Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   ABFU34_RS05160 Genome accession   NZ_CP155966
Coordinates   1232313..1233575 (-) Length   420 a.a.
NCBI ID   WP_228442817.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani strain BXC#143     
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 1194759..1252166 1232313..1233575 within 0


Gene organization within MGE regions


Location: 1194759..1252166
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU34_RS04985 (ABFU34_04975) - 1196235..1197515 (+) 1281 WP_228442796.1 SidA/IucD/PvdA family monooxygenase -
  ABFU34_RS04990 (ABFU34_04980) - 1197569..1197820 (+) 252 WP_228442797.1 hypothetical protein -
  ABFU34_RS04995 (ABFU34_04985) - 1198239..1198616 (-) 378 WP_228442798.1 hypothetical protein -
  ABFU34_RS05000 (ABFU34_04990) - 1198613..1198927 (-) 315 WP_228442799.1 hypothetical protein -
  ABFU34_RS05005 (ABFU34_04995) - 1198984..1199746 (-) 763 Protein_970 hypothetical protein -
  ABFU34_RS05010 (ABFU34_05000) - 1199908..1200189 (+) 282 WP_373046018.1 helix-turn-helix domain-containing protein -
  ABFU34_RS05015 (ABFU34_05005) dndC 1200359..1201489 (+) 1131 WP_228442802.1 DNA phosphorothioation system sulfurtransferase DndC -
  ABFU34_RS05020 (ABFU34_05010) - 1201511..1201726 (+) 216 WP_082346685.1 DNA modification system-associated small protein -
  ABFU34_RS05025 (ABFU34_05015) dndD 1201716..1203794 (+) 2079 WP_228442803.1 DNA sulfur modification protein DndD -
  ABFU34_RS05030 (ABFU34_05020) - 1203796..1205325 (+) 1530 WP_228442804.1 ATP-binding protein -
  ABFU34_RS05035 (ABFU34_05025) - 1205358..1205693 (+) 336 WP_228442805.1 hypothetical protein -
  ABFU34_RS05040 (ABFU34_05030) - 1205877..1207277 (-) 1401 WP_228442806.1 site-specific integrase -
  ABFU34_RS05045 (ABFU34_05035) - 1207825..1208049 (+) 225 WP_053051249.1 hypothetical protein -
  ABFU34_RS05050 (ABFU34_05040) - 1208446..1208926 (+) 481 Protein_979 RadC family protein -
  ABFU34_RS05055 (ABFU34_05045) - 1209176..1209835 (+) 660 WP_228442836.1 DUF1629 domain-containing protein -
  ABFU34_RS05060 (ABFU34_05050) - 1209872..1213864 (+) 3993 WP_228442807.1 hypothetical protein -
  ABFU34_RS05065 (ABFU34_05055) - 1213906..1214556 (+) 651 WP_228442808.1 hypothetical protein -
  ABFU34_RS05070 (ABFU34_05060) - 1214925..1215464 (+) 540 WP_228442809.1 hypothetical protein -
  ABFU34_RS05075 (ABFU34_05065) - 1215464..1216705 (+) 1242 WP_228442810.1 DGQHR domain-containing protein -
  ABFU34_RS05080 (ABFU34_05070) - 1216733..1217863 (+) 1131 WP_228442811.1 ParB N-terminal domain-containing protein -
  ABFU34_RS05085 (ABFU34_05075) - 1218132..1218461 (-) 330 WP_228442812.1 hypothetical protein -
  ABFU34_RS05090 (ABFU34_05080) - 1218728..1220323 (+) 1596 WP_228442813.1 MobA/MobL family protein -
  ABFU34_RS05095 (ABFU34_05085) - 1220376..1220717 (-) 342 WP_228442814.1 hypothetical protein -
  ABFU34_RS05100 (ABFU34_05090) - 1221539..1221793 (+) 255 WP_228442815.1 hypothetical protein -
  ABFU34_RS05105 (ABFU34_05095) - 1222083..1222313 (-) 231 WP_181920809.1 hypothetical protein -
  ABFU34_RS05110 (ABFU34_05100) - 1222377..1222523 (+) 147 WP_076054137.1 hypothetical protein -
  ABFU34_RS05115 (ABFU34_05105) - 1222707..1223102 (+) 396 WP_042594933.1 hypothetical protein -
  ABFU34_RS05120 (ABFU34_05110) - 1223193..1223585 (+) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  ABFU34_RS05125 (ABFU34_05115) glgX 1224111..1226240 (-) 2130 WP_228442816.1 glycogen debranching protein GlgX -
  ABFU34_RS05130 (ABFU34_05120) rimK 1226733..1227608 (+) 876 WP_116921527.1 30S ribosomal protein S6--L-glutamate ligase -
  ABFU34_RS05135 (ABFU34_05125) - 1228258..1228935 (+) 678 WP_003490678.1 response regulator transcription factor -
  ABFU34_RS05140 (ABFU34_05130) - 1228928..1230258 (+) 1331 Protein_997 sensor histidine kinase -
  ABFU34_RS05145 (ABFU34_05135) - 1230357..1230612 (-) 256 Protein_998 SymE family type I addiction module toxin -
  ABFU34_RS05150 (ABFU34_05140) coaE 1230806..1231429 (-) 624 WP_225042504.1 dephospho-CoA kinase -
  ABFU34_RS05155 (ABFU34_05145) - 1231443..1232306 (-) 864 WP_040940797.1 A24 family peptidase -
  ABFU34_RS05160 (ABFU34_05150) pilC 1232313..1233575 (-) 1263 WP_228442817.1 type II secretion system F family protein Machinery gene
  ABFU34_RS05165 (ABFU34_05155) pilA/pilAI 1233926..1234333 (+) 408 WP_228442818.1 pilin Machinery gene
  ABFU34_RS05170 (ABFU34_05160) - 1234466..1234852 (+) 387 WP_373046337.1 pilin -
  ABFU34_RS05175 (ABFU34_05165) - 1234911..1236731 (+) 1821 WP_323539564.1 hypothetical protein -
  ABFU34_RS05180 (ABFU34_05170) - 1236840..1237598 (+) 759 WP_228442820.1 class I SAM-dependent methyltransferase -
  ABFU34_RS05185 (ABFU34_05175) - 1237696..1238781 (+) 1086 WP_407463960.1 glycosyltransferase family 9 protein -
  ABFU34_RS05190 (ABFU34_05180) - 1238784..1239626 (-) 843 WP_228442822.1 glycosyltransferase -
  ABFU34_RS05195 (ABFU34_05185) - 1239620..1240792 (-) 1173 WP_228442823.1 glycosyltransferase -
  ABFU34_RS05200 (ABFU34_05190) - 1240777..1241640 (-) 864 WP_228442824.1 glycosyltransferase -
  ABFU34_RS05205 (ABFU34_05195) - 1241690..1242541 (-) 852 WP_108133901.1 glycosyltransferase family 2 protein -
  ABFU34_RS05210 (ABFU34_05200) pilB 1242697..1244433 (+) 1737 WP_040940802.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU34_RS05215 (ABFU34_05205) pilR 1245818..1247212 (-) 1395 WP_012437607.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU34_RS05220 (ABFU34_05210) - 1247421..1249043 (-) 1623 WP_407470555.1 sensor histidine kinase -
  ABFU34_RS05225 (ABFU34_05215) sucC 1249277..1250446 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU34_RS05230 (ABFU34_05220) sucD 1250471..1251346 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  ABFU34_RS05235 (ABFU34_05225) - 1251483..1251860 (+) 378 WP_019237352.1 CopG family ribbon-helix-helix protein -
  ABFU34_RS05240 (ABFU34_05230) - 1251864..1252166 (+) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 420 a.a.        Molecular weight: 45810.26 Da        Isoelectric Point: 10.2311

>NTDB_id=1000405 ABFU34_RS05160 WP_228442817.1 1232313..1233575(-) (pilC) [Xanthomonas campestris pv. raphani strain BXC#143]
MSAVRSTIKNKPASISAEQLMSPFVWEGTDKRGVKMKGEQVARNANMLRAELRRQGITPSVVKAKPKPLFGAAGKKITPK
EIAFFSRQMATMMKSGVPIVGSLEIIGNGHKNPRMKQMVGQIRTDIEGGSSLHEAISKHPVQFDELYRNLIKAGEGAGVL
ETVLDTIASYKENLEALKGKIKKALFYPAMVVAVALLVSSILLIWVVPQFEDVFKGFGAELPAFTQLIVNASRFMVSYWW
LMLLVIVGSIVGFIFAYKRSLAMQHGMDRLVLKVPIIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNSVYE
KAVLRMREDVSVGYPVNVSMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYYEQEVNNAVDALSSLIEPLIMVFIGTV
VGGMVIGMYLPIFKLASVVG

Nucleotide


Download         Length: 1263 bp        

>NTDB_id=1000405 ABFU34_RS05160 WP_228442817.1 1232313..1233575(-) (pilC) [Xanthomonas campestris pv. raphani strain BXC#143]
ATGTCGGCAGTCCGTAGCACCATCAAGAACAAACCGGCGAGCATTAGCGCCGAACAACTCATGAGCCCGTTTGTCTGGGA
GGGGACAGACAAGCGCGGCGTGAAGATGAAGGGCGAGCAGGTGGCCCGCAACGCCAACATGCTGCGGGCCGAACTCCGCC
GGCAAGGCATCACGCCCAGCGTCGTCAAGGCCAAGCCAAAGCCATTGTTCGGGGCGGCAGGCAAGAAGATCACGCCGAAG
GAAATTGCGTTCTTCAGCCGTCAGATGGCCACCATGATGAAGTCGGGCGTGCCGATTGTCGGGTCGCTGGAGATCATCGG
CAATGGTCACAAGAACCCGCGCATGAAGCAGATGGTGGGGCAGATCCGTACCGACATCGAAGGCGGATCTTCGCTGCACG
AAGCGATAAGCAAGCATCCAGTGCAGTTTGACGAGCTGTATCGCAACCTGATCAAGGCCGGCGAAGGCGCTGGTGTGCTG
GAAACCGTCCTGGATACTATCGCCTCATACAAAGAGAACCTGGAAGCCCTTAAGGGCAAAATCAAGAAGGCCCTGTTCTA
CCCTGCCATGGTCGTGGCAGTTGCCCTGCTGGTCAGCTCGATCCTGTTGATCTGGGTTGTTCCGCAGTTCGAGGATGTGT
TCAAGGGATTTGGCGCGGAACTGCCGGCATTCACCCAACTGATCGTCAATGCGTCCCGATTCATGGTCTCGTATTGGTGG
CTGATGCTGCTTGTGATCGTCGGTTCGATCGTGGGTTTCATCTTTGCCTATAAGCGCTCGCTTGCGATGCAGCATGGTAT
GGATCGGTTGGTGCTCAAGGTACCGATCATCGGCCAGATCATGCACAACAGCTCGATTGCGCGTTTTGCGCGCACTACTG
CGGTGACCTTCAAGGCAGGCGTGCCGTTGGTCGAAGCACTGGGCATCGTCGCCGGCGCCACTGGTAACTCGGTGTACGAG
AAAGCCGTGTTGCGCATGCGCGAGGATGTCTCGGTGGGCTATCCGGTCAACGTGTCGATGAAACAGGTCAATCTGTTCCC
GCATATGGTGATCCAGATGACGGCAATCGGCGAGGAAGCGGGCGCATTGGACGCCATGCTGTTCAAGGTGGCCGAGTACT
ACGAGCAGGAAGTGAACAATGCGGTGGACGCATTGAGCAGCCTCATCGAACCCCTGATCATGGTGTTCATTGGTACAGTA
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

43.719

94.762

0.414
  pilG Neisseria meningitidis 44/76-A

43.108

95

0.41
  pilC Vibrio cholerae strain A1552

41.814

94.524

0.395
  pilC Vibrio campbellii strain DS40M4

39.798

94.524

0.376

Multiple sequence alignment