Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200369
Name   oriT_ICEPinKCOM1741-1 in_silico
Organism   Prevotella intermedia strain KCOM 1741
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP024733 (28890..29091 [-], 202 nt)
oriT length   202 nt
IRs (inverted repeats)      102..107, 120..125  (GCTTCC..GGAAGC)
 13..19, 24..30  (TATGTTC..GAACATA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 202 nt

>oriT_ICEPinKCOM1741-1
CCGACGGATTTTTATGTTCGCCTGAACATAGCAAGATGTCTTTTCAGCCGCTCAAAACGTTTTGAGCAGCCACGAAAAGCACTTGCCCTTGCAGGGGGCGGGCTTCCTCTCCGAAGTCGGGAAGCTTTTCAAACCTGCGGTGTCTGTGACCCCAAGCGGCGGCTTATGCCGTCCATCCGCTAAATCCAAAGTTTATATGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14395 GenBank   ATV39401
Name   Relaxase_CUB95_12610_ICEPinKCOM1741-1 insolico UniProt ID   _
Length   416 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 416 a.a.        Molecular weight: 46998.42 Da        Isoelectric Point: 9.5255

>ATV39401.1 relaxase [Prevotella intermedia]
MVAKISVGKSLYGALAYNGEKINEAKGRLLTTNRIYNDGTGTVDIRKAMEGFLACMPEHTRVEKPVLHIS
LNPHPDDVLTDTELQDIAREYLEKLGYGDQPYLIVKHEDIDRHHLHIVTINVDEKGRRLNQDFLFRRSDR
IRRELEQKYGLHPAERKNQRIENPLRKVDASAGDVKRQVGNTVKALSGQYRFQTMGEYRALLSLYNMTVE
EARGNVCGREYHGLVYSVTDDAGNKTGNPFKSSLFGKSAGYEAVQKKFARSKQEIKDRKLADMTKRTVLS
VLEGTYDKEKFVSRLREKGIDTVLRYTEEGRIYGATFIDHRTGCVLNGSRMGKELSANALQEHFTLPYAG
QPPIPLSVPVETVEDMREQTASDHENTAGGIGLLTPEGPAVDAEEEAFIRAMQRKKKKKRRKGLGM

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(10-180)


  Protein structure



No available structure.




T4CP

ID   16903 GenBank   ATV39400
Name   t4cp2_CUB95_12605_ICEPinKCOM1741-1 insolico UniProt ID   _
Length   669 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 669 a.a.        Molecular weight: 76611.67 Da        Isoelectric Point: 7.8098

>ATV39400.1 conjugal transfer protein TraG [Prevotella intermedia]
MSQQEDDLRALAKIMDFLRAVSIILVVMNVYWFCYEAIRLWSVDIGVVDRILMNFNRTAGLFRSILYTKL
FAVLLLALSCLGTKGVKGEKITWGRIWTALAAGFVLFFLNWWILALPLPVEAVTGLYVLTVGTGYVCLLM
GGLWMSRLLKHNFMDDVFNNENESFMQETRLIESEYSVNLPTRFYYRKRWNNGWINVVNPFRASIVLGTP
GSGKSYAVVNNFIKQQIEKGFSMYVYDFKFSDLSTIAYNHLLNHPEGYKVKPKFYVINFDDPRRSHRCNP
IHPDFMEDITDAYESAYTIMLNLNKSWVQKQGDFFVESPIILFAAIIWYLKIFQNGKYCTFPHAIEFLNR
RYEDIFPILTSYPELENYLSPFMDAWLGGAAEQLMGQIASAKIPLSRMISPQLYWVMSDSEFTLDINNPK
EPKILCVGNNPDRQNIYGAALGLYNSRIVKLINKKGMLKSSVIIDELPTIYFKGLDNLIATARSNKVAVC
LGFQDFSQLVRDYGDKEAKVVMNTVGNIFSGQVVGETAKTLSERFGKVLQKRQSISINRQDVSTSINTQM
DALIPPSKISGLTQGMFVGSVSDNFNERIEQKIFHCEIVVDAEKVKREEKAYKPIPVITDFTDEDGKDCM
KETVQANYRRIKEEVKQIVADELERIAGDENLKHLLQQK

  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: 624223..634796

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CUB95_12610 619346..620596 - 1251 ATV39401 relaxase -
CUB95_12615 620575..621000 - 426 ATV39552 MobA protein -
CUB95_12620 621271..621402 - 132 Protein_557 hypothetical protein -
CUB95_12625 621423..622472 + 1050 ATV39402 ParA family protein -
CUB95_12630 622475..622915 + 441 ATV39403 DUF3408 domain-containing protein -
CUB95_12635 622918..623265 + 348 ATV39404 DUF3408 domain-containing protein -
CUB95_12640 623298..624020 + 723 ATV39553 conjugal transfer protein TraD -
CUB95_12645 624223..624534 + 312 ATV39405 DUF4134 domain-containing protein traE
CUB95_12650 624545..624877 + 333 ATV39406 DUF4133 domain-containing protein traF
CUB95_12655 624874..627378 + 2505 ATV39407 TraG family conjugative transposon ATPase virb4
CUB95_12660 627428..627808 + 381 ATV39408 DUF3876 domain-containing protein traH
CUB95_12665 627832..628461 + 630 ATV39409 DUF4141 domain-containing protein traI
CUB95_12670 628465..629469 + 1005 ATV39410 conjugative transposon protein TraJ traJ
CUB95_12675 629501..630124 + 624 ATV39411 conjugative transposon protein TraK traK
CUB95_12680 630131..630439 + 309 ATV39412 DUF3989 domain-containing protein traL
CUB95_12685 630420..631769 + 1350 ATV39413 conjugative transposon protein TraM traM
CUB95_12690 631825..632811 + 987 ATV39414 conjugative transposon protein TraN traN
CUB95_12695 632814..633389 + 576 ATV39415 conjugal transfer protein TraO traO
CUB95_12700 633398..634267 + 870 ATV39416 DNA primase traP
CUB95_12705 634293..634796 + 504 ATV39417 DUF3872 domain-containing protein traQ
CUB95_12710 634793..635320 + 528 ATV39418 lysozyme -
CUB95_12715 635384..635605 - 222 ATV39419 hypothetical protein -
CUB95_12720 635723..636031 - 309 ATV39420 hypothetical protein -
CUB95_12725 636077..636322 - 246 ATV39421 hypothetical protein -
CUB95_12730 636319..636552 - 234 ATV39422 DUF3873 domain-containing protein -
CUB95_12735 636573..636830 - 258 ATV39423 hypothetical protein -
CUB95_12740 636855..638144 - 1290 ATV39424 PcfJ-like protein -
CUB95_12745 638147..638569 - 423 ATV39425 PcfK-like protein -
CUB95_12750 638583..638804 - 222 ATV39426 hypothetical protein -
CUB95_12755 638816..639031 - 216 ATV39427 hypothetical protein -
CUB95_12760 638937..639182 + 246 ATV39428 hypothetical protein -
CUB95_12765 639488..639679 + 192 ATV39429 hypothetical protein -

Host bacterium

ID   326 Element type   ICE (Integrative and conjugative element)
Element name   ICEPinKCOM1741-1 GenBank   CP024733
Element size   737408 bp Coordinate of oriT [Strand]   28890..29091 [-]
Host bacterium   Prevotella intermedia strain KCOM 1741 Coordinate of element   592106..640400

Cargo genes

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