Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   NYR99_RS17120 Genome accession   NZ_CP103840
Coordinates   3923921..3925183 (+) Length   420 a.a.
NCBI ID   WP_316687921.1    Uniprot ID   -
Organism   Xanthomonas dyei strain 22-325     
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 3914943..3951804 3923921..3925183 within 0


Gene organization within MGE regions


Location: 3914943..3951804
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NYR99_RS17075 (NYR99_17040) - 3914943..3915794 (+) 852 WP_316687912.1 glycosyltransferase family 2 protein -
  NYR99_RS17080 (NYR99_17045) - 3915846..3916706 (+) 861 WP_316687913.1 glycosyltransferase family 2 protein -
  NYR99_RS17085 (NYR99_17050) - 3916691..3917866 (+) 1176 WP_316687914.1 glycosyltransferase -
  NYR99_RS17090 (NYR99_17055) - 3917860..3918702 (+) 843 WP_316687915.1 glycosyltransferase -
  NYR99_RS17095 (NYR99_17060) - 3918705..3919631 (-) 927 WP_316687916.1 glycosyltransferase family 9 protein -
  NYR99_RS17100 (NYR99_17065) - 3919888..3920646 (-) 759 WP_316687917.1 class I SAM-dependent methyltransferase -
  NYR99_RS17105 (NYR99_17070) - 3920770..3922590 (-) 1821 WP_316687918.1 hypothetical protein -
  NYR99_RS17110 (NYR99_17075) - 3922649..3923071 (-) 423 WP_316687919.1 pilin -
  NYR99_RS17115 (NYR99_17085) pilA/pilAI 3923172..3923570 (-) 399 WP_316687920.1 pilin Machinery gene
  NYR99_RS17120 (NYR99_17090) pilC 3923921..3925183 (+) 1263 WP_316687921.1 type II secretion system F family protein Machinery gene
  NYR99_RS17125 (NYR99_17095) - 3925190..3926053 (+) 864 WP_115513691.1 A24 family peptidase -
  NYR99_RS17130 (NYR99_17100) coaE 3926067..3926687 (+) 621 WP_316687922.1 dephospho-CoA kinase -
  NYR99_RS17135 (NYR99_17105) - 3926841..3931622 (+) 4782 WP_316687923.1 RHS repeat-associated core domain-containing protein -
  NYR99_RS17140 (NYR99_17110) - 3932259..3932662 (+) 404 Protein_3274 SymE family type I addiction module toxin -
  NYR99_RS17145 (NYR99_17115) - 3932738..3933028 (+) 291 WP_228325572.1 DUF1778 domain-containing protein -
  NYR99_RS17150 (NYR99_17120) - 3933025..3933516 (+) 492 WP_316687924.1 GNAT family N-acetyltransferase -
  NYR99_RS17155 (NYR99_17125) - 3933661..3934995 (-) 1335 WP_316687925.1 HAMP domain-containing sensor histidine kinase -
  NYR99_RS17160 (NYR99_17130) - 3934988..3935665 (-) 678 WP_003490678.1 response regulator transcription factor -
  NYR99_RS17165 (NYR99_17135) - 3935684..3936268 (-) 585 WP_316688070.1 hypothetical protein -
  NYR99_RS17170 (NYR99_17140) rimK 3936372..3937277 (-) 906 WP_167455844.1 30S ribosomal protein S6--L-glutamate ligase -
  NYR99_RS17175 (NYR99_17145) glgX 3937745..3939877 (+) 2133 WP_316688074.1 glycogen debranching protein GlgX -
  NYR99_RS17180 (NYR99_17150) - 3940432..3940824 (-) 393 WP_104617555.1 H-NS family nucleoid-associated regulatory protein -
  NYR99_RS17185 (NYR99_17155) - 3940913..3941305 (-) 393 WP_316688076.1 hypothetical protein -
  NYR99_RS17190 (NYR99_17160) - 3941848..3942393 (-) 546 WP_104617557.1 hypothetical protein -
  NYR99_RS17195 (NYR99_17165) - 3942563..3942847 (+) 285 WP_316688080.1 hypothetical protein -
  NYR99_RS17200 (NYR99_17170) - 3943456..3943797 (+) 342 WP_316688082.1 hypothetical protein -
  NYR99_RS17205 (NYR99_17175) - 3943862..3944143 (+) 282 WP_228325566.1 DUF6516 family protein -
  NYR99_RS17210 (NYR99_17180) - 3944151..3944519 (+) 369 WP_316688084.1 transcriptional regulator -
  NYR99_RS17215 (NYR99_17185) - 3944593..3945228 (-) 636 Protein_3289 hypothetical protein -
  NYR99_RS17220 (NYR99_17190) - 3945298..3946400 (+) 1103 WP_316688085.1 IS3 family transposase -
  NYR99_RS17225 (NYR99_17195) - 3946601..3947278 (+) 678 WP_316688086.1 hypothetical protein -
  NYR99_RS17230 (NYR99_17200) - 3947500..3948990 (+) 1491 WP_316688088.1 hypothetical protein -
  NYR99_RS17235 (NYR99_17205) - 3949309..3950118 (-) 810 WP_316688091.1 hypothetical protein -

Sequence

Protein


Download         Length: 420 a.a.        Molecular weight: 45767.15 Da        Isoelectric Point: 10.2311

>NTDB_id=725905 NYR99_RS17120 WP_316687921.1 3923921..3925183(+) (pilC) [Xanthomonas dyei strain 22-325]
MSAVRSTIKNKPATINAEQLMSPFVWEGTDKRGVKMKGEQVARNANMLRAELRRQGITPSVVKAKPKPLFGAAGKKITPK
EIAFFSRQMATMMKSGVPIVGSLEIIGNGHKNPRMKQMVGQIRTDIEGGSSLHEAVSKHPVQFDELYRNLIKAGEGAGVL
ETVLDTIASYKENLEALKGKIKKALFYPAMVVAVALLVSSILLIWVVPQFEDVFKGFGAELPAFTQLIVNASRFMVSYWW
LMLLVVVGSAVGFIFAYKRSIAMQHAMDRVVLKVPIIGQIMHNSSIARFARTTAVTFKAGVPLVEALGIVAGATGNSVYE
KAVLRMREDVSVGYPVNVSMKQVNLFPHMVVQMTAIGEEAGALDAMLFKVAEYYEQEVNNAVDALSSLIEPLIMVFIGTV
VGGMVIGMYLPIFKLASVVG

Nucleotide


Download         Length: 1263 bp        

>NTDB_id=725905 NYR99_RS17120 WP_316687921.1 3923921..3925183(+) (pilC) [Xanthomonas dyei strain 22-325]
ATGTCGGCAGTCCGTAGTACCATCAAGAACAAACCGGCGACCATCAACGCCGAGCAACTCATGAGCCCGTTCGTCTGGGA
GGGAACGGACAAGCGCGGCGTGAAGATGAAGGGCGAGCAGGTTGCCCGCAACGCCAACATGCTGCGGGCCGAGCTCCGCC
GGCAAGGCATCACACCCAGCGTTGTCAAGGCCAAGCCCAAGCCGCTATTCGGGGCAGCAGGCAAGAAAATCACGCCGAAG
GAAATTGCGTTCTTCAGTCGTCAGATGGCCACCATGATGAAGTCGGGCGTCCCGATTGTCGGGTCGCTGGAGATCATCGG
CAATGGTCATAAAAATCCGCGAATGAAACAGATGGTCGGGCAGATCCGTACTGACATCGAAGGCGGCTCCTCGCTACACG
AGGCGGTGAGCAAGCATCCGGTGCAGTTTGACGAGCTGTATCGCAACCTGATCAAGGCGGGCGAAGGGGCTGGTGTGCTG
GAAACCGTCCTGGACACCATTGCCTCATACAAAGAGAACCTGGAAGCCCTCAAGGGCAAGATCAAGAAGGCACTGTTCTA
TCCTGCAATGGTCGTGGCAGTCGCCCTATTGGTCAGCTCGATTCTATTGATCTGGGTCGTTCCGCAGTTCGAGGACGTGT
TCAAAGGGTTTGGTGCGGAACTGCCTGCATTCACTCAGCTAATCGTCAATGCATCCCGATTCATGGTTTCGTATTGGTGG
CTGATGCTACTTGTCGTCGTCGGCTCGGCTGTGGGCTTCATCTTTGCCTATAAGCGCTCCATTGCAATGCAGCATGCTAT
GGATCGTGTAGTACTCAAGGTGCCGATCATCGGACAGATCATGCACAACAGCTCGATTGCACGTTTTGCGCGGACTACTG
CGGTGACCTTCAAGGCGGGCGTGCCACTTGTAGAGGCTCTTGGCATTGTCGCCGGCGCTACTGGCAATTCGGTGTATGAA
AAAGCTGTGTTACGCATGCGCGAGGATGTGTCGGTGGGTTATCCGGTCAACGTGTCGATGAAACAGGTCAATCTGTTCCC
ACACATGGTGGTTCAGATGACAGCAATCGGTGAAGAAGCTGGTGCATTGGATGCCATGTTGTTCAAGGTGGCTGAGTACT
ACGAGCAGGAAGTGAACAATGCGGTCGATGCATTGAGCAGCCTCATCGAACCCTTGATCATGGTGTTCATTGGTACAGTA
GTCGGTGGCATGGTCATCGGCATGTACCTGCCAATCTTCAAGCTCGCTTCGGTGGTTGGATAA

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 Pseudomonas stutzeri DSM 10701

52.764

94.762

0.5
  pilC Legionella pneumophila strain ERS1305867

50.852

97.857

0.498
  pilC Acinetobacter baylyi ADP1

51.741

95.714

0.495
  pilC Acinetobacter baumannii D1279779

49.507

96.667

0.479
  pilG Neisseria gonorrhoeae MS11

44.361

95

0.421
  pilG Neisseria meningitidis 44/76-A

43.86

95

0.417
  pilC Vibrio cholerae strain A1552

41.058

94.524

0.388
  pilC Vibrio campbellii strain DS40M4

39.798

94.524

0.376