Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100078 |
| Name | oriT_pHTbeta  |
| Organism | Enterococcus faecium |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_007594 (30409..30600 [-], 192 nt) |
| oriT length | 192 nt |
| IRs (inverted repeats) | IR1: 38..49, 52..64 (TAGCACCTTCCT..AGGAAGGTGGCTA) IR2: 65..71, 75..81 (AGTTGGC..GCCAACT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note |
oriT sequence
Download Length: 192 nt
>oriT_pHTbeta
CCAAAGAATTAATGCAAAGAGCATAAGGGAAAACTAATAGCACCTTCCTAAAGGAAGGTGGCTAAGTTGGCTGTGCCAACTGGTTTTCTTTCAAAATCACTTCATATTTTTTGCTATCACAAAAAAATCCATTTTCGACCTATTTTCGGTCATAATATAGTACCTACTTTTGGTCATAGTTTCGTCCGTAGT
CCAAAGAATTAATGCAAAGAGCATAAGGGAAAACTAATAGCACCTTCCTAAAGGAAGGTGGCTAAGTTGGCTGTGCCAACTGGTTTTCTTTCAAAATCACTTCATATTTTTTGCTATCACAAAAAAATCCATTTTCGACCTATTTTCGGTCATAATATAGTACCTACTTTTGGTCATAGTTTCGTCCGTAGT
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Tomita H et al. (2005) Genetic analysis of transfer-related regions of the vancomycin resistance Enterococcus conjugative plasmid pHTbeta: identification of oriT and a putative relaxase gene. J Bacteriol. 187(22):7727-37. [PMID:16267297]
Relaxase
| ID | 73 | GenBank | YP_398676 |
| Name | ORF34_pHTbeta  |
UniProt ID | Q33E54 |
| Length | 506 a.a. | PDB ID | |
| Note | putative relaxase/nickase | ||
Relaxase protein sequence
Download Length: 506 a.a. Molecular weight: 60652.14 Da Isoelectric Point: 9.4204
>YP_398676.1 putative relaxase/nickase (plasmid) [Enterococcus faecium]
MTEHIFNRKSASIILKAKFETGKNKKKNHMVELQKFVDYISRQEAIRQDKLDHDYSEDELNELARIEKAL
EKIEQETDQPVIKDLREMDKYIDYMTRKKAILENVDNEIVNGAFSNTKRYITKKDISKIKESVIEAKNNG
SVMFQDVISFDNDFLVREGYYNPETNELNENILYEATKSMMGKMQEKEELVDPFWFATIHRNTEHIHIHV
TAMERKNTREIMEYDGVLQARGKRKQSTLDDMIFKFGSKILDRTNEFEKISKLRKEVPLELKQSVKDSLI
QLYVENNSRYDKELVKYLKELKKEIPSTTRGYNELPEETKEKIDEVTNYMTKDNPKRKEYDRMTKEIDEL
YQTTYGKRYNPQEYYLNRKKDFNARMGNAVVGQIKLLKQSEEKNLKSNELKNLLDGKKLNVKFDREKPEF
KTKYAKQSYDDFQKRLEERQLAREKNEVHFKKISEKFKDKKLIRKIDRVINDDLNMYRAKNDYEVAQRMI
EQEKMRQAREFEIGMN
MTEHIFNRKSASIILKAKFETGKNKKKNHMVELQKFVDYISRQEAIRQDKLDHDYSEDELNELARIEKAL
EKIEQETDQPVIKDLREMDKYIDYMTRKKAILENVDNEIVNGAFSNTKRYITKKDISKIKESVIEAKNNG
SVMFQDVISFDNDFLVREGYYNPETNELNENILYEATKSMMGKMQEKEELVDPFWFATIHRNTEHIHIHV
TAMERKNTREIMEYDGVLQARGKRKQSTLDDMIFKFGSKILDRTNEFEKISKLRKEVPLELKQSVKDSLI
QLYVENNSRYDKELVKYLKELKKEIPSTTRGYNELPEETKEKIDEVTNYMTKDNPKRKEYDRMTKEIDEL
YQTTYGKRYNPQEYYLNRKKDFNARMGNAVVGQIKLLKQSEEKNLKSNELKNLLDGKKLNVKFDREKPEF
KTKYAKQSYDDFQKRLEERQLAREKNEVHFKKISEKFKDKKLIRKIDRVINDDLNMYRAKNDYEVAQRMI
EQEKMRQAREFEIGMN
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q33E54 |
Reference
[1] Tomita H et al. (2005) Genetic analysis of transfer-related regions of the vancomycin resistance Enterococcus conjugative plasmid pHTbeta: identification of oriT and a putative relaxase gene. J Bacteriol. 187(22):7727-37. [PMID:16267297]
T4CP
| ID | 73 | GenBank | YP_398664 |
| Name | VirD4_pHT beta |
UniProt ID | Q33E66 |
| Length | 952 a.a. | PDB ID | _ |
| Note | Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, secretion, and vesicular transport]; COG3505 | ||
T4CP protein sequence
Download Length: 952 a.a. Molecular weight: 108263.13 Da Isoelectric Point: 7.8218
>YP_398664.1 hypothetical protein pHTbeta_22 (plasmid) [Enterococcus faecium]
MKLVQNNEVKERKNGFVKNSNKILGKLKKVGSFKKNKYHTGKIEGEDLPKSLQDKLNVPLVFIGVFLGSI
VFLAITYLLNFLKALLVAIGQSESGLLGVEFDPKFSLAYLKPLGDTKQYFMCAVVAVIGVAYLIYGKLNH
ESEKNLVYGQKGDSRLSTIKEIKRDYHEIPEKTEVYDGIGGVPISHYQDKYYIDRDTVNTVVLGASRSGK
GETFVVPLLDNLSRAKIQSNMVVNDPKGELFSASKETLEKRGYRVLVLNIDDPLESMSFNPLQLVIDSWA
NKDYHEASKRANTLTSMLFASGMGTDNEFFYKSAKSAVNAIILTIVEHCFNNDCIEKITMYNVAQMLNEL
GSLFYTDPKTGKEKNALDEYFNTLPQGNQAKIQYGSTSFAGDKAKGSILSTASQGIEMFTSDLFGKLTSK
MSIDLKEIGFPKSIQFKVNTNLVGKRISISFLRKENDVIRLIKKYRVKVKALGLCVLNFNEYLQDGDMLD
IRYEEEKSRAWYRIEFPKKQANSHDTSLVTKKFKSGKNYSDLEISTLRLKYTDQPTAVFMVIPDYDPSNH
VLASIFISQLYTELASNCKQTPDKKCFRRVHFLLDEFGNMPAIDNMDGIMTVCLGRNMLFDLVIQSYSQL
ETRYDKAFKTIKENCQNHILIMSNDEETIEEISKKCGHKTTINRSASSKHLDTDSSVTSSAEQERVITVE
RASQLIEGEQIILRNLHRQDTKRNKIRPFPIFNTKETNMPYRYQFLAEDFDTQRDINEIDIACEHINLSL
QDNQIPYARFIKDLKTRLEYSIINNIPISEEDYQDYRNLSGSQQTINEEELLKLVNTEVKSQDMEGQVLS
EQEMKINIYLKESQKEAIELVKVINGRLADENSADMVIKTINSQVLDTPFIQSLINDSIAIHNVQESKDQ
IMILEQQLANAYELAVLKTKNSILKNKIIKLKNAMTKLAKAI
MKLVQNNEVKERKNGFVKNSNKILGKLKKVGSFKKNKYHTGKIEGEDLPKSLQDKLNVPLVFIGVFLGSI
VFLAITYLLNFLKALLVAIGQSESGLLGVEFDPKFSLAYLKPLGDTKQYFMCAVVAVIGVAYLIYGKLNH
ESEKNLVYGQKGDSRLSTIKEIKRDYHEIPEKTEVYDGIGGVPISHYQDKYYIDRDTVNTVVLGASRSGK
GETFVVPLLDNLSRAKIQSNMVVNDPKGELFSASKETLEKRGYRVLVLNIDDPLESMSFNPLQLVIDSWA
NKDYHEASKRANTLTSMLFASGMGTDNEFFYKSAKSAVNAIILTIVEHCFNNDCIEKITMYNVAQMLNEL
GSLFYTDPKTGKEKNALDEYFNTLPQGNQAKIQYGSTSFAGDKAKGSILSTASQGIEMFTSDLFGKLTSK
MSIDLKEIGFPKSIQFKVNTNLVGKRISISFLRKENDVIRLIKKYRVKVKALGLCVLNFNEYLQDGDMLD
IRYEEEKSRAWYRIEFPKKQANSHDTSLVTKKFKSGKNYSDLEISTLRLKYTDQPTAVFMVIPDYDPSNH
VLASIFISQLYTELASNCKQTPDKKCFRRVHFLLDEFGNMPAIDNMDGIMTVCLGRNMLFDLVIQSYSQL
ETRYDKAFKTIKENCQNHILIMSNDEETIEEISKKCGHKTTINRSASSKHLDTDSSVTSSAEQERVITVE
RASQLIEGEQIILRNLHRQDTKRNKIRPFPIFNTKETNMPYRYQFLAEDFDTQRDINEIDIACEHINLSL
QDNQIPYARFIKDLKTRLEYSIINNIPISEEDYQDYRNLSGSQQTINEEELLKLVNTEVKSQDMEGQVLS
EQEMKINIYLKESQKEAIELVKVINGRLADENSADMVIKTINSQVLDTPFIQSLINDSIAIHNVQESKDQ
IMILEQQLANAYELAVLKTKNSILKNKIIKLKNAMTKLAKAI
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q33E66 |
Reference
[1] Tomita H et al. (2005) Genetic analysis of transfer-related regions of the vancomycin resistance Enterococcus conjugative plasmid pHTbeta: identification of oriT and a putative relaxase gene. J Bacteriol. 187(22):7727-37. [PMID:16267297]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 11474..39441
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HXB78_RS00045 (pHTbeta_10) | 6755..10384 | + | 3630 | WP_011377358 | SpaA isopeptide-forming pilin-related protein | - |
| HXB78_RS00050 (pHTbeta_11) | 10444..10806 | + | 363 | WP_002338167 | hypothetical protein | - |
| HXB78_RS00055 (pHTbeta_12) | 10820..10972 | + | 153 | WP_011377359 | hypothetical protein | - |
| HXB78_RS00060 (pHTbeta_13) | 11040..11462 | + | 423 | WP_002338169 | hypothetical protein | - |
| HXB78_RS00065 (pHTbeta_14) | 11474..12889 | + | 1416 | WP_011377361 | CpaF/VirB11 family protein | virB11 |
| HXB78_RS00070 (pHTbeta_15) | 12906..13721 | + | 816 | WP_080106305 | hypothetical protein | - |
| HXB78_RS00075 (pHTbeta_16) | 13721..14518 | + | 798 | WP_002338172 | hypothetical protein | - |
| HXB78_RS00080 (pHTbeta_17) | 14536..14898 | + | 363 | WP_002338173 | hypothetical protein | - |
| HXB78_RS00085 (pHTbeta_18) | 14912..15058 | + | 147 | WP_002326866 | hypothetical protein | - |
| HXB78_RS00090 | 15070..15291 | + | 222 | WP_002338174 | hypothetical protein | - |
| HXB78_RS00095 (pHTbeta_19) | 15310..15585 | + | 276 | WP_002311852 | TrbC/VirB2 family protein | virB2 |
| HXB78_RS00100 (pHTbeta_20) | 15694..17520 | + | 1827 | WP_011377363 | hypothetical protein | - |
| HXB78_RS00105 (pHTbeta_21) | 17533..18249 | + | 717 | WP_011377364 | hypothetical protein | - |
| HXB78_RS00110 (pHTbeta_22) | 18262..21120 | + | 2859 | WP_011377365 | VirD4-like conjugal transfer protein, CD1115 family | - |
| HXB78_RS00115 (pHTbeta_23) | 21228..23912 | + | 2685 | WP_238792833 | pLS20_p028 family conjugation system transmembrane protein | - |
| HXB78_RS00120 (pHTbeta_24) | 23936..24271 | + | 336 | WP_181404974 | DUF5592 family protein | - |
| HXB78_RS00125 (pHTbeta_25) | 24268..24885 | + | 618 | WP_002311858 | hypothetical protein | virb4 |
| HXB78_RS00130 (pHTbeta_26) | 24902..25369 | + | 468 | WP_011377368 | hypothetical protein | - |
| HXB78_RS00135 (pHTbeta_27) | 25385..27340 | + | 1956 | WP_002311860 | tra protein | virb4 |
| HXB78_RS00140 (pHTbeta_28) | 27362..28498 | + | 1137 | WP_002311861 | bifunctional lytic transglycosylase/C40 family peptidase | orf14 |
| HXB78_RS00145 (pHTbeta_29) | 28512..29162 | + | 651 | WP_011377369 | hypothetical protein | - |
| HXB78_RS00150 (pHTbeta_30) | 29176..30072 | + | 897 | WP_011377370 | hypothetical protein | - |
| HXB78_RS00155 (pHTbeta_31) | 30108..30338 | + | 231 | WP_002311864 | hypothetical protein | - |
| HXB78_RS00160 (pHTbeta_32) | 30689..30985 | + | 297 | WP_010776936 | hypothetical protein | - |
| HXB78_RS00165 (pHTbeta_33) | 30982..31449 | + | 468 | WP_011377371 | hypothetical protein | - |
| HXB78_RS00170 (pHTbeta_34) | 31466..33052 | + | 1587 | WP_238792822 | MobP2 family relaxase | - |
| HXB78_RS00175 (pHTbeta_35) | 33074..33403 | + | 330 | WP_002311869 | hypothetical protein | - |
| HXB78_RS00180 (pHTbeta_36) | 33405..33668 | + | 264 | WP_002338155 | hypothetical protein | - |
| HXB78_RS00185 (pHTbeta_37) | 33890..34756 | + | 867 | WP_011377373 | hypothetical protein | - |
| HXB78_RS00190 (pHTbeta_38) | 34911..36737 | + | 1827 | WP_011377374 | ArdC-like ssDNA-binding domain-containing protein | - |
| HXB78_RS00195 (pHTbeta_39) | 36742..37815 | + | 1074 | WP_181404969 | hypothetical protein | - |
| HXB78_RS00200 (pHTbeta_40) | 37824..38081 | + | 258 | WP_011377376 | hypothetical protein | - |
| HXB78_RS00205 (pHTbeta_41) | 38122..38412 | + | 291 | WP_011377377 | hypothetical protein | - |
| HXB78_RS00210 (pHTbeta_42) | 38437..39441 | + | 1005 | WP_011377378 | DUF3991 domain-containing protein | traP |
| HXB78_RS00215 (pHTbeta_43) | 39466..39822 | + | 357 | WP_181404970 | hypothetical protein | - |
| HXB78_RS00220 (pHTbeta_45) | 40284..40502 | + | 219 | WP_011377380 | hypothetical protein | - |
| HXB78_RS00225 (pHTbeta_46) | 40539..40856 | + | 318 | WP_011377381 | hypothetical protein | - |
| HXB78_RS00230 (pHTbeta_47) | 40867..41064 | + | 198 | WP_011377382 | hypothetical protein | - |
| HXB78_RS00235 (pHTbeta_48) | 41061..42029 | + | 969 | WP_011377383 | zeta toxin family protein | - |
| HXB78_RS00240 (pHTbeta_49) | 42270..43442 | + | 1173 | WP_181404971 | hypothetical protein | - |
Host bacterium
| ID | 73 | GenBank | NC_007594 |
| Plasmid name | pHT beta | Incompatibility group | - |
| Plasmid size | 52890 bp | Coordinate of oriT [Strand] | 30409..30600 [-] |
| Host baterium | Enterococcus faecium |
Cargo genes
| Drug resistance gene | carry Tn1546-like transposons encoding vancomycin resistance |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | AcrIIA1 |