Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103410 |
| Name | oriT_pSDP9R-tetX4  |
| Organism | Klebsiella sp. strain SDP9R |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_MW940621 (942..1023 [-], 82 nt) |
| oriT length | 82 nt |
| IRs (inverted repeats) | 27..32, 35..40 (GCCACC..GGTGGC) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 82 nt
>oriT_pSDP9R-tetX4
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2542 | GenBank | WP_032440569 |
| Name | Relaxase_KR398_RS00005_pSDP9R-tetX4 |
UniProt ID | A0A7G3L4G1 |
| Length | 642 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 642 a.a. Molecular weight: 74384.24 Da Isoelectric Point: 8.3203
>WP_032440569.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacterales]
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDERFQRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVICQHNLMSVETAAMEMNSIAMQNTHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSPRSAEMVKQSVQTSYSDKLHVRDRGA
RAERRQARADARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASDNI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGSFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDDRYYD
DVRHNDDSSYKP
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDERFQRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVICQHNLMSVETAAMEMNSIAMQNTHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNIVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNAMFREKNASWEKLHQVMNDAGLML
ETSGKGLIVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSPRSAEMVKQSVQTSYSDKLHVRDRGA
RAERRQARADARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIALKAERQKLYDEGMMRPLTYRAWTEQQALHGDQAALSQLRGWSYRQNRKNRTPQASDNI
IYCAPADDTSLLKADGYEARLHRDGAVVYSRQGQDAIIDRGDRVEVINPYDDGDLNTRIAVDMVAWKSGE
RVEFSRDGSFAYAAGDAVAAHNLHHRDSIIVPSDREQYDYTREKFNQLKGRYTDSEREALRQQYDDRYYD
DVRHNDDSSYKP
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A7G3L4G1 |
T4CP
| ID | 2327 | GenBank | WP_032440593 |
| Name | trbC_KR398_RS00310_pSDP9R-tetX4 |
UniProt ID | _ |
| Length | 730 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 730 a.a. Molecular weight: 82679.78 Da Isoelectric Point: 6.3201
>WP_032440593.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacterales]
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPNTVQRATQLLSLAAAVLTETRGRYRVEYPEP
EKLSVKKDELEKYQHIHQSAVTQQADGFSY
MQQKQKPVDAARLQRQVHQSMVEEMAYRTGPLLLAIIAIFGAAIVWPVLLWAAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLNRHMEKAAGVFYTGYERTLDGGREIWLRMDDLTRHLI
LMATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFLWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTIIDPTETAEFAAKSAGMEYQAIQDSMEYRAGAIGGSYADTGRVTVQEKPKLPFDELQALN
QGEQATVFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLSHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPNTVQRATQLLSLAAAVLTETRGRYRVEYPEP
EKLSVKKDELEKYQHIHQSAVTQQADGFSY
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 48059..69992
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| KR398_RS00295 (GJFFNDAI_00060) | 43822..44448 | - | 627 | WP_254913868 | RepA family replication protein | - |
| KR398_RS00300 (GJFFNDAI_00061) | 45023..45274 | - | 252 | WP_113394424 | hypothetical protein | - |
| KR398_RS00305 (GJFFNDAI_00062) | 45286..45819 | - | 534 | WP_032440594 | phospholipase D family protein | - |
| KR398_RS00310 (GJFFNDAI_00063) | 45865..48057 | - | 2193 | WP_032440593 | F-type conjugative transfer protein TrbC | - |
| KR398_RS00315 (GJFFNDAI_00064) | 48059..49180 | - | 1122 | WP_052455213 | thioredoxin fold domain-containing protein | trbB |
| KR398_RS00320 (GJFFNDAI_00065) | 49161..50579 | - | 1419 | WP_063666705 | hypothetical protein | trbA |
| KR398_RS00325 (GJFFNDAI_00066) | 50681..51304 | - | 624 | WP_032440592 | plasmid IncI1-type surface exclusion protein ExcA | - |
| KR398_RS00330 (GJFFNDAI_00067) | 51370..53514 | - | 2145 | WP_032440591 | DotA/TraY family protein | traY |
| KR398_RS00335 (GJFFNDAI_00068) | 53556..54137 | - | 582 | WP_050597335 | conjugal transfer protein TraX | - |
| KR398_RS00340 (GJFFNDAI_00069) | 54134..55330 | - | 1197 | WP_032440590 | conjugal transfer protein TraW | traW |
| KR398_RS00345 (GJFFNDAI_00070) | 55340..58387 | - | 3048 | WP_032440589 | conjugal transfer protein | traU |
| KR398_RS00350 (GJFFNDAI_00071) | 58397..58960 | - | 564 | WP_045325070 | hypothetical protein | traT |
| KR398_RS00355 (GJFFNDAI_00072) | 59004..59405 | - | 402 | WP_032440588 | DUF6750 family protein | traR |
| KR398_RS00360 (GJFFNDAI_00073) | 59461..59994 | - | 534 | WP_032440587 | conjugal transfer protein TraQ | traQ |
| KR398_RS00365 (GJFFNDAI_00074) | 60004..60723 | - | 720 | WP_050597333 | conjugal transfer protein TraP | traP |
| KR398_RS00370 (GJFFNDAI_00075) | 60730..62070 | - | 1341 | WP_032440586 | conjugal transfer protein TraO | traO |
| KR398_RS00375 (GJFFNDAI_00076) | 62074..63177 | - | 1104 | WP_077264204 | DotH/IcmK family type IV secretion protein | traN |
| KR398_RS00380 (GJFFNDAI_00077) | 63188..63856 | - | 669 | WP_032440585 | DotI/IcmL/TraM family protein | traM |
| KR398_RS00385 (GJFFNDAI_00078) | 63928..64281 | - | 354 | WP_032440584 | hypothetical protein | traL |
| KR398_RS00390 (GJFFNDAI_00079) | 64315..67728 | - | 3414 | WP_052145516 | LPD7 domain-containing protein | - |
| KR398_RS00395 (GJFFNDAI_00080) | 67746..68012 | - | 267 | WP_032440577 | IcmT/TraK family protein | traK |
| KR398_RS00400 (GJFFNDAI_00081) | 68009..69196 | - | 1188 | WP_077255878 | plasmid transfer ATPase TraJ | - |
| KR398_RS00405 (GJFFNDAI_00082) | 69174..69992 | - | 819 | WP_032440576 | type IV secretory system conjugative DNA transfer family protein | traI |
| KR398_RS00410 (GJFFNDAI_00083) | 69989..70453 | - | 465 | WP_225546581 | DotD/TraH family lipoprotein | - |
| KR398_RS00415 (GJFFNDAI_00084) | 70479..70958 | - | 480 | WP_032440574 | lytic transglycosylase domain-containing protein | - |
| KR398_RS00420 (GJFFNDAI_00086) | 71690..71917 | - | 228 | WP_032440573 | hypothetical protein | - |
| KR398_RS00425 (GJFFNDAI_00087) | 72527..73369 | + | 843 | WP_032440572 | helix-turn-helix domain-containing protein | - |
| KR398_RS00430 (GJFFNDAI_00088) | 73444..74358 | + | 915 | WP_223289764 | hypothetical protein | - |
| KR398_RS00435 (GJFFNDAI_00089) | 74441..74845 | + | 405 | WP_223289767 | molybdopterin-dependent oxidoreductase | - |
Host bacterium
| ID | 3853 | GenBank | NZ_MW940621 |
| Plasmid name | pSDP9R-tetX4 | Incompatibility group | IncFII |
| Plasmid size | 78159 bp | Coordinate of oriT [Strand] | 942..1023 [-] |
| Host baterium | Klebsiella sp. strain SDP9R |
Cargo genes
| Drug resistance gene | tet(X4) |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |