Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   QMY62_RS05695 Genome accession   NZ_CP125656
Coordinates   1353220..1354953 (+) Length   577 a.a.
NCBI ID   WP_283269167.1    Uniprot ID   -
Organism   Xanthomonas campestris strain GBBC 3139     
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 1309668..1362762 1353220..1354953 within 0


Gene organization within MGE regions


Location: 1309668..1362762
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  QMY62_RS05495 (QMY62_05495) - 1311224..1311970 (-) 747 WP_167766520.1 hypothetical protein -
  QMY62_RS05500 (QMY62_05500) - 1311986..1312849 (-) 864 WP_167766519.1 hypothetical protein -
  QMY62_RS05505 (QMY62_05505) - 1313320..1313700 (-) 381 WP_209271700.1 hypothetical protein -
  QMY62_RS05510 (QMY62_05510) - 1313697..1314011 (-) 315 WP_283269132.1 hypothetical protein -
  QMY62_RS05515 (QMY62_05515) - 1314054..1314815 (-) 762 WP_283269134.1 hypothetical protein -
  QMY62_RS05520 (QMY62_05520) - 1314917..1315258 (+) 342 WP_167766516.1 helix-turn-helix transcriptional regulator -
  QMY62_RS05525 (QMY62_05525) dndC 1315429..1316559 (+) 1131 WP_167766515.1 DNA phosphorothioation system sulfurtransferase DndC -
  QMY62_RS21800 - 1316580..1316795 (+) 216 WP_167766514.1 DNA modification system-associated small protein -
  QMY62_RS05530 (QMY62_05530) dndD 1316785..1318863 (+) 2079 WP_167766513.1 DNA sulfur modification protein DndD -
  QMY62_RS05535 (QMY62_05535) - 1318865..1320394 (+) 1530 WP_209271699.1 DndE family protein -
  QMY62_RS05540 (QMY62_05540) - 1320421..1320756 (+) 336 WP_167766512.1 hypothetical protein -
  QMY62_RS05545 (QMY62_05545) - 1320939..1322183 (-) 1245 Protein_1070 site-specific integrase -
  QMY62_RS05550 (QMY62_05550) - 1322249..1323351 (+) 1103 Protein_1071 IS3-like element IS1404 family transposase -
  QMY62_RS05555 (QMY62_05555) - 1323385..1323543 (-) 159 Protein_1072 integrase -
  QMY62_RS05560 (QMY62_05560) - 1324089..1324304 (+) 216 WP_167766510.1 hypothetical protein -
  QMY62_RS05565 (QMY62_05565) radC 1324628..1325191 (+) 564 WP_283269635.1 DNA repair protein RadC -
  QMY62_RS05570 (QMY62_05570) - 1325330..1325926 (+) 597 WP_345782097.1 DUF1629 domain-containing protein -
  QMY62_RS05575 (QMY62_05575) - 1325960..1329982 (+) 4023 WP_283269140.1 hypothetical protein -
  QMY62_RS05580 (QMY62_05580) - 1330022..1330672 (+) 651 WP_167766506.1 hypothetical protein -
  QMY62_RS05585 (QMY62_05585) - 1331021..1332973 (+) 1953 WP_283269142.1 hypothetical protein -
  QMY62_RS05590 (QMY62_05590) - 1333027..1334253 (+) 1227 WP_167766504.1 hypothetical protein -
  QMY62_RS05600 (QMY62_05600) - 1335651..1337246 (+) 1596 WP_345782102.1 MobA/MobL family protein -
  QMY62_RS05605 (QMY62_05605) - 1337299..1337640 (-) 342 WP_283269146.1 hypothetical protein -
