Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200370
Name   oriT_ICEPinKCOM2033-1 in_silico
Organism   Prevotella intermedia strain KCOM 2033
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP024696 (30068..30264 [-], 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_ICEPinKCOM2033-1
ACGGATTTTTATGTTCACCTGAACATAGCAAGATGTCTTTTCAGCCGCTCAAAATATTTTGAGCAGCCACGAAAAGCACTTGCCCTTGCAGGGGGCGGGCTTTCCCTCCGAAGTCGGGAAGCCTTTCAGAACTGCGGTGCTGTAATCCGAAGCGGCGGCTTATGCCGTCAATCCGCTAAATCCAAAGTAATATGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14396 GenBank   ATV53720
Name   Relaxase_CTM50_12240_ICEPinKCOM2033-1 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

>ATV53720.1 relaxase [Prevotella intermedia]
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   16904 GenBank   ATV53719
Name   t4cp2_CTM50_12235_ICEPinKCOM2033-1 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

>ATV53719.1 conjugal transfer protein TraG [Prevotella intermedia]
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: 2736069..2746624

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CTM50_12240 2731198..2732445 - 1248 ATV53720 relaxase -
CTM50_12245 2732424..2732852 - 429 ATV53721 MobA protein -
CTM50_12250 2732849..2733073 - 225 ATV53945 hypothetical protein -
CTM50_12255 2733122..2733289 - 168 ATV53722 hypothetical protein -
CTM50_12260 2733274..2734323 + 1050 ATV53723 ParA family protein -
CTM50_12265 2734326..2734766 + 441 ATV53946 hypothetical protein -
CTM50_12270 2734769..2735122 + 354 ATV53724 conjugal transfer protein TraB -
CTM50_12275 2735139..2735867 + 729 ATV53725 conjugal transfer protein TraD -
CTM50_12280 2736069..2736386 + 318 ATV53726 conjugal transfer protein TraE traE
CTM50_12285 2736397..2736729 + 333 ATV53727 conjugal transfer protein TraF traF
CTM50_12290 2736726..2739230 + 2505 ATV53728 conjugal transfer protein TraG virb4
CTM50_12295 2739271..2739651 + 381 ATV53729 conjugal transfer protein TraH traH
CTM50_12300 2739675..2740304 + 630 ATV53730 hypothetical protein traI
CTM50_12305 2740308..2741312 + 1005 ATV53731 conjugative transposon protein TraJ traJ
CTM50_12310 2741344..2741967 + 624 ATV53732 conjugative transposon protein TraK traK
CTM50_12315 2741974..2742282 + 309 ATV53733 conjugal transfer protein TraL traL
CTM50_12320 2742263..2743615 + 1353 ATV53734 conjugative transposon protein TraM traM
CTM50_12325 2743650..2744636 + 987 ATV53735 conjugative transposon protein TraN traN
CTM50_12330 2744639..2745214 + 576 ATV53736 conjugal transfer protein TraO traO
CTM50_12335 2745222..2746124 + 903 ATV53737 DNA primase traP
CTM50_12340 2746121..2746624 + 504 ATV53738 conjugal transfer protein TraQ traQ
CTM50_12345 2746621..2747148 + 528 ATV53739 lysozyme -
CTM50_12350 2747357..2747602 + 246 ATV53947 hypothetical protein -
CTM50_12355 2747636..2747944 - 309 ATV53948 hypothetical protein -
CTM50_12360 2747998..2748243 - 246 ATV53740 hypothetical protein -
CTM50_12365 2748240..2748473 - 234 ATV53741 DUF3873 domain-containing protein -
CTM50_12370 2748493..2748750 - 258 ATV53742 hypothetical protein -
CTM50_12375 2748775..2750106 - 1332 ATV53743 hypothetical protein -
CTM50_12380 2750103..2750519 - 417 ATV53744 PcfK-like protein -
CTM50_12385 2750533..2750754 - 222 ATV53950 hypothetical protein -
CTM50_12390 2750766..2750981 - 216 ATV53949 hypothetical protein -
CTM50_12395 2750887..2751131 + 245 Protein_2416 hypothetical protein -
CTM50_12400 2751143..2751553 - 411 ATV53745 hypothetical protein -

Host bacterium

ID   327 Element type   ICE (Integrative and conjugative element)
Element name   ICEPinKCOM2033-1 GenBank   CP024696
Element size   2777805 bp Coordinate of oriT [Strand]   30068..30264 [-]
Host bacterium   Prevotella intermedia strain KCOM 2033 Coordinate of element   2702780..2752400

Cargo genes

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