Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   115794
Name   oriT_64A:C|unnamed3 in_silico
Organism   Citrobacter portucalensis strain 64A:C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP134687 (21281..21386 [-], 106 nt)
oriT length   106 nt
IRs (inverted repeats)      30..35, 41..46  (CCGCCG..CGGCGG)
Location of nic site      _
Conserved sequence flanking the
  nic site  
 
 _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 106 nt

>oriT_64A:C|unnamed3
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase


ID   10116 GenBank   WP_004187323
Name   traI_RIK60_RS25305_64A:C|unnamed3 insolico UniProt ID   A0A3U8KUL3
Length   659 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 659 a.a.        Molecular weight: 75179.89 Da        Isoelectric Point: 9.9948

>WP_004187323.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK

  Protein domains


Predicted by InterproScan.

(86-334)


  Protein structure


Source ID Structure
AlphaFold DB A0A3U8KUL3


T4CP


ID   11821 GenBank   WP_004206885
Name   t4cp2_RIK60_RS25605_64A:C|unnamed3 insolico UniProt ID   _
Length   695 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 695 a.a.        Molecular weight: 79538.91 Da        Isoelectric Point: 4.8317

>WP_004206885.1 MULTISPECIES: conjugal transfer protein TrbC [Enterobacterales]
MQQESVDSKKVLRPDGSFMEWFLTPNVQFGLLAILTVLGLFLPFTMLLSILILPPLMVAFTDRKFRPPLR
MPKDCEMFDDTLTTETQAEYRLGPIRIPHKVRERKKAKGILYVGYERGRLFGRELWLNMTDLLRHMVFFG
TTGSGKTETFYGFIVNFLLWCRGYCLSDGKADNKLAFATWSLARRFGREDDYYVLNLLTGSIDRFVNLVK
QESIPAQSNSVNLFSVAPPTFIIQLMESMLPQVGGDSAQWQDTAKAMMSALINALCYKRARGELLLSQRT
IQKNMSLPAMAALYVEAKKNGWHSEGYAALESYLENTPGFLLANAEYPETWEARAFEQHNYMSRQFLKTL
SLFNETYGHVFPEDSGDIRMDDIFHNDRILIVMIPSLELSRGEAATLGRLYVTLQRMTISKDLGYQLEGK
KEEVLLTHALNNQAPYGLIYDELGQYFTSGMDTLSAQMRSLEKMGVFSSQDHPSLARGANGEVDSLIANT
RVKYFESIEDRKTFEILRETVGQDYYSELSGQEAEHGTFSKTVREGDLYQIREKDRVNIRELRKQTEGQG
VISFQDALVRSAAFYIPDNEKFSSELPMRINRFIEVLPPSPATLYSIYPERKDDELAETNPDAMRFPPIK
LFGYDKAANSLLEKIEVFYELQCGAISPEEMSVCLFELFAEWLDGTETDDVLYHQEDDLFPMIEM

  Protein domains



No domain identified.


  Protein structure



No available structure.




T4SS


T4SS were predicted by using oriTfinder2.

Region 1: 1977..18485

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RIK60_RS25215 (RIK60_25215) 1384..1980 - 597 WP_015060003 hypothetical protein -
RIK60_RS25220 (RIK60_25220) 1977..3185 - 1209 WP_011091082 conjugal transfer protein TraW traW
RIK60_RS25225 (RIK60_25225) 3182..6232 - 3051 WP_004187482 hypothetical protein traU
RIK60_RS25230 (RIK60_25230) 6229..6723 - 495 WP_004187480 hypothetical protein -
RIK60_RS25235 (RIK60_25235) 6769..7158 - 390 WP_004187479 DUF6750 family protein traR
RIK60_RS25240 (RIK60_25240) 7175..7705 - 531 WP_004187478 conjugal transfer protein TraQ traQ
RIK60_RS25245 (RIK60_25245) 7729..8433 - 705 WP_015060002 conjugal transfer protein TraP traP
RIK60_RS25250 (RIK60_25250) 8445..9794 - 1350 WP_004187474 conjugal transfer protein TraO traO
RIK60_RS25255 (RIK60_25255) 9806..10957 - 1152 WP_004187471 DotH/IcmK family type IV secretion protein traN
RIK60_RS25260 (RIK60_25260) 10966..11679 - 714 WP_004187467 DotI/IcmL family type IV secretion protein traM
RIK60_RS25265 (RIK60_25265) 11747..12157 + 411 WP_004187465 H-NS family nucleoid-associated regulatory protein -
RIK60_RS25270 (RIK60_25270) 12186..12341 + 156 WP_172693602 Hha/YmoA family nucleoid-associated regulatory protein -
RIK60_RS25275 (RIK60_25275) 12342..12854 - 513 WP_011091071 hypothetical protein traL
RIK60_RS25280 (RIK60_25280) 12820..16257 - 3438 WP_015586048 LPD7 domain-containing protein -
RIK60_RS25285 (RIK60_25285) 16282..16542 - 261 WP_004187310 IcmT/TraK family protein traK
RIK60_RS25290 (RIK60_25290) 16532..17695 - 1164 WP_004187313 plasmid transfer ATPase TraJ virB11
RIK60_RS25295 (RIK60_25295) 17706..18485 - 780 WP_004187315 type IV secretory system conjugative DNA transfer family protein traI
RIK60_RS25300 (RIK60_25300) 18482..18982 - 501 WP_004187320 DotD/TraH family lipoprotein -
RIK60_RS25305 (RIK60_25305) 18996..20975 - 1980 WP_004187323 TraI/MobA(P) family conjugative relaxase -
RIK60_RS25310 (RIK60_25310) 20962..21489 - 528 WP_172740549 plasmid mobilization protein MobA -
RIK60_RS25315 (RIK60_25315) 21524..21919 + 396 WP_019725163 hypothetical protein -
RIK60_RS25320 (RIK60_25320) 22421..22957 - 537 WP_004187332 hypothetical protein -
RIK60_RS25325 (RIK60_25325) 23090..23401 - 312 WP_004187333 hypothetical protein -


Host bacterium


ID   16227 GenBank   NZ_CP134687
Plasmid name   64A:C|unnamed3 Incompatibility group   IncL/M
Plasmid size   64903 bp Coordinate of oriT [Strand]   21281..21386 [-]
Host baterium   Citrobacter portucalensis strain 64A:C

Cargo genes


Drug resistance gene   blaOXA-48
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -