Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   JM952_RS05240 Genome accession   NZ_CP069085
Coordinates   1238713..1239969 (-) Length   418 a.a.
NCBI ID   WP_011038215.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. campestris strain BJSJQ20200612     
Function   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 1193623..1238997 1238713..1239969 flank -284


Gene organization within MGE regions


Location: 1193623..1239969
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  JM952_RS04990 (JM952_05005) - 1195227..1195655 (+) 429 WP_145998822.1 hypothetical protein -
  JM952_RS04995 (JM952_05010) - 1196040..1196828 (-) 789 WP_145998823.1 hypothetical protein -
  JM952_RS05000 (JM952_05015) - 1196902..1197795 (-) 894 WP_145998824.1 hypothetical protein -
  JM952_RS05005 (JM952_05020) - 1197961..1198341 (-) 381 WP_172973787.1 hypothetical protein -
  JM952_RS05010 (JM952_05025) - 1198338..1198652 (-) 315 WP_218065344.1 hypothetical protein -
  JM952_RS05015 (JM952_05030) - 1198702..1199463 (-) 762 WP_100666316.1 hypothetical protein -
  JM952_RS05020 (JM952_05035) - 1199641..1199940 (+) 300 WP_230428394.1 helix-turn-helix transcriptional regulator -
  JM952_RS05025 (JM952_05040) - 1200009..1200440 (+) 432 WP_100666318.1 hypothetical protein -
  JM952_RS05030 (JM952_05045) - 1200445..1200897 (-) 453 WP_145998825.1 hypothetical protein -
  JM952_RS05035 (JM952_05050) - 1201100..1202500 (-) 1401 WP_218065345.1 site-specific integrase -
  JM952_RS05040 (JM952_05055) - 1203108..1203623 (-) 516 WP_100666321.1 hypothetical protein -
  JM952_RS05045 (JM952_05060) - 1203712..1204197 (+) 486 WP_145998826.1 hypothetical protein -
  JM952_RS05050 (JM952_05065) - 1204330..1205814 (-) 1485 WP_100666322.1 hypothetical protein -
  JM952_RS05055 (JM952_05070) - 1205894..1206859 (-) 966 WP_145998827.1 hypothetical protein -
  JM952_RS05060 (JM952_05075) - 1207249..1207509 (+) 261 WP_145998828.1 hypothetical protein -
  JM952_RS05065 (JM952_05080) - 1207496..1207993 (-) 498 WP_152091502.1 hypothetical protein -
  JM952_RS05070 (JM952_05085) - 1208103..1208633 (-) 531 WP_152091503.1 hypothetical protein -
  JM952_RS05075 (JM952_05090) - 1208668..1209480 (-) 813 WP_152091504.1 hypothetical protein -
  JM952_RS05080 (JM952_05095) - 1209477..1209785 (-) 309 WP_152091505.1 hypothetical protein -
  JM952_RS05085 (JM952_05100) radC 1209996..1210475 (+) 480 WP_152091506.1 DNA repair protein RadC -
  JM952_RS05090 (JM952_05105) - 1210544..1210720 (+) 177 WP_172973789.1 hypothetical protein -
  JM952_RS05095 (JM952_05110) - 1210940..1211581 (+) 642 WP_152091507.1 DUF1629 domain-containing protein -
  JM952_RS05100 (JM952_05115) - 1211617..1214202 (+) 2586 WP_218065346.1 XVIPCD domain-containing protein -
  JM952_RS05105 (JM952_05120) - 1214442..1215245 (-) 804 WP_230428395.1 hypothetical protein -
  JM952_RS05110 (JM952_05125) - 1215529..1216035 (-) 507 WP_230428396.1 hypothetical protein -
  JM952_RS05115 (JM952_05130) - 1216112..1216747 (+) 636 WP_230428397.1 hypothetical protein -
  JM952_RS05120 (JM952_05135) - 1216865..1217023 (+) 159 WP_172973790.1 hypothetical protein -
  JM952_RS05130 (JM952_05145) - 1219092..1219568 (-) 477 WP_152091510.1 hypothetical protein -
  JM952_RS05135 (JM952_05150) - 1219730..1220476 (-) 747 WP_218065347.1 ATP-dependent endonuclease -
  JM952_RS05140 (JM952_05155) - 1221098..1221099 (-) 2 WP_087942062.1 IS5 family transposase -
  JM952_RS05145 (JM952_05160) - 1221344..1222555 (-) 1212 WP_218065348.1 AAA family ATPase -
  JM952_RS05150 (JM952_05165) traD 1223091..1223390 (-) 300 WP_100666201.1 conjugal transfer protein TraD -
  JM952_RS05155 (JM952_05170) - 1223657..1225252 (+) 1596 WP_100666199.1 MobA/MobL family protein -
  JM952_RS05160 (JM952_05175) - 1225305..1225646 (-) 342 WP_100666197.1 hypothetical protein -
  JM952_RS05165 (JM952_05180) - 1226340..1226768 (+) 429 WP_012437589.1 hypothetical protein -
  JM952_RS05170 (JM952_05185) - 1227011..1227241 (-) 231 WP_157382680.1 hypothetical protein -
  JM952_RS05175 (JM952_05190) - 1227305..1227451 (+) 147 WP_040940792.1 hypothetical protein -
  JM952_RS05180 (JM952_05195) - 1227636..1228031 (+) 396 WP_016945003.1 hypothetical protein -
  JM952_RS05185 (JM952_05200) - 1228122..1228514 (+) 393 WP_012437593.1 H-NS family nucleoid-associated regulatory protein -
  JM952_RS05190 (JM952_05205) glgX 1229048..1231177 (-) 2130 WP_016945001.1 glycogen debranching protein GlgX -
  JM952_RS05195 (JM952_05210) rimK 1231671..1232546 (+) 876 WP_016945000.1 30S ribosomal protein S6--L-glutamate ligase -
  JM952_RS05200 (JM952_05215) - 1232769..1233242 (+) 474 WP_012437597.1 hypothetical protein -
  JM952_RS05205 (JM952_05220) - 1233273..1233950 (+) 678 WP_003490678.1 response regulator transcription factor -
  JM952_RS05210 (JM952_05225) - 1233943..1235277 (+) 1335 WP_012437598.1 HAMP domain-containing sensor histidine kinase -
  JM952_RS05215 (JM952_05230) - 1235420..1235911 (-) 492 WP_011038220.1 GNAT family N-acetyltransferase -
  JM952_RS05220 (JM952_05235) - 1235908..1236198 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  JM952_RS05225 (JM952_05240) - 1236273..1236674 (-) 402 WP_019237348.1 SymE family type I addiction module toxin -
  JM952_RS05230 (JM952_05245) coaE 1237206..1237829 (-) 624 WP_011038217.1 dephospho-CoA kinase -
  JM952_RS05235 (JM952_05250) - 1237843..1238706 (-) 864 WP_011038216.1 A24 family peptidase -
  JM952_RS05240 (JM952_05255) pilC 1238713..1239969 (-) 1257 WP_011038215.1 type II secretion system F family protein Machinery gene

Sequence

Protein


Download         Length: 418 a.a.        Molecular weight: 45907.37 Da        Isoelectric Point: 10.3359

>NTDB_id=532278 JM952_RS05240 WP_011038215.1 1238713..1239969(-) (pilC) [Xanthomonas campestris pv. campestris strain BJSJQ20200612]
MSIARSSMKKQPIDRNVNEMVPFVWEGTDKRGIKMKGEQPARNANMLRAELRRQGITPLVVKTKPKPLFGAAGKKISSKD
IAFFSRQMATMMKSGVPIVGSLEIIGEGHKNPRMKKMVGQIRTDIEGGSSLHEAISRHPVQFDDLYRNLVRAGEGAGVLE
TVLDTVANYKENIEALKGKIKKALFYPAMVMAVAIIVSGILLVFVVPQFEDVFKGFGAELPAFTQMIVAASRFMVSYWWL
MLLGSIAAIAGFIFAYKRSPRMRHGMDRLVLKVPVIGQIMHNSSIARFARTTAVTFKAGVPLVEALSIVAGATGNKVYEE
AVLRMRDDVSVGYPVNMAMKQVNLFPHMVVQMTSIGEEAGALDAMLFKVAEYFEQEVNNAVDALSSLLEPLIMVFIGTIV
GGMVIGMYLPIFKLGSVV

Nucleotide


Download         Length: 1257 bp        

>NTDB_id=532278 JM952_RS05240 WP_011038215.1 1238713..1239969(-) (pilC) [Xanthomonas campestris pv. campestris strain BJSJQ20200612]
ATGTCAATCGCTCGTAGCAGCATGAAGAAGCAGCCGATAGACCGGAACGTAAACGAGATGGTCCCATTTGTCTGGGAGGG
TACGGACAAGCGCGGCATCAAGATGAAGGGGGAACAACCTGCTCGCAACGCGAACATGCTCCGCGCTGAGCTTCGGCGGC
AGGGCATCACACCTTTAGTTGTAAAGACGAAGCCTAAGCCGCTTTTCGGCGCCGCTGGCAAGAAAATTTCTTCAAAAGAT
ATCGCATTTTTCAGTCGCCAGATGGCAACAATGATGAAGTCGGGCGTACCTATTGTTGGATCGCTTGAAATCATCGGAGA
GGGGCACAAAAATCCCCGCATGAAAAAAATGGTTGGTCAAATTAGGACCGACATTGAAGGAGGGTCTTCACTCCATGAAG
CAATTTCTAGGCATCCAGTCCAATTCGACGACCTCTATCGAAATTTGGTACGAGCAGGCGAAGGTGCCGGCGTTCTAGAA
ACCGTTTTAGACACAGTTGCAAATTACAAAGAAAACATTGAAGCACTGAAGGGAAAAATAAAGAAAGCTTTATTTTATCC
TGCAATGGTAATGGCCGTTGCAATTATTGTGAGCGGAATATTACTTGTATTTGTTGTCCCGCAATTTGAAGACGTATTCA
AAGGATTCGGAGCAGAACTACCAGCTTTCACTCAGATGATCGTCGCGGCGTCGCGTTTCATGGTGTCTTATTGGTGGCTT
ATGCTACTTGGTAGCATCGCAGCAATTGCAGGATTCATTTTTGCTTACAAGCGCTCGCCTCGCATGCGACATGGAATGGA
TAGATTGGTCTTGAAGGTCCCAGTCATTGGCCAGATCATGCATAATAGCTCTATCGCCCGATTTGCGCGAACCACTGCCG
TTACGTTCAAAGCTGGCGTTCCTTTAGTTGAAGCCTTGAGCATTGTGGCTGGCGCCACCGGTAATAAAGTTTATGAGGAA
GCTGTGCTTCGTATGCGCGATGATGTCTCGGTAGGCTACCCTGTCAACATGGCGATGAAGCAGGTCAATCTTTTCCCACA
CATGGTGGTTCAGATGACCTCGATCGGCGAAGAAGCTGGCGCCCTGGATGCCATGTTGTTCAAAGTGGCTGAATATTTCG
AGCAAGAAGTTAATAACGCCGTGGATGCATTGAGCAGCTTACTGGAACCATTGATCATGGTTTTTATTGGCACAATTGTG
GGCGGCATGGTCATTGGCATGTATCTTCCCATCTTCAAACTTGGCTCAGTGGTCTAA

Domains

Predicted by InterproScan.

Type II secretion system (T2SS), protein F (T2SSF)

(84-207)

Type II secretion system (T2SS), protein F (T2SSF)

(288-410)


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
  pilC Pseudomonas stutzeri DSM 10701

53.788

94.737

0.51
  pilC Acinetobacter baylyi ADP1

53.401

94.976

0.507
  pilC Acinetobacter baumannii D1279779

51.741

96.172

0.498
  pilC Legionella pneumophila strain ERS1305867

50.493

97.129

0.49
  pilG Neisseria gonorrhoeae MS11

44.836

94.976

0.426
  pilG Neisseria meningitidis 44/76-A

44.332

94.976

0.421
  pilC Vibrio cholerae strain A1552

42.172

94.737

0.4
  pilC Vibrio campbellii strain DS40M4

39.141

94.737

0.371