Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   SriyCCGPB3_RS16860 Genome accession   NZ_CP155568
Coordinates   3634034..3635764 (-) Length   576 a.a.
NCBI ID   WP_153855680.1    Uniprot ID   -
Organism   Stenotrophomonas riyadhensis strain ESTM1A_MKCTX4_10a     
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)
Genomic island 3622937..3656129 3634034..3635764 within 0


Gene organization within MGE regions


Location: 3622937..3656129
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  SriyCCGPB3_RS16810 (SriyCCGPB3_003356) - 3622937..3623122 (+) 186 WP_141097650.1 hypothetical protein -
  SriyCCGPB3_RS16815 (SriyCCGPB3_003357) - 3623181..3623855 (+) 675 WP_141097651.1 hypothetical protein -
  SriyCCGPB3_RS16820 (SriyCCGPB3_003358) - 3623849..3624862 (+) 1014 WP_049447473.1 hypothetical protein -
  SriyCCGPB3_RS16825 (SriyCCGPB3_003359) - 3624856..3625872 (+) 1017 WP_350259520.1 TraB/GumN family protein -
  SriyCCGPB3_RS16830 (SriyCCGPB3_003360) - 3626191..3626460 (+) 270 WP_110713349.1 hypothetical protein -
  SriyCCGPB3_RS16835 (SriyCCGPB3_003361) - 3626512..3628269 (+) 1758 WP_350259521.1 ABC transporter transmembrane domain-containing protein -
  SriyCCGPB3_RS16840 (SriyCCGPB3_003362) sucD 3628387..3629262 (-) 876 WP_005410793.1 succinate--CoA ligase subunit alpha -
  SriyCCGPB3_RS16845 (SriyCCGPB3_003363) sucC 3629283..3630452 (-) 1170 WP_004154430.1 ADP-forming succinate--CoA ligase subunit beta -
  SriyCCGPB3_RS16850 (SriyCCGPB3_003364) - 3630858..3632471 (+) 1614 WP_164162034.1 ATP-binding protein -
  SriyCCGPB3_RS16855 (SriyCCGPB3_003365) pilR 3632532..3633905 (+) 1374 WP_110713353.1 sigma-54 dependent transcriptional regulator Regulator
  SriyCCGPB3_RS16860 (SriyCCGPB3_003366) pilB 3634034..3635764 (-) 1731 WP_153855680.1 type IV-A pilus assembly ATPase PilB Machinery gene
  SriyCCGPB3_RS16865 (SriyCCGPB3_003367) - 3635980..3636387 (-) 408 WP_180854230.1 pilin -
  SriyCCGPB3_RS16870 (SriyCCGPB3_003368) pilA2 3636513..3636962 (-) 450 WP_153855678.1 pilin Machinery gene
  SriyCCGPB3_RS16875 (SriyCCGPB3_003369) pilC 3637317..3638576 (+) 1260 WP_180854231.1 type II secretion system F family protein Machinery gene
  SriyCCGPB3_RS16880 (SriyCCGPB3_003370) - 3638585..3639448 (+) 864 WP_010481503.1 A24 family peptidase -
  SriyCCGPB3_RS16885 (SriyCCGPB3_003371) coaE 3639460..3640071 (+) 612 WP_350259522.1 dephospho-CoA kinase -
  SriyCCGPB3_RS16890 (SriyCCGPB3_003372) - 3640201..3640587 (-) 387 WP_350259523.1 hypothetical protein -
  SriyCCGPB3_RS16895 (SriyCCGPB3_003373) - 3641012..3642994 (-) 1983 WP_350259524.1 DUF2235 domain-containing protein -
  SriyCCGPB3_RS16900 (SriyCCGPB3_003374) - 3643174..3643770 (-) 597 WP_350259525.1 DUF3304 domain-containing protein -
  SriyCCGPB3_RS16905 (SriyCCGPB3_003375) - 3643798..3644898 (-) 1101 WP_350259526.1 DUF2235 domain-containing protein -
  SriyCCGPB3_RS16910 (SriyCCGPB3_003376) - 3644940..3645548 (-) 609 WP_180860819.1 DUF3304 domain-containing protein -
  SriyCCGPB3_RS16915 (SriyCCGPB3_003377) - 3645739..3646449 (-) 711 WP_350259527.1 DUF4123 domain-containing protein -
  SriyCCGPB3_RS16920 (SriyCCGPB3_003378) tssI 3646547..3649156 (-) 2610 WP_350259528.1 type VI secretion system tip protein TssI/VgrG -
  SriyCCGPB3_RS16925 (SriyCCGPB3_003379) - 3649379..3649795 (-) 417 WP_350259529.1 hypothetical protein -
  SriyCCGPB3_RS16930 (SriyCCGPB3_003380) - 3650066..3651436 (-) 1371 WP_350259530.1 HAMP domain-containing sensor histidine kinase -
  SriyCCGPB3_RS16935 (SriyCCGPB3_003381) - 3651399..3652076 (-) 678 WP_005410804.1 response regulator transcription factor -
  SriyCCGPB3_RS16940 (SriyCCGPB3_003382) - 3652089..3652574 (-) 486 WP_110713376.1 hypothetical protein -
  SriyCCGPB3_RS16945 (SriyCCGPB3_003383) rimK 3652860..3653738 (-) 879 WP_110713377.1 30S ribosomal protein S6--L-glutamate ligase -
  SriyCCGPB3_RS16950 (SriyCCGPB3_003384) - 3653868..3654305 (+) 438 WP_110713379.1 thioesterase family protein -
  SriyCCGPB3_RS16955 (SriyCCGPB3_003385) - 3654306..3655460 (-) 1155 WP_350259531.1 hypothetical protein -
  SriyCCGPB3_RS16960 (SriyCCGPB3_003386) - 3655605..3656129 (+) 525 WP_350259532.1 hypothetical protein -

