Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120579
Name   oriT_pCF2_OXA48 in_silico
Organism   Citrobacter freundii strain CF2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP133849 (25130..25235 [+], 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_pCF2_OXA48
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12962 GenBank   WP_326971574
Name   Relaxase_RHA96_RS01980_pCF2_OXA48 insolico UniProt ID   _
Length   323 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 323 a.a.        Molecular weight: 36857.73 Da        Isoelectric Point: 9.9196

>WP_326971574.1 relaxase/mobilization nuclease domain-containing protein [Citrobacter freundii]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKRATSLPTNIKTRRRLLRRVWYLTRRNIP

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(53-303)


  Protein structure



No available structure.




T4CP

ID   15221 GenBank   WP_004206885
Name   t4cp2_RHA96_RS02105_pCF2_OXA48 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: 28030..55373

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RHA96_RS01960 (RHA96_01960) 23115..23426 + 312 WP_004187333 hypothetical protein -
RHA96_RS01965 (RHA96_01965) 23559..24095 + 537 WP_004187332 hypothetical protein -
RHA96_RS01970 (RHA96_01970) 24597..24992 - 396 WP_019725163 hypothetical protein -
RHA96_RS01975 (RHA96_01975) 25027..25554 + 528 WP_172740549 plasmid mobilization protein MobA -
RHA96_RS01980 (RHA96_01980) 25541..26512 + 972 WP_326971574 relaxase/mobilization nuclease domain-containing protein -
RHA96_RS01985 (RHA96_01985) 26518..27519 + 1002 WP_326971575 hypothetical protein -
RHA96_RS01990 (RHA96_01990) 27533..28033 + 501 WP_004187320 DotD/TraH family lipoprotein -
RHA96_RS01995 (RHA96_01995) 28030..28809 + 780 WP_004187315 type IV secretory system conjugative DNA transfer family protein traI
RHA96_RS02000 (RHA96_02000) 28820..29983 + 1164 WP_004187313 plasmid transfer ATPase TraJ virB11
RHA96_RS02005 (RHA96_02005) 29973..30233 + 261 WP_004187310 IcmT/TraK family protein traK
RHA96_RS02010 (RHA96_02010) 30258..33695 + 3438 WP_015586048 LPD7 domain-containing protein -
RHA96_RS02015 (RHA96_02015) 33661..34173 + 513 WP_011091071 hypothetical protein traL
RHA96_RS02020 (RHA96_02020) 34174..34386 - 213 WP_305953721 Hha/YmoA family nucleoid-associated regulatory protein -
RHA96_RS02025 (RHA96_02025) 34358..34768 - 411 WP_004187465 H-NS family nucleoid-associated regulatory protein -
RHA96_RS02030 (RHA96_02030) 34836..35549 + 714 WP_004187467 DotI/IcmL family type IV secretion protein traM
RHA96_RS02035 (RHA96_02035) 35558..36709 + 1152 WP_004187471 DotH/IcmK family type IV secretion protein traN
RHA96_RS02040 (RHA96_02040) 36721..38070 + 1350 WP_004187474 conjugal transfer protein TraO traO
RHA96_RS02045 (RHA96_02045) 38082..38786 + 705 WP_015060002 conjugal transfer protein TraP traP
RHA96_RS02050 (RHA96_02050) 38810..39340 + 531 WP_004187478 conjugal transfer protein TraQ traQ
RHA96_RS02055 (RHA96_02055) 39357..39746 + 390 WP_004187479 DUF6750 family protein traR
RHA96_RS02060 (RHA96_02060) 39792..40286 + 495 WP_004187480 hypothetical protein -
RHA96_RS02065 (RHA96_02065) 40283..43333 + 3051 WP_004187482 hypothetical protein traU
RHA96_RS02070 (RHA96_02070) 43330..44538 + 1209 WP_011091082 conjugal transfer protein TraW traW
RHA96_RS02075 (RHA96_02075) 44535..45131 + 597 WP_015060003 hypothetical protein -
RHA96_RS02080 (RHA96_02080) 45124..47319 + 2196 WP_015062834 DotA/TraY family protein traY
RHA96_RS02085 (RHA96_02085) 47321..47974 + 654 WP_015060005 hypothetical protein -
RHA96_RS02090 (RHA96_02090) 48055..48285 + 231 WP_011091085 IncL/M type plasmid replication protein RepC -
RHA96_RS02095 (RHA96_02095) 48581..49636 + 1056 WP_015060006 plasmid replication initiator RepA -
RHA96_RS02100 (RHA96_02100) 50859..50954 + 96 WP_004206884 DinQ-like type I toxin DqlB -
RHA96_RS02105 (RHA96_02105) 51005..53092 - 2088 WP_004206885 conjugal transfer protein TrbC -
RHA96_RS02110 (RHA96_02110) 53105..54055 - 951 WP_004206886 DsbC family protein trbB
RHA96_RS02115 (RHA96_02115) 54066..55373 - 1308 WP_015059988 hypothetical protein trbA
RHA96_RS02120 (RHA96_02120) 55373..55768 - 396 WP_004187436 lytic transglycosylase domain-containing protein -
RHA96_RS02125 (RHA96_02125) 55873..56223 - 351 WP_124065455 DUF1496 domain-containing protein -
RHA96_RS02130 (RHA96_02130) 56336..56770 + 435 Protein_76 CPBP family intramembrane glutamate endopeptidase -
RHA96_RS02135 (RHA96_02135) 56785..57993 - 1209 WP_001206290 IS4-like element IS10A family transposase -
RHA96_RS02140 (RHA96_02140) 58296..59207 + 912 WP_015586033 LysR family transcriptional regulator -
RHA96_RS02145 (RHA96_02145) 59509..60306 - 798 WP_015059991 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-48 -

Host bacterium

ID   21008 GenBank   NZ_CP133849
Plasmid name   pCF2_OXA48 Incompatibility group   IncL/M
Plasmid size   63586 bp Coordinate of oriT [Strand]   25130..25235 [+]
Host baterium   Citrobacter freundii strain CF2

Cargo genes

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