Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200387
Name   oriT_ICERanRCAD0179-1 in_silico
Organism   Riemerella anatipestifer strain RCAD0179 Scaffold4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   QXQM01000004 (18949..19145 [+], 197 nt)
oriT length   197 nt
IRs (inverted repeats)      10..17, 20..27  (TATGTTCA..TGAACATA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 197 nt

>oriT_ICERanRCAD0179-1
ACGGATTTTTATGTTCACCTGAACATAGCAAGATGTCTTTTCAGCCGCTCAAAATATTTTGAGCAGCCACGAAAAGCACTTGCCCTTGCAGGGGGCGGGCTTTCCCTCCGAAGTCGGGAAGCCTTTCAGAACTGCGGTGCTGTAATCCGAAGCGGCGGCTTATGCCGTCAATCCGCTAAATCCAAAGTAATATGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14414 GenBank   MSN90297
Name   Relaxase_D1Y74_04675_ICERanRCAD0179-1 insolico UniProt ID   _
Length   415 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 415 a.a.        Molecular weight: 46563.08 Da        Isoelectric Point: 9.8931

>MSN90297.1 relaxase [Riemerella anatipestifer]
MVAKISVGSSLYGAIAYNGEKINEAQGRLLTTNRIYNDGSGTVDIGKAMEGFLTFLPPQMKIEKPVVHIS
LNPHPEDVLTDIELQNIAREYLEKLGFGNQPYLVFKHEDIDRHHLHIVTVNVDENGKRLNRDFLYRRSDR
IRRELEQKYGLHPAERKNQRLDNPLRKVAASAGDVKKQVGNTVKALNGQYRFQTMGEYRALLSLYNMTVE
EARGNVRGREYHGLVYSVTDDKGNKVGNPFKSSLFGKSAGYEAVQKKFVRSKSEIKDRKLADMTKRTVLS
VLQGTYDKDKFVSQLKEKGIDTVLRYTEEGRIYGATFIDHRTGCVLNGSRMGKELSANALQEHFTLPYAG
QPPIPLSIPVDAADKAHGQTAYDSEDISGGMGLLTPEGPAVDAEEEAFIRAMKRKKKKKRKGLGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(64-184)


  Protein structure



No available structure.




T4CP

ID   16936 GenBank   MSN90298
Name   t4cp2_D1Y74_04680_ICERanRCAD0179-1 insolico UniProt ID   _
Length   672 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 672 a.a.        Molecular weight: 77086.10 Da        Isoelectric Point: 7.1001

>MSN90298.1 conjugal transfer protein TraG [Riemerella anatipestifer]
MSQQEDDLRALAKIMDFLRAVSIILVVMNVYWFCYEAIRLWGVNIGVVDKILLNFDRTAGLFHSILYTKL
FSVLLLALSCLGTKGVKGEKITWGRIWTAFAVGFVLFFLNWWLLPLPLPLEAVTGLYVLTIGTGYVCLLM
GGLWMSRLLKHNLMEDVFNNENESFMQETRLIESEYSVNLPTRFYYRKRWNNGWINVVNPFRASIVLGTP
GSGKSYAVVNNFIKQQIEKGFSQYIYDFKYPDLSTIAYNHLLNHPDGYKVKPKFYVINFDDPRRSHRCNP
IHPDFMEDITDAYESAYTIMLNLNKTWVQKQGDFFVESPIILFASIIWYLKIYQNGKFCTFPHAIEFLNR
RYEDIFPILTSYPELENYLSPFMDAWLGGAAEQLMGQIASAKIPLSRMISPQLYWVMSDSEFTLDINNPE
EPKILCVGNNPDRQNIYGAALGLYNSRIVKLINKKGMLKSSVIIDELPTIYFKGLDNLIATARSNKVAVC
LGFQDFSQLVRDYGDKEAKVVMNTVGNIFSGQVVGETAKTLSERFGKVLQKRQSISINRQDVSTSINTQM
DALIPPSKISGLTQGMFVGSVSDNFNERIEQKIFHCEIVVDAEKVKREESAYKKIPVITNFTDEDGNDRM
KETVQANYRRIKEEVKQIVQEELERIKNDPVLCKLLPDNETV

  Protein domains


Predicted by InterproScan.

YWFCY protein (YWFCY)

(6-150)

TraM recognition site of TraD and TraG (TraG-D_C)

(462-572)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60072..70627

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
D1Y74_04520 55143..55553 + 411 MSN90268 hypothetical protein -
D1Y74_04525 55565..55809 - 245 Protein_45 hypothetical protein -
D1Y74_04530 55715..55930 + 216 MSN90269 hypothetical protein -
D1Y74_04535 55942..56163 + 222 MSN90270 hypothetical protein -
D1Y74_04540 56177..56593 + 417 MSN90271 PcfK-like protein -
D1Y74_04545 56590..57921 + 1332 MSN90272 hypothetical protein -
D1Y74_04550 57946..58203 + 258 MSN90273 hypothetical protein -
D1Y74_04555 58223..58456 + 234 MSN90274 DUF3873 domain-containing protein -
D1Y74_04560 58453..58698 + 246 MSN90275 hypothetical protein -
D1Y74_04565 58752..59060 + 309 MSN90276 hypothetical protein -
D1Y74_04570 59094..59339 - 246 MSN90277 hypothetical protein -
D1Y74_04575 59548..60075 - 528 MSN90278 lysozyme -
D1Y74_04580 60072..60575 - 504 MSN90279 DUF3872 domain-containing protein traQ
D1Y74_04585 60572..61474 - 903 MSN90280 DNA primase traP
D1Y74_04590 61482..62057 - 576 MSN90281 conjugal transfer protein TraO traO
D1Y74_04595 62060..63046 - 987 MSN90282 conjugative transposon protein TraN traN
D1Y74_04600 63081..64433 - 1353 MSN90283 conjugative transposon protein TraM traM
D1Y74_04605 64414..65352 - 939 Protein_61 conjugative transposon protein TraK -
D1Y74_04610 65384..66388 - 1005 MSN90284 conjugative transposon protein TraJ traJ
D1Y74_04615 66392..67021 - 630 MSN90285 DUF4141 domain-containing protein traI
D1Y74_04620 67045..67425 - 381 MSN90286 DUF3876 domain-containing protein traH
D1Y74_04625 67466..69970 - 2505 MSN90287 TraG family conjugative transposon ATPase virb4
D1Y74_04630 69967..70299 - 333 MSN90288 DUF4133 domain-containing protein traF
D1Y74_04635 70310..70627 - 318 MSN90289 DUF4134 domain-containing protein traE
D1Y74_04640 70829..71557 - 729 MSN90290 conjugal transfer protein TraD -
D1Y74_04645 71574..71927 - 354 MSN90291 DUF3408 domain-containing protein -
D1Y74_04650 71930..72370 - 441 MSN90292 DUF3408 domain-containing protein -
D1Y74_04655 72373..73422 - 1050 MSN90293 ParA family protein -
D1Y74_04660 73407..73574 + 168 MSN90294 hypothetical protein -
D1Y74_04665 73623..73847 + 225 MSN90295 hypothetical protein -
D1Y74_04670 73844..74272 + 429 MSN90296 MobA protein -
D1Y74_04675 74251..75498 + 1248 MSN90297 relaxase -

Host bacterium

ID   344 Element type   ICE (Integrative and conjugative element)
Element name   ICERanRCAD0179-1 GenBank   QXQM01000004
Element size   208058 bp Coordinate of oriT [Strand]   18949..19145 [+]
Host bacterium   Riemerella anatipestifer strain RCAD0179 Scaffold4 Coordinate of element   54705..103871

Cargo genes

Drug resistance gene   tet(Q)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA9