Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   CDO11_RS08410 Genome accession   NZ_CP021789
Coordinates   1651934..1653193 (-) Length   419 a.a.
NCBI ID   WP_011408067.1    Uniprot ID   A0A0K0GIM7
Organism   Xanthomonas oryzae pv. oryzae strain PXO61     
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 1643206..1657832 1651934..1653193 within 0


Gene organization within MGE regions


Location: 1643206..1657832
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  CDO11_RS24875 - 1643206..1643535 (+) 330 WP_125168748.1 hypothetical protein -
  CDO11_RS08350 (CDO11_08175) - 1643612..1645045 (+) 1434 Protein_1513 RHS repeat-associated core domain-containing protein -
  CDO11_RS08355 (CDO11_08180) - 1645051..1645419 (+) 369 WP_011408064.1 DUF6869 domain-containing protein -
  CDO11_RS08360 (CDO11_08185) - 1645589..1646557 (-) 969 WP_011258802.1 IS5-like element ISXo1 family transposase -
  CDO11_RS08365 - 1646653..1646820 (+) 168 Protein_1516 IS701 family transposase -
  CDO11_RS08375 (CDO11_08195) - 1646938..1647159 (+) 222 Protein_1517 IS4 family transposase -
  CDO11_RS08380 (CDO11_08200) - 1647249..1648205 (+) 957 WP_041182041.1 IS30-like element IS1112a family transposase -
  CDO11_RS08385 (CDO11_08205) - 1648189..1648491 (+) 303 WP_158645227.1 hypothetical protein -
  CDO11_RS08395 (CDO11_08210) - 1649052..1650371 (-) 1320 WP_109181905.1 IS701-like element ISXo15 family transposase -
  CDO11_RS08400 (CDO11_08215) coaE 1650442..1651050 (-) 609 WP_011258357.1 dephospho-CoA kinase -
  CDO11_RS08405 (CDO11_08220) - 1651064..1651927 (-) 864 WP_011258358.1 A24 family peptidase -
  CDO11_RS08410 (CDO11_08225) pilC 1651934..1653193 (-) 1260 WP_011408067.1 type II secretion system F family protein Machinery gene
  CDO11_RS08415 (CDO11_08230) pilA2 1653548..1653973 (+) 426 WP_011408068.1 pilin Machinery gene
  CDO11_RS08420 (CDO11_08235) - 1654108..1655697 (+) 1590 WP_011408069.1 phosphoethanolamine transferase -
  CDO11_RS08425 (CDO11_08240) - 1655708..1656337 (+) 630 WP_011408070.1 hypothetical protein -
  CDO11_RS26070 (CDO11_08245) - 1656307..1657832 (+) 1526 Protein_1527 hypothetical protein -

Sequence

Protein


Download         Length: 419 a.a.        Molecular weight: 46058.56 Da        Isoelectric Point: 10.2301

>NTDB_id=233562 CDO11_RS08410 WP_011408067.1 1651934..1653193(-) (pilC) [Xanthomonas oryzae pv. oryzae strain PXO61]
MSVARSAIKKQPVDRNTSMLQTFIWEGADKRGVKMKGEQTARNANMLRAELRRQGIVPSMVKQKPKPLFGGAGKKITPKE
IAFFSRQMATMMKSGVPIVSSLEIIGEGHKNPRMKKMVGQIRTDIEGGSSLYESISKHPVQFDELYRNLVRAGEGAGVLE
TVLETVATYKENIEALKGKIKKALFYPAMVVAVAIIVSAILLIFVVPQFEEVFKSFGAELPAFTQLLVNASRFMVSYWWL
MLIVTVGSVVGFIFAYKRSPRMQHGLDRLILKVPVIGQIMHNSAIARFARTTAVTFKAGVPLVEALGIVAGATGNKLYEE
AVFRMRDDVSVGYPVNMAMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYFEEEVNNAVDALSSLLEPLIMVFIGTIV
GGMVIGMYLPIFKLGAVVG

Nucleotide


Download         Length: 1260 bp        

>NTDB_id=233562 CDO11_RS08410 WP_011408067.1 1651934..1653193(-) (pilC) [Xanthomonas oryzae pv. oryzae strain PXO61]
ATGTCAGTCGCGCGTAGCGCCATCAAGAAGCAACCGGTCGACCGGAACACCAGCATGCTGCAGACCTTCATTTGGGAAGG
GGCTGACAAGCGTGGCGTGAAGATGAAGGGAGAGCAGACAGCCCGCAACGCCAATATGTTGCGAGCAGAGCTGCGCCGTC
AGGGCATCGTGCCCAGCATGGTGAAGCAAAAGCCGAAGCCTCTGTTCGGAGGGGCGGGGAAGAAAATTACCCCTAAAGAA
ATTGCGTTCTTTAGCCGCCAGATGGCGACGATGATGAAGTCGGGCGTGCCCATCGTCAGTTCGTTGGAGATCATTGGCGA
GGGACACAAGAACCCACGCATGAAAAAAATGGTCGGCCAGATCAGGACAGATATCGAGGGTGGATCCTCGCTCTACGAGT
CCATCAGCAAACATCCCGTTCAGTTTGACGAGCTCTACCGCAACCTCGTCCGCGCGGGCGAAGGCGCTGGCGTACTGGAG
ACAGTCCTCGAAACGGTCGCTACCTACAAAGAAAACATTGAAGCTCTGAAGGGCAAGATCAAAAAGGCACTGTTCTACCC
TGCCATGGTGGTTGCAGTGGCAATCATCGTGAGTGCGATTTTGCTCATCTTCGTGGTGCCTCAGTTCGAGGAAGTATTCA
AGAGCTTCGGTGCCGAACTACCGGCATTCACTCAGCTCCTCGTCAACGCATCGCGCTTCATGGTCAGCTATTGGTGGTTG
ATGCTGATAGTGACAGTTGGATCTGTCGTTGGCTTCATCTTTGCCTACAAACGTTCTCCACGGATGCAGCATGGACTTGA
TCGATTGATCCTCAAGGTGCCCGTAATCGGGCAGATCATGCACAACAGTGCGATTGCACGCTTTGCACGGACCACTGCAG
TGACATTCAAGGCAGGCGTTCCTCTAGTTGAGGCACTTGGGATCGTAGCTGGCGCTACTGGCAATAAGCTTTATGAAGAG
GCTGTTTTCAGGATGCGGGACGATGTGTCTGTGGGTTACCCGGTCAACATGGCGATGAAACAGGTGAACCTATTTCCACA
CATGGTTATTCAAATGACTGCGATTGGCGAAGAAGCCGGCGCACTTGATGCAATGCTCTTCAAAGTGGCTGAATACTTTG
AGGAGGAGGTCAATAATGCCGTGGATGCACTCAGCAGCCTGCTCGAGCCACTGATCATGGTCTTCATCGGCACGATCGTC
GGCGGCATGGTCATCGGCATGTATCTTCCGATCTTCAAACTCGGCGCAGTGGTGGGTTAA

Domains

Predicted by InterproScan.

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

(288-410)

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

(84-207)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A0K0GIM7

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

53.202

96.897

0.516
  pilC Pseudomonas stutzeri DSM 10701

53.283

94.511

0.504
  pilC Acinetobacter baylyi ADP1

50.37

96.659

0.487
  pilC Acinetobacter baumannii D1279779

50.37

96.659

0.487
  pilG Neisseria gonorrhoeae MS11

43.921

96.181

0.422
  pilG Neisseria meningitidis 44/76-A

43.424

96.181

0.418
  pilC Vibrio cholerae strain A1552

40.75

95.465

0.389
  pilC Vibrio campbellii strain DS40M4

39

95.465

0.372

Multiple sequence alignment