Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106816 |
| Name | oriT_pSme442-208  |
| Organism | Sinorhizobium meliloti strain BIM B-442D |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP123004 (121327..121382 [-], 56 nt) |
| oriT length | 56 nt |
| IRs (inverted repeats) | 4..9, 22..27 (GGAAAG..CTTTCC) |
| Location of nic site | 35..36 |
| Conserved sequence flanking the nic site |
TCCTGCCTCT |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 56 nt
>oriT_pSme442-208
GCAGGAAAGGGCGTAGCACATCTTTCCGTATCCTGCCTCTCCAAATTGTCAGGGGA
GCAGGAAAGGGCGTAGCACATCTTTCCGTATCCTGCCTCTCCAAATTGTCAGGGGA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 4547 | GenBank | WP_088195322 |
| Name | virD4_QC756_RS18920_pSme442-208 |
UniProt ID | _ |
| Length | 563 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 563 a.a. Molecular weight: 63011.38 Da Isoelectric Point: 9.2690
>WP_088195322.1 type IV secretion system ATPase VirD4 [Sinorhizobium meliloti]
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILLVQQMVSVRDRQHYGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILAMPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QKSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPTPLMIADERF
SHV
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILLVQQMVSVRDRQHYGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILAMPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QKSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPTPLMIADERF
SHV
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 4548 | GenBank | WP_127668867 |
| Name | t4cp2_QC756_RS19030_pSme442-208 |
UniProt ID | _ |
| Length | 673 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 673 a.a. Molecular weight: 75288.99 Da Isoelectric Point: 9.6588
>WP_127668867.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium meliloti]
MTKQLQAFYLLFCVGTAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
MVPALLVAGLVAYIGLKPTSSPLGDAAFQDMASLRRAKWFRKQGHIFGRVGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENRMILLIEGQRPIFGEKLRFFETQPFKSAEAFSQANIPQVPEVDYLAPKPVPATTP
EYAKGGDPSVEIPSLAPAKEKKPLTAAAAEAVPVKAERAAEEKAAAPAKRLDAMEARIKAIEEGLKPKAA
QLKEVVETKAEKLGDKSPTKRRNIMDIFSATVPDPVEVGVTAE
MTKQLQAFYLLFCVGTAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
MVPALLVAGLVAYIGLKPTSSPLGDAAFQDMASLRRAKWFRKQGHIFGRVGRNILRTKDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRQNGSQVFLFAPGSEKTNSYNPLDFIRPERGNRT
TDIQNIASILVPENTESENSVWQATAQQVLAGVISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENRMILLIEGQRPIFGEKLRFFETQPFKSAEAFSQANIPQVPEVDYLAPKPVPATTP
EYAKGGDPSVEIPSLAPAKEKKPLTAAAAEAVPVKAERAAEEKAAAPAKRLDAMEARIKAIEEGLKPKAA
QLKEVVETKAEKLGDKSPTKRRNIMDIFSATVPDPVEVGVTAE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 93868..103281
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| QC756_RS18815 (QC756_18815) | 89777..90007 | - | 231 | Protein_98 | transposase | - |
| QC756_RS18820 (QC756_18820) | 90039..91436 | - | 1398 | WP_017263436 | IS1182 family transposase | - |
| QC756_RS18825 (QC756_18825) | 91504..92261 | - | 758 | Protein_100 | IS256-like element ISRm5 family transposase | - |
| QC756_RS18830 (QC756_18830) | 92315..92908 | - | 594 | WP_088195327 | type IV secretory system conjugative DNA transfer family protein | - |
| QC756_RS18835 (QC756_18835) | 92892..93083 | + | 192 | Protein_102 | Lrp/AsnC ligand binding domain-containing protein | - |
| QC756_RS18840 (QC756_18840) | 93142..93438 | + | 297 | WP_164816899 | hypothetical protein | - |
| QC756_RS18845 (QC756_18845) | 93868..94575 | + | 708 | WP_033049347 | type IV secretion system lytic transglycosylase VirB1 | virB1 |
| QC756_RS18850 (QC756_18850) | 94589..94951 | + | 363 | WP_014528518 | pilin major subunit VirB2 | virB2 |
| QC756_RS18855 (QC756_18855) | 94948..95274 | + | 327 | WP_003537077 | type IV secretion system protein VirB3 | virB3 |
| QC756_RS18860 (QC756_18860) | 95274..97643 | + | 2370 | WP_088195326 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| QC756_RS18865 (QC756_18865) | 97657..98340 | + | 684 | WP_003537081 | pilin minor subunit VirB5 | traI |
| QC756_RS18870 (QC756_18870) | 98421..99308 | + | 888 | WP_088195325 | type IV secretion system protein | virB6 |
