Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   ATY46_RS07825 Genome accession   NZ_CP013676
Coordinates   1620513..1622246 (+) Length   577 a.a.
NCBI ID   WP_011408072.1    Uniprot ID   A0A0K0GIN1
Organism   Xanthomonas oryzae pv. oryzae strain PXO282     
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 1605407..1629359 1620513..1622246 within 0


Gene organization within MGE regions


Location: 1605407..1629359
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ATY46_RS26600 - 1605556..1605855 (+) 300 WP_125168747.1 hypothetical protein -
  ATY46_RS26605 - 1605852..1606181 (+) 330 WP_125168748.1 hypothetical protein -
  ATY46_RS07765 (ATY46_07495) - 1606258..1607691 (+) 1434 Protein_1479 RHS repeat-associated core domain-containing protein -
  ATY46_RS24580 - 1607697..1608065 (+) 369 WP_011408064.1 DUF6869 domain-containing protein -
  ATY46_RS07770 (ATY46_07500) - 1608235..1609203 (-) 969 WP_011409177.1 IS5-like element ISXo1 family transposase -
  ATY46_RS26610 - 1609299..1609466 (+) 168 Protein_1482 IS701 family transposase -
  ATY46_RS07775 (ATY46_07505) - 1609584..1609805 (+) 222 Protein_1483 IS4 family transposase -
  ATY46_RS07780 (ATY46_07510) - 1609895..1610851 (+) 957 WP_041182041.1 IS30-like element IS1112a family transposase -
  ATY46_RS24590 - 1610835..1611137 (+) 303 WP_158645227.1 hypothetical protein -
  ATY46_RS07785 (ATY46_07515) - 1611698..1613017 (-) 1320 WP_155296483.1 IS701 family transposase -
  ATY46_RS07790 (ATY46_07520) coaE 1613088..1613696 (-) 609 WP_011258357.1 dephospho-CoA kinase -
  ATY46_RS07795 (ATY46_07525) - 1613710..1614573 (-) 864 WP_011258358.1 A24 family peptidase -
  ATY46_RS07800 (ATY46_07530) pilC 1614580..1615839 (-) 1260 WP_011408067.1 type II secretion system F family protein Machinery gene
  ATY46_RS07805 (ATY46_07535) pilA2 1616193..1616618 (+) 426 WP_011408068.1 pilin Machinery gene
  ATY46_RS07810 (ATY46_07540) - 1616753..1618342 (+) 1590 WP_069959793.1 phosphoethanolamine transferase -
  ATY46_RS07815 (ATY46_07545) - 1618413..1618982 (+) 570 WP_229001934.1 hypothetical protein -
  ATY46_RS07820 (ATY46_07550) - 1618952..1620478 (+) 1527 WP_042464666.1 membrane protein -
  ATY46_RS07825 (ATY46_07555) pilB 1620513..1622246 (+) 1734 WP_011408072.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ATY46_RS27830 (ATY46_07560) - 1622255..1622515 (-) 261 WP_011408073.1 Fic family protein -
  ATY46_RS27835 - 1622603..1622764 (-) 162 WP_153296778.1 hypothetical protein -
  ATY46_RS07835 - 1622826..1623032 (-) 207 WP_027703281.1 YhfG family protein -
  ATY46_RS07840 (ATY46_07565) pilR 1623105..1624556 (-) 1452 WP_173340383.1 sigma-54 dependent transcriptional regulator Regulator
  ATY46_RS07845 (ATY46_07570) - 1624827..1626440 (-) 1614 WP_011258366.1 HAMP domain-containing sensor histidine kinase -
  ATY46_RS07850 (ATY46_07575) sucC 1626674..1627843 (+) 1170 WP_011258367.1 ADP-forming succinate--CoA ligase subunit beta -
  ATY46_RS07855 (ATY46_07580) sucD 1627868..1628743 (+) 876 WP_011258368.1 succinate--CoA ligase subunit alpha -
  ATY46_RS07860 (ATY46_07585) - 1629063..1629359 (+) 297 WP_011408075.1 hypothetical protein -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62970.00 Da        Isoelectric Point: 5.4513

>NTDB_id=163874 ATY46_RS07825 WP_011408072.1 1620513..1622246(+) (pilB) [Xanthomonas oryzae pv. oryzae strain PXO282]
MNSVSTTNLVGITGIARRLVQDGALEETAARTAMEQAAAAKVPLPQWFAENRLVSASQLAAANAVEFGMPLMDVSVFDAN
QNAVKLVSEELLQKYHVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNASFGSSLG
NDDEEMGDLDVSTGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLSQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIDKLGYEPDQQK
LFLEAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPEQVANMELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMK
ASQGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=163874 ATY46_RS07825 WP_011408072.1 1620513..1622246(+) (pilB) [Xanthomonas oryzae pv. oryzae strain PXO282]
ATGAATTCAGTATCTACAACCAACCTCGTTGGCATCACCGGCATCGCTCGTCGCCTTGTGCAGGATGGCGCCCTGGAGGA
AACCGCTGCGCGGACAGCGATGGAACAGGCGGCCGCTGCCAAGGTGCCGCTGCCGCAGTGGTTTGCCGAGAACAGGCTGG
TGTCGGCGTCGCAGCTTGCGGCGGCCAATGCAGTGGAATTTGGCATGCCACTGATGGATGTGTCTGTGTTCGACGCTAAC
CAGAACGCAGTCAAGCTAGTCAGCGAGGAGTTGCTCCAGAAGTACCATGTGCTGCCGCTGTTCAAGCGCGGCAATCGGTT
GTTTGTGGGAGTGAGCAACCCGACTCAGACCCGTGCACTAGATGACATCAAGTTTCATACGAATCTGGTCGTCGAGCCGA
TTCTTGTCGATGAGGACCAAATCCGTCGCACATTGGAGCAGTGGCAGGCAAGCAATGCCTCATTTGGATCATCGCTTGGC
AACGACGACGAGGAAATGGGGGATCTGGACGTCTCCACCGGCGACGAAGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGCGACGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGGGCCTCGGACA
TCCATTTCGAGCCGTACGAAGACGACTACCGGGTGCGGTTGCGGATCGACGGGTTGCTGAAGAACGTGGCCAAGGCGCCG
GTGAAGCTGAGCCAGCGCATCGCGGCGCGTTTGAAGGTGATGTCGCAGCTGGATATCGCCGAGAAGCGGGTGCCGCAGGA
CGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGACTTCCGTGTCAGCACCTTGCCGACCCTGTTCGGTGAGA
AGGTGGTGCTGCGTATCCTGGACGGCAGCGCGGCCAAGCTGGGCATCGACAAGCTGGGCTACGAGCCGGACCAACAGAAG
CTGTTCCTGGAAGCGATCCACAAGCCGTACGGCATGGTGCTGGTGACCGGGCCGACCGGCTCGGGCAAGACGGTGTCGCT
GTACACGGCGCTGGGCATCCTCAACGATGAGACGCGCAACATCTCCACCGCCGAGGATCCGGTCGAAATTCGCCTGCCTG
GCGTCAACCAGGTGCAGCAGAACAACAAGCGCGGCATGACCTTCGCCGCGGCGCTGCGTTCGTTCCTGCGACAGGATCCG
GACATCATCATGGTTGGCGAAATCCGCGACCTGGAAACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGTCACATGGT
GCTGTCCACGCTGCATACCAACGATGCGCCGCAGACCATCGCGCGTCTGATGAACATGGGGATCGCGCCGTACAACATCA
CCTCGTCGGTGACCTTGGTGATCGCGCAGCGTCTGGCGCGGCGGTTGTGCAATAACTGCAAGCGCAAGTCGACGTTGCCG
GAGCATGCACTGCTGGCGGAAGGCTTTACGCCGGAGCAGGTCGCGAATATGGAGCTTTATGAAGCCGTGGGTTGCGACGA
GTGCACCGAGGGCTACAAGGGCCGTACCGGTATCTATCAGGTGATGCCGATGACCGACGAAATCGGCGCGATCGTGCTGG
AAGGCGGCAATGCGATGCAGATTGCCGAGGCCGCTCAGAAGATCGGCATCCGGGACTTGCGGCAGTCGGCGTTGATGAAG
GCCTCGCAAGGCGTGACCAGCCTGGCCGAGATCAATCGGGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(201-468)

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

(49-152)


Secondary structure

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



3D structure

Source ID Structure
  AlphaFold DB A0A0K0GIN1

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

57.042

98.44

0.562
  pilB Acinetobacter baumannii D1279779

56.69

98.44

0.558
  pilB Legionella pneumophila strain ERS1305867

52.465

98.44

0.516
  pilB Vibrio cholerae strain A1552

49.74

100

0.497
  pilF Neisseria gonorrhoeae MS11

49.648

98.44

0.489
  pilB Vibrio campbellii strain DS40M4

46.046

98.614

0.454
  pilB Vibrio parahaemolyticus RIMD 2210633

46.359

97.574

0.452
  pilB Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

39.394

91.508

0.36

Multiple sequence alignment