Sequence

Protein


Download         Length: 576 a.a.        Molecular weight: 62084.07 Da        Isoelectric Point: 6.0426

>NTDB_id=997817 SriyCCGPB3_RS16860 WP_153855680.1 3634034..3635764(-) (pilB) [Stenotrophomonas riyadhensis strain ESTM1A_MKCTX4_10a]
MNAVTTANLVGITGLARRLVQDGALDEASARDAMAKAAAARQPLPTWFAQNKVVGAAQLAAANAVEFGMPLFDVSTFDAS
QNAMSLVSEELLRKHNVLPLFKRGGKLFVGTSNPTHSLDEIKFHTNLVVEPIIVDEDQIRRTLEQWHASHDTLGDALGGD
DEGMGNLEVAAGDEDLGAGGDSGIDAKGDDTPVVKFVNKVLVDAIRKGASDIHFEPYEDDYRVRLRIDGLLKMVARAPVK
LNQRIAARLKVMAQLDIAEKRVPQDGRIKLNLSKSKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIDKLGYEPDQQKLF
LEAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDPDI
IMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCGNCKKPSDLPAH
ALLAEGFTQAQLDAGVQLYEAVGCDECTEGYKGRTGLYQVMPMTDEIATIVLAGGNALQIAEAAQQIGVNDLRQSALKKA
AAGITSLAEINRVTKD

