Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilB   Type   Machinery gene
Locus tag   ABFU63_RS05420 Genome accession   NZ_CP155987
Coordinates   1282675..1284405 (+) Length   576 a.a.
NCBI ID   WP_057671826.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. campestris strain LMG 08081     
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 1234786..1291160 1282675..1284405 within 0


Gene organization within MGE regions


Location: 1234786..1291160
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU63_RS05200 (ABFU63_05195) - 1234786..1236666 (+) 1881 WP_019237331.1 integrase arm-type DNA-binding domain-containing protein -
  ABFU63_RS05205 (ABFU63_05200) - 1236851..1237270 (+) 420 WP_019237332.1 hypothetical protein -
  ABFU63_RS05210 (ABFU63_05205) - 1237303..1238304 (+) 1002 WP_407365473.1 XVIPCD domain-containing protein -
  ABFU63_RS05215 (ABFU63_05210) - 1238375..1239025 (-) 651 WP_011038252.1 LysR substrate-binding domain-containing protein -
  ABFU63_RS05220 (ABFU63_05215) - 1239128..1239421 (+) 294 WP_011038251.1 helix-turn-helix domain-containing protein -
  ABFU63_RS05225 (ABFU63_05220) - 1239449..1240333 (-) 885 WP_057671621.1 LysR family transcriptional regulator -
  ABFU63_RS05230 (ABFU63_05225) - 1241086..1245111 (-) 4026 WP_075287146.1 helix-turn-helix domain-containing protein -
  ABFU63_RS05235 (ABFU63_05230) - 1245659..1248922 (-) 3264 WP_057671623.1 ATP-binding protein -
  ABFU63_RS05240 (ABFU63_05235) - 1249013..1249144 (+) 132 Protein_1012 IS5/IS1182 family transposase -
  ABFU63_RS05245 (ABFU63_05240) - 1250113..1251651 (+) 1539 WP_011038243.1 MASE1 domain-containing protein -
  ABFU63_RS05250 (ABFU63_05245) - 1252673..1253320 (+) 648 WP_016848927.1 hypothetical protein -
  ABFU63_RS05255 (ABFU63_05250) - 1253352..1254491 (+) 1140 WP_017117946.1 type IV secretion system protein -
  ABFU63_RS05260 (ABFU63_05255) - 1254569..1255108 (+) 540 WP_225443876.1 DUF4189 domain-containing protein -
  ABFU63_RS05265 (ABFU63_05260) - 1255506..1256036 (+) 531 WP_407365474.1 hypothetical protein -
  ABFU63_RS05270 (ABFU63_05265) - 1256033..1256692 (+) 660 WP_057671625.1 hypothetical protein -
  ABFU63_RS05275 (ABFU63_05270) - 1256689..1258071 (+) 1383 WP_057671628.1 DUF6792 domain-containing protein -
  ABFU63_RS05280 (ABFU63_05275) - 1258175..1258602 (+) 428 Protein_1020 type IV secretion system protein -
  ABFU63_RS05285 (ABFU63_05280) - 1259031..1260163 (+) 1133 WP_139115401.1 IS3-like element ISXca1 family transposase -
  ABFU63_RS05290 (ABFU63_05285) - 1260182..1260733 (+) 552 Protein_1022 IS3 family transposase -
  ABFU63_RS05295 (ABFU63_05290) - 1261282..1261761 (+) 480 WP_075286085.1 RadC family protein -
  ABFU63_RS05300 (ABFU63_05295) - 1261832..1262023 (+) 192 WP_221261829.1 hypothetical protein -
  ABFU63_RS05305 (ABFU63_05300) - 1262657..1262812 (+) 156 WP_186009287.1 hypothetical protein -
  ABFU63_RS05310 (ABFU63_05305) - 1263801..1264226 (+) 426 Protein_1026 XVIPCD domain-containing protein -
  ABFU63_RS05315 (ABFU63_05310) - 1264254..1264508 (-) 255 WP_057671639.1 hypothetical protein -
  ABFU63_RS05320 (ABFU63_05315) - 1264775..1266370 (+) 1596 WP_192012501.1 MobA/MobL family protein -
  ABFU63_RS05325 (ABFU63_05320) - 1266443..1266811 (-) 369 WP_225443877.1 transcriptional regulator -
  ABFU63_RS05330 (ABFU63_05325) - 1266819..1267100 (-) 282 WP_011348355.1 DUF6516 family protein -
  ABFU63_RS05335 (ABFU63_05330) - 1267166..1267507 (-) 342 WP_081020748.1 hypothetical protein -
  ABFU63_RS05340 (ABFU63_05335) - 1268233..1268583 (+) 351 WP_225443878.1 hypothetical protein -
  ABFU63_RS05345 (ABFU63_05340) - 1268882..1269112 (-) 231 WP_157382680.1 hypothetical protein -
  ABFU63_RS05350 (ABFU63_05345) - 1269176..1269322 (+) 147 WP_040940792.1 hypothetical protein -
  ABFU63_RS05355 (ABFU63_05350) - 1269507..1269902 (+) 396 WP_042594933.1 hypothetical protein -
  ABFU63_RS05360 (ABFU63_05355) - 1269993..1270385 (+) 393 WP_012437593.1 H-NS family nucleoid-associated regulatory protein -
  ABFU63_RS05365 (ABFU63_05360) glgX 1270920..1273049 (-) 2130 WP_057671651.1 glycogen debranching protein GlgX -
  ABFU63_RS05370 (ABFU63_05365) rimK 1273542..1274417 (+) 876 WP_016945000.1 30S ribosomal protein S6--L-glutamate ligase -
  ABFU63_RS05375 (ABFU63_05370) - 1275067..1275744 (+) 678 WP_003490678.1 response regulator transcription factor -
  ABFU63_RS05380 (ABFU63_05375) - 1275737..1277071 (+) 1335 WP_057671653.1 HAMP domain-containing sensor histidine kinase -
  ABFU63_RS05385 (ABFU63_05380) - 1277214..1277705 (-) 492 WP_011038220.1 GNAT family N-acetyltransferase -
  ABFU63_RS05390 (ABFU63_05385) - 1277702..1277992 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  ABFU63_RS05395 (ABFU63_05390) - 1278067..1278468 (-) 402 WP_040940795.1 SymE family type I addiction module toxin -
  ABFU63_RS05400 (ABFU63_05395) coaE 1279000..1279623 (-) 624 WP_011038217.1 dephospho-CoA kinase -
  ABFU63_RS05405 (ABFU63_05400) - 1279637..1280500 (-) 864 WP_057671659.1 A24 family peptidase -
  ABFU63_RS05410 (ABFU63_05405) pilC 1280507..1281769 (-) 1263 WP_057671824.1 type II secretion system F family protein Machinery gene
  ABFU63_RS05415 (ABFU63_05410) pilA 1282111..1282539 (+) 429 WP_057671660.1 pilin Machinery gene
  ABFU63_RS05420 (ABFU63_05415) pilB 1282675..1284405 (+) 1731 WP_057671826.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU63_RS05430 (ABFU63_05425) pilR 1284824..1286218 (-) 1395 WP_057671663.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU63_RS05435 (ABFU63_05430) - 1286427..1288037 (-) 1611 WP_057671664.1 PAS domain-containing sensor histidine kinase -
  ABFU63_RS05440 (ABFU63_05435) sucC 1288271..1289440 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU63_RS05445 (ABFU63_05440) sucD 1289465..1290340 (+) 876 WP_057671668.1 succinate--CoA ligase subunit alpha -
  ABFU63_RS05450 (ABFU63_05445) - 1290444..1290854 (+) 411 WP_029217117.1 CopG family ribbon-helix-helix protein -
  ABFU63_RS05455 (ABFU63_05450) - 1290858..1291160 (+) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 576 a.a.        Molecular weight: 62599.69 Da        Isoelectric Point: 5.6001

>NTDB_id=1000774 ABFU63_RS05420 WP_057671826.1 1282675..1284405(+) (pilB) [Xanthomonas campestris pv. campestris strain LMG 08081]
MSAVAANLVGITGIARRLVQDGALDEISARTAMDQAAAAKTPLPQWFSERKLVSASQLAAANAVEFGMPLMDVSVFDASQ
NAVKLVSEELLQKYQVLPLFKRGNRLFVGVSNPTQTRALDDIKFHTNLVVEPILVDEDQIRRTLEQWQASNAALGSSLGS
DDDDIGDLDVSAGDEDMGAGGDSGVDAKGDDTPVVKFVNKVLVDAIRRGASDIHFEPYEDDYRVRLRIDGLLKNVAKAPV
KLNQRIAARLKVMSQLDIAEKRVPQDGRIKLNLSKTKQIDFRVSTLPTLFGEKVVLRILDASAAKLGIEKLGYEADQQKL
FLDAIHKPYGMVLVTGPTGSGKTVSLYTALGILNDETRNISTAEDPVEIRLPGVNQVQQNVKRGMTFAAALRSFLRQDPD
IIMVGEIRDLETAEIAIKAAQTGHMVLSTLHTNDAPQTIARLMNMGIAPYNITSSVTLVIAQRLARRLCNNCKRKSTLPE
HALLAEGFTPEQVANIDLYEAVGCDECTEGYKGRTGIYQVMPMTDEIGAIVLEGGNAMQIAEAAQKIGIRDLRQSALMKA
SHGVTSLAEINRVTKD

Nucleotide


Download         Length: 1731 bp        

>NTDB_id=1000774 ABFU63_RS05420 WP_057671826.1 1282675..1284405(+) (pilB) [Xanthomonas campestris pv. campestris strain LMG 08081]
ATGAGTGCAGTCGCGGCGAACTTAGTAGGAATTACAGGCATTGCACGCCGCCTAGTGCAAGACGGAGCGCTTGATGAAAT
AAGTGCCCGTACCGCCATGGACCAAGCCGCGGCAGCGAAGACTCCGCTTCCCCAATGGTTCTCAGAGAGAAAGCTGGTTT
CCGCGTCTCAACTGGCTGCAGCCAACGCAGTCGAGTTCGGCATGCCTCTCATGGACGTTTCCGTGTTCGATGCTAGTCAG
AACGCGGTCAAGCTGGTCAGTGAGGAGTTGCTCCAGAAGTATCAGGTGCTGCCGCTGTTCAAGCGCGGCAACCGGTTGTT
TGTGGGAGTGAGCAACCCGACCCAGACACGGGCGCTGGACGACATCAAGTTCCACACTAACTTGGTGGTCGAGCCGATTC
TGGTCGACGAGGACCAGATCCGTCGCACGCTAGAGCAGTGGCAGGCCAGTAACGCCGCGCTCGGCTCGTCGCTGGGGAGC
GACGATGACGATATAGGCGATCTAGACGTGTCCGCCGGGGACGAGGACATGGGCGCCGGCGGGGATTCCGGGGTCGATGC
CAAGGGCGATGACACGCCGGTGGTGAAGTTCGTCAACAAGGTGCTGGTGGATGCGATCCGGCGGGGAGCCTCGGACATCC
ATTTCGAGCCCTATGAAGATGACTACCGGGTGCGGTTGCGGATCGATGGGCTGTTGAAGAACGTGGCCAAGGCGCCGGTG
AAGCTCAACCAGCGCATCGCGGCGCGCCTGAAGGTGATGTCGCAGCTGGACATCGCCGAGAAGCGGGTGCCGCAGGACGG
GCGCATCAAGCTCAACCTGTCCAAGACCAAGCAGATCGATTTTCGCGTGAGCACCTTGCCGACCTTGTTCGGCGAGAAGG
TGGTGTTGCGTATCCTGGACGCCAGTGCGGCCAAGCTCGGTATCGAGAAGCTGGGCTATGAGGCGGACCAGCAGAAGCTG
TTCCTGGATGCGATCCACAAGCCCTACGGCATGGTGCTGGTGACCGGGCCGACCGGTTCGGGCAAGACGGTGTCGCTGTA
TACCGCGCTCGGGATTCTCAACGACGAGACGCGCAATATTTCCACGGCCGAGGATCCGGTCGAAATCCGCTTGCCCGGCG
TCAATCAGGTGCAGCAGAACGTCAAGCGGGGCATGACGTTTGCGGCGGCGCTGCGCTCGTTCCTGCGTCAGGACCCGGAC
ATCATCATGGTCGGCGAAATCCGCGACCTGGAGACGGCCGAGATTGCGATCAAGGCGGCGCAGACGGGCCACATGGTGCT
GTCGACGTTGCACACCAACGATGCGCCGCAGACCATTGCGCGTCTGATGAACATGGGCATCGCGCCGTACAACATCACCT
CGTCGGTGACCCTGGTCATCGCGCAGCGCTTGGCGCGGCGCTTGTGCAACAACTGCAAGCGCAAGTCGACGCTGCCGGAA
CATGCGCTGCTGGCGGAAGGCTTTACGCCGGAGCAGGTTGCGAACATCGACCTCTATGAAGCGGTCGGTTGCGATGAGTG
CACGGAAGGCTACAAGGGCCGTACCGGCATCTATCAGGTGATGCCGATGACCGACGAGATCGGTGCGATCGTGCTGGAAG
GCGGCAATGCGATGCAGATCGCCGAGGCCGCACAGAAGATCGGTATCCGCGACCTGCGCCAGTCGGCGTTGATGAAGGCT
TCGCACGGGGTGACCAGCCTGGCCGAAATCAATCGTGTGACCAAGGACTGA

Domains

Predicted by InterproScan.

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

(49-152)

Type II/IV secretion system protein (T2SSE)

(200-467)


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

56.338

98.611

0.556
  pilB Acinetobacter baylyi ADP1

55.282

98.611

0.545
  pilB Legionella pneumophila strain ERS1305867

52.083

100

0.521
  pilF Neisseria gonorrhoeae MS11

49.12

98.611

0.484
  pilB Vibrio cholerae strain A1552

49.817

94.792

0.472
  pilB Vibrio campbellii strain DS40M4

46.046

98.785

0.455
  pilB Vibrio parahaemolyticus RIMD 2210633

46.333

97.049

0.45
  pilB/pilB1 Synechocystis sp. PCC 6803

35.41

100

0.375

Multiple sequence alignment