Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120285
Name   oriT_pCf164_CTX-M-8 in_silico
Organism   Citrobacter freundii strain Cf164
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN187903 (35473..35577 [-], 105 nt)
oriT length   105 nt
IRs (inverted repeats)      32..37, 40..45  (GCCGGC..GCCGGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 105 nt

>oriT_pCf164_CTX-M-8
AGTACGGGACAAGATGTGTTTTTGGTACACCGCCGGCACGCCGGCAGTGACGCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTAT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12760 GenBank   WP_004206924
Name   traI_H5D58_RS00175_pCf164_CTX-M-8 insolico UniProt ID   A0A2V4FJ40
Length   659 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 659 a.a.        Molecular weight: 75087.84 Da        Isoelectric Point: 10.0285

>WP_004206924.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLTRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQSTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFAGIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQLRSESDDKFNPK

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(86-334)


  Protein structure


Source ID Structure
AlphaFold DB A0A2V4FJ40


T4CP

ID   14980 GenBank   WP_004206885
Name   t4cp2_H5D58_RS00060_pCf164_CTX-M-8 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: 5426..32675

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5D58_RS00015 1544..1876 - 333 Protein_2 peroxidase-related enzyme -
H5D58_RS00020 1871..2260 - 390 Protein_3 DUF4158 domain-containing protein -
H5D58_RS00025 2422..2979 + 558 WP_001217881 recombinase family protein -
H5D58_RS00030 3162..4022 + 861 WP_000027057 broad-spectrum class A beta-lactamase TEM-1 -
H5D58_RS00035 4161..4463 - 303 WP_085327671 histidine phosphatase family protein -
H5D58_RS00040 4531..4926 + 396 WP_015062852 DUF1496 domain-containing protein -
H5D58_RS00045 5031..5426 + 396 WP_004187436 lytic transglycosylase domain-containing protein -
H5D58_RS00050 5426..6733 + 1308 WP_015059988 hypothetical protein trbA
H5D58_RS00055 6744..7694 + 951 WP_004206886 DsbC family protein trbB
H5D58_RS00060 7707..9794 + 2088 WP_004206885 conjugal transfer protein TrbC -
H5D58_RS00460 9845..9940 - 96 WP_004206884 DinQ-like type I toxin DqlB -
H5D58_RS00065 11167..12234 - 1068 WP_024190316 plasmid replication initiator RepA -
H5D58_RS00070 12519..12749 - 231 WP_004187496 IncL/M type plasmid replication protein RepC -
H5D58_RS00075 12823..13476 - 654 WP_004206935 hypothetical protein -
H5D58_RS00080 13479..15659 - 2181 WP_004187492 DotA/TraY family protein traY
H5D58_RS00085 15652..16302 - 651 WP_004187488 hypothetical protein -
H5D58_RS00090 16299..17507 - 1209 WP_004187486 conjugal transfer protein TraW traW
H5D58_RS00095 17504..20554 - 3051 WP_011154474 conjugative transfer protein traU
H5D58_RS00100 20551..21045 - 495 WP_085327669 hypothetical protein -
H5D58_RS00105 21091..21480 - 390 WP_011154472 DUF6750 family protein traR
H5D58_RS00110 21497..22027 - 531 WP_004187478 conjugal transfer protein TraQ traQ
H5D58_RS00115 22051..22755 - 705 WP_045342064 conjugal transfer protein TraP traP
H5D58_RS00120 22767..24116 - 1350 WP_004206932 conjugal transfer protein TraO traO
H5D58_RS00125 24128..25279 - 1152 WP_015062843 DotH/IcmK family type IV secretion protein traN
H5D58_RS00130 25288..26070 - 783 WP_004206929 DotI/IcmL family type IV secretion protein traM
H5D58_RS00135 26069..26479 + 411 WP_004187465 H-NS family nucleoid-associated regulatory protein -
H5D58_RS00140 26466..26663 + 198 WP_004187464 Hha/YmoA family nucleoid-associated regulatory protein -
H5D58_RS00145 26664..27218 - 555 WP_011154467 hypothetical protein traL
H5D58_RS00445 27142..30447 - 3306 WP_220178452 LPD7 domain-containing protein -
H5D58_RS00155 30472..30732 - 261 WP_004187310 IcmT/TraK family protein traK
H5D58_RS00160 30722..31885 - 1164 WP_045342066 plasmid transfer ATPase TraJ virB11
H5D58_RS00165 31896..32675 - 780 WP_004187315 type IV secretory system conjugative DNA transfer family protein traI
H5D58_RS00170 32672..33172 - 501 WP_004206925 DotD/TraH family lipoprotein -
H5D58_RS00175 33186..35165 - 1980 WP_004206924 TraI/MobA(P) family conjugative relaxase -
H5D58_RS00180 35152..35469 - 318 WP_004206923 plasmid mobilization protein MobA -
H5D58_RS00185 35745..36110 + 366 WP_004206922 hypothetical protein -
H5D58_RS00190 36611..37147 - 537 WP_004206920 hypothetical protein -
H5D58_RS00195 37280..37591 - 312 WP_004187333 hypothetical protein -

Host bacterium

ID   20714 GenBank   NZ_MN187903
Plasmid name   pCf164_CTX-M-8 Incompatibility group   IncL/M
Plasmid size   68453 bp Coordinate of oriT [Strand]   35473..35577 [-]
Host baterium   Citrobacter freundii strain Cf164

Cargo genes

Drug resistance gene   blaTEM-1A, blaCTX-M-8
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -