Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   XCR_RS15570 Genome accession   NC_017271
Coordinates   3649514..3651250 (-) Length   578 a.a.
NCBI ID   WP_043921911.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani 756C     
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 3641705..3700042 3649514..3651250 within 0


Gene organization within MGE regions


Location: 3641705..3700042
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  XCR_RS15530 (XCR_3435) - 3641705..3642007 (-) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -
  XCR_RS15535 (XCR_3436) - 3642011..3642421 (-) 411 WP_029628876.1 DNA-binding protein -
  XCR_RS15540 (XCR_3437) sucD 3642525..3643400 (-) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  XCR_RS15545 (XCR_3438) sucC 3643425..3644594 (-) 1170 WP_014508701.1 ADP-forming succinate--CoA ligase subunit beta -
  XCR_RS15550 (XCR_3439) - 3644828..3646438 (+) 1611 WP_014508702.1 HAMP domain-containing sensor histidine kinase -
  XCR_RS15555 (XCR_3440) pilR 3646647..3648041 (+) 1395 WP_043921909.1 sigma-54 dependent transcriptional regulator Regulator
  XCR_RS23200 - 3648233..3648595 (+) 363 WP_148263072.1 hypothetical protein -
  XCR_RS15565 (XCR_3443) - 3648540..3649331 (+) 792 WP_202796265.1 toxin -
  XCR_RS15570 (XCR_3444) pilB 3649514..3651250 (-) 1737 WP_043921911.1 type IV-A pilus assembly ATPase PilB Machinery gene
  XCR_RS15575 pilA2 3651388..3651819 (-) 432 WP_043922199.1 pilin Machinery gene
  XCR_RS15580 - 3652168..3653425 (+) 1258 Protein_3088 type II secretion system F family protein -
  XCR_RS15585 (XCR_3447) - 3653432..3654295 (+) 864 WP_011038216.1 A24 family peptidase -
  XCR_RS15590 (XCR_3448) coaE 3654309..3654932 (+) 624 WP_014508710.1 dephospho-CoA kinase -
  XCR_RS15595 - 3655465..3655866 (+) 402 WP_043921912.1 SymE family type I addiction module toxin -
  XCR_RS15600 (XCR_3450) - 3655941..3656231 (+) 291 WP_014508712.1 DUF1778 domain-containing protein -
  XCR_RS15605 (XCR_3451) - 3656228..3656719 (+) 492 WP_014508713.1 GNAT family N-acetyltransferase -
  XCR_RS15610 (XCR_3452) - 3656862..3658196 (-) 1335 WP_012437598.1 HAMP domain-containing sensor histidine kinase -
  XCR_RS15615 (XCR_3453) - 3658189..3658866 (-) 678 WP_003490678.1 response regulator transcription factor -
  XCR_RS15620 (XCR_3455) rimK 3659516..3660391 (-) 876 WP_043921913.1 30S ribosomal protein S6--L-glutamate ligase -
  XCR_RS15625 (XCR_3456) glgX 3660883..3663012 (+) 2130 WP_014508716.1 glycogen debranching protein GlgX -
  XCR_RS15630 (XCR_3458) - 3663554..3663946 (-) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  XCR_RS15635 (XCR_3459) - 3664037..3664432 (-) 396 WP_042594933.1 hypothetical protein -
  XCR_RS23705 (XCR_3460) - 3664608..3664763 (-) 156 WP_042594934.1 hypothetical protein -
  XCR_RS23900 - 3664881..3665222 (-) 342 WP_237704751.1 hypothetical protein -
  XCR_RS15645 (XCR_3462) - 3665355..3665726 (-) 372 WP_014508721.1 hypothetical protein -
  XCR_RS22275 - 3666410..3666751 (+) 342 WP_080565911.1 hypothetical protein -
  XCR_RS15650 (XCR_3463) - 3666804..3668414 (-) 1611 WP_014508722.1 MobA/MobL family protein -
  XCR_RS15655 traD 3668682..3669008 (+) 327 WP_043921914.1 conjugal transfer protein TraD -
  XCR_RS22280 - 3669271..3669540 (+) 270 WP_237704833.1 HNH endonuclease -
  XCR_RS15660 (XCR_3464) - 3669534..3670091 (+) 558 WP_014508723.1 hypothetical protein -
  XCR_RS23905 (XCR_3465) - 3670139..3671374 (+) 1236 WP_237704752.1 HNH endonuclease -
  XCR_RS15670 (XCR_3466) - 3671386..3672012 (-) 627 WP_162470855.1 hypothetical protein -
  XCR_RS15675 (XCR_3467) - 3672077..3676042 (-) 3966 WP_014508726.1 hypothetical protein -
  XCR_RS15680 - 3676080..3676718 (-) 639 WP_043921915.1 DUF1629 domain-containing protein -
  XCR_RS22285 (XCR_3469) - 3676851..3678215 (-) 1365 WP_014508728.1 DNA double-strand break repair nuclease NurA -
  XCR_RS15690 (XCR_3470) - 3678218..3680308 (-) 2091 WP_014508729.1 DUF87 domain-containing protein -
  XCR_RS15695 - 3680322..3681212 (-) 891 WP_033836759.1 DNA adenine methylase -
  XCR_RS23910 - 3681430..3681621 (-) 192 WP_080565913.1 hypothetical protein -
  XCR_RS15700 (XCR_3471) radC 3681691..3682170 (-) 480 WP_014508730.1 DNA repair protein RadC -
  XCR_RS15705 - 3682573..3682797 (-) 225 WP_039405436.1 hypothetical protein -
  XCR_RS15710 (XCR_3472) - 3682991..3683437 (+) 447 WP_014508731.1 hypothetical protein -
  XCR_RS15715 (XCR_3473) - 3684013..3685413 (+) 1401 WP_014508732.1 site-specific integrase -
  XCR_RS15720 (XCR_3474) - 3685765..3687180 (+) 1416 WP_014508733.1 hypothetical protein -
  XCR_RS15725 (XCR_3475) - 3687181..3688416 (-) 1236 WP_202796266.1 abortive infection family protein -
  XCR_RS15730 (XCR_3476) - 3688461..3689654 (-) 1194 WP_014508735.1 GIY-YIG nuclease family protein -
  XCR_RS15735 (XCR_3477) - 3689647..3691752 (-) 2106 WP_043921917.1 DEAD/DEAH box helicase -
  XCR_RS15740 (XCR_3478) - 3691749..3694535 (-) 2787 WP_043921918.1 DNA methyltransferase -
  XCR_RS15745 (XCR_3479) - 3694873..3695196 (-) 324 WP_108723645.1 helix-turn-helix transcriptional regulator -
  XCR_RS15750 (XCR_3480) - 3695301..3696053 (+) 753 WP_014508739.1 hypothetical protein -
  XCR_RS15755 (XCR_3481) - 3696096..3696410 (+) 315 WP_014508740.1 hypothetical protein -
  XCR_RS15760 (XCR_3482) - 3696407..3696787 (+) 381 WP_193387299.1 hypothetical protein -
  XCR_RS23210 - 3697046..3698044 (-) 999 WP_148263074.1 hypothetical protein -
  XCR_RS15770 - 3698081..3698263 (-) 183 WP_141762696.1 hypothetical protein -

Sequence

Protein


Download         Length: 578 a.a.        Molecular weight: 62655.76 Da        Isoelectric Point: 5.6039

>NTDB_id=45763 XCR_RS15570 WP_043921911.1 3649514..3651250(-) (pilB) [Xanthomonas campestris pv. raphani 756C]
MSAGVSVNLVGITGIARRLVQDGVLEEAAARSAMDQAGSAKVPLPQWFSEKKLVTAAQLAAANAVEFGMPLLDVSAFDAS
QNAVKLVSEELLQKYQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNASLGSSLG
DDDDDMGDLDVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLNQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIEKLGYEADQQK
LFLEAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPAQIAAGIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALM
KASHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1737 bp        

>NTDB_id=45763 XCR_RS15570 WP_043921911.1 3649514..3651250(-) (pilB) [Xanthomonas campestris pv. raphani 756C]
ATGAGTGCTGGAGTTTCTGTCAATCTCGTTGGCATAACAGGAATCGCCAGGCGCTTGGTCCAAGACGGTGTTCTAGAGGA
AGCTGCTGCACGATCTGCAATGGATCAGGCGGGTAGTGCCAAAGTACCGTTGCCCCAATGGTTTTCTGAGAAAAAGTTGG
TGACGGCTGCTCAGCTAGCTGCAGCCAACGCTGTCGAGTTCGGTATGCCGCTACTTGATGTGTCGGCGTTCGACGCCAGC
CAGAATGCGGTCAAGCTAGTCAGTGAAGAGTTGCTCCAGAAATATCAAGTGCTGCCTTTGTTCAAACGCGGCAACCGGTT
GTTCGTGGGGGTGAGCAACCCGACTCAGACCAGGGCGCTGGACGATATCAAGTTCCATACGAACCTGGTGGTCGAGCCTA
TCCTGGTCGACGAGGACCAGATTCGTCGCACCTTGGAGCAGTGGCAGGCCAGCAATGCGTCGCTTGGCTCATCGCTCGGT
GACGACGATGACGACATGGGGGATTTGGACGTGTCGGCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGCGATGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGGACA
TCCATTTCGAGCCGTATGAAGACGACTATCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCG
GTGAAGCTCAACCAGCGCATCGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGA
CGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGCGTGAGCACCTTGCCGACCTTGTTCGGCGAAA
AGGTTGTGCTGCGTATCCTGGACGGCAGCGCGGCCAAGCTCGGCATCGAGAAGCTGGGCTACGAGGCGGACCAGCAGAAG
CTATTCCTGGAGGCGATCCACAAACCCTACGGCATGGTGCTGGTGACCGGGCCGACCGGTTCGGGCAAGACGGTGTCGTT
GTACACGGCACTCGGCATCCTCAACGACGAGACGCGCAACATCTCCACCGCCGAGGACCCGGTGGAAATCCGGTTGCCCG
GCGTCAATCAGGTGCAGCAGAACAACAAGCGCGGCATGACCTTCGCCGCGGCGCTGCGTTCGTTCTTGCGCCAGGATCCG
GACATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCCGCGCAGACCGGTCACATGGT
GCTGTCCACGCTGCACACCAACGATGCGCCGCAGACCATCGCGCGTTTGATGAACATGGGCATCGCGCCTTACAACATCA
CCTCGTCGGTGACCCTGGTGATCGCGCAGCGTCTGGCGCGGCGCCTGTGCAACAACTGCAAGCGCAAATCGACCTTGCCC
GAGCATGCGTTGCTGGCCGAAGGCTTCACGCCTGCGCAGATCGCTGCCGGGATCGAGCTGTATGAGGCGGTCGGTTGCGA
CGAGTGTACCGAAGGCTACAAGGGCCGTACCGGCATCTATCAGGTGATGCCGATGACGGACGAAATCGGCGCGATCGTGC
TGGAAGGCGGCAATGCGATGCAGATCGCCGAGGCTGCGCAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTAATG
AAGGCTTCGCACGGCGTGACCAGCCTGGCCGAAATCAATCGGGTGACGAAGGATTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(201-468)

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

(50-153)


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

54.754

98.27

0.538
  pilB Legionella pneumophila strain ERS1305867

52.021

98.443

0.512
  pilF Neisseria gonorrhoeae MS11

49.12

98.27

0.483
  pilB Vibrio cholerae strain A1552

48.174

99.481

0.479
  pilB Vibrio parahaemolyticus RIMD 2210633

46.25

96.886

0.448
  pilB Vibrio campbellii strain DS40M4

45.518

98.443

0.448
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

39.924

91.003

0.363
  pilF Thermus thermophilus HB27

40.192

89.965

0.362

Multiple sequence alignment