Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   ABFU54_RS04860 Genome accession   NZ_CP155971
Coordinates   1156733..1158469 (+) Length   578 a.a.
NCBI ID   WP_407470240.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani strain bglFP 6791     
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 1136400..1166190 1156733..1158469 within 0


Gene organization within MGE regions


Location: 1136400..1166190
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU54_RS04760 (ABFU54_04745) - 1136400..1136546 (+) 147 WP_076054137.1 hypothetical protein -
  ABFU54_RS04765 (ABFU54_04750) - 1136730..1137125 (+) 396 WP_042594933.1 hypothetical protein -
  ABFU54_RS04770 (ABFU54_04755) - 1137216..1137608 (+) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  ABFU54_RS04775 (ABFU54_04760) glgX 1138134..1140263 (-) 2130 WP_228431836.1 glycogen debranching protein GlgX -
  ABFU54_RS04780 (ABFU54_04765) rimK 1140756..1141630 (+) 875 Protein_926 30S ribosomal protein S6--L-glutamate ligase -
  ABFU54_RS04785 (ABFU54_04770) - 1142280..1142957 (+) 678 WP_003490678.1 response regulator transcription factor -
  ABFU54_RS04790 (ABFU54_04775) - 1142950..1144284 (+) 1335 WP_019237347.1 HAMP domain-containing sensor histidine kinase -
  ABFU54_RS04795 (ABFU54_04780) - 1144383..1144638 (-) 256 Protein_929 SymE family type I addiction module toxin -
  ABFU54_RS04800 (ABFU54_04785) coaE 1144832..1145455 (-) 624 WP_225042504.1 dephospho-CoA kinase -
  ABFU54_RS04805 (ABFU54_04790) - 1145469..1146332 (-) 864 WP_040940797.1 A24 family peptidase -
  ABFU54_RS04810 (ABFU54_04795) pilC 1146339..1147601 (-) 1263 WP_104570928.1 type II secretion system F family protein Machinery gene
  ABFU54_RS04815 (ABFU54_04800) pilA/pilAI 1147952..1148350 (+) 399 WP_104570927.1 pilin Machinery gene
  ABFU54_RS04820 (ABFU54_04805) - 1148451..1148873 (+) 423 WP_104570926.1 pilin -
  ABFU54_RS04825 (ABFU54_04810) - 1148932..1150752 (+) 1821 WP_323540341.1 hypothetical protein -
  ABFU54_RS04830 (ABFU54_04815) - 1150876..1151634 (+) 759 WP_323534158.1 class I SAM-dependent methyltransferase -
  ABFU54_RS04835 (ABFU54_04820) - 1152131..1152817 (+) 687 WP_258872788.1 glycosyltransferase family 9 protein -
  ABFU54_RS04840 (ABFU54_04825) - 1152820..1153662 (-) 843 WP_147308817.1 glycosyltransferase -
  ABFU54_RS04845 (ABFU54_04830) - 1153656..1154828 (-) 1173 WP_181920810.1 glycosyltransferase -
  ABFU54_RS04850 (ABFU54_04835) - 1154813..1155676 (-) 864 WP_323540340.1 glycosyltransferase -
  ABFU54_RS04855 (ABFU54_04840) - 1155726..1156577 (-) 852 WP_108133901.1 glycosyltransferase family 2 protein -
  ABFU54_RS04860 (ABFU54_04845) pilB 1156733..1158469 (+) 1737 WP_407470240.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU54_RS04865 (ABFU54_04850) pilR 1159854..1161248 (-) 1395 WP_012437607.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU54_RS04870 (ABFU54_04855) - 1161457..1163067 (-) 1611 WP_323540339.1 ATP-binding protein -
  ABFU54_RS04875 (ABFU54_04860) sucC 1163301..1164470 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU54_RS04880 (ABFU54_04865) sucD 1164495..1165370 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  ABFU54_RS04885 (ABFU54_04870) - 1165474..1165884 (+) 411 WP_029628876.1 CopG family ribbon-helix-helix protein -
  ABFU54_RS04890 (ABFU54_04875) - 1165888..1166190 (+) 303 WP_323540338.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 578 a.a.        Molecular weight: 62809.00 Da        Isoelectric Point: 5.4508

>NTDB_id=1000495 ABFU54_RS04860 WP_407470240.1 1156733..1158469(+) (pilB) [Xanthomonas campestris pv. raphani strain bglFP 6791]
MNAVISANLVGITGIARRLVQDGALDETAARTAMEQAASARVPLPQWFAERKLVTASQLAAANAVEFGMPLMDVSVFDAS
QNAVKLVSEELLQKYQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSMG
DDDEGMGDLDVSTGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLSQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVDTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQK
LFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKAPLP
EHALLAEGFTAEQIAAGIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQRIGIRDLRQSALV
KAAHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1737 bp        

>NTDB_id=1000495 ABFU54_RS04860 WP_407470240.1 1156733..1158469(+) (pilB) [Xanthomonas campestris pv. raphani strain bglFP 6791]
ATGAACGCAGTGATCTCAGCCAATCTCGTTGGCATAACCGGCATAGCTCGTCGGCTGGTTCAAGACGGCGCACTTGATGA
AACGGCGGCCCGTACCGCCATGGAGCAAGCTGCTTCAGCCAGGGTTCCTCTGCCCCAGTGGTTTGCGGAGAGAAAGTTAG
TGACTGCATCCCAGCTTGCCGCCGCAAACGCGGTTGAGTTTGGCATGCCTCTGATGGACGTTTCCGTGTTCGATGCCAGC
CAGAACGCGGTCAAGCTGGTCAGCGAGGAGTTGCTCCAGAAGTACCAGGTGCTACCGCTGTTCAAGCGCGGCAACCGGTT
GTTCGTGGGGGTGAGCAATCCGACCCAGACCAGGGCGCTGGACGACATCAAGTTCCATACCAATCTGGTGGTCGAGCCGA
TCCTGGTCGACGAGGATCAGATCCGTCGCACCTTGGAGCAGTGGCAGGCCAGCAATGCGGCGCTTGGCTCGTCGATGGGT
GACGACGACGAGGGGATGGGGGATCTGGACGTCTCCACCGGCGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGCGACGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCGTCCGACA
TCCATTTCGAGCCGTACGAAGACGACTACCGGGTGCGCTTGCGGATCGATGGCCTCCTGAAGAATGTGGCCAAGGCGCCG
GTGAAGTTGAGCCAGCGCATTGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGA
TGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTGGACACCTTGCCGACCCTGTTCGGCGAGA
AGGTGGTGCTGCGTATCCTGGACGCGAGTGCGGCCAAGCTGGGCATTGAGAAGCTGGGCTATGAGGCGGATCAGCAAAAG
CTGTTCCTGGATGCGATCCACAAGCCTTACGGCATGGTGCTGGTGACCGGGCCAACCGGTTCGGGCAAGACGGTGTCGTT
GTATACGGCGCTGGGCATCCTCAACGATGAGACGCGCAACATCTCCACGGCCGAGGATCCGGTCGAAATCCGCTTGCCTG
GTGTCAATCAGGTGCAGCAAAACGTCAAGCGCGGCATGACGTTTGCTGCGGCGTTGCGCTCGTTCCTGCGCCAGGATCCG
GACATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGTCACATGGT
GTTGTCGACGCTGCATACCAACGATGCGCCACAGACCATCGCGCGTCTGATGAACATGGGCATTGCGCCGTACAACATCA
CTTCGTCGGTGACCTTGGTCATTGCGCAGCGTCTGGCGCGGCGTTTGTGCAACAACTGCAAGCGCAAGGCGCCGCTGCCG
GAGCATGCGTTGCTGGCCGAAGGGTTTACCGCAGAGCAGATCGCTGCCGGAATCGAACTGTACGAGGCGGTCGGCTGCGA
TGAGTGCACCGAAGGCTACAAGGGGCGTACCGGTATCTACCAGGTGATGCCGATGACCGACGAGATCGGCGCGATCGTAC
TGGAAGGCGGCAACGCGATGCAGATCGCCGAGGCGGCGCAGAGGATCGGCATCCGCGATTTGCGGCAGTCGGCGCTGGTG
AAGGCGGCGCATGGGGTGACGAGCCTGGCGGAGATCAATCGGGTGACGAAGGACTGA

Domains

Predicted by InterproScan.

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

(50-153)

Type II/IV secretion system protein (T2SSE)

(201-468)


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 baumannii D1279779

55.81

98.27

0.548
  pilB Acinetobacter baylyi ADP1

55.106

98.27

0.542
  pilB Legionella pneumophila strain ERS1305867

51.845

98.443

0.51
  pilB Vibrio cholerae strain A1552

48.87

99.481

0.486
  pilF Neisseria gonorrhoeae MS11

47.711

98.27

0.469
  pilB Vibrio campbellii strain DS40M4

45.518

98.443

0.448
  pilB Vibrio parahaemolyticus RIMD 2210633

45.567

97.578

0.445
  pilB/pilB1 Synechocystis sp. PCC 6803

35.61

100

0.379
  pilF Thermus thermophilus HB27

40.307

90.138

0.363

Multiple sequence alignment