Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   GDM11_RS05530 Genome accession   NZ_AP019684
Coordinates   1251361..1253094 (+) Length   577 a.a.
NCBI ID   WP_012437606.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. campestris strain MAFF302021     
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 1199923..1251326 1251361..1253094 flank 35


Gene organization within MGE regions


Location: 1199923..1253094
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  GDM11_RS05255 (Xcc3_10330) - 1201527..1201955 (+) 429 WP_145998822.1 hypothetical protein -
  GDM11_RS05260 (Xcc3_10340) - 1202340..1203128 (-) 789 WP_145998823.1 hypothetical protein -
  GDM11_RS05265 - 1203202..1204095 (-) 894 WP_145998824.1 hypothetical protein -
  GDM11_RS05270 (Xcc3_10350) - 1204261..1204641 (-) 381 WP_172973787.1 hypothetical protein -
  GDM11_RS05275 (Xcc3_10360) - 1204638..1204952 (-) 315 WP_100666315.1 hypothetical protein -
  GDM11_RS05280 (Xcc3_10370) - 1205002..1205763 (-) 762 WP_100666316.1 hypothetical protein -
  GDM11_RS05285 (Xcc3_10380) - 1205941..1206240 (+) 300 WP_230428394.1 helix-turn-helix domain-containing protein -
  GDM11_RS05290 (Xcc3_10390) - 1206252..1206740 (+) 489 WP_230431642.1 ADP-dependent glucokinase/phosphofructokinase -
  GDM11_RS05295 (Xcc3_10400) - 1206745..1207197 (-) 453 WP_145998825.1 hypothetical protein -
  GDM11_RS05300 (Xcc3_10410) - 1207400..1208800 (-) 1401 WP_100666320.1 site-specific integrase -
  GDM11_RS05305 (Xcc3_10420) - 1209410..1209925 (-) 516 WP_100666321.1 hypothetical protein -
  GDM11_RS05310 (Xcc3_10430) - 1210014..1210499 (+) 486 WP_145998826.1 hypothetical protein -
  GDM11_RS05315 (Xcc3_10440) - 1210632..1212116 (-) 1485 WP_100666322.1 hypothetical protein -
  GDM11_RS05320 (Xcc3_10450) - 1212196..1213161 (-) 966 WP_145998827.1 hypothetical protein -
  GDM11_RS05325 (Xcc3_10460) - 1213551..1213811 (+) 261 WP_145998828.1 hypothetical protein -
  GDM11_RS05330 (Xcc3_10470) - 1213798..1214295 (-) 498 WP_152091502.1 hypothetical protein -
  GDM11_RS05335 (Xcc3_10480) - 1214405..1214935 (-) 531 WP_152091503.1 hypothetical protein -
  GDM11_RS05340 (Xcc3_10490) - 1214970..1215782 (-) 813 WP_152091504.1 AbiJ-NTD4 domain-containing protein -
  GDM11_RS05345 (Xcc3_10500) - 1215779..1216087 (-) 309 WP_152091505.1 hypothetical protein -
  GDM11_RS05350 (Xcc3_10510) - 1216298..1216777 (+) 480 WP_152091506.1 JAB domain-containing protein -
  GDM11_RS22890 (Xcc3_10520) - 1216846..1217022 (+) 177 WP_172973789.1 hypothetical protein -
  GDM11_RS05355 (Xcc3_10530) - 1217242..1217883 (+) 642 WP_152091507.1 DUF1629 domain-containing protein -
  GDM11_RS05360 (Xcc3_10540) - 1217919..1220477 (+) 2559 WP_152091508.1 XVIPCD domain-containing protein -
  GDM11_RS05365 (Xcc3_10550) - 1220487..1221589 (-) 1103 Protein_1003 IS3-like element IS1404 family transposase -
  GDM11_RS05370 (Xcc3_10570) - 1222114..1222752 (-) 639 WP_232053528.1 hypothetical protein -
  GDM11_RS05375 (Xcc3_10580) - 1223036..1223542 (-) 507 WP_230428396.1 hypothetical protein -
  GDM11_RS05380 (Xcc3_10590) - 1223619..1224254 (+) 636 WP_230428397.1 hypothetical protein -
  GDM11_RS22895 (Xcc3_10600) - 1224372..1224530 (+) 159 WP_172973790.1 hypothetical protein -
  GDM11_RS05390 (Xcc3_10650) - 1226598..1227074 (-) 477 WP_152091510.1 hypothetical protein -
  GDM11_RS05395 (Xcc3_10660) - 1227235..1229208 (-) 1974 WP_152091511.1 ATP-dependent nuclease -
  GDM11_RS05405 (Xcc3_10670) - 1229744..1230043 (-) 300 WP_100666201.1 conjugal transfer protein TraD -
  GDM11_RS05410 (Xcc3_10680) - 1230310..1231905 (+) 1596 WP_100666199.1 MobA/MobL family protein -
  GDM11_RS05415 (Xcc3_10690) - 1231958..1232299 (-) 342 WP_100666197.1 hypothetical protein -
  GDM11_RS05420 - 1232993..1233421 (+) 429 WP_012437589.1 hypothetical protein -
  GDM11_RS22900 (Xcc3_10710) - 1233664..1233894 (-) 231 WP_157382680.1 hypothetical protein -
  GDM11_RS05425 (Xcc3_10720) - 1233958..1234104 (+) 147 WP_040940792.1 hypothetical protein -
  GDM11_RS05430 (Xcc3_10730) - 1234289..1234684 (+) 396 WP_016945003.1 hypothetical protein -
  GDM11_RS05435 (Xcc3_10740) - 1234775..1235167 (+) 393 WP_012437593.1 H-NS family nucleoid-associated regulatory protein -
  GDM11_RS05445 (Xcc3_10750) glgX 1235701..1237830 (-) 2130 WP_011038223.1 glycogen debranching protein GlgX -
  GDM11_RS05450 (Xcc3_10760) rimK 1238324..1239199 (+) 876 WP_016945000.1 30S ribosomal protein S6--L-glutamate ligase -
  GDM11_RS05455 (Xcc3_10770) - 1239422..1239895 (+) 474 WP_012437597.1 hypothetical protein -
  GDM11_RS05460 (Xcc3_10780) - 1239926..1240603 (+) 678 WP_003490678.1 response regulator transcription factor -
  GDM11_RS05465 (Xcc3_10790) - 1240596..1241930 (+) 1335 WP_012437598.1 sensor histidine kinase -
  GDM11_RS05470 (Xcc3_10800) - 1242073..1242564 (-) 492 WP_011038220.1 GNAT family N-acetyltransferase -
  GDM11_RS05475 (Xcc3_10810) - 1242561..1242851 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  GDM11_RS05480 (Xcc3_10820) - 1242926..1243327 (-) 402 WP_012437599.1 SymE family type I addiction module toxin -
  GDM11_RS05490 (Xcc3_10830) coaE 1243859..1244482 (-) 624 WP_011038217.1 dephospho-CoA kinase -
  GDM11_RS05495 (Xcc3_10840) - 1244496..1245359 (-) 864 WP_012437600.1 prepilin peptidase -
  GDM11_RS05500 - 1245366..1246627 (-) 1262 Protein_1029 type II secretion system F family protein -
  GDM11_RS05505 (Xcc3_10870) comP 1246979..1247392 (+) 414 WP_012437602.1 pilin Machinery gene
  GDM11_RS05510 (Xcc3_10880) - 1247611..1249122 (+) 1512 WP_256729490.1 phosphoethanolamine transferase -
  GDM11_RS05515 (Xcc3_10890) - 1249133..1249762 (+) 630 WP_012437604.1 hypothetical protein -
  GDM11_RS23760 - 1249732..1251326 (+) 1595 Protein_1033 spermidine synthase -
  GDM11_RS05530 (Xcc3_10920) pilB 1251361..1253094 (+) 1734 WP_012437606.1 type IV-A pilus assembly ATPase PilB Machinery gene

Sequence

Protein


Download         Length: 577 a.a.        Molecular weight: 62661.87 Da        Isoelectric Point: 5.7669

>NTDB_id=73221 GDM11_RS05530 WP_012437606.1 1251361..1253094(+) (pilB) [Xanthomonas campestris pv. campestris strain MAFF302021]
MNSVATTNLVGITGIARRLVQDGALEEAAARTAMEQAAAAKVPLPQWFAEKKLVSAAQLAAANAVEFGMPLMDVSVFDAS
QNAVKLVSEELLQKHQVLPLFKRGNRLFVGVSNPTQTKALDDIKFHTNLVVEPILVDEDQIRRTLEQWQAGNASFGSALG
GDDEEMGDLDVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAP
VKLNQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQK
LFLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDP
DIIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLP
EHALLAEGFTPEQVANIELYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMK
ASHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1734 bp        

>NTDB_id=73221 GDM11_RS05530 WP_012437606.1 1251361..1253094(+) (pilB) [Xanthomonas campestris pv. campestris strain MAFF302021]
ATGAATTCAGTAGCTACCACTAACCTCGTTGGCATCACCGGCATCGCTCGTCGCCTCGTGCAGGATGGCGCCCTGGAGGA
AGCCGCTGCGCGGACGGCGATGGAACAGGCGGCCGCTGCCAAGGTGCCGCTGCCGCAGTGGTTTGCCGAGAAGAAGCTGG
TGTCGGCGGCGCAGCTGGCGGCGGCCAATGCCGTGGAATTCGGCATGCCGCTAATGGATGTGTCGGTGTTTGACGCTAGT
CAGAACGCGGTGAAGCTGGTAAGTGAAGAGTTGCTCCAGAAGCATCAGGTGTTGCCGCTGTTCAAGCGCGGCAACCGATT
GTTTGTGGGGGTGAGCAACCCGACGCAGACCAAGGCATTGGACGACATCAAGTTCCATACCAACTTGGTGGTGGAGCCAA
TTCTGGTCGATGAGGACCAGATCCGTAGGACGTTGGAGCAATGGCAGGCAGGAAACGCGTCCTTTGGCTCGGCGCTTGGT
GGCGACGACGAGGAGATGGGGGACCTAGACGTGTCCGCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGA
TGCCAAGGGTGATGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGTCGGGGAGCCTCGGACA
TCCATTTCGAGCCGTATGAAGACGACTACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCG
GTGAAGCTCAACCAGCGCATCGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGA
CGGGCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGATTTTCGCGTGAGCACCTTGCCGACCTTGTTCGGCGAAA
AGGTGGTGCTGCGTATCCTGGACGCCAGTGCGGCCAAGCTCGGTATCGAGAAGCTGGGCTATGAGGCGGACCAGCAGAAG
CTGTTCCTGGATGCGATCCACAAGCCCTACGGCATGGTGCTGGTGACCGGGCCGACCGGTTCGGGCAAGACGGTGTCGCT
GTATACCGCGCTCGGGATTCTCAACGACGAGACGCGCAACATTTCCACGGCCGAGGATCCGGTCGAAATCCGCCTGCCTG
GCGTCAATCAGGTGCAGCAGAACGTCAAGCGGGGCATGACGTTTGCCGCTGCGCTGCGCTCGTTCCTGCGTCAGGACCCG
GACATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATCGCGATCAAGGCGGCGCAGACCGGCCACATGGT
GCTGTCGACGCTGCACACCAACGATGCGCCGCAAACCATTGCGCGTCTGATGAACATGGGTATCGCACCGTACAACATCA
CCTCCTCGGTGACCTTGGTCATCGCGCAGCGCCTGGCGCGGCGGCTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCG
GAACATGCGCTGCTGGCGGAAGGCTTTACGCCGGAGCAGGTTGCGAACATCGAGCTCTATGAAGCGGTCGGTTGCGATGA
GTGCACGGAAGGCTACAAGGGCCGTACCGGCATCTATCAGGTAATGCCGATGACCGATGAAATCGGCGCGATCGTGCTGG
AAGGCGGCAATGCGATGCAGATCGCCGAGGCCGCACAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTGATGAAG
GCTTCGCACGGCGTCACCAGCCTCGCCGAGATCAATCGTGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

Type II/IV secretion system protein (T2SSE)

(201-468)

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

(49-150)


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

56.514

98.44

0.556
  pilB Acinetobacter baylyi ADP1

55.652

99.653

0.555
  pilB Legionella pneumophila strain ERS1305867

52.465

98.44

0.516
  pilB Vibrio cholerae strain A1552

49.567

100

0.496
  pilF Neisseria gonorrhoeae MS11

49.12

98.44

0.484
  pilB Vibrio campbellii strain DS40M4

46.046

98.614

0.454
  pilB Vibrio parahaemolyticus RIMD 2210633

46.333

96.88

0.449

Multiple sequence alignment