Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SCD_RS12185 Genome accession   NC_022357
Coordinates   2520275..2521990 (+) Length   571 a.a.
NCBI ID   WP_009205467.1    Uniprot ID   S6B749
Organism   Sulfuricella denitrificans skB26     
Function   power the assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
ICE 2512739..2521990 2520275..2521990 within 0


Gene organization within MGE regions


Location: 2512739..2521990
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SCD_RS12140 (SCD_00736) xerD 2512739..2513635 (-) 897 WP_009205458.1 site-specific tyrosine recombinase XerD -
  SCD_RS12145 (SCD_00737) - 2513613..2514083 (-) 471 WP_023506992.1 methylated-DNA--[protein]-cysteine S-methyltransferase -
  SCD_RS12150 (SCD_00738) rplS 2514315..2514698 (-) 384 WP_009205460.1 50S ribosomal protein L19 -
  SCD_RS12155 (SCD_00739) trmD 2514717..2515454 (-) 738 WP_232504463.1 tRNA (guanosine(37)-N1)-methyltransferase TrmD -
  SCD_RS12160 (SCD_00740) rimM 2515484..2515963 (-) 480 WP_009205462.1 ribosome maturation factor RimM -
  SCD_RS12165 (SCD_00741) rpsP 2515977..2516219 (-) 243 WP_009205463.1 30S ribosomal protein S16 -
  SCD_RS12170 (SCD_00742) ffh 2516303..2517646 (-) 1344 WP_009205464.1 signal recognition particle protein -
  SCD_RS12175 (SCD_00743) - 2518010..2518837 (+) 828 WP_009205465.1 inner membrane protein YpjD -
  SCD_RS12180 (SCD_00744) - 2518928..2520199 (+) 1272 WP_023506993.1 HlyC/CorC family transporter -
  SCD_RS12185 (SCD_00745) pilB 2520275..2521990 (+) 1716 WP_009205467.1 type IV-A pilus assembly ATPase PilB Machinery gene

Sequence

Protein


Download         Length: 571 a.a.        Molecular weight: 62340.48 Da        Isoelectric Point: 5.0738

>NTDB_id=62196 SCD_RS12185 WP_009205467.1 2520275..2521990(+) (pilB) [Sulfuricella denitrificans skB26]
MAAATTSTKLSGLANALVQSGRLLEADAEAIQSQAGVDETGFVTQLVQSKKMSSLEVAEFAARTFGFPLLDLTAIDADHL
PNDVLDAKLIRSRRVLALQKRGNRLFIATSDPANLRALDDVRFKTSLTVEPVVVEDDKLGKLIDKIAEATDTTLQNLAGD
DINLEFTDEEALAQKDEGASAEIDDAPVVRFLQKILLDAINAGVSDIHFEPYEKYYRIRYRLDGILSEVAQPPLAIKEKL
SSRIKVISKLDISEKRVPQDGRMKLVLSKNRAIDFRVSTLPTLYGEKIVMRILDPSSATLGVDALGYEPDQKEFLLNAVR
RPYGMVLVTGPTGSGKTVSLYTCLNILNEPGVNISTAEDPAEINLPGVNQVNVNDKAGLTFSAALKSFLRQDPDVIMVGE
IRDLETADISIKAAQTGHMVLSTLHTNDAPGTLTRLMNMGVAPFNIASAVILITAQRLARRLCKCKQPIEIPREALLRAG
YTEEDLDGSWQPYGHIGCEICKGTGYKGRVGIYQVMPISDEMSRIIMKNGTAHDIADQAKREGIRDLRQSGLIKVKAGLT
TLEEIEAVTNE

Nucleotide


Download         Length: 1716 bp        

>NTDB_id=62196 SCD_RS12185 WP_009205467.1 2520275..2521990(+) (pilB) [Sulfuricella denitrificans skB26]
ATGGCAGCAGCAACAACTTCGACCAAGCTTAGCGGACTGGCCAACGCACTGGTTCAAAGCGGGCGCCTGCTGGAGGCCGA
TGCCGAAGCTATTCAGTCCCAGGCTGGCGTCGATGAAACCGGCTTTGTTACCCAGTTGGTGCAAAGCAAAAAAATGAGTT
CCCTGGAGGTTGCAGAATTTGCTGCGCGGACATTCGGCTTTCCCCTGCTGGATTTGACTGCTATCGATGCGGATCACCTG
CCCAATGATGTGCTCGATGCCAAGCTGATCAGAAGCCGGCGCGTTCTGGCCCTGCAAAAGCGCGGCAATCGCCTGTTTAT
CGCCACCTCCGATCCAGCCAACCTGCGCGCCCTGGACGATGTGCGCTTCAAAACCAGCCTCACGGTTGAGCCGGTGGTAG
TAGAAGACGACAAACTCGGCAAGCTGATAGACAAAATTGCCGAAGCTACTGACACTACCCTGCAGAATCTGGCTGGCGAT
GACATCAACCTTGAATTCACCGACGAGGAAGCGCTGGCGCAAAAAGATGAGGGCGCCAGCGCGGAAATCGACGACGCCCC
AGTCGTCCGTTTCCTCCAGAAAATTCTGCTGGACGCGATCAATGCCGGCGTTTCAGACATCCATTTTGAACCCTACGAAA
AATACTACCGCATCCGCTATCGCCTCGACGGCATACTCTCCGAAGTAGCGCAACCGCCCCTGGCAATCAAGGAAAAGCTC
TCATCCCGCATCAAAGTGATTTCCAAGCTCGACATTTCTGAGAAACGGGTGCCTCAGGACGGCCGAATGAAGCTGGTGCT
GTCCAAGAACCGCGCCATTGACTTCCGCGTCAGCACTCTGCCTACTCTGTACGGCGAAAAAATCGTGATGCGGATTCTCG
ACCCGTCCAGCGCCACGCTGGGTGTTGATGCCCTGGGCTACGAGCCGGACCAAAAAGAGTTTCTGCTCAATGCCGTCCGC
CGCCCTTATGGCATGGTGCTGGTAACCGGGCCAACCGGCAGTGGCAAAACCGTATCGCTTTATACCTGCCTGAATATCCT
GAACGAACCCGGCGTTAACATCTCCACCGCGGAAGACCCAGCTGAGATCAACCTTCCCGGCGTCAACCAGGTTAACGTCA
ACGACAAGGCTGGACTGACCTTCTCCGCAGCACTCAAGTCCTTTCTGCGTCAAGACCCGGATGTCATCATGGTGGGTGAG
ATCCGCGACCTGGAAACGGCGGACATCTCGATCAAGGCAGCGCAAACCGGCCACATGGTTCTGTCCACCCTGCACACCAA
CGATGCTCCAGGCACCTTGACCCGTCTGATGAACATGGGAGTCGCCCCTTTCAACATCGCCTCCGCAGTCATCCTGATTA
CCGCACAGCGTCTGGCGCGGCGCCTGTGCAAGTGCAAACAGCCCATCGAAATTCCCAGAGAAGCACTATTGCGTGCCGGC
TATACCGAAGAGGATCTCGACGGCAGTTGGCAGCCTTATGGCCATATCGGTTGTGAAATCTGCAAGGGCACCGGCTACAA
GGGGCGAGTCGGCATCTACCAAGTCATGCCGATCAGCGACGAAATGAGCCGCATCATCATGAAAAACGGCACCGCGCATG
ACATCGCCGACCAGGCAAAGCGCGAAGGTATTCGCGACCTACGTCAATCCGGACTGATCAAAGTAAAAGCCGGACTGACA
ACGCTGGAAGAAATCGAAGCCGTCACCAACGAGTAA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(194-461)

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

(46-149)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB S6B749

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

54.435

100

0.548
  pilB Acinetobacter baylyi ADP1

54.101

100

0.543
  pilF Neisseria gonorrhoeae MS11

54.211

99.825

0.541
  pilB Legionella pneumophila strain ERS1305867

51.641

100

0.524
  pilB Vibrio cholerae strain A1552

48.746

97.723

0.476
  pilB Vibrio parahaemolyticus RIMD 2210633

47.443

99.299

0.471
  pilB Vibrio campbellii strain DS40M4

46.479

99.475

0.462
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

41.288

92.469

0.382
  pilF Thermus thermophilus HB27

40.075

93.52

0.375
  pilB/pilB1 Synechocystis sp. PCC 6803

41.036

87.916

0.361

Multiple sequence alignment