Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100852 |
| Name | oriT_pKPGJ-3d  |
| Organism | Klebsiella variicola strain GJ3 |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP017288 (14402..14507 [+], 106 nt) |
| oriT length | 106 nt |
| IRs (inverted repeats) | 18..35, 41..58 (GTTTTTGGAGTACCGCCG..CGGCGGCCATCCAAAAAC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 106 nt
>oriT_pKPGJ-3d
AGTATGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCATCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
AGTATGGGACAAGATGTGTTTTTGGAGTACCGCCGACACGCGGCGGCCATCCAAAAACGTCTTGGTCAGGGCAAGCCCCGACACCCCCTAACGAGGTTAGCTATCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 924 | GenBank | WP_077138896 |
| Name | PutativerelaxaseofpKPGJ-3d |
UniProt ID | A0A1Q1E692 |
| Length | 659 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 659 a.a. Molecular weight: 75388.24 Da Isoelectric Point: 10.0411
>WP_077138896.1 TraI/MobA(P) family conjugative relaxase [Klebsiella variicola]
MVIPKIIEGRRDKKSSFAQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLIRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQNTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFSKDTLHQACRLLELKNGWSHSNGAYVVNE
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNFIHVSAGLREAKSWDDVHK
TFADIGLRFEKAQGKKGYVITHEHQNLKTAVKASLVFNKAQYTLKSMEERFGEYQPSRIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPTYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPYTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSLRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSENDDKFKPK
MVIPKIIEGRRDKKSSFAQLIKYMADKPSQELTDTVQPTPETALAVKSDMFEGLNNYLIRKQKVISTPVD
VEPGVQRVVVGDVTCQYNTFSLDGAAQEMNSVSQQNTRCKDPVMHYVLSWPDYEKPNDDQVFDSVKFTLA
SMGMSDHQYVAAIHRDTDNLHVHVAVNRINPQTYKAASSSFSKDTLHQACRLLELKNGWSHSNGAYVVNE
RQQIVRNPHSKKERGNWRSLDRINKMENKEGVETLYRYIVGDEQVGGSRQNFIHVSAGLREAKSWDDVHK
TFADIGLRFEKAQGKKGYVITHEHQNLKTAVKASLVFNKAQYTLKSMEERFGEYQPSRIEPAKVSVFKTA
YTPGAYRRDANKRLQRKIERAEERMLLKGRYRAYRNNLPTYSPDKDRIADEYRKIAQHTRLVKNNVRHSV
SDPYTRKLMYNLAEFKRLQAVANLRLSLREERNGFRAANPRLSYREWVEQEALKGDKAALSQMRGFAYSS
RKKEKYKQQLVEQIGFNRTFNAITSHDRDDVAVMASARHGVKPRLLKDGTVIFERDGKPVAADRGHIVLT
ESNGIDKEKTADLAIALTIAGKAKSLRVDGDGEFKELCCNRIVDAAVNHNHPVAQGITFTDAAQQAYAQN
EKHRLIREQNNSKNEMQFRSENDDKFKPK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 17303..45078
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| BBD65_RS01845 (BBD65_27765) | 12389..12700 | + | 312 | WP_011091065 | hypothetical protein | - |
| BBD65_RS01850 (BBD65_27770) | 12833..13369 | + | 537 | WP_077138895 | hypothetical protein | - |
| BBD65_RS01855 (BBD65_27775) | 13869..14264 | - | 396 | WP_171972704 | MobC | - |
| BBD65_RS31475 | 14299..14826 | + | 528 | WP_227516820 | plasmid mobilization protein MobA | - |
| BBD65_RS01865 (BBD65_27785) | 14813..16792 | + | 1980 | WP_077138896 | TraI/MobA(P) family conjugative relaxase | - |
| BBD65_RS01870 (BBD65_27790) | 16806..17306 | + | 501 | WP_077138897 | DotD/TraH family lipoprotein | - |
| BBD65_RS01875 (BBD65_27795) | 17303..18082 | + | 780 | WP_004187315 | type IV secretory system conjugative DNA transfer family protein | traI |
| BBD65_RS01880 (BBD65_27800) | 18093..19256 | + | 1164 | WP_077138898 | plasmid transfer ATPase TraJ | virB11 |
| BBD65_RS01885 (BBD65_27805) | 19246..19506 | + | 261 | WP_004187310 | IcmT/TraK family protein | traK |
| BBD65_RS31480 | 19531..22836 | + | 3306 | WP_227516821 | LPD7 domain-containing protein | - |
| BBD65_RS01895 (BBD65_27815) | 22802..23314 | + | 513 | WP_011091071 | hypothetical protein | traL |
| BBD65_RS31795 | 23315..23527 | - | 213 | WP_306458688 | Hha/YmoA family nucleoid-associated regulatory protein | - |
| BBD65_RS01905 (BBD65_27820) | 23499..23909 | - | 411 | WP_040027863 | H-NS family nucleoid-associated regulatory protein | - |
| BBD65_RS01910 (BBD65_27825) | 23977..24690 | + | 714 | WP_227516822 | DotI/IcmL family type IV secretion protein | traM |
| BBD65_RS01915 | 24699..25850 | + | 1152 | WP_077138900 | DotH/IcmK family type IV secretion protein | traN |
| BBD65_RS01920 (BBD65_27835) | 25862..27211 | + | 1350 | WP_077138901 | conjugal transfer protein TraO | traO |
| BBD65_RS01925 (BBD65_27840) | 27223..27927 | + | 705 | WP_077138902 | conjugal transfer protein TraP | traP |
| BBD65_RS01930 (BBD65_27845) | 27951..28481 | + | 531 | WP_004187478 | conjugal transfer protein TraQ | traQ |
| BBD65_RS01935 (BBD65_27850) | 28498..28887 | + | 390 | WP_011154472 | DUF6750 family protein | traR |
| BBD65_RS01940 (BBD65_27855) | 28933..29427 | + | 495 | WP_004187480 | hypothetical protein | - |
| BBD65_RS01945 (BBD65_27860) | 29424..32474 | + | 3051 | WP_077138903 | conjugal transfer protein | traU |
| BBD65_RS01950 (BBD65_27865) | 32471..33679 | + | 1209 | WP_011091082 | conjugal transfer protein TraW | traW |
| BBD65_RS01955 (BBD65_27870) | 33676..34272 | + | 597 | WP_077138904 | TraX-like protein | - |
| BBD65_RS01960 (BBD65_27875) | 34265..36460 | + | 2196 | WP_077138905 | DotA/TraY family protein | traY |
| BBD65_RS01965 (BBD65_27880) | 36462..37115 | + | 654 | WP_077138906 | hypothetical protein | - |
| BBD65_RS01970 (BBD65_27885) | 37196..37426 | + | 231 | WP_011091085 | IncL/M type plasmid replication protein RepC | - |
| BBD65_RS01975 (BBD65_27890) | 37723..38778 | + | 1056 | WP_224052343 | plasmid replication initiator RepA | - |
| BBD65_RS31765 | 40003..40098 | + | 96 | WP_004206884 | DinQ-like type I toxin DqlB | - |
| BBD65_RS01980 (BBD65_27895) | 40153..40662 | - | 510 | WP_023302492 | MucR family transcriptional regulator | - |
| BBD65_RS01985 (BBD65_27900) | 40710..42797 | - | 2088 | WP_011091092 | hypothetical protein | - |
| BBD65_RS01990 (BBD65_27905) | 42810..43760 | - | 951 | WP_004187441 | DsbC family protein | trbB |
| BBD65_RS01995 (BBD65_27910) | 43771..45078 | - | 1308 | WP_015062796 | hypothetical protein | trbA |
| BBD65_RS02000 (BBD65_27915) | 45086..45472 | - | 387 | WP_228146396 | lytic transglycosylase domain-containing protein | - |
| BBD65_RS02005 (BBD65_27920) | 45577..45960 | - | 384 | WP_032451295 | DUF1496 domain-containing protein | - |
| BBD65_RS02010 (BBD65_27925) | 46040..46693 | + | 654 | WP_039592068 | type II CAAX endopeptidase family protein | - |
| BBD65_RS02015 (BBD65_27930) | 46846..47280 | + | 435 | WP_015062799 | translesion error-prone DNA polymerase V autoproteolytic subunit | - |
| BBD65_RS02020 (BBD65_27935) | 47268..48533 | + | 1266 | WP_077138907 | translesion error-prone DNA polymerase V subunit UmuC | - |
| BBD65_RS02025 (BBD65_27940) | 48556..49404 | - | 849 | WP_060453257 | 3'-5' exonuclease | - |
| BBD65_RS02030 (BBD65_27945) | 49407..49727 | - | 321 | WP_021561451 | hypothetical protein | - |
Host bacterium
| ID | 1312 | GenBank | NZ_CP017288 |
| Plasmid name | pKPGJ-3d | Incompatibility group | IncL/M |
| Plasmid size | 58665 bp | Coordinate of oriT [Strand] | 14402..14507 [+] |
| Host baterium | Klebsiella variicola strain GJ3 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |