Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   ABFU05_RS05080 Genome accession   NZ_CP156015
Coordinates   1215950..1217212 (-) Length   420 a.a.
NCBI ID   WP_104570928.1    Uniprot ID   -
Organism   Xanthomonas campestris pv. raphani strain 0576     
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 1205219..1235886 1215950..1217212 within 0


Gene organization within MGE regions


Location: 1205219..1235886
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  ABFU05_RS05025 (ABFU05_05020) - 1205715..1205945 (-) 231 WP_181920809.1 hypothetical protein -
  ABFU05_RS05030 (ABFU05_05025) - 1206009..1206155 (+) 147 WP_076054137.1 hypothetical protein -
  ABFU05_RS05035 (ABFU05_05030) - 1206339..1206734 (+) 396 WP_042594933.1 hypothetical protein -
  ABFU05_RS05040 (ABFU05_05035) - 1206825..1207217 (+) 393 WP_011038224.1 H-NS family nucleoid-associated regulatory protein -
  ABFU05_RS05045 (ABFU05_05040) glgX 1207743..1209872 (-) 2130 WP_274299339.1 glycogen debranching protein GlgX -
  ABFU05_RS05050 (ABFU05_05045) rimK 1210366..1211241 (+) 876 WP_076054142.1 30S ribosomal protein S6--L-glutamate ligase -
  ABFU05_RS05055 (ABFU05_05050) - 1211891..1212568 (+) 678 WP_003490678.1 response regulator transcription factor -
  ABFU05_RS05060 (ABFU05_05055) - 1212561..1213895 (+) 1335 WP_019237347.1 HAMP domain-containing sensor histidine kinase -
  ABFU05_RS05065 (ABFU05_05060) - 1213994..1214249 (-) 256 Protein_984 SymE family type I addiction module toxin -
  ABFU05_RS05070 (ABFU05_05065) coaE 1214443..1215066 (-) 624 WP_225042504.1 dephospho-CoA kinase -
  ABFU05_RS05075 (ABFU05_05070) - 1215080..1215943 (-) 864 WP_011038216.1 A24 family peptidase -
  ABFU05_RS05080 (ABFU05_05075) pilC 1215950..1217212 (-) 1263 WP_104570928.1 type II secretion system F family protein Machinery gene
  ABFU05_RS05085 (ABFU05_05080) pilA/pilAI 1217563..1217961 (+) 399 WP_104570927.1 pilin Machinery gene
  ABFU05_RS05090 (ABFU05_05085) - 1218062..1218484 (+) 423 WP_104570926.1 pilin -
  ABFU05_RS05095 (ABFU05_05090) - 1218543..1220363 (+) 1821 WP_147308815.1 hypothetical protein -
  ABFU05_RS05100 (ABFU05_05095) - 1220487..1221245 (+) 759 WP_274299340.1 bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG -
  ABFU05_RS05105 (ABFU05_05100) - 1221742..1222428 (+) 687 WP_258872788.1 glycosyltransferase family 9 protein -
  ABFU05_RS05110 (ABFU05_05105) - 1222431..1223273 (-) 843 WP_147308817.1 glycosyltransferase -
  ABFU05_RS05115 (ABFU05_05110) - 1223267..1224439 (-) 1173 WP_181920810.1 glycosyltransferase -
  ABFU05_RS05120 (ABFU05_05115) - 1224424..1225287 (-) 864 WP_116921534.1 glycosyltransferase -
  ABFU05_RS05125 (ABFU05_05120) - 1225337..1226188 (-) 852 WP_108133901.1 glycosyltransferase family 2 protein -
  ABFU05_RS05130 (ABFU05_05125) pilB 1226344..1228077 (+) 1734 WP_274299341.1 type IV-A pilus assembly ATPase PilB Machinery gene
  ABFU05_RS05135 (ABFU05_05130) - 1228260..1229051 (-) 792 WP_407467098.1 zeta toxin family protein -
  ABFU05_RS05140 (ABFU05_05135) - 1228996..1229352 (-) 357 WP_139328384.1 hypothetical protein -
  ABFU05_RS05145 (ABFU05_05140) pilR 1229550..1230944 (-) 1395 WP_043921909.1 sigma-54 dependent transcriptional regulator Regulator
  ABFU05_RS05150 (ABFU05_05145) - 1231153..1232763 (-) 1611 WP_070690016.1 PAS domain-containing sensor histidine kinase -
  ABFU05_RS05155 (ABFU05_05150) sucC 1232997..1234166 (+) 1170 WP_011038209.1 ADP-forming succinate--CoA ligase subunit beta -
  ABFU05_RS05160 (ABFU05_05155) sucD 1234191..1235066 (+) 876 WP_011038208.1 succinate--CoA ligase subunit alpha -
  ABFU05_RS05165 (ABFU05_05160) - 1235170..1235580 (+) 411 WP_323475224.1 CopG family ribbon-helix-helix protein -
  ABFU05_RS05170 (ABFU05_05165) - 1235584..1235886 (+) 303 WP_011038207.1 type II toxin-antitoxin system RelE/ParE family toxin -

Sequence

Protein


Download         Length: 420 a.a.        Molecular weight: 45799.15 Da        Isoelectric Point: 10.2311

>NTDB_id=1001216 ABFU05_RS05080 WP_104570928.1 1215950..1217212(-) (pilC) [Xanthomonas campestris pv. raphani strain 0576]
MSAVRSTTKNKPASISAEQQMSPFVWEGTDKRGVKMKGEQVARNANMLRAELRRQGITPSVVKAKPKPLFGAAGKKITPK
EIAFFSRQMATMMKSGVPIVGSLEIIGNGHKNPRMKQMVGQIRTDIEGGSSLHEAVSKHPVQFDELYRNLIKAGEGAGVL
ETVLDTIASYKENLEALKGKIKKALFYPAMVVAVALLVSSILLIWVVPQFEDVFKGFGAELPAFTQLIVNASRFMVSYWW
LMLLVIVGSLVGFIFAYKRSLAMQHGMDRLVLKVPIIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNSVYE
KAVLRMREDVSVGYPVNVSMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYYEQEVNNAVDALSSLIEPLIMVFIGTV
VGGMVIGMYLPIFKLASVVG

Nucleotide


Download         Length: 1263 bp        

>NTDB_id=1001216 ABFU05_RS05080 WP_104570928.1 1215950..1217212(-) (pilC) [Xanthomonas campestris pv. raphani strain 0576]
ATGTCGGCAGTCCGCAGCACCACCAAAAACAAACCGGCGAGCATCAGCGCCGAACAGCAGATGAGTCCGTTCGTCTGGGA
GGGAACAGACAAGCGCGGTGTGAAGATGAAAGGTGAACAGGTCGCCCGCAACGCCAATATGTTGCGTGCGGAACTCCGCC
GGCAGGGCATTACGCCCAGCGTTGTTAAGGCAAAGCCTAAGCCACTGTTCGGGGCGGCAGGCAAGAAGATCACGCCGAAG
GAAATTGCGTTCTTCAGCCGTCAGATGGCCACTATGATGAAGTCGGGCGTCCCGATTGTCGGGTCGCTGGAGATCATCGG
CAATGGTCACAAAAACCCGCGCATGAAGCAGATGGTCGGGCAGATCCGTACCGACATCGAGGGCGGCTCTTCGCTGCACG
AAGCGGTAAGCAAGCATCCGGTGCAGTTCGACGAGCTGTACCGCAACCTGATCAAGGCGGGCGAAGGCGCTGGTGTGCTG
GAAACCGTCCTGGATACTATCGCCTCATACAAAGAGAACCTGGAAGCCCTTAAGGGCAAAATCAAGAAGGCCCTGTTCTA
CCCTGCCATGGTCGTGGCAGTTGCCCTGCTGGTCAGCTCGATCCTGTTGATCTGGGTTGTTCCGCAGTTCGAGGATGTGT
TCAAGGGATTTGGCGCGGAACTGCCGGCATTCACCCAACTGATCGTCAATGCGTCCAGATTCATGGTCTCGTATTGGTGG
CTGATGCTGCTTGTGATCGTCGGCTCGCTTGTGGGCTTCATCTTTGCCTACAAGCGATCACTTGCAATGCAGCATGGCAT
GGATCGGTTGGTACTCAAGGTACCCATCATCGGCCAGATCATGCACAACAGCTCGATTGCGCGTTTTGCGCGCACTACCG
CGGTGACCTTCAAGGCAGGCGTGCCGCTGGTCGAAGCACTGGGCATCGTCGCTGGCGCCACCGGCAACTCGGTGTACGAG
AAAGCAGTATTGCGCATGCGCGAGGATGTGTCGGTGGGCTATCCGGTCAACGTGTCGATGAAACAGGTCAACCTGTTTCC
GCATATGGTGATCCAGATGACGGCGATCGGCGAGGAGGCGGGCGCATTGGACGCCATGCTGTTCAAAGTTGCCGAATACT
ACGAGCAGGAAGTGAACAATGCGGTGGACGCACTGAGCAGCCTCATCGAACCCCTGATCATGGTGTTCATTGGTACAGTA
GTCGGCGGCATGGTCATCGGCATGTACCTGCCCATCTTCAAGCTCGCTTCGGTAGTTGGATAA

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

52.488

95.714

0.502
  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

50.369

96.905

0.488
  pilG Neisseria gonorrhoeae MS11

42.857

98.333

0.421
  pilG Neisseria meningitidis 44/76-A

42.271

98.571

0.417
  pilC Vibrio cholerae strain A1552

41.562

94.524

0.393
  pilC Vibrio campbellii strain DS40M4

39.9

95.476

0.381

Multiple sequence alignment