Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   EBA25_RS08280 Genome accession   NZ_CP033188
Coordinates   1620586..1622319 (+) Length   577 a.a.
NCBI ID   WP_011408072.1    Uniprot ID   A0A0K0GIN1
Organism   Xanthomonas oryzae pv. oryzae strain PXO513     
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 1599483..1620551 1620586..1622319 flank 35


Gene organization within MGE regions


Location: 1599483..1622319
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  EBA25_RS25150 - 1599483..1601120 (+) 1638 WP_243739232.1 hypothetical protein -
  EBA25_RS25155 - 1601210..1603972 (+) 2763 WP_243739233.1 RHS repeat-associated core domain-containing protein -
  EBA25_RS08175 - 1603972..1604460 (+) 489 WP_128415435.1 DUF6714 family protein -
  EBA25_RS08180 (EBA25_08165) - 1604512..1605480 (+) 969 WP_011258802.1 IS5-like element ISXo1 family transposase -
  EBA25_RS08185 - 1605629..1605928 (+) 300 WP_125168747.1 hypothetical protein -
  EBA25_RS08190 - 1605925..1606254 (+) 330 WP_125168748.1 hypothetical protein -
  EBA25_RS08195 (EBA25_08170) - 1606331..1607764 (+) 1434 Protein_1473 RHS repeat-associated core domain-containing protein -
  EBA25_RS08200 (EBA25_08175) - 1607770..1608138 (+) 369 WP_133260527.1 DUF6869 domain-containing protein -
  EBA25_RS08205 (EBA25_08180) - 1608308..1609276 (-) 969 WP_011409545.1 IS5-like element ISXo1 family transposase -
  EBA25_RS08210 (EBA25_08185) - 1609372..1609539 (+) 168 Protein_1476 IS701 family transposase -
  EBA25_RS08220 (EBA25_08195) - 1609657..1609878 (+) 222 Protein_1477 IS4 family transposase -
  EBA25_RS08225 (EBA25_08200) - 1609968..1610924 (+) 957 WP_041182041.1 IS30-like element IS1112a family transposase -
  EBA25_RS08230 (EBA25_08205) - 1610908..1611210 (+) 303 WP_158645227.1 hypothetical protein -
  EBA25_RS08240 (EBA25_08215) - 1611771..1613090 (-) 1320 WP_133260528.1 IS701-like element ISXo15 family transposase -
  EBA25_RS08245 (EBA25_08220) coaE 1613161..1613769 (-) 609 WP_011258357.1 dephospho-CoA kinase -
  EBA25_RS08250 (EBA25_08225) - 1613783..1614646 (-) 864 WP_011258358.1 A24 family peptidase -
  EBA25_RS08255 (EBA25_08230) pilC 1614653..1615912 (-) 1260 WP_011408067.1 type II secretion system F family protein Machinery gene
  EBA25_RS08260 (EBA25_08235) pilA2 1616267..1616692 (+) 426 WP_011408068.1 pilin Machinery gene
  EBA25_RS08265 (EBA25_08240) - 1616827..1618416 (+) 1590 WP_011408069.1 phosphoethanolamine transferase -
  EBA25_RS08270 (EBA25_08245) - 1618427..1619056 (+) 630 WP_011408070.1 hypothetical protein -
  EBA25_RS25765 (EBA25_08250) - 1619026..1620551 (+) 1526 Protein_1487 hypothetical protein -
  EBA25_RS08280 (EBA25_08255) pilB 1620586..1622319 (+) 1734 WP_011408072.1 type IV-A pilus assembly ATPase PilB Machinery gene

Sequence

Protein


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

>NTDB_id=322254 EBA25_RS08280 WP_011408072.1 1620586..1622319(+) (pilB) [Xanthomonas oryzae pv. oryzae strain PXO513]
MNSVSTTNLVGITGIARRLVQDGALEETAARTAMEQAAAAKVPLPQWFAENRLVSASQLAAANAVEFGMPLMDVSVFDAN
QNAVKLVSEELLQKYHVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNASFGSSLG
NDDEEMGDLDVSTGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLSQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDGSAAKLGIDKLGYEPDQQK
LFLEAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNNKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPEQVANMELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMK
ASQGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=322254 EBA25_RS08280 WP_011408072.1 1620586..1622319(+) (pilB) [Xanthomonas oryzae pv. oryzae strain PXO513]
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