Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200475
Name   oriT_ICECmeCH34-1 in_silico
Organism   Cupriavidus metallidurans CH34
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP000352 (8299..8616 [-], 318 nt)
oriT length   318 nt
IRs (inverted repeats)      238..243, 251..256  (CCAGCC..GGCTGG)
 199..206, 215..222  (TAAAAGGC..GCCTTTTA)
 197..202, 207..212  (TTTAAA..TTTAAA)
Location of nic site      44..45
Conserved sequence flanking the
  nic site    		  TCGTGCCTGC
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 318 nt

>oriT_ICECmeCH34-1
CCATGGCCGATCGATCGTGCTTGCGCCAGCGAAGAAAGGTCGTGCCTGCGCCAGTGGTCTGCTGGGCCAGCTCGACGGGAAGCAGGTGGAAGGGATGCCCGCACGCCTGTGGCAGCACCTGTCGCTGCGCCAGGGCAATCAACTCGTCGCGCATGGCGAAGCACTGGCTGGCCCAGGCCTCGAAGTCCCCTTTACCTTTAAAAGGCTTTAAAAGGCCTTTTAGAGAGGCCGCGTGTTCCAGCCGCATGAAGGCTGGCTGTTCCAGACGACGGAAGTAGCGCGGTTCGCGGTTCGGGTCGCTCATGCCGGTTCGTCCTC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14512 GenBank   ABF09241
Name   TraI_2_Rmet_2364_ICECmeCH34-1 insolico UniProt ID   _
Length   680 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 680 a.a.        Molecular weight: 74533.78 Da        Isoelectric Point: 7.8320

>ABF09241.1 relaxase [Cupriavidus metallidurans CH34]
MTLESHPVPRYTETVKGQRAEMARERGARGKALPRKGQKASRSARHQDTHMLSLFQRKRPAVATAPTPPP
ASDLPKGLMRPESAASLLATPRRQKLLEHIWQRTSLSRKQFAVLYRAPLERYAELVQAFPASESHHHAYP
GGMLDHGLEIVAYALKLRQSHLLPIGASPEDQAAQAEAWTAAVAYAALLHDIGKIAVDLHVELADGSLWH
PWYGPLHQPYRFRYRDDREYRLHSAATGLLYRQLLDTQLLDWLSDYRDLWGPLLYVLAGQYEHAGVLGEL
VVQADRASVAQELGGDPARAMAAPKHALQRKLLDGLRYLLKEELKLNQPEASDGWLTEDALWLVSKTVSD
KLRAHLLSQGIDGIPANNTAVFNVLQDHGMLQPTLDGKAVWRATVTSNAGWTHSFTLLRLAPALIWEAGE
RPAPFAGTVAIDTSPVEKHAAAASSPEVAAKPTPGGQESPPWEGGSAADPIIAPLAEAMPDVMEDLLTMV
GMGDSSATQQDESTIPTELSATRPEAPPPSIVASSPSSPAPAATPAATTVQPSGEHFMAWLKQGIASRRL
IINDAKALVHTVSDTAYLVSPGVFQRYAQEHPQLAAIARQEKLEPWQWAQKRFEKLAAHRKQASGLNIWT
CHVSGPRKSRQLHGYLLTQPGALFERVPPNNPYLCLFNEEAGREVSLAAK

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(77-389)

Putative conjugal transfer nickase/helicase TraI C-term (TraI_2_C)

(543-665)


  Protein structure



No available structure.




T4CP

ID   17128 GenBank   ABF09213
Name   virD4_Rmet_2336_ICECmeCH34-1 insolico UniProt ID   _
Length   729 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 729 a.a.        Molecular weight: 80777.58 Da        Isoelectric Point: 7.3460

>ABF09213.1 VirD4, Type IV secretory pathway, VirD4 components [Cupriavidus metallidurans CH34]
MSGKQPVEVLLRPAVELYTVAACAGAAFLCLVAPWSLALSPAMGIGSALAFGAYGAIRYRDARIILRYRR
NIRRLPRYVMTSKDVPVSQQRLFVGRGFLWEQKHTHRLMQTYRPEFRRYVEPTPAYRLTRRLEERLEFAP
LPLSRLPKLTGWDAPFNPVRPLPPVGGLPRLHGIEPDEVDVSLPLGERVGHSLVLGTTRVGKTRLAELFV
TQDIRRRNAAGEHEVVIVIDPKGDADLLKRMYVEAQRAGREGEFYIFHLGWPEISARYNAVGRFGRISEV
ATRIAGQLSGEGNSAAFREFAWRFVNIIARALVELGQRPDYMLIQRHVINIDALFIEYAQHYFAKTEPKA
WEVIVQIEAKLNEKNIPRNMIGREKRVVALEQYLSQARNYDPVLDGLRSAVRYDKTYFDKIVASLLPLLE
KLTSGKIAQLLAPNYSDLADPRPIFDWMQVIRKRAVVYVGLDALSDAEVAAAVGNSMFSDLVSVAGHIYK
HGIDDGLPGASAGARVPINVHADEFNELMGDEFIPLINKGGGAGLQVTAYTQTLSDIEARIGNRAKAGQV
IGNFNNLFMLRVRETATAELLTRQLPKVEVYTTTIVSGATDSSDIRGATDFTSNTQDRISMASVPMIEPS
HVVGLPKGQCFALLQGGQLWKVRMPLPAPDPDEVMPTDLQQLAGYMRQSYSEATQWWEFTSSAALPHAAL
PDDLLDDAAPAEPDAVATGADDSTGEAAP

  Protein domains


Predicted by InterproScan.

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

(508-636)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2545874..2573458

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Rmet_2327 2541444..2542553 + 1110 ABF09204 putative adenine-specific DNA methyltransferase -
Rmet_2328 2542604..2542924 + 321 ABF09205 conserved hypothetical protein -
Rmet_2329 2543014..2543319 + 306 ABF09206 conserved hypothetical protein -
Rmet_2330 2543456..2545735 + 2280 ABF09207 Putative plasmid-related DNA/RNA helicase -
Rmet_2331 2545874..2546473 + 600 ABF09208 pilL lipoprotein (type IV pili) tfc2
Rmet_2332 2546470..2547114 + 645 ABF09209 conserved putative exported protein -
Rmet_2333 2547127..2547864 + 738 ABF09210 conserved putative exported protein tfc3
Rmet_2334 2547846..2548436 + 591 ABF09211 putative lytic transglycosylase, catalytic virB1
Rmet_2335 2548433..2548981 + 549 ABF09212 putative exported protein tfc5
Rmet_2336 2548986..2551175 + 2190 ABF09213 VirD4, Type IV secretory pathway, VirD4 components -
Rmet_2337 2551172..2551921 + 750 ABF09214 conserved hypothetical protein; putative membrane protein tfc7
Rmet_2338 2551962..2554586 - 2625 ABF09215 conserved hypothetical protein -
Rmet_2339 2554596..2555321 - 726 ABF09216 conserved hypothetical protein -
Rmet_2340 2555360..2556262 - 903 ABF09217 conserved hypothetical protein -
Rmet_2341 2556262..2556915 - 654 ABF09218 conserved hypothetical protein -
Rmet_6523 2556759..2557229 - 471 ADC45130 conserved hypothetical protein -
Rmet_2342 2557226..2558140 - 915 ABF09219 putative AAA ATPase, central region -
Rmet_2343 2558158..2558733 - 576 ABF09220 conserved hypothetical protein -
Rmet_2344 2558730..2559200 - 471 ABF09221 putative excisionase -
Rmet_2345 2559404..2559787 + 384 ABF09222 conserved hypothetical protein tfc8
Rmet_2346 2559784..2560017 + 234 ABF09223 conserved hypothetical protein tfc9
Rmet_2347 2560034..2560393 + 360 ABF09224 conserved hypothetical protein tfc10
Rmet_2348 2560406..2560804 + 399 ABF09225 conserved hypothetical protein tfc11
Rmet_2349 2560801..2561493 + 693 ABF09226 conserved hypothetical protein tfc12
Rmet_2350 2561490..2562401 + 912 ABF09227 conserved hypothetical protein tfc13
Rmet_2351 2562391..2563809 + 1419 ABF09228 conserved hypothetical protein tfc14
Rmet_2352 2563790..2564230 + 441 ABF09229 Putative secreted protein tfc15
Rmet_2353 2564230..2567121 + 2892 ABF09230 Type IV secretory pathway, VirB4 components virb4
Rmet_2354 2567146..2567910 + 765 ABF09231 putative exported protein -
Rmet_2355 2568086..2568580 + 495 ABF09232 DNA binding protein, possibly associated to lesions -
Rmet_2356 2568745..2569191 + 447 ABF09233 conserved hypothetical protein; putative exported protein tfc24
Rmet_2357 2569188..2570138 + 951 ABF09234 putative exported protein tfc23
Rmet_2358 2570148..2571542 + 1395 ABF09235 putative membrane protein tfc22
Rmet_2359 2571539..2571895 + 357 ABF09236 putative membrane protein tfc18
Rmet_2360 2571911..2573458 + 1548 ABF09237 conserved hypothetical protein (membrane) tfc19
Rmet_2361 2573474..2573833 - 360 ABF09238 conserved hypothetical protein -
Rmet_2362 2573907..2574539 - 633 ABF09239 conserved hypothetical protein -
Rmet_2363 2574552..2575178 - 627 ABF09240 conserved hypothetical protein -
Rmet_2364 2575344..2577386 + 2043 ABF09241 relaxase -
Rmet_2365 2577434..2578429 - 996 ABF09242 putative transcriptional regulator -

Host bacterium

ID   420 Element type   ICE (Integrative and conjugative element)
Element name   ICECmeCH34-1 GenBank   CP000352
Element size   3928089 bp Coordinate of oriT [Strand]   8299..8616 [-]
Host bacterium   Cupriavidus metallidurans CH34 Coordinate of element   2508632..2618212

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   pbrA, merR2, merT
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA3