Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 102977 |
| Name | oriT_pB-3002cz  |
| Organism | Klebsiella pneumoniae strain Kpn-3002cz |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KJ958926 (81173..81254 [-], 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_pB-3002cz
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC
CGGGACAGGATATGTTTTGTATTACCGCCACCACGGTGGCAGCAATCCAAAACTCCTGGTCAGGGCGAAGCCCCGACACCCC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2232 | GenBank | WP_015632446 |
| Name | Relaxase_HTC85_RS00415_pB-3002cz |
UniProt ID | R4WBX2 |
| Length | 642 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 642 a.a. Molecular weight: 74631.63 Da Isoelectric Point: 9.3060
>WP_015632446.1 MULTISPECIES: TraI/MobA(P) family conjugative relaxase [Enterobacteriaceae]
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDQRFRRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVTCQHNLMSVETAAMEMNSIAMQNLHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNLVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNTMFREKNASWEKLHQVMNDAGLML
EPSGKGLVVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSSRSAEMVKQSVQTPYSDRLHVRDRGA
RAERRQARAEARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIELKAERRKLYDEGRMRPLTYRAWTEQQALHGDQAALSQLRGWAYRQNRKNRTPQASDSI
IFCAPADDTSLIKADGYDARLYRDGAVVYSRHGQDAIIDRGDRVEVINPYDNGDLNTRIAVDMVAWKSGE
RIEFSRDGSFAYAAGDAVAAHNLHHRDSILVPSNREQYDYTREKFNQLKGRYTDREREAVRQQYDNRYYD
DVRHNDDNSYKP
MNAIIPPKRRDRKSSFVQLVAYVSVRDDVPLKDELKEDQRFRRPSRSRQAIFDRLVDYMNRSEGTIIEQI
SDMTPEGDIRCSVDGVTCQHNLMSVETAAMEMNSIAMQNLHVKDAVYHYILSWQEDENPSDDQVFDSVKH
SLKRLGMEEHQYVAAIHRDTDNLHVHIAANRVHPVSYRAANVWNDADKLQRTCRELELKHGFKVDNGSWV
RDADNNLVRARKGYRNAPRSARQLEHFSDKESLHHFAVQHVRKPVNTMFREKNASWEKLHQVMNDAGLML
EPSGKGLVVRDVCGDEKLAVKSSRVHPGMTLSRLEPALGTFVPSSRSAEMVKQSVQTPYSDRLHVRDRGA
RAERRQARAEARIDLRERYEKYRNAWKKPDLHAAERFRAVSAAFKEQKTHIRDNEKDAHMRKLMYHIVEF
EREKSMAALRIELKAERRKLYDEGRMRPLTYRAWTEQQALHGDQAALSQLRGWAYRQNRKNRTPQASDSI
IFCAPADDTSLIKADGYDARLYRDGAVVYSRHGQDAIIDRGDRVEVINPYDNGDLNTRIAVDMVAWKSGE
RIEFSRDGSFAYAAGDAVAAHNLHHRDSILVPSNREQYDYTREKFNQLKGRYTDREREAVRQQYDNRYYD
DVRHNDDNSYKP
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | R4WBX2 |
T4CP
| ID | 1920 | GenBank | WP_015632442 |
| Name | trbC_HTC85_RS00380_pB-3002cz |
UniProt ID | _ |
| Length | 730 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 730 a.a. Molecular weight: 82688.74 Da Isoelectric Point: 5.8919
>WP_015632442.1 MULTISPECIES: F-type conjugative transfer protein TrbC [Enterobacteriaceae]
MQQKQKPVDAARLQRQVHQGMVEEMAYRTGPLLLAIIVIFGAAIVWPVLLWVAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLSRHMDNAAGVFYTGYERMLDGGREIWLRMDDLTRHLI
LLATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFIWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTITDPTETAEFAAKSAGMEYQAIQDSMEYRPGAISGSYADTGRVTVQEKSKLPFDELQTLN
QGEQATIFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLAHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPDAVQRATQLLSLAASVLTETRGRYSVEYPEP
EKLSVKKDEFEKYQHIHQSAVTQQADGFVY
MQQKQKPVDAARLQRQVHQGMVEEMAYRTGPLLLAIIVIFGAAIVWPVLLWVAIPVMLVWVPMFMLNEFR
MPARMPMDMDRLDPSTETMRPGKLLGFLPVTKLSRHMDNAAGVFYTGYERMLDGGREIWLRMDDLTRHLI
LLATTGAGKTEMLLGFVLNALCWAKGLIFSDGKAQNDVWFAVASLSRRFGREDDLRLLNYITGGQSRSQR
LLENDKSRQQSNNTNPFALAQETYITQLMDSMMPEAGNDRTWQEKAKGMNQVLTKALIYKSRKEQKVMSQ
RLIQEYLSLDKFAELYLQAEAEEWHEEIRTGLRNYLSTSVPGFDMSLITKPSEWSQEARNQHGYLTSQYN
RMLSLFSDTYGHVFSSGAGDIDLRDVVHNDRILVILIPALELSASEALTLGRLTTSQLAMILSQDLGERM
EGKAEDILVIKKFRDRFPFIWLADEVGSYYSDTIGQLATQVRSLGYALVLAGQDLQKLKTAVGDKLWTLL
GNMFTRIFGTITDPTETAEFAAKSAGMEYQAIQDSMEYRPGAISGSYADTGRVTVQEKSKLPFDELQTLN
QGEQATIFKGAVIRNNALYIADDDKITDKDVRINRFVEVEWPTYDSLAHLLPAKVRRDRPRPASINRIMA
IVKNDKIRHAPDSMIIQDGVLYAIADEAMYFDEVAPTPPDAVQRATQLLSLAASVLTETRGRYSVEYPEP
EKLSVKKDEFEKYQHIHQSAVTQQADGFVY
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 51471..73312
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HTC85_RS00245 | 47024..47410 | - | 387 | WP_015632417 | acyl-CoA thioesterase | - |
| HTC85_RS00250 | 47410..47895 | - | 486 | WP_015632418 | hypothetical protein | - |
| HTC85_RS00255 | 47862..48440 | - | 579 | WP_015632419 | hypothetical protein | - |
| HTC85_RS00260 | 48708..49241 | + | 534 | WP_015632420 | transcription termination/antitermination NusG family protein | - |
| HTC85_RS00265 | 49259..49462 | + | 204 | WP_032495743 | hypothetical protein | - |
| HTC85_RS00270 | 49496..49807 | + | 312 | WP_015632421 | hypothetical protein | - |
| HTC85_RS00275 | 50505..50984 | + | 480 | WP_015632423 | lytic transglycosylase domain-containing protein | - |
| HTC85_RS00280 | 51007..51474 | + | 468 | WP_015632424 | DotD/TraH family lipoprotein | - |
| HTC85_RS00285 | 51471..52289 | + | 819 | WP_015632425 | type IV secretory system conjugative DNA transfer family protein | traI |
| HTC85_RS00290 | 52267..53454 | + | 1188 | WP_032495744 | plasmid transfer ATPase TraJ | virB11 |
| HTC85_RS00295 | 53451..53717 | + | 267 | WP_032441926 | IcmT/TraK family protein | traK |
| HTC85_RS00300 | 53735..57058 | + | 3324 | WP_032495745 | LPD7 domain-containing protein | - |
| HTC85_RS00305 | 57092..57445 | + | 354 | WP_015632427 | hypothetical protein | traL |
| HTC85_RS00310 | 57481..58185 | + | 705 | WP_015632428 | DotI/IcmL/TraM family protein | traM |
| HTC85_RS00315 | 58196..59299 | + | 1104 | WP_015632429 | DotH/IcmK family type IV secretion protein | traN |
| HTC85_RS00320 | 59303..60643 | + | 1341 | WP_015632430 | conjugal transfer protein TraO | traO |
| HTC85_RS00325 | 60649..61368 | + | 720 | WP_015632431 | conjugal transfer protein TraP | traP |
| HTC85_RS00330 | 61378..61911 | + | 534 | WP_015632432 | conjugal transfer protein TraQ | traQ |
| HTC85_RS00335 | 61965..62366 | + | 402 | WP_015632433 | DUF6750 family protein | traR |
| HTC85_RS00340 | 62410..62973 | + | 564 | WP_032495746 | hypothetical protein | traT |
| HTC85_RS00345 | 62992..66030 | + | 3039 | WP_335904770 | ATP-binding protein | - |
| HTC85_RS00350 | 66077..67237 | + | 1161 | WP_032495747 | conjugal transfer protein TraW | traW |
| HTC85_RS00355 | 67234..67815 | + | 582 | WP_015632437 | conjugal transfer protein TraX | - |
| HTC85_RS00360 | 67857..70001 | + | 2145 | WP_015632438 | DotA/TraY family protein | traY |
| HTC85_RS00365 | 70067..70690 | + | 624 | WP_015632439 | plasmid IncI1-type surface exclusion protein ExcA | - |
| HTC85_RS00370 | 70792..72210 | + | 1419 | WP_015632440 | hypothetical protein | trbA |
| HTC85_RS00375 | 72158..73312 | + | 1155 | WP_015632441 | thioredoxin fold domain-containing protein | trbB |
| HTC85_RS00380 | 73314..75506 | + | 2193 | WP_015632442 | F-type conjugative transfer protein TrbC | - |
| HTC85_RS00385 | 75552..75857 | + | 306 | WP_015632443 | phospholipase D-like domain-containing protein | - |
| HTC85_RS00390 | 75880..77469 | - | 1590 | WP_015632444 | IS66 family transposase | - |
| HTC85_RS00395 | 77499..77848 | - | 350 | Protein_78 | IS66 family insertion sequence element accessory protein TnpB | - |
| HTC85_RS00400 | 77845..78252 | - | 408 | WP_015632445 | transposase | - |
Host bacterium
| ID | 3420 | GenBank | NZ_KJ958926 |
| Plasmid name | pB-3002cz | Incompatibility group | IncFII |
| Plasmid size | 97649 bp | Coordinate of oriT [Strand] | 81173..81254 [-] |
| Host baterium | Klebsiella pneumoniae strain Kpn-3002cz |
Cargo genes
| Drug resistance gene | aac(6')-Ib, blaNDM-1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |