Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100234
Name   oriT_pCTX-M3 experimental
Organism   Citrobacter freundii
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_004464 (31616..31721 [+], 106 nt)
oriT length   106 nt
IRs (inverted repeats)      18..35, 41..58  (GTTTTTGGAGTACCGCCG..CGGCGGCCGTCCAAAAAC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  ACATCTTGT
Note   

  oriT sequence  


Download         Length: 106 nt

>oriT_pCTX-M3
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Michał Dmowski et al. (2018) Characteristics of the Conjugative Transfer System of the IncM Plasmid pCTX-M3 and Identification of Its Putative Regulators. Journal of bacteriology. 200(18):e00234-18. [PMID:29986941]


Relaxase

ID   305 GenBank   NP_775011
Name   NikB_pCTX-M3 insolico UniProt ID   Q8GFT3
Length   658 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 658 a.a.        Molecular weight: 75135.84 Da        Isoelectric Point: 10.0285

>NP_775011.1 putative nickase (plasmid) [Citrobacter freundii]
MIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVDV
EPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLAS
MGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVNDR
QQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHKT
FADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTAY
TPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPVYSPDKDRIADEYRKIAQHTRLVKNNVRHSVS
DPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSSR
KKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLTE
SNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQNE
KHRLIREQNNSKNEMQFRSERDDKFNPK

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(85-333)


  Protein structure


Source ID Structure
AlphaFold DB Q8GFT3


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 34517..53620

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HKK50_RS00250 (pCTX-M3_048) 29601..29912 + 312 WP_011091065 hypothetical protein -
HKK50_RS00255 (pCTX-M3_049) 30045..30581 + 537 WP_011091066 hypothetical protein -
HKK50_RS00260 (pCTX-M3_050) 31082..31447 - 366 WP_011091067 hypothetical protein -
HKK50_RS00550 31462..32040 + 579 WP_223811519 plasmid mobilization protein MobA -
HKK50_RS00270 (pCTX-M3_052) 32027..34006 + 1980 WP_050868819 TraI/MobA(P) family conjugative relaxase -
HKK50_RS00275 (pCTX-M3_053) 34020..34520 + 501 WP_004187320 DotD/TraH family lipoprotein -
HKK50_RS00280 (pCTX-M3_054) 34517..35296 + 780 WP_004187315 type IV secretory system conjugative DNA transfer family protein traI
HKK50_RS00285 (pCTX-M3_055) 35307..36470 + 1164 WP_004187313 plasmid transfer ATPase TraJ virB11
HKK50_RS00290 (pCTX-M3_056) 36460..36720 + 261 WP_004187310 IcmT/TraK family protein traK
HKK50_RS00555 36745..39957 + 3213 WP_011091070 LPD7 domain-containing protein -
HKK50_RS00300 (pCTX-M3_058) 39881..40435 + 555 WP_011154467 hypothetical protein traL
HKK50_RS00305 40436..40633 - 198 WP_004187464 Hha/YmoA family nucleoid-associated regulatory protein -
HKK50_RS00310 40620..41030 - 411 WP_004187465 H-NS family nucleoid-associated regulatory protein -
HKK50_RS00315 (pCTX-M3_060) 41029..41811 + 783 WP_011091073 DotI/IcmL family type IV secretion protein traM
HKK50_RS00320 (pCTX-M3_061) 41820..42971 + 1152 WP_011091074 DotH/IcmK family type IV secretion protein traN
HKK50_RS00325 (pCTX-M3_062) 42983..44332 + 1350 WP_011091075 conjugal transfer protein TraO traO
HKK50_RS00330 (pCTX-M3_063) 44344..45048 + 705 WP_011091076 conjugal transfer protein TraP traP
HKK50_RS00335 (pCTX-M3_064) 45072..45602 + 531 WP_011091077 conjugal transfer protein TraQ traQ
HKK50_RS00340 (pCTX-M3_065) 45619..46008 + 390 WP_011091078 DUF6750 family protein traR
HKK50_RS00345 (pCTX-M3_067) 46054..46548 + 495 WP_011091080 hypothetical protein -
HKK50_RS00350 (pCTX-M3_068) 46545..49595 + 3051 WP_011091081 hypothetical protein traU
HKK50_RS00355 (pCTX-M3_069) 49592..50800 + 1209 WP_011091082 conjugal transfer protein TraW traW
HKK50_RS00360 (pCTX-M3_070) 50797..51447 + 651 WP_011091083 hypothetical protein -
HKK50_RS00365 (pCTX-M3_071) 51440..53620 + 2181 WP_004187492 DotA/TraY family protein traY
HKK50_RS00370 (pCTX-M3_072) 53623..54276 + 654 WP_011091084 hypothetical protein -
HKK50_RS00375 (pCTX-M3_073) 54333..54581 + 249 WP_015062836 IncL/M type plasmid replication protein RepC -
HKK50_RS00380 (pCTX-M3_075) 54867..55934 + 1068 WP_050868820 plasmid replication initiator RepA -
HKK50_RS00385 (pCTX-M3_076) 56938..57798 - 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -

Host bacterium

ID   696 GenBank   NC_004464
Plasmid name   pCTX-M3 Incompatibility group   IncL/M
Plasmid size   89468 bp Coordinate of oriT [Strand]   31616..31721 [+]
Host baterium   Citrobacter freundii

Cargo genes

Drug resistance gene   blaCTX-M-3, blaTEM-1B, aac(3)-IId, dfrA12, aadA2, qacE, sul1, armA, msr(E), mph(E)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -