Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilC   Type   Machinery gene
Locus tag   NYR97_RS02480 Genome accession   NZ_CP103836
Coordinates   610657..611913 (+) Length   418 a.a.
NCBI ID   WP_212580037.1    Uniprot ID   -
Organism   Xanthomonas hydrangeae strain 22-323     
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 607076..670091 610657..611913 within 0


Gene organization within MGE regions


Location: 607076..670091
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  NYR97_RS02460 (NYR97_02445) - 607076..607258 (+) 183 WP_316696530.1 YhfG family protein -
  NYR97_RS02465 (NYR97_02450) - 607255..607872 (+) 618 WP_316696532.1 Fic family protein -
  NYR97_RS02470 (NYR97_02455) pilB 607881..609617 (-) 1737 WP_316696533.1 type IV-A pilus assembly ATPase PilB Machinery gene
  NYR97_RS02475 (NYR97_02460) - 609874..610305 (-) 432 WP_316696535.1 pilin -
  NYR97_RS02480 (NYR97_02465) pilC 610657..611913 (+) 1257 WP_212580037.1 type II secretion system F family protein Machinery gene
  NYR97_RS02485 (NYR97_02470) - 611920..612783 (+) 864 WP_316696538.1 A24 family peptidase -
  NYR97_RS02490 (NYR97_02475) coaE 612797..613429 (+) 633 WP_316696539.1 dephospho-CoA kinase -
  NYR97_RS02495 (NYR97_02480) - 613691..618460 (+) 4770 WP_316696540.1 RHS repeat-associated core domain-containing protein -
  NYR97_RS02500 (NYR97_02485) - 618465..618917 (+) 453 WP_316696542.1 hypothetical protein -
  NYR97_RS02505 (NYR97_02490) - 619349..619750 (+) 402 WP_316696544.1 SymE family type I addiction module toxin -
  NYR97_RS02510 (NYR97_02495) - 619825..620115 (+) 291 WP_316696546.1 DUF1778 domain-containing protein -
  NYR97_RS02515 (NYR97_02500) - 620112..620603 (+) 492 WP_316696548.1 GNAT family N-acetyltransferase -
  NYR97_RS02520 (NYR97_02505) - 620752..622086 (-) 1335 WP_210763036.1 HAMP domain-containing sensor histidine kinase -
  NYR97_RS02525 (NYR97_02510) - 622079..622756 (-) 678 WP_006448355.1 response regulator transcription factor -
  NYR97_RS02530 (NYR97_02515) - 622787..623260 (-) 474 WP_316696552.1 hypothetical protein -
  NYR97_RS02535 (NYR97_02520) rimK 623485..624390 (-) 906 WP_205393974.1 30S ribosomal protein S6--L-glutamate ligase -
  NYR97_RS02540 (NYR97_02525) glgX 624897..627029 (+) 2133 WP_316696555.1 glycogen debranching protein GlgX -
  NYR97_RS02545 (NYR97_02530) - 627385..627777 (-) 393 WP_205393972.1 H-NS family nucleoid-associated regulatory protein -
  NYR97_RS02550 (NYR97_02535) - 627866..628261 (-) 396 WP_205393971.1 hypothetical protein -
  NYR97_RS02555 (NYR97_02540) - 628594..629703 (+) 1110 WP_316696557.1 hypothetical protein -
  NYR97_RS02560 (NYR97_02545) - 629868..630125 (+) 258 WP_205393969.1 hypothetical protein -
  NYR97_RS02565 (NYR97_02550) - 630133..630417 (-) 285 WP_043889393.1 hypothetical protein -
  NYR97_RS02570 (NYR97_02555) - 630872..633118 (+) 2247 WP_210763034.1 methyl-accepting chemotaxis protein -
  NYR97_RS02575 (NYR97_02560) - 633328..633750 (-) 423 WP_316696562.1 YqaA family protein -
  NYR97_RS02580 (NYR97_02565) - 633852..634769 (-) 918 WP_316696564.1 LysR family transcriptional regulator -
  NYR97_RS02585 (NYR97_02570) - 634883..636076 (+) 1194 WP_316696566.1 serine hydrolase domain-containing protein -
  NYR97_RS02590 (NYR97_02575) - 636073..637287 (+) 1215 WP_316696568.1 MFS transporter -
  NYR97_RS02595 (NYR97_02580) - 637308..637646 (+) 339 WP_316696570.1 GNAT family N-acetyltransferase -
  NYR97_RS02600 (NYR97_02585) - 637787..638164 (-) 378 WP_316696572.1 helix-turn-helix domain-containing protein -
  NYR97_RS02605 (NYR97_02590) - 638287..639150 (+) 864 WP_316696574.1 NAD(P)H-binding protein -
  NYR97_RS02610 (NYR97_02595) - 639147..639791 (+) 645 WP_316696575.1 DsbA family protein -
  NYR97_RS02615 (NYR97_02600) - 639788..640654 (+) 867 WP_316696576.1 SDR family NAD(P)-dependent oxidoreductase -
  NYR97_RS02620 (NYR97_02605) - 640701..641585 (-) 885 WP_316696577.1 arginase family protein -
  NYR97_RS02625 (NYR97_02610) - 641637..642827 (-) 1191 WP_316696578.1 MFS transporter -
  NYR97_RS02630 (NYR97_02615) - 642856..643830 (-) 975 WP_316696579.1 zinc-binding dehydrogenase -
  NYR97_RS02635 (NYR97_02620) - 643961..644860 (+) 900 WP_316696581.1 LysR family transcriptional regulator -
  NYR97_RS02640 (NYR97_02625) - 644989..645789 (-) 801 WP_316696583.1 hypothetical protein -
  NYR97_RS02645 (NYR97_02630) - 646966..647379 (+) 414 Protein_526 methyl-accepting chemotaxis protein -
  NYR97_RS02650 (NYR97_02635) - 647594..647785 (+) 192 WP_316696585.1 hypothetical protein -
  NYR97_RS02655 (NYR97_02640) - 648909..650060 (-) 1152 WP_316696586.1 cytochrome c peroxidase -
  NYR97_RS02660 (NYR97_02645) - 650099..652873 (-) 2775 WP_316696588.1 TonB-dependent receptor plug domain-containing protein -
  NYR97_RS02665 (NYR97_02650) - 652933..653652 (-) 720 WP_316696590.1 FecR domain-containing protein -
  NYR97_RS02670 (NYR97_02655) - 653900..654394 (-) 495 WP_176342022.1 sigma-70 family RNA polymerase sigma factor -
  NYR97_RS02675 (NYR97_02660) - 654647..655378 (-) 732 WP_316696593.1 hypothetical protein -
  NYR97_RS02680 (NYR97_02665) - 655972..657321 (-) 1350 WP_316696595.1 hypothetical protein -
  NYR97_RS02685 (NYR97_02670) - 657433..658932 (+) 1500 WP_316696597.1 MFS transporter -
  NYR97_RS02690 (NYR97_02675) - 658937..659500 (+) 564 WP_316696598.1 TetR family transcriptional regulator -
  NYR97_RS02695 (NYR97_02680) - 659670..660807 (-) 1138 Protein_536 IS3 family transposase -
  NYR97_RS02700 (NYR97_02685) - 660858..661867 (-) 1010 Protein_537 IS3 family transposase -
  NYR97_RS02705 (NYR97_02690) - 661934..663868 (-) 1935 WP_316696600.1 hypothetical protein -
  NYR97_RS02710 (NYR97_02695) - 663869..664678 (-) 810 WP_316696603.1 PP2C family serine/threonine-protein phosphatase -
  NYR97_RS02715 (NYR97_02700) - 664678..665352 (-) 675 WP_316696605.1 VWA domain-containing protein -
  NYR97_RS02720 (NYR97_02705) - 666134..666416 (+) 283 Protein_541 hypothetical protein -
  NYR97_RS02725 (NYR97_02710) - 666463..666741 (+) 279 WP_316696607.1 hypothetical protein -
  NYR97_RS02730 (NYR97_02715) - 667151..667471 (+) 321 WP_316696609.1 hypothetical protein -
  NYR97_RS02735 - 668039..668254 (+) 216 Protein_544 hypothetical protein -
  NYR97_RS02740 (NYR97_02720) - 668393..668572 (+) 180 WP_316696611.1 hypothetical protein -
  NYR97_RS02745 (NYR97_02725) - 668748..669017 (-) 270 WP_316696613.1 hypothetical protein -

Sequence

Protein


Download         Length: 418 a.a.        Molecular weight: 45546.71 Da        Isoelectric Point: 10.2788

>NTDB_id=725845 NYR97_RS02480 WP_212580037.1 610657..611913(+) (pilC) [Xanthomonas hydrangeae strain 22-323]
MSAVRSAIKNKPTAQVDQMSPFVWEGTDKRGVKMKGEQTAKNANLLRAELRRQGITPTVVKVKPKPLFGSAGQKVTSKDI
SFFSRQMATMMKSGVPIVGALEIIGSGHKNPRMRSMVGQIRSDIEGGSSLHEAISRHPVQFDELYRNLVKAGEGAGVLET
VLDTVATYKENLEALKGKIKKALFYPATVVAVALLVSSILLIFVVPQFEDVFKGFGAELPAFTQMIVNASRFMVSWWWLI
LFIVVGAVVGFIYAYKRSPSMQHGMDRLVLKVPIIGKIMHNSSIARFSRTTAVTFKAGVPLVEALSIVAGATGNSVYEKA
VLRMRDDVSVGYPVNVAMKQVNLFPHMVVQMTAIGEEAGALDAMLFKVAEYFEQEVNNAVDALSSLIEPLIMIFIGTVVG
GMVIGMYLPIFKLATVVG

Nucleotide


Download         Length: 1257 bp        

>NTDB_id=725845 NYR97_RS02480 WP_212580037.1 610657..611913(+) (pilC) [Xanthomonas hydrangeae strain 22-323]
ATGTCAGCAGTACGTAGTGCCATCAAAAACAAACCGACCGCACAGGTAGATCAGATGAGTCCGTTTGTCTGGGAGGGAAC
AGACAAGCGCGGCGTCAAGATGAAAGGCGAGCAAACGGCCAAGAATGCAAATTTGCTACGCGCAGAATTGCGACGCCAGG
GCATTACGCCGACCGTTGTCAAGGTGAAGCCCAAGCCGCTGTTCGGCTCTGCTGGTCAGAAGGTGACTTCAAAGGACATT
TCGTTCTTCAGCCGGCAAATGGCAACAATGATGAAGTCCGGTGTACCGATCGTCGGTGCGCTGGAGATCATTGGCAGCGG
CCACAAAAACCCGCGCATGCGTAGCATGGTTGGACAGATTCGTAGCGATATCGAAGGTGGCTCATCGCTGCACGAGGCAA
TCAGCAGGCACCCGGTGCAGTTCGACGAACTGTATCGAAACCTGGTCAAGGCTGGCGAAGGCGCCGGCGTCCTTGAGACG
GTGCTGGACACCGTGGCTACCTATAAAGAGAACCTGGAAGCATTAAAGGGAAAGATCAAGAAGGCCCTGTTCTATCCCGC
AACGGTGGTCGCGGTAGCGCTTTTGGTCAGCTCAATTCTGCTGATCTTTGTCGTGCCGCAATTTGAAGACGTTTTCAAAG
GCTTCGGTGCGGAACTTCCTGCGTTCACCCAGATGATCGTCAATGCATCAAGGTTCATGGTGTCTTGGTGGTGGTTGATC
TTGTTTATCGTAGTCGGCGCGGTGGTTGGCTTCATTTATGCGTACAAGCGCTCCCCATCAATGCAACACGGCATGGACCG
TCTAGTGCTCAAGGTGCCGATTATTGGCAAGATAATGCACAACAGCTCGATCGCCCGCTTTTCCCGCACCACAGCCGTGA
CATTCAAGGCTGGCGTGCCGCTGGTCGAGGCACTGAGCATTGTTGCTGGCGCCACGGGTAACTCAGTCTACGAGAAAGCT
GTGCTGCGCATGCGAGACGATGTATCGGTAGGCTACCCAGTCAACGTCGCGATGAAGCAGGTCAACCTGTTCCCGCACAT
GGTGGTGCAGATGACTGCCATCGGCGAAGAGGCAGGTGCACTTGACGCCATGTTGTTTAAGGTCGCCGAGTACTTCGAGC
AGGAGGTCAATAACGCGGTCGACGCCCTCAGTAGCTTGATCGAACCACTCATCATGATATTCATTGGTACCGTTGTCGGC
GGCATGGTCATCGGCATGTACCTGCCTATTTTCAAGCTAGCCACTGTAGTTGGATAA

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

51.816

98.804

0.512
  pilC Acinetobacter baumannii D1279779

51.741

96.172

0.498
  pilC Acinetobacter baylyi ADP1

50.985

97.129

0.495
  pilC Legionella pneumophila strain ERS1305867

50.985

97.129

0.495
  pilG Neisseria gonorrhoeae MS11

44.221

95.215

0.421
  pilG Neisseria meningitidis 44/76-A

43.86

95.455

0.419
  pilC Vibrio cholerae strain A1552

41.832

96.651

0.404
  pilC Vibrio campbellii strain DS40M4

40.648

95.933

0.39