  QMY62_RS05610 (QMY62_05610) - 1338297..1338713 (+) 417 WP_283269148.1 hypothetical protein -
  QMY62_RS05615 (QMY62_05615) - 1339003..1339233 (-) 231 WP_283269150.1 hypothetical protein -
  QMY62_RS05620 (QMY62_05620) - 1339297..1339443 (+) 147 WP_116889157.1 hypothetical protein -
  QMY62_RS05625 (QMY62_05625) - 1339628..1340023 (+) 396 WP_011038225.1 hypothetical protein -
  QMY62_RS05630 (QMY62_05630) - 1340114..1340506 (+) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  QMY62_RS05635 (QMY62_05635) glgX 1341045..1343174 (-) 2130 WP_283269153.1 glycogen debranching protein GlgX -
  QMY62_RS05640 (QMY62_05640) rimK 1343667..1344542 (+) 876 WP_011038222.1 30S ribosomal protein S6--L-glutamate ligase -
  QMY62_RS05645 (QMY62_05645) - 1345192..1345869 (+) 678 WP_003490678.1 response regulator transcription factor -
  QMY62_RS05650 (QMY62_05650) - 1345862..1347196 (+) 1335 WP_012437598.1 HAMP domain-containing sensor histidine kinase -
  QMY62_RS05655 (QMY62_05655) - 1347339..1347830 (-) 492 WP_223646366.1 GNAT family N-acetyltransferase -
  QMY62_RS05660 (QMY62_05660) - 1347827..1348117 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  QMY62_RS05665 (QMY62_05665) - 1348193..1348594 (-) 402 WP_283269159.1 SymE family type I addiction module toxin -
  QMY62_RS05670 (QMY62_05670) coaE 1349123..1349746 (-) 624 WP_228424129.1 dephospho-CoA kinase -
  QMY62_RS05675 (QMY62_05675) - 1349760..1350623 (-) 864 WP_040940797.1 A24 family peptidase -
  QMY62_RS05680 (QMY62_05680) pilC 1350630..1351832 (-) 1203 WP_283269162.1 type II secretion system F family protein Machinery gene
  QMY62_RS05685 (QMY62_05685) comP 1352237..1352668 (+) 432 WP_024939397.1 pilin Machinery gene
  QMY62_RS05690 (QMY62_05690) - 1352765..1353178 (+) 414 WP_283269165.1 pilin -
  QMY62_RS05695 (QMY62_05695) pilB 1353220..1354953 (+) 1734 WP_283269167.1 type IV-A pilus assembly ATPase PilB Machinery gene
  QMY62_RS05700 (QMY62_05700) - 1355136..1355873 (-) 738 WP_283269169.1 zeta toxin family protein -
  QMY62_RS05705 (QMY62_05705) - 1355873..1356235 (-) 363 WP_217694196.1 hypothetical protein -
  QMY62_RS05710 (QMY62_05710) - 1356427..1357820 (-) 1394 Protein_1103 sigma-54 dependent transcriptional regulator -
  QMY62_RS05715 (QMY62_05715) - 1358029..1359639 (-) 1611 WP_283269172.1 HAMP domain-containing sensor histidine kinase -
  QMY62_RS05720 (QMY62_05720) sucC 1359873..1361042 (+) 1170 WP_012437609.1 ADP-forming succinate--CoA ligase subunit beta -
  QMY62_RS05725 (QMY62_05725) sucD 1361067..1361942 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  QMY62_RS05730 (QMY62_05730) - 1362046..1362456 (+) 411 WP_029217117.1 DNA-binding protein -
  QMY62_RS05735 (QMY62_05735) - 1362460..1362762 (+) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62836.97 Da        Isoelectric Point: 5.5885

>NTDB_id=832117 QMY62_RS05695 WP_283269167.1 1353220..1354953(+) (pilB) [Xanthomonas campestris strain GBBC 3139]
MNAAISSNLVGITGIARRLVQDGALDEANARAAMDHAAQAKVPLPQWFAEKKLVTAAQLASANAVEFGMPLMDVSVFDAS
QNAVKLVSEELLQKYQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSLG
DDDDEMGDLDVSTGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLNQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQK
LFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMK
ASHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=832117 QMY62_RS05695 WP_283269167.1 1353220..1354953(+) (pilB) [Xanthomonas campestris strain GBBC 3139]
ATGAACGCTGCAATCAGCTCAAATCTAGTTGGAATTACCGGCATCGCGCGGCGTCTTGTTCAGGATGGTGCGTTAGATGA
AGCGAACGCACGTGCGGCAATGGATCATGCGGCCCAGGCTAAAGTTCCGTTGCCGCAATGGTTCGCCGAAAAGAAGCTCG
TAACAGCAGCGCAGCTCGCCTCTGCCAATGCAGTTGAGTTCGGTATGCCACTGATGGATGTGTCGGTGTTCGACGCCAGC
CAGAACGCGGTCAAACTGGTCAGCGAAGAGTTGCTCCAGAAGTACCAGGTGCTGCCGCTGTTCAAGCGCGGCAACCGGTT
GTTCGTGGGGGTGAGCAACCCGACCCAGACCAGGGCGCTGGACGATATCAAGTTCCACACCAATCTGGTGGTCGAGCCGA
TCCTGGTCGACGAAGACCAGATCCGTCGCACATTGGAGCAGTGGCAGGCCAGCAATGCGGCGCTCGGCTCCTCGCTCGGC
GACGACGATGATGAGATGGGGGATCTGGACGTCTCCACCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGCGATGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGGACA
TCCATTTCGAGCCCTATGAAGATGACTACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCG
GTGAAGCTCAACCAGCGCATCGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGA
CGGGCGCATCAAGCTCAATCTGTCCAAGACCAAGCAGATCGACTTCCGTGTGAGCACCTTGCCAACCCTGTTCGGCGAGA
AGGTGGTGTTGCGTATCCTGGACGCCAGTGCGGCCAAGCTCGGTATCGAGAAGCTGGGCTATGAGGCGGACCAGCAGAAG
CTGTTCCTGGATGCGATCCACAAGCCCTACGGCATGGTGCTGGTGACCGGGCCGACTGGTTCGGGCAAGACGGTGTCGCT
GTATACCGCGCTCGGGATTCTCAACGACGAGACGCGCAATATTTCCACGGCTGAGGATCCGGTCGAAATCCGCTTGCCCG
GCGTCAATCAGGTGCAGCAGAACGTCAAGCGGGGCATGACGTTTGCGGCGGCGCTGCGCTCGTTCCTGCGTCAGGACCCG
GACATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACCGGCCATATGGT
GCTGTCGACACTGCACACCAACGATGCGCCGCAAACCATTGCGCGTCTGATGAACATGGGTATCGCGCCGTACAACATCA
CCTCGTCGGTGACGCTGGTCATCGCGCAGCGCCTGGCGCGGCGGCTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCG
GAACATGCGCTGCTGGCGGAAGGCTTTACGCCGGAGCAGGTTGCGAACATCGAGCTGTATGAAGCGGTCGGTTGCGATGA
GTGCACGGAAGGCTACAAGGGCCGTACCGGCATCTATCAGGTGATGCCGATGACCGATGAAATCGGCGCGATCGTGCTGG
AAGGCGGCAATGCGATGCAGATCGCCGAGGCTGCGCAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTGATGAAG
GCTTCGCACGGCGTGACCAGCCTGGCCGAAATCAATCGGGTGACGAAGGATTGA

Domains

Predicted by InterproScan.

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

(49-153)

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

98.44

0.549
  pilB Acinetobacter baylyi ADP1

55.634

98.44

0.548
  pilB Legionella pneumophila strain ERS1305867

51.215

99.827

0.511
  pilB Vibrio cholerae strain A1552

48.174

99.653

0.48
  pilF Neisseria gonorrhoeae MS11

48.239

98.44

0.475
  pilB Vibrio campbellii strain DS40M4

45.343

98.614

0.447
  pilB Vibrio parahaemolyticus RIMD 2210633

45.293

97.574

0.442
  pilB/pilB1 Synechocystis sp. PCC 6803

35.41

100

0.374