Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   ACCQ09_RS05225 Genome accession   NZ_CP167854
Coordinates   1239840..1241102 (-) Length   420 a.a.
NCBI ID   WP_040940798.1    Uniprot ID   -
Organism   Xanthomonas sp. NCPPB 2586     
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 1202955..1259697 1239840..1241102 within 0


Gene organization within MGE regions


Location: 1202955..1259697
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ACCQ09_RS05035 (ACCQ09_05035) - 1203795..1204028 (+) 234 WP_162866359.1 hypothetical protein -
  ACCQ09_RS05040 (ACCQ09_05040) - 1204025..1204591 (+) 567 WP_162866360.1 hypothetical protein -
  ACCQ09_RS05045 (ACCQ09_05045) - 1204710..1205045 (-) 336 WP_040940781.1 hypothetical protein -
  ACCQ09_RS05050 (ACCQ09_05050) - 1205042..1205356 (-) 315 WP_014090899.1 hypothetical protein -
  ACCQ09_RS05055 (ACCQ09_05055) - 1205406..1206167 (-) 762 WP_040942245.1 hypothetical protein -
  ACCQ09_RS05060 (ACCQ09_05060) - 1206329..1206610 (+) 282 WP_040940782.1 helix-turn-helix domain-containing protein -
  ACCQ09_RS05065 (ACCQ09_05065) dndC 1206742..1207899 (+) 1158 WP_228427691.1 DNA phosphorothioation system sulfurtransferase DndC -
  ACCQ09_RS05070 (ACCQ09_05070) - 1207920..1208135 (+) 216 WP_014090894.1 DNA modification system-associated small protein -
  ACCQ09_RS05075 (ACCQ09_05075) dndD 1208125..1210203 (+) 2079 WP_014090893.1 DNA sulfur modification protein DndD -
  ACCQ09_RS05080 (ACCQ09_05080) - 1210205..1211734 (+) 1530 WP_040940783.1 DndE family protein -
  ACCQ09_RS05085 (ACCQ09_05085) - 1211794..1212156 (-) 363 WP_080640037.1 type II toxin-antitoxin system RnlB family antitoxin -
  ACCQ09_RS05090 (ACCQ09_05090) - 1212153..1213052 (-) 900 WP_372386272.1 RNase LS family HEPN domain-containing protein -
  ACCQ09_RS05095 (ACCQ09_05095) - 1213278..1214678 (-) 1401 WP_040940784.1 site-specific integrase -
  ACCQ09_RS05100 (ACCQ09_05100) - 1215224..1215448 (+) 225 WP_040940785.1 hypothetical protein -
  ACCQ09_RS05105 (ACCQ09_05105) - 1215817..1216296 (+) 480 WP_040940786.1 RadC family protein -
  ACCQ09_RS05110 (ACCQ09_05110) - 1216577..1217206 (+) 630 WP_040942248.1 DUF1629 domain-containing protein -
  ACCQ09_RS05115 (ACCQ09_05115) - 1217242..1221198 (+) 3957 WP_040940787.1 MAP7 domain-containing protein -
  ACCQ09_RS05120 (ACCQ09_05120) - 1221263..1221889 (+) 627 WP_197708550.1 hypothetical protein -
  ACCQ09_RS05125 (ACCQ09_05125) - 1221901..1223136 (-) 1236 WP_040940788.1 HNH endonuclease -
  ACCQ09_RS05130 (ACCQ09_05130) - 1223184..1223744 (-) 561 WP_040942250.1 hypothetical protein -
  ACCQ09_RS05135 (ACCQ09_05135) - 1223738..1224088 (-) 351 WP_078515451.1 HNH endonuclease -
  ACCQ09_RS05140 (ACCQ09_05140) - 1224270..1224596 (-) 327 WP_040940789.1 hypothetical protein -
  ACCQ09_RS05145 (ACCQ09_05145) - 1224863..1226458 (+) 1596 WP_040940790.1 MobA/MobL family protein -
  ACCQ09_RS05150 (ACCQ09_05150) - 1226511..1226852 (-) 342 WP_040940791.1 hypothetical protein -
  ACCQ09_RS05155 (ACCQ09_05155) - 1227554..1227982 (+) 429 WP_012437589.1 hypothetical protein -
  ACCQ09_RS05160 (ACCQ09_05160) - 1228225..1228455 (-) 231 WP_162866361.1 hypothetical protein -
  ACCQ09_RS05165 (ACCQ09_05165) - 1228519..1228665 (+) 147 WP_040940792.1 hypothetical protein -
  ACCQ09_RS05170 (ACCQ09_05170) - 1228850..1229245 (+) 396 WP_042594933.1 hypothetical protein -
  ACCQ09_RS05175 (ACCQ09_05175) - 1229336..1229728 (+) 393 WP_012437593.1 H-NS family nucleoid-associated regulatory protein -
  ACCQ09_RS05180 (ACCQ09_05180) glgX 1230253..1232382 (-) 2130 WP_016945001.1 glycogen debranching protein GlgX -
  ACCQ09_RS05185 (ACCQ09_05185) rimK 1232875..1233750 (+) 876 WP_011038222.1 30S ribosomal protein S6--L-glutamate ligase -
  ACCQ09_RS05190 (ACCQ09_05190) - 1234400..1235077 (+) 678 WP_003490678.1 response regulator transcription factor -
  ACCQ09_RS05195 (ACCQ09_05195) - 1235070..1236404 (+) 1335 WP_057671653.1 HAMP domain-containing sensor histidine kinase -
  ACCQ09_RS05200 (ACCQ09_05200) - 1236547..1237038 (-) 492 WP_040940794.1 GNAT family N-acetyltransferase -
  ACCQ09_RS05205 (ACCQ09_05205) - 1237035..1237325 (-) 291 WP_011038219.1 DUF1778 domain-containing protein -
  ACCQ09_RS05210 (ACCQ09_05210) - 1237400..1237801 (-) 402 WP_040940795.1 SymE family type I addiction module toxin -
  ACCQ09_RS05215 (ACCQ09_05215) coaE 1238333..1238956 (-) 624 WP_040940796.1 dephospho-CoA kinase -
  ACCQ09_RS05220 (ACCQ09_05220) - 1238970..1239833 (-) 864 WP_040940797.1 A24 family peptidase -
  ACCQ09_RS05225 (ACCQ09_05225) pilC 1239840..1241102 (-) 1263 WP_040940798.1 type II secretion system F family protein Machinery gene
  ACCQ09_RS05230 (ACCQ09_05230) pilA/pilAI 1241454..1241852 (+) 399 WP_040940799.1 pilin Machinery gene
  ACCQ09_RS05235 (ACCQ09_05235) - 1241957..1242379 (+) 423 WP_040940800.1 pilin -
  ACCQ09_RS05240 (ACCQ09_05240) - 1242438..1244258 (+) 1821 WP_162866362.1 hypothetical protein -
  ACCQ09_RS05245 (ACCQ09_05245) - 1244382..1245140 (+) 759 WP_080640038.1 class I SAM-dependent methyltransferase -
  ACCQ09_RS05250 (ACCQ09_05250) - 1245562..1246323 (+) 762 WP_162866363.1 glycosyltransferase family 9 protein -
  ACCQ09_RS05255 (ACCQ09_05255) - 1246326..1247168 (-) 843 WP_162866364.1 glycosyltransferase -
  ACCQ09_RS05260 (ACCQ09_05260) - 1247162..1248334 (-) 1173 WP_162866365.1 glycosyltransferase -
  ACCQ09_RS05265 (ACCQ09_05265) - 1248319..1249182 (-) 864 WP_080640041.1 glycosyltransferase -
  ACCQ09_RS05270 (ACCQ09_05270) - 1249232..1250083 (-) 852 WP_108133901.1 glycosyltransferase family 2 protein -
  ACCQ09_RS05275 (ACCQ09_05275) pilB 1250239..1251975 (+) 1737 WP_040940802.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ACCQ09_RS05280 (ACCQ09_05280) pilR 1253360..1254754 (-) 1395 WP_040940803.1 sigma-54 dependent transcriptional regulator Regulator
  ACCQ09_RS05285 (ACCQ09_05285) - 1254964..1256574 (-) 1611 WP_227971326.1 HAMP domain-containing sensor histidine kinase -
  ACCQ09_RS05290 (ACCQ09_05290) sucC 1256808..1257977 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ACCQ09_RS05295 (ACCQ09_05295) sucD 1258002..1258877 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  ACCQ09_RS05300 (ACCQ09_05300) - 1258981..1259391 (+) 411 WP_029217117.1 CopG family ribbon-helix-helix protein -
  ACCQ09_RS05305 (ACCQ09_05305) - 1259395..1259697 (+) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 420 a.a.        Molecular weight: 45811.20 Da        Isoelectric Point: 10.2311

>NTDB_id=1039874 ACCQ09_RS05225 WP_040940798.1 1239840..1241102(-) (pilC) [Xanthomonas sp. NCPPB 2586]
MSAVRSTIKNKPASISAEQQMSPFVWEGTDKRGVKMKGEQVARNANMLRAELRRQGITPSVVKAKPKPLFGAAGKKITPK
EIAFFSRQMATMMKSGVPIVGSLEIIGNGHKNPRMKQMVGQIRTDIEGGSSLHEAVSKHPVQFDELYRNLIKAGEGAGVL
ETVLDTIASYKENLEALKGKIKKALFYPAMVVAVALLVSSILLIWVVPQFEDVFKGFGAELPAFTQLIVNASRFMVSYWW
LMLLVIVGSIVGFIFAYKRSLAMQHGMDRLVLKVPIIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNSVYE
KAVLRMREDVSVGYPVNVSMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYYEQEVNNAVDALSSLIEPLIMVFIGTV
VGGMVIGMYLPIFKLASVVG

Nucleotide


Download         Length: 1263 bp        

>NTDB_id=1039874 ACCQ09_RS05225 WP_040940798.1 1239840..1241102(-) (pilC) [Xanthomonas sp. NCPPB 2586]
ATGTCGGCAGTCCGCAGCACCATCAAAAACAAACCGGCGAGCATCAGCGCCGAACAGCAGATGAGTCCGTTCGTCTGGGA
GGGAACAGACAAGCGCGGCGTGAAGATGAAAGGCGAACAGGTCGCCCGCAACGCCAATATGTTGCGTGCGGAACTCCGCC
GGCAGGGCATTACGCCCAGCGTTGTGAAGGCAAAGCCTAAGCCACTGTTCGGGGCGGCAGGCAAGAAGATCACGCCGAAG
GAAATTGCGTTCTTCAGCCGTCAGATGGCCACCATGATGAAGTCGGGCGTGCCAATTGTCGGGTCGCTGGAGATCATCGG
CAATGGTCACAAGAACCCGCGCATGAAGCAGATGGTCGGGCAGATCCGTACCGACATCGAAGGCGGATCTTCGCTGCACG
AAGCGGTAAGCAAGCATCCGGTGCAGTTCGACGAGCTGTATCGCAACCTGATCAAGGCCGGCGAAGGCGCTGGTGTGCTG
GAAACCGTCCTGGATACCATTGCCTCGTACAAGGAGAACCTGGAAGCCCTGAAGGGCAAGATCAAGAAGGCCTTGTTCTA
CCCCGCGATGGTCGTGGCAGTGGCTTTGTTGGTGAGCTCGATACTCTTGATCTGGGTCGTTCCGCAGTTCGAGGACGTGT
TCAAGGGGTTTGGCGCGGAACTGCCGGCGTTTACCCAATTGATCGTCAATGCGTCCCGATTCATGGTCTCGTATTGGTGG
CTGATGCTGCTTGTGATCGTCGGCTCGATCGTGGGCTTCATCTTTGCCTACAAGCGATCGCTTGCAATGCAGCATGGCAT
GGATCGGTTGGTGCTCAAGGTACCGATCATCGGCCAGATCATGCACAACAGCTCGATTGCGCGTTTTGCGCGCACTACTG
CGGTGACCTTCAAGGCAGGCGTGCCGTTGGTCGAAGCACTGGGCATCGTCGCCGGCGCCACTGGTAACTCGGTGTACGAG
AAAGCCGTGTTGCGCATGCGCGAGGATGTCTCGGTGGGCTATCCGGTCAACGTGTCGATGAAACAGGTCAACCTGTTTCC
GCATATGGTGATCCAGATGACGGCGATCGGCGAGGAAGCGGGCGCATTGGACGCCATGCTGTTCAAGGTGGCCGAGTACT
ACGAGCAAGAAGTGAACAATGCGGTGGACGCATTGAGCAGCCTCATCGAACCCCTGATCATGGTGTTCATTGGTACAGTA
GTCGGCGGCATGGTCATCGGCATGTACCTGCCCATCTTCAAGCTCGCTTCGGTGGTTGGATAA

Domains

Predicted by InterproScan.

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

(85-208)

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

(289-411)


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 Acinetobacter baylyi ADP1

52.736

95.714

0.505
  pilC Legionella pneumophila strain ERS1305867

51.095

97.857

0.5
  pilC Pseudomonas stutzeri DSM 10701

52.513

94.762

0.498
  pilC Acinetobacter baumannii D1279779

50.614

96.905

0.49
  pilG Neisseria gonorrhoeae MS11

43.099

98.333

0.424
  pilG Neisseria meningitidis 44/76-A

42.512

98.571

0.419
  pilC Vibrio cholerae strain A1552

41.814

94.524

0.395
  pilC Vibrio campbellii strain DS40M4

39.651

95.476

0.379

Multiple sequence alignment