Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   AMD13_RS16905 Genome accession   NZ_CP008995
Coordinates   3820407..3821663 (+) Length   418 a.a.
NCBI ID   WP_040107659.1    Uniprot ID   A0AAI7ZHE3
Organism   Xanthomonas citri pv. citri strain NT17     
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 3822349..3871395 3820407..3821663 flank 686


Gene organization within MGE regions


Location: 3820407..3871395
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  AMD13_RS16905 (J169_03429) pilC 3820407..3821663 (+) 1257 WP_040107659.1 type II secretion system F family protein Machinery gene
  AMD13_RS16910 (J169_03430) - 3821670..3822533 (+) 864 WP_003491180.1 A24 family peptidase -
  AMD13_RS16915 (J169_03431) coaE 3822547..3823155 (+) 609 WP_011052129.1 dephospho-CoA kinase -
  AMD13_RS16920 (J169_03432) - 3823379..3827902 (+) 4524 WP_040107660.1 RHS repeat-associated core domain-containing protein -
  AMD13_RS16925 (J169_03433) - 3828537..3828902 (+) 366 WP_075150055.1 SymE family type I addiction module toxin -
  AMD13_RS16935 (J169_03435) - 3828916..3830060 (+) 1145 WP_087943921.1 IS3-like element ISXac3 family transposase -
  AMD13_RS24010 - 3830086..3830172 (+) 87 Protein_3244 SymE family type I addiction module toxin -
  AMD13_RS16940 (J169_03436) - 3830275..3831609 (-) 1335 WP_003490680.1 HAMP domain-containing sensor histidine kinase -
  AMD13_RS16945 (J169_03437) - 3831602..3832279 (-) 678 WP_003490678.1 response regulator transcription factor -
  AMD13_RS16950 (J169_03438) - 3832305..3832781 (-) 477 WP_011052133.1 hypothetical protein -
  AMD13_RS16955 (J169_03439) rimK 3832959..3833875 (-) 917 Protein_3248 30S ribosomal protein S6--L-glutamate ligase -
  AMD13_RS16960 (J169_03440) glgX 3834339..3836471 (+) 2133 WP_011052136.1 glycogen debranching protein GlgX -
  AMD13_RS16965 (J169_03441) - 3837101..3837493 (-) 393 WP_003490669.1 H-NS family nucleoid-associated regulatory protein -
  AMD13_RS16970 (J169_03442) - 3837584..3837976 (-) 393 WP_003490667.1 hypothetical protein -
  AMD13_RS16975 (J169_03443) - 3838087..3838746 (-) 660 WP_015463531.1 thermonuclease family protein -
  AMD13_RS16980 (J169_03444) - 3839646..3840008 (+) 363 WP_015463532.1 hypothetical protein -
  AMD13_RS16985 (J169_03445) mobQ 3840055..3841647 (-) 1593 WP_011052141.1 MobQ family relaxase -
  AMD13_RS24020 (J169_03446) - 3841904..3842230 (+) 327 WP_015463533.1 conjugal transfer protein TraD -
  AMD13_RS16990 (J169_03447) - 3842800..3843033 (-) 234 WP_015463534.1 hypothetical protein -
  AMD13_RS16995 (J169_03448) - 3843586..3844290 (-) 705 WP_011052145.1 hypothetical protein -
  AMD13_RS24995 (J169_03449) - 3844999..3846873 (+) 1875 WP_146198386.1 hypothetical protein -
  AMD13_RS17000 (J169_03450) - 3846782..3849367 (-) 2586 WP_011052147.1 XVIPCD domain-containing protein -
  AMD13_RS17005 (J169_03451) - 3849403..3850059 (-) 657 WP_040107661.1 DUF1629 domain-containing protein -
  AMD13_RS17010 (J169_03452) - 3850189..3850605 (+) 417 WP_015463535.1 hypothetical protein -
  AMD13_RS17015 (J169_03453) radC 3850707..3851186 (-) 480 WP_015463536.1 DNA repair protein RadC -
  AMD13_RS17020 (J169_RS17075) - 3851582..3851806 (-) 225 WP_015472627.1 hypothetical protein -
  AMD13_RS17025 (J169_03455) - 3851918..3852796 (-) 879 WP_015472628.1 hypothetical protein -
  AMD13_RS17030 (J169_03456) - 3853021..3853479 (-) 459 WP_011052152.1 chemotaxis transducer -
  AMD13_RS17035 (J169_03457) - 3853575..3854498 (+) 924 WP_011052153.1 hypothetical protein -
  AMD13_RS17040 (J169_03458) - 3854671..3855936 (-) 1266 WP_011052154.1 PAS domain-containing sensor histidine kinase -
  AMD13_RS17045 (J169_03459) - 3856021..3856389 (+) 369 WP_011052155.1 response regulator -
  AMD13_RS17050 (J169_RS17105) - 3856739..3857023 (-) 285 WP_040107790.1 hypothetical protein -
  AMD13_RS17055 (J169_03460) - 3857884..3858150 (+) 267 WP_234705867.1 hypothetical protein -
  AMD13_RS17060 (J169_RS17115) - 3858688..3859131 (-) 444 WP_011052159.1 BLUF domain-containing protein -
  AMD13_RS24045 (J169_03461) - 3859838..3861433 (-) 1596 WP_011052160.1 N-acetylmuramoyl-L-alanine amidase -
  AMD13_RS17070 (J169_03462) - 3862079..3862546 (-) 468 WP_011052161.1 hypothetical protein -
  AMD13_RS17075 (J169_03463) - 3862543..3863001 (-) 459 WP_011052162.1 hypothetical protein -
  AMD13_RS17080 (J169_03464) - 3863361..3864296 (+) 936 Protein_3275 integrase -
  AMD13_RS17090 (J169_03466) - 3864367..3865454 (+) 1088 WP_087943923.1 IS3-like element ISXac2 family transposase -
  AMD13_RS17095 (J169_03467) - 3865493..3865951 (+) 459 Protein_3277 integrase -
  AMD13_RS17100 (J169_03468) - 3866134..3867063 (-) 930 WP_011052165.1 Kiwa anti-phage protein KwaB-like domain-containing protein -
  AMD13_RS17105 (J169_03469) - 3867060..3867644 (-) 585 WP_015463543.1 hypothetical protein -
  AMD13_RS17110 (J169_03470) - 3867874..3868212 (-) 339 WP_011052167.1 helix-turn-helix transcriptional regulator -
  AMD13_RS17115 (J169_03471) - 3868324..3869085 (+) 762 WP_015463544.1 hypothetical protein -
  AMD13_RS17120 (J169_03472) - 3869132..3869446 (+) 315 WP_011052169.1 hypothetical protein -
  AMD13_RS17125 (J169_03473) - 3869443..3869823 (+) 381 WP_011052170.1 hypothetical protein -
  AMD13_RS17130 (J169_03474) - 3869894..3871159 (-) 1266 WP_050752415.1 PAS domain-containing sensor histidine kinase -
  AMD13_RS25845 - 3871244..3871366 (+) 123 WP_306345870.1 hypothetical protein -

Sequence

Protein


Download         Length: 418 a.a.        Molecular weight: 45374.73 Da        Isoelectric Point: 10.2788

>NTDB_id=125995 AMD13_RS16905 WP_040107659.1 3820407..3821663(+) (pilC) [Xanthomonas citri pv. citri strain NT17]
MSAARSVVKTKTAASAEQMSPFVWEGTDKRGVKMKGEQTARNANLLRAELRRQGITPLVVKVKPKPLFGAAGKKVSAKDI
SFFSRQMATMMKSGVPIVGALEIIGSGQKNPRMRTMVGQIRTDIEGGASLYEAVSKHPVQFDELYRNLVKAGEGAGVLET
VLDTVATYKENLEALKGKIKKALFYPAMVMAVAMLVSAILLVWVVPQFEDVFKGFGAELPAFTQMIVNLSRFMVSWWWLM
LFALVGAAIGSVFAYKRSPAMQHGMDRLVLKVPIIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNSVYEKA
VLRMREDVSVGYPVNVAMKQVNLFPHMVVQMTAIGEEAGALDAMLFKVAEYFEQEVNNAVDALSSLIEPLIMVFIGTIVG
GMVIGMYLPIFKLASVVG

Nucleotide


Download         Length: 1257 bp        

>NTDB_id=125995 AMD13_RS16905 WP_040107659.1 3820407..3821663(+) (pilC) [Xanthomonas citri pv. citri strain NT17]
ATGTCAGCAGCACGTAGCGTAGTCAAGACGAAGACCGCCGCATCGGCGGAGCAGATGAGTCCGTTTGTCTGGGAGGGGAC
AGACAAGCGCGGCGTCAAGATGAAAGGCGAACAAACGGCCCGCAATGCAAATCTGCTGCGCGCCGAGTTACGGCGCCAGG
GCATTACTCCTCTCGTCGTGAAAGTTAAGCCGAAACCACTATTCGGCGCTGCCGGAAAGAAAGTTTCCGCAAAAGACATT
TCATTTTTCAGCCGACAGATGGCAACCATGATGAAGTCCGGCGTGCCGATTGTCGGCGCGCTGGAGATCATTGGCAGCGG
CCAAAAGAATCCGCGCATGCGCACAATGGTCGGACAGATTAGGACAGATATCGAAGGGGGGGCATCGCTCTACGAAGCCG
TAAGCAAGCACCCGGTGCAATTTGATGAGCTCTATCGGAATTTGGTCAAGGCAGGCGAAGGCGCAGGGGTACTGGAAACT
GTGCTCGACACCGTCGCCACTTACAAAGAAAACCTTGAAGCCCTGAAAGGCAAGATCAAGAAGGCACTGTTCTACCCTGC
CATGGTAATGGCAGTGGCGATGTTGGTCAGTGCAATCCTGCTTGTTTGGGTGGTTCCCCAATTTGAAGATGTCTTCAAGG
GCTTTGGAGCGGAGCTGCCTGCGTTCACACAGATGATCGTCAACCTGTCTCGCTTTATGGTGTCTTGGTGGTGGCTGATG
CTGTTCGCACTTGTTGGCGCTGCGATTGGGTCTGTTTTCGCATACAAGCGTTCACCAGCAATGCAACATGGCATGGACCG
CCTGGTGCTAAAAGTGCCGATCATTGGTCAGATCATGCACAACAGCTCAATTGCAAGATTCGCCCGGACGACGGCGGTGA
CCTTCAAGGCCGGCGTACCGCTAGTCGAGGCGCTGGGCATCGTGGCCGGTGCTACAGGTAATTCGGTCTACGAAAAAGCA
GTACTGCGCATGCGCGAAGACGTCTCCGTGGGCTACCCGGTCAACGTCGCGATGAAACAGGTCAACCTGTTTCCGCATAT
GGTGGTGCAGATGACCGCCATCGGTGAAGAAGCGGGCGCGCTGGATGCCATGCTGTTCAAGGTAGCGGAGTATTTCGAGC
AGGAAGTCAACAACGCGGTCGATGCGCTCAGCAGCCTGATCGAACCCCTGATCATGGTGTTCATTGGTACCATCGTCGGC
GGCATGGTCATCGGCATGTACCTGCCTATCTTCAAGCTCGCCTCGGTGGTTGGATAA

Domains

Predicted by InterproScan.

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

(287-409)

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

(83-206)


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 Pseudomonas stutzeri DSM 10701

53.086

96.89

0.514
  pilC Acinetobacter baylyi ADP1

51.843

97.368

0.505
  pilC Acinetobacter baumannii D1279779

51.613

96.411

0.498
  pilC Legionella pneumophila strain ERS1305867

52.525

94.737

0.498
  pilG Neisseria meningitidis 44/76-A

42.963

96.89

0.416
  pilG Neisseria gonorrhoeae MS11

42.822

96.651

0.414
  pilC Vibrio cholerae strain A1552

41.814

94.976

0.397
  pilC Vibrio campbellii strain DS40M4

39.95

96.411

0.385

Multiple sequence alignment