Nucleotide


Download         Length: 1731 bp        

>NTDB_id=997817 SriyCCGPB3_RS16860 WP_153855680.1 3634034..3635764(-) (pilB) [Stenotrophomonas riyadhensis strain ESTM1A_MKCTX4_10a]
ATGAACGCCGTAACCACCGCCAATCTCGTCGGCATCACCGGCCTGGCCCGTCGCCTGGTCCAGGATGGTGCGCTGGACGA
GGCTTCCGCCCGCGATGCCATGGCCAAGGCTGCCGCCGCCCGGCAGCCGCTGCCGACCTGGTTCGCGCAGAACAAGGTGG
TTGGGGCAGCCCAGCTGGCAGCTGCCAACGCGGTCGAGTTCGGCATGCCGCTGTTCGACGTATCCACGTTCGACGCCAGC
CAGAACGCCATGAGCCTGGTCAGTGAGGAGCTGCTGCGGAAACACAATGTGCTGCCGCTGTTCAAGCGCGGCGGCAAGCT
GTTCGTCGGCACCAGCAACCCGACCCACTCGCTGGATGAGATCAAGTTCCACACCAACCTGGTGGTGGAGCCGATCATCG
TCGATGAGGACCAGATCCGCCGGACGTTGGAGCAGTGGCACGCCAGCCATGACACCCTCGGTGACGCCCTGGGTGGCGAC
GACGAGGGCATGGGAAACCTGGAAGTCGCGGCTGGCGACGAGGACCTGGGGGCCGGTGGCGACTCCGGCATCGACGCCAA
GGGTGACGACACCCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGCAAGGGCGCTTCGGACATCCACT
TCGAACCCTACGAAGACGATTACCGGGTGCGCCTGCGCATCGACGGCCTGCTGAAGATGGTGGCGCGCGCGCCGGTGAAA
TTGAACCAGCGCATTGCCGCGCGCCTGAAGGTGATGGCGCAGCTGGATATCGCCGAGAAGCGCGTGCCGCAGGACGGTCG
CATCAAGTTGAACCTGTCCAAGTCCAAGCAGATCGACTTCCGCGTCAGCACGCTGCCGACCCTGTTCGGCGAGAAGGTGG
TGCTGCGTATCCTCGATGGCAGCGCGGCCAAGCTGGGCATCGACAAGCTGGGTTACGAGCCGGACCAGCAGAAGCTGTTC
CTGGAAGCCATCCACAAGCCCTACGGCATGGTGCTGGTGACCGGCCCGACCGGTTCGGGCAAGACGGTGTCGCTGTATAC
CGCGCTGGGCATCCTCAACGATGAGACGCGCAACATCTCCACCGCCGAAGACCCGGTGGAAATCCGCCTGCCCGGCGTCA
ACCAGGTGCAGCAGAACAACAAGCGCGGCATGACCTTCGCGGCGGCGCTGCGCTCGTTCCTGCGACAGGATCCGGACATC
ATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGCCACATGGTGCTGTC
CACCCTGCATACCAACGATGCGCCGCAGACCATCGCGCGACTGATGAACATGGGTATTGCGCCCTACAACATCACCAGCT
CGGTGACGCTGGTGATCGCCCAGCGCCTGGCGCGCCGGCTGTGCGGCAACTGCAAGAAGCCTTCCGATCTTCCCGCGCAC
GCGTTGCTGGCCGAGGGCTTCACCCAGGCGCAGTTGGATGCAGGCGTGCAGTTGTACGAGGCGGTGGGCTGCGATGAGTG
CACTGAGGGCTACAAGGGCCGTACCGGGCTTTACCAGGTGATGCCGATGACCGATGAGATCGCCACCATCGTGCTGGCTG
GCGGTAATGCGCTGCAGATTGCCGAGGCAGCGCAGCAGATCGGGGTGAATGATCTGCGCCAATCCGCGCTGAAGAAGGCG
GCGGCGGGCATCACCAGCCTGGCCGAGATCAATCGCGTTACCAAGGATTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(199-466)

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

(49-150)


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

54.452

100

0.552
  pilB Acinetobacter baumannii D1279779

55.517

99.132

0.55
  pilB Legionella pneumophila strain ERS1305867

52.548

98.785

0.519
  pilF Neisseria gonorrhoeae MS11

49.296

98.611

0.486
  pilB Vibrio cholerae strain A1552

48.517

99.479

0.483
  pilB Vibrio parahaemolyticus RIMD 2210633

45.804

99.306

0.455
  pilB Vibrio campbellii strain DS40M4

45.167

98.785

0.446

Multiple sequence alignment