGTAAAGGACTGCTCACAGAAGAGCAGCTCTCCGA
AGCAGTATCCCAATCACGCAAAAATCGGCATTCATTGGTCACTACTCTTGTGATCAGTAAGCTAATATCTGCAAGAGAAA
TTGCAGAGCTTTGTTATGAAGAATACGGCACGCCGCTTCTGGATTTAGCCGAGTTTGATGTTTCCAGCATTCCCGAAGAT
TTTCTCAATAAAAAGCTCATCGAGAAGCACCGCTGCCTGCCACTGTTTAAGCGTGGCAACCGGCTGTATATAGGTACATC
TGACCCCACCAACATTCCCGCACTGGAAGATTTTCAGTTTTCAGCAGGTTTGCACGCCGAAGCTATTTTGGTGGAAGACG
ATAAGCTTGCCAAAGCGCTGGAGAAAATCCTTGAAGAAGACATCAGCGCTCTGGATTTGGGGGGCTTGGACGAAGAAGCT
CTTGCTGGCATTGAAGTTACTGATACCGACAAGCGCCCGGAAAATGATAATGAAGGCGCCGACGATGCCCCAATAGTTAT
CTATATCAACAAGATTTTGACAGATGCTATTCGCCGCGGCGCATCAGATTTGCACTTTGAACCTTATGAGAAGCGCTACC
GCATCCGTTTTCGTATCGATGGCATTTTGCATGAAGTGTCTGAGCCGCCGATTAACCTCTCAGGGCGCATTTCTGCACGC
TTAAAGGTGATGTCAAAACTCGACATTGCCGAGCGCCGCCTGCCCCAAGATGGCCGCATAAAGATGAAACTCAGCCGCAC
CAAGAGCATCGATTTTCGGGTAAGTACCCTGCCGACGCTCTGGGGCGAAAAAATTGTAATGCGTATTCTGGACTCCTCTT
CTGCCCAGCTTGGTATCGAGAAGCTCGGTTACGAGCCAGACCAAAAGCAGCTGTACCTCGATAACCTCGCTAAACCCCAG
GGCATGATTCTGGTGACCGGCCCCACAGGCTCGGGTAAAACCGTATCCCTGTACACCGGCCTTAATATCCTCAATACCGA
AGAGCGCAACATTTCCACCGCCGAAGACCCGGTAGAAATAAACCTTGAAGGCGTGAATCAGGTTCACATTAATAACAAGG
CAGGACTTACATTTGCGTCTGCTTTGCGATCGTTTTTGCGTCAGGACCCTGACGTGGTGATGGTGGGGGAAATCAGGGAT
TTGGAAACCGCCGAGATTGCCATTAAGGCAGCTCAAACCGGCCACTTGGTGTTATCCACCCTGCACACCAACTCTGCCGC
CGAAACCCTTACCCGTCTTTTAAATATGGGGGTGCCGGGCTATAACATCGCGAGCTCGGTGAATTTGATTATTGCCCAGC
GCCTCGCTAGGCGCCTGTGCCCAGAGTGTAAACAACCGGAAGAGATCCCCAATCACGAACTGGAGCGCCTGGGTTTTAAT
CAGGCGCAGATTGCCGAAGGCTTCACCGCTTTTAAGCCCTGCGGCTGCGATTTATGTTCCGGTGGTTATAAAGGTCGCGT
GGGTATTTATGAAGTCATGCCCATGAGTGATGAAATTGCAAGGGTCATTATGGAAGGCGGTAATTCGCTTGAAATTGCTC
GCATGGCCAAGTCTCAGGGCGTAAGGGACCTGCGCTTATCAGGGCTCCTTAAGGTGATACAAGGCGTAACCAGTATTGCA
GAGGTTAACCGCGTGACCAGTTTTTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(191-458)

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
  AlphaFold DB A1S2H4

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

58.363

98.944

0.577
  pilB Acinetobacter baumannii D1279779

58.259

99.12

0.577
  pilB Legionella pneumophila strain ERS1305867

55.83

99.648

0.556
  pilB Vibrio parahaemolyticus RIMD 2210633

52.389

99.472

0.521
  pilB Vibrio cholerae strain A1552

52.05

98.768

0.514
  pilB Vibrio campbellii strain DS40M4

51.779

98.944

0.512
  pilF Neisseria gonorrhoeae MS11

49.204

99.472

0.489
  pilB/pilB1 Synechocystis sp. PCC 6803

37.355

100

0.398
  pilF Thermus thermophilus HB27

38.693

99.648

0.386
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

38.043

97.183

0.37

Multiple sequence alignment