Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   APY30_RS17040 Genome accession   NZ_CP013006
Coordinates   3761657..3762916 (+) Length   419 a.a.
NCBI ID   WP_033836749.1    Uniprot ID   A0A7Z7NHG2
Organism   Xanthomonas citri pv. malvacearum strain XcmN1003     
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 3763670..3787043 3761657..3762916 flank 754


Gene organization within MGE regions


Location: 3761657..3787043
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  APY30_RS17040 (APY30_16275) pilC 3761657..3762916 (+) 1260 WP_033836749.1 type II secretion system F family protein Machinery gene
  APY30_RS17045 (APY30_16280) - 3762923..3763786 (+) 864 WP_003491180.1 A24 family peptidase -
  APY30_RS17050 (APY30_16285) coaE 3763800..3764408 (+) 609 WP_005915836.1 dephospho-CoA kinase -
  APY30_RS17055 (APY30_16290) - 3765333..3769394 (+) 4062 WP_190276429.1 RHS repeat-associated core domain-containing protein -
  APY30_RS24420 - 3769391..3769777 (+) 387 WP_125825481.1 hypothetical protein -
  APY30_RS17065 (APY30_16300) - 3770418..3771505 (+) 1088 WP_089504397.1 IS3-like element ISXac2 family transposase -
  APY30_RS17075 (APY30_16315) - 3772742..3773098 (+) 357 Protein_3185 type I toxin-antitoxin system SymE family toxin -
  APY30_RS17080 (APY30_16320) - 3773201..3774535 (-) 1335 WP_005917998.1 HAMP domain-containing sensor histidine kinase -
  APY30_RS17085 (APY30_16325) - 3774528..3775205 (-) 678 WP_003490678.1 response regulator transcription factor -
  APY30_RS17090 (APY30_16330) - 3775231..3775707 (-) 477 WP_033479676.1 hypothetical protein -
  APY30_RS17095 (APY30_16335) rimK 3775885..3776802 (-) 918 WP_168950233.1 30S ribosomal protein S6--L-glutamate ligase -
  APY30_RS17100 (APY30_16340) glgX 3777266..3779398 (+) 2133 WP_005922313.1 glycogen debranching protein GlgX -
  APY30_RS17110 (APY30_16345) - 3780031..3780423 (-) 393 WP_003490669.1 H-NS family nucleoid-associated regulatory protein -
  APY30_RS17115 (APY30_16350) - 3780514..3780906 (-) 393 WP_005918499.1 hypothetical protein -
  APY30_RS17120 (APY30_16355) - 3781017..3781676 (-) 660 WP_003490665.1 thermonuclease family protein -
  APY30_RS24435 - 3781895..3782080 (+) 186 WP_150130653.1 hypothetical protein -
  APY30_RS17125 - 3782148..3782396 (+) 249 WP_005918502.1 hypothetical protein -
  APY30_RS17130 (APY30_16360) - 3782900..3783274 (+) 375 WP_033836750.1 hypothetical protein -
  APY30_RS17135 (APY30_16365) - 3783318..3784907 (-) 1590 WP_033836751.1 MobA/MobL family protein -
  APY30_RS17140 - 3785166..3785492 (+) 327 WP_033836752.1 hypothetical protein -
  APY30_RS17145 - 3785756..3786025 (+) 270 WP_223301056.1 HNH endonuclease -
  APY30_RS17150 (APY30_16375) - 3786019..3786579 (+) 561 WP_033836753.1 hypothetical protein -

Sequence

Protein


Download         Length: 419 a.a.        Molecular weight: 45878.36 Da        Isoelectric Point: 10.3363

>NTDB_id=159126 APY30_RS17040 WP_033836749.1 3761657..3762916(+) (pilC) [Xanthomonas citri pv. malvacearum strain XcmN1003]
MSVARNVIKKQPADRSNSQMQPFVWEGTDKRGIKMKGEQAARNVNMLRAELRRQGITPTVVKPKPKPLFGAAGKKVGPKD
IAFFSRQMATMMKSGVPIVGSLEIIGEGHKNPRMRKMVGQIRTDIEGGSSLHEAISKHPVQFDELYRNLVRAGEGAGVLE
TVLDTVANYKENIEALKGKIKKALFYPAMVVAVALIVSAILLIFVVPQFEEVFKGFGAELPAFTQMIVAASRFMISYWWL
MLLVIGGAITGFIFAYKRSPRMQHGMDRLVLKVPVIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNKVYEE
AVLRMRDDVSVGYPVNMAMKQVNLFPHMVIQMTAIGEEAGALDAMLFKVAEYFEQEVNNAVDALSSLLEPMIMVFIGTIV
GGMVIGMYLPIFKLGAVVG

Nucleotide


Download         Length: 1260 bp        

>NTDB_id=159126 APY30_RS17040 WP_033836749.1 3761657..3762916(+) (pilC) [Xanthomonas citri pv. malvacearum strain XcmN1003]
ATGTCAGTCGCGCGTAACGTAATCAAAAAACAGCCAGCCGACCGAAGCAACAGCCAGATGCAGCCTTTTGTATGGGAGGG
GACGGATAAGCGTGGCATCAAGATGAAAGGGGAGCAGGCGGCGCGCAATGTGAACATGTTGCGTGCAGAGCTTCGTCGCC
AGGGCATTACGCCCACTGTCGTCAAGCCCAAGCCCAAACCACTTTTTGGCGCTGCCGGCAAAAAAGTGGGCCCTAAGGAC
ATTGCGTTTTTCAGTCGTCAGATGGCAACTATGATGAAGTCCGGCGTTCCCATCGTAGGATCGCTTGAGATCATTGGCGA
GGGGCACAAAAACCCACGAATGAGGAAAATGGTCGGCCAGATAAGGACCGACATTGAAGGCGGCTCTTCACTGCATGAAG
CGATCAGCAAGCATCCGGTACAGTTTGACGAGCTCTACCGCAACCTTGTCCGCGCGGGAGAGGGCGCAGGCGTGCTGGAG
ACAGTCTTAGACACAGTCGCCAATTACAAAGAAAACATTGAGGCCTTGAAAGGCAAGATCAAGAAGGCGCTCTTCTACCC
CGCAATGGTCGTTGCAGTCGCCCTCATTGTTAGCGCCATCTTGCTCATTTTTGTTGTTCCACAGTTCGAAGAAGTCTTCA
AAGGGTTTGGAGCCGAACTTCCCGCGTTCACACAGATGATCGTTGCGGCATCTCGCTTCATGATCAGCTACTGGTGGCTA
ATGCTGCTCGTCATCGGTGGCGCGATTACCGGCTTCATCTTCGCTTACAAGCGCTCACCTCGCATGCAACATGGCATGGA
TCGCCTGGTCTTGAAGGTGCCTGTCATCGGCCAAATTATGCATAACAGTTCCATTGCAAGGTTTGCGCGCACGACCGCCG
TGACCTTCAAGGCTGGCGTTCCGCTCGTGGAAGCACTCGGCATTGTTGCGGGGGCGACTGGTAACAAAGTTTATGAAGAA
GCAGTGCTGCGCATGCGTGACGACGTATCGGTGGGCTATCCAGTCAACATGGCCATGAAGCAGGTCAACCTGTTCCCACA
CATGGTTATTCAAATGACTGCGATTGGCGAGGAAGCAGGCGCACTGGATGCCATGCTGTTTAAGGTTGCTGAGTATTTCG
AGCAGGAGGTCAACAATGCCGTGGATGCGTTGAGCAGCCTGCTTGAACCAATGATCATGGTGTTCATCGGCACCATCGTC
GGCGGCATGGTCATCGGCATGTATCTTCCGATCTTCAAACTCGGCGCAGTGGTTGGATAA

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 A0A7Z7NHG2

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 Pseudomonas stutzeri DSM 10701

54.293

94.511

0.513
  pilC Acinetobacter baylyi ADP1

52.97

96.42

0.511
  pilC Legionella pneumophila strain ERS1305867

51.605

96.659

0.499
  pilC Acinetobacter baumannii D1279779

51.238

96.42

0.494
  pilG Neisseria gonorrhoeae MS11

44.638

95.704

0.427
  pilG Neisseria meningitidis 44/76-A

44.14

95.704

0.422
  pilC Vibrio cholerae strain A1552

41.5

95.465

0.396
  pilC Vibrio campbellii strain DS40M4

39.702

96.181

0.382
  pilC Thermus thermophilus HB27

37.905

95.704

0.363

Multiple sequence alignment