Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200351
Name   oriT_ICEBdoHS2_L_2_B_045b-1 in_silico
Organism   Bacteroides dorei isolate HS2_L_2_B_045b
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP009057 (18499..18695 [+], 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_ICEBdoHS2_L_2_B_045b-1
ACGGATTTTTATGTTCACCTGAACATAGCAAGATGTCTTTTCAGCCGCTCAAAATATTTTGAGCAGCCACGAAAAGCACTTGCCCTTGCAGGGGGCGGGCTTTCCCTCCGAAGTCGGGAAGCCTTTCAGAACTGCGGTGCTGTAATCCGAAGCGGCGGCTTATGCCGTCAATCCGCTAAATCCAAAGTAATATGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14377 GenBank   ALA73093
Name   Relaxase_IY41_06110_ICEBdoHS2_L_2_B_045b-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

>ALA73093.1 relaxase [Phocaeicola dorei]
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   16872 GenBank   ALA73094
Name   t4cp2_IY41_06115_ICEBdoHS2_L_2_B_045b-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

>ALA73094.1 conjugal transfer protein TraG [Phocaeicola dorei]
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: 1642551..1653106

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IY41_05970 1637634..1637897 - 264 ALA73068 hypothetical protein -
IY41_05975 1638194..1638409 + 216 ALA73069 hypothetical protein -
IY41_05980 1638656..1639072 + 417 ALA73070 PcfK-like protein -
IY41_05985 1639069..1640400 + 1332 ALA73071 hypothetical protein -
IY41_05990 1640425..1640682 + 258 ALA73072 hypothetical protein -
IY41_05995 1640702..1640935 + 234 ALA73073 hypothetical protein -
IY41_06000 1640932..1641177 + 246 ALA73074 hypothetical protein -
IY41_06005 1641231..1641539 + 309 ALA73075 hypothetical protein -
IY41_06010 1641573..1641962 - 390 ALA76030 hypothetical protein -
IY41_06015 1642027..1642554 - 528 ALA73076 lysozyme -
IY41_06020 1642551..1643054 - 504 ALA73077 conjugal transfer protein TraQ traQ
IY41_06025 1643051..1643953 - 903 ALA73078 DNA primase traP
IY41_06030 1643961..1644536 - 576 ALA73079 conjugal transfer protein TraO traO
IY41_06035 1644539..1645525 - 987 ALA73080 conjugal transfer protein traN
IY41_06040 1645560..1646912 - 1353 ALA73081 conjugal transfer protein traM
IY41_06045 1646893..1647201 - 309 ALA73082 conjugal transfer protein TraL traL
IY41_06050 1647208..1647831 - 624 ALA73083 conjugal transfer protein traK
IY41_06055 1647863..1648867 - 1005 ALA73084 conjugal transfer protein traJ
IY41_06060 1648871..1649500 - 630 ALA73085 hypothetical protein traI
IY41_06065 1649524..1649904 - 381 ALA73086 conjugal transfer protein TraH traH
IY41_06070 1649945..1652449 - 2505 ALA73087 conjugal transfer protein TraG virb4
IY41_06075 1652446..1652778 - 333 ALA73088 conjugal transfer protein TraF traF
IY41_06080 1652789..1653106 - 318 ALA73089 conjugal transfer protein TraE traE
IY41_06085 1653308..1654036 - 729 ALA76031 conjugal transfer protein TraD -
IY41_06090 1654053..1654406 - 354 ALA73090 conjugal transfer protein TraB -
IY41_06095 1654409..1654849 - 441 ALA73091 protein found in conjugate transposon -
IY41_06100 1654852..1655613 - 762 ALA76032 conjugal transfer protein TraA -
IY41_06105 1656323..1656751 + 429 ALA73092 MobA protein -
IY41_06110 1656730..1657977 + 1248 ALA73093 relaxase -

Host bacterium

ID   308 Element type   ICE (Integrative and conjugative element)
Element name   ICEBdoHS2_L_2_B_045b-1 GenBank   CP009057
Element size   5444912 bp Coordinate of oriT [Strand]   18499..18695 [+]
Host bacterium   Bacteroides dorei isolate HS2_L_2_B_045b Coordinate of element   1637634..1686354

Cargo genes

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