Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100443
Name   oriT_pNDM-HK in_silico
Organism   Escherichia coli
Sequence Completeness      core
NCBI accession of oriT (coordinates [strand])   NC_019063 (65764..65869 [+], 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    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 106 nt

>oriT_pNDM-HK
AGTACGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCGTCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   514 GenBank   YP_006952501
Name   Nickase_pNDM-HK insolico UniProt ID   F1CNQ2
Length   659 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 659 a.a.        Molecular weight: 75223.04 Da        Isoelectric Point: 9.9948

>YP_006952501.1 putative nickase (plasmid) [Escherichia coli]
MVIPKIIEGRRDKKSSFGQLIKYMADKPSQELTDTVQPTPETVLAVKSDMFEGLNNYLIRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQNTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFTKDTLHQACRLLELKNGWSHSNGAYVVND
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNLIHVSAGLREAKSWDDVHK
TFADIGLRVEKAQGKKGYVITHEHQNQKTAVKASLVFNKAQYTLKSMEERFGEYQPSHIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPIYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPHTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSVRVDGDGEFKELCCNRIVDAAVNHNLPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSESDDKFNPK

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(87-334)

Large polyvalent protein-associated domain 7 (LPD7)

(530-630)


  Protein structure


Source ID Structure
AlphaFold DB F1CNQ2


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 68665..88083

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS772_RS00430 (D616_p59094) 63750..64061 + 312 WP_015058934 hypothetical protein -
HS772_RS00435 (D616_p59095) 64194..64730 + 537 WP_015058935 hypothetical protein -
HS772_RS00440 (D616_p59054) 65231..65626 - 396 WP_015058936 hypothetical protein -
HS772_RS00565 65625..66188 + 564 WP_227537722 plasmid mobilization protein MobA -
HS772_RS00450 (D616_p59052) 66175..68154 + 1980 WP_015058937 TraI/MobA(P) family conjugative relaxase -
HS772_RS00455 (D616_p59051) 68168..68668 + 501 WP_004187320 DotD/TraH family lipoprotein -
HS772_RS00460 (D616_p59050) 68665..69444 + 780 WP_015058938 type IV secretory system conjugative DNA transfer family protein traI
HS772_RS00465 (D616_p59049) 69455..70618 + 1164 WP_004187313 plasmid transfer ATPase TraJ virB11
HS772_RS00470 (D616_p59048) 70608..70868 + 261 WP_004187310 IcmT/TraK family protein traK
HS772_RS00570 70893..74420 + 3528 WP_015058939 LPD7 domain-containing protein -
HS772_RS00480 (D616_p59040) 74344..74898 + 555 WP_015243643 hypothetical protein traL
HS772_RS00485 74899..75096 - 198 WP_004187464 Hha/YmoA family nucleoid-associated regulatory protein -
HS772_RS00490 75083..75493 - 411 WP_004187465 H-NS family nucleoid-associated regulatory protein -
HS772_RS00495 (D616_p59046) 75492..76274 + 783 WP_015058941 DotI/IcmL family type IV secretion protein traM
HS772_RS00500 (D616_p59045) 76283..77434 + 1152 WP_011091074 DotH/IcmK family type IV secretion protein traN
HS772_RS00505 (D616_p59044) 77446..78795 + 1350 WP_015058942 conjugal transfer protein TraO traO
HS772_RS00510 (D616_p59043) 78807..79511 + 705 WP_015243644 conjugal transfer protein TraP traP
HS772_RS00515 (D616_p59042) 79535..80065 + 531 WP_011091077 conjugal transfer protein TraQ traQ
HS772_RS00520 (D616_p59041) 80082..80471 + 390 WP_011091078 DUF6750 family protein traR
HS772_RS00525 (D616_p59097) 80517..81011 + 495 WP_015243645 hypothetical protein -
HS772_RS00530 (D616_p59098) 81008..84058 + 3051 WP_011091081 hypothetical protein traU
HS772_RS00535 (D616_p59099) 84055..85263 + 1209 WP_011091082 conjugal transfer protein TraW traW
HS772_RS00540 (D616_p59100) 85260..85910 + 651 WP_011091083 hypothetical protein -
HS772_RS00545 (D616_p59101) 85903..88083 + 2181 WP_004187492 DotA/TraY family protein traY
HS772_RS00550 (D616_p59102) 88086..88739 + 654 WP_011091084 hypothetical protein -

Host bacterium

ID   904 GenBank   NC_019063
Plasmid name   pNDM-HK Incompatibility group   IncL/M
Plasmid size   88803 bp Coordinate of oriT [Strand]   65764..65869 [+]
Host baterium   Escherichia coli

Cargo genes

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