Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   IYN96_RS05500 Genome accession   NZ_CP064871
Coordinates   1188812..1190071 (-) Length   419 a.a.
NCBI ID   WP_047340536.1    Uniprot ID   -
Organism   Xanthomonas oryzae pv. oryzicola strain YN01     
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)
ICE 1153563..1188714 1188812..1190071 flank 98


Gene organization within MGE regions


Location: 1153563..1190071
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  IYN96_RS05330 (IYN96_05320) - 1154618..1155013 (-) 396 WP_229689316.1 hypothetical protein -
  IYN96_RS05335 (IYN96_05325) - 1155228..1156628 (-) 1401 WP_047340378.1 site-specific integrase -
  IYN96_RS05340 (IYN96_05330) - 1157259..1157921 (-) 663 WP_047340377.1 hypothetical protein -
  IYN96_RS05345 (IYN96_05335) - 1157926..1159593 (-) 1668 WP_047340376.1 adenylosuccinate synthetase -
  IYN96_RS05350 (IYN96_05340) - 1159586..1160131 (-) 546 WP_047340588.1 AAA family ATPase -
  IYN96_RS05355 (IYN96_05345) radC 1160560..1161039 (+) 480 WP_047340375.1 DNA repair protein RadC -
  IYN96_RS05360 (IYN96_05350) - 1161111..1161302 (+) 192 WP_031422191.1 hypothetical protein -
  IYN96_RS05365 (IYN96_05355) - 1161816..1162091 (+) 276 WP_136614812.1 hypothetical protein -
  IYN96_RS21485 - 1163089..1163505 (+) 417 Protein_1018 XVIPCD domain-containing protein -
  IYN96_RS05375 (IYN96_05365) - 1163591..1165300 (+) 1710 WP_240113097.1 KAP family NTPase -
  IYN96_RS05380 - 1165362..1166117 (+) 756 WP_031422202.1 hypothetical protein -
  IYN96_RS05385 (IYN96_05375) qatC 1166114..1167421 (+) 1308 WP_033485369.1 Qat anti-phage system QueC-like protein QatC -
  IYN96_RS05390 (IYN96_05380) qatD 1167421..1168161 (+) 741 WP_033485367.1 Qat anti-phage system TatD family nuclease QatD -
  IYN96_RS05395 (IYN96_05385) - 1168225..1168479 (-) 255 WP_033485366.1 hypothetical protein -
  IYN96_RS05400 (IYN96_05390) - 1168745..1170340 (+) 1596 WP_047340394.1 MobA/MobL family protein -
  IYN96_RS05405 (IYN96_05395) - 1170393..1170734 (-) 342 WP_047340393.1 hypothetical protein -
  IYN96_RS05410 (IYN96_05400) - 1171439..1172405 (+) 967 WP_044750250.1 IS5-like element ISXo1 family transposase -
  IYN96_RS05415 (IYN96_05405) - 1172603..1173956 (-) 1354 Protein_1027 IS5 family transposase -
  IYN96_RS05420 (IYN96_05410) - 1174275..1174886 (+) 612 WP_044749921.1 thermonuclease family protein -
  IYN96_RS05425 (IYN96_05415) - 1175108..1175389 (+) 282 WP_229689374.1 hypothetical protein -
  IYN96_RS05430 (IYN96_05420) - 1175480..1175872 (+) 393 WP_011409118.1 H-NS family nucleoid-associated regulatory protein -
  IYN96_RS05435 (IYN96_05425) - 1176432..1176433 (-) 2 WP_144406551.1 IS5 family transposase -
  IYN96_RS05440 (IYN96_05430) - 1176843..1177799 (-) 957 WP_048483755.1 IS30-like element IS1112a family transposase -
  IYN96_RS05445 (IYN96_05435) - 1178215..1179066 (-) 852 WP_044749924.1 IS1595 family transposase -
  IYN96_RS05450 (IYN96_05440) glgX 1179163..1181295 (-) 2133 WP_014504336.1 glycogen debranching protein GlgX -
  IYN96_RS05455 (IYN96_05445) rimK 1181770..1182687 (+) 918 WP_014504335.1 30S ribosomal protein S6--L-glutamate ligase -
  IYN96_RS05460 (IYN96_05450) - 1182900..1183289 (+) 390 WP_014504334.1 hypothetical protein -
  IYN96_RS05465 (IYN96_05455) - 1183367..1184044 (+) 678 WP_003490678.1 response regulator transcription factor -
  IYN96_RS05470 (IYN96_05460) - 1184037..1185371 (+) 1335 WP_047340105.1 HAMP domain-containing sensor histidine kinase -
  IYN96_RS21490 - 1185470..1185765 (-) 296 Protein_1039 SymE family type I addiction module toxin -
  IYN96_RS05480 (IYN96_05470) - 1185899..1186942 (-) 1044 Protein_1040 IS3 family transposase -
  IYN96_RS05485 (IYN96_05475) - 1187072..1187236 (+) 165 Protein_1041 IS701 family transposase -
  IYN96_RS05490 (IYN96_05480) coaE 1187320..1187928 (-) 609 WP_014504326.1 dephospho-CoA kinase -
  IYN96_RS05495 (IYN96_05485) - 1187942..1188805 (-) 864 WP_047340103.1 A24 family peptidase -
  IYN96_RS05500 (IYN96_05490) pilC 1188812..1190071 (-) 1260 WP_047340536.1 type II secretion system F family protein Machinery gene

Sequence

Protein


Download         Length: 419 a.a.        Molecular weight: 46094.63 Da        Isoelectric Point: 10.2301

>NTDB_id=505485 IYN96_RS05500 WP_047340536.1 1188812..1190071(-) (pilC) [Xanthomonas oryzae pv. oryzicola strain YN01]
MSVARSAIKKQPVDRNTSMLQTFIWEGADKRGVKMKGEQTARNANMLRAELRRQGIVPSMVKQKPKPLFGAAGKKITPKE
IAFFSRQMATMMKSGVPIVSSLEIIGEGHKNPRMKKMVGQIRTDIEGGSSLYESISKHPVQFDELYRNLVRAGEGAGVLE
TVLETVATYKENIEALKGKIKKAMFYPAMVVAVAIIVSAILLIFVVPQFEEVFKSFGAELPAFTQLLVNASRFMVSYWWL
MLMVTVGSVVGFIFAYKRSPRMQHGLDRLILKVPVIGQIMHNSAIARFARTTAVTFKAGVPLVEALGIVAGATGNKLYEE
AVFRMRDDVSVGYPVNMAMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYFEDEVNNAVDALSSLLEPLIMVFIGTIV
GGMVIGMYLPIFKLGAVVG

Nucleotide


Download         Length: 1260 bp        

>NTDB_id=505485 IYN96_RS05500 WP_047340536.1 1188812..1190071(-) (pilC) [Xanthomonas oryzae pv. oryzicola strain YN01]
ATGTCAGTCGCGCGTAGCGCCATCAAGAAGCAACCGGTCGACCGAAACACCAGCATGCTGCAGACCTTCATTTGGGAAGG
GGCTGACAAGCGTGGCGTGAAGATGAAGGGAGAGCAGACAGCCCGCAACGCCAATATGTTGCGAGCAGAGCTGCGCCGTC
AGGGTATCGTGCCCAGCATGGTGAAGCAAAAGCCGAAGCCTCTGTTCGGAGCGGCGGGGAAGAAAATTACCCCTAAAGAA
ATTGCGTTCTTTAGCCGCCAGATGGCGACGATGATGAAGTCGGGCGTGCCCATCGTCAGTTCGTTGGAGATCATTGGCGA
GGGACACAAGAACCCACGCATGAAAAAAATGGTCGGCCAGATCAGGACAGATATCGAGGGTGGATCCTCGCTCTACGAGT
CCATCAGCAAACATCCCGTTCAGTTTGACGAGCTCTATCGCAACCTCGTCCGCGCGGGCGAAGGCGCTGGCGTACTGGAG
ACAGTCCTCGAAACGGTCGCTACCTACAAAGAAAACATTGAAGCCCTGAAGGGCAAGATCAAAAAGGCAATGTTCTACCC
TGCCATGGTGGTTGCGGTGGCAATCATCGTGAGTGCGATTTTGCTCATCTTCGTGGTGCCTCAGTTCGAGGAAGTATTCA
AGAGCTTCGGTGCCGAACTACCGGCATTCACTCAGCTCCTCGTCAACGCATCGCGCTTCATGGTCAGCTATTGGTGGTTG
ATGCTGATGGTGACAGTTGGATCTGTCGTTGGCTTCATCTTTGCCTACAAACGTTCTCCACGGATGCAGCATGGACTTGA
TCGATTGATCCTCAAGGTGCCCGTAATCGGGCAGATCATGCACAACAGTGCGATTGCACGCTTTGCACGGACCACTGCAG
TGACATTCAAGGCAGGCGTTCCTCTAGTTGAGGCACTTGGGATCGTAGCTGGCGCTACTGGCAATAAGCTTTATGAAGAG
GCTGTTTTCAGGATGCGGGACGATGTGTCTGTGGGTTACCCGGTCAACATGGCGATGAAACAGGTAAACCTATTTCCACA
CATGGTTATTCAAATGACTGCGATTGGCGAAGAAGCCGGCGCACTTGATGCAATGCTCTTCAAAGTGGCTGAATACTTTG
AGGATGAGGTCAATAATGCCGTGGATGCACTCAGCAGCCTGCTCGAGCCACTGATCATGGTCTTCATCGGCACGATCGTC
GGCGGCATGGTCATCGGCATGTATCTTCCGATCTTCAAACTCGGCGCAGTGGTGGGTTAA

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 Legionella pneumophila strain ERS1305867

52.709

96.897

0.511
  pilC Pseudomonas stutzeri DSM 10701

53.788

94.511

0.508
  pilC Acinetobacter baylyi ADP1

50.617

96.659

0.489
  pilC Acinetobacter baumannii D1279779

50.37

96.659

0.487
  pilG Neisseria gonorrhoeae MS11

43.358

95.227

0.413
  pilG Neisseria meningitidis 44/76-A

42.75

95.465

0.408
  pilC Vibrio cholerae strain A1552

40.25

95.465

0.384
  pilC Vibrio campbellii strain DS40M4

38.75

95.465

0.37