| QC756_RS18875 (QC756_18875) | 99341..99508 | + | 168 | WP_003537091 | type IV secretion system lipoprotein VirB7 | - |
| QC756_RS18880 (QC756_18880) | 99495..100208 | + | 714 | WP_003537093 | type IV secretion system protein VirB8 | virB8 |
| QC756_RS18885 (QC756_18885) | 100205..101086 | + | 882 | WP_127515308 | P-type conjugative transfer protein VirB9 | virB9 |
| QC756_RS18890 (QC756_18890) | 101083..102201 | + | 1119 | WP_127515306 | type IV secretion system protein VirB10 | virB10 |
| QC756_RS18895 (QC756_18895) | 102241..103281 | + | 1041 | WP_003537101 | P-type DNA transfer ATPase VirB11 | virB11 |
| QC756_RS18900 (QC756_18900) | 103950..105479 | + | 1530 | WP_280097634 | IS21 family transposase | - |
| QC756_RS18905 (QC756_18905) | 105492..106229 | + | 738 | WP_012477343 | IS21-like element helper ATPase IstB | - |
| QC756_RS18910 (QC756_18910) | 106417..106568 | + | 152 | Protein_117 | integrase | - |
| QC756_RS18915 (QC756_18915) | 107106..107831 | + | 726 | WP_003537873 | response regulator | - |
Region 2: 130771..141748
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| QC756_RS19010 (QC756_19010) | 126752..127099 | - | 348 | WP_012477217 | IS66 family insertion sequence element accessory protein TnpB | - |
| QC756_RS19015 (QC756_19015) | 127096..127470 | - | 375 | WP_012477218 | transposase | - |
| QC756_RS19020 (QC756_19020) | 127585..127932 | + | 348 | WP_234836685 | ester cyclase | - |
| QC756_RS19025 (QC756_19025) | 127990..128700 | - | 711 | WP_318884588 | hypothetical protein | - |
| QC756_RS19030 (QC756_19030) | 128753..130774 | - | 2022 | WP_127668867 | type IV secretory system conjugative DNA transfer family protein | - |
| QC756_RS19035 (QC756_19035) | 130771..131799 | - | 1029 | WP_280097619 | P-type DNA transfer ATPase VirB11 | virB11 |
| QC756_RS19040 (QC756_19040) | 131780..132991 | - | 1212 | WP_127515494 | type IV secretion system protein VirB10 | virB10 |
| QC756_RS19045 (QC756_19045) | 132991..133800 | - | 810 | WP_127515493 | P-type conjugative transfer protein VirB9 | virB9 |
| QC756_RS19050 (QC756_19050) | 133797..134492 | - | 696 | WP_127515491 | type IV secretion system protein | virB8 |
| QC756_RS19055 (QC756_19055) | 134531..135559 | - | 1029 | WP_127515489 | type IV secretion system protein | virB6 |
| QC756_RS19060 (QC756_19060) | 135575..135802 | - | 228 | WP_127515487 | hypothetical protein | - |
| QC756_RS19065 (QC756_19065) | 135792..136493 | - | 702 | WP_127668865 | type IV secretion system protein | - |
| QC756_RS19070 (QC756_19070) | 136505..137593 | - | 1089 | WP_127668872 | lytic transglycosylase domain-containing protein | - |
| QC756_RS19075 (QC756_19075) | 137590..138345 | - | 756 | Protein_150 | type VI secretion protein | - |
| QC756_RS19085 (QC756_19085) | 139398..141104 | - | 1707 | Protein_152 | VirB4 family type IV secretion system protein | - |
| QC756_RS19090 (QC756_19090) | 141107..141406 | - | 300 | WP_020479309 | VirB3 family type IV secretion system protein | virB3 |
| QC756_RS19095 (QC756_19095) | 141410..141748 | - | 339 | WP_127515462 | TrbC/VirB2 family protein | virB2 |
| QC756_RS19100 (QC756_19100) | 141760..142671 | - | 912 | WP_164822253 | lytic transglycosylase domain-containing protein | - |
| QC756_RS19105 (QC756_19105) | 142894..143502 | + | 609 | WP_127668864 | hypothetical protein | - |
| QC756_RS19110 (QC756_19110) | 143499..144035 | + | 537 | WP_127668863 | thermonuclease family protein | - |
| QC756_RS19115 (QC756_19115) | 144032..144733 | + | 702 | WP_127668862 | thermonuclease family protein | - |
| QC756_RS19120 (QC756_19120) | 144791..145138 | + | 348 | WP_234838964 | hypothetical protein | - |
| QC756_RS19125 (QC756_19125) | 145140..145733 | + | 594 | WP_127668860 | hypothetical protein | - |
| QC756_RS19130 (QC756_19130) | 145753..146169 | + | 417 | WP_127515526 | hypothetical protein | - |
Host bacterium
| ID | 7253 | GenBank | NZ_CP123004 |
| Plasmid name | pSme442-208 | Incompatibility group | - |
| Plasmid size | 208285 bp | Coordinate of oriT [Strand] | 121327..121382 [-] |
| Host baterium | Sinorhizobium meliloti strain BIM B-442D |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | htpB |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |