Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200057 |
| Name | oriT_R391  |
| Organism | Providencia rettgeri |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | AY090559 (5428..5726 [+], 299 nt) |
| oriT length | 299 nt |
| IRs (inverted repeats) | 178..192, 216..230 (ATCGAGACGCCAAAC..GTTTGGCGTTTCGAT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | _ |
oriT sequence
Download Length: 299 nt
GCTCTGTTTGGCGGTGGATGACTGAGCCAAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTCGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTCAGGCATTTATATGTGAAATCGGGCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGTGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTAGTTTTGGTTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Reference
[1] Wozniak RA et al. (2009) Comparative ICE genomics: insights into the evolution of the SXT/R391 family of ICEs. PLoS Genet. 5(12):e1000786. [PMID:20041216]
[2] Ceccarelli D et al. (2008) Identification of the origin of transfer (oriT) and a new gene required for mobilization of the SXT/R391 family of integrating conjugative elements. J Bacteriol. 190(15):5328-38. [PMID:18539733]
Relaxase
| ID | 271 | GenBank | AAM08003 |
| Name | TraI_R391  |
UniProt ID | Q8RL15 |
| Length | 716 a.a. | PDB ID | |
| Note | _ | ||
Relaxase protein sequence
Download Length: 716 a.a. Molecular weight: 79958.22 Da Isoelectric Point: 5.4572
MFKNLFFQTKALPELSSQLDADIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTTNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDLEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWLRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSSVRLFSKSEWEATRQTQAEPQSRSSEHSDL
PEASSSIEHRKSTESPSTNSSEQDDELRLASDVNNPQATENAPGDGCEKPNNSYDGAISNNVNQYDTEAL
NLPESLAWLPEASSALVMVGEQILIRYPDAVRPWCAPRKLLAELSQLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKRLIALIDISKQGTEPAAAIQNEEALQRPSRTKTTNAQAKEPATRAERKQKPIAPNAK
SSTDPKYVQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANAHGIPAGQLLRGISASDEC
QFDEGETVLFTAHAKR
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q8RL15 |
Reference
[1] Ceccarelli D et al. (2008) Identification of the origin of transfer (oriT) and a new gene required for mobilization of the SXT/R391 family of integrating conjugative elements. J Bacteriol. 190(15):5328-38. [PMID:18539733]
T4CP
| ID | 271 | GenBank | AAM08004 |
| Name | TraD_R391 |
UniProt ID | Q8RL14 |
| Length | 606 a.a. | PDB ID | _ |
| Note | putative coupling protein involved in conjugal transfer | ||
T4CP protein sequence
Download Length: 606 a.a. Molecular weight: 67069.90 Da Isoelectric Point: 6.7826
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVNDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FSARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q8RL14 |
Reference
[1] Ceccarelli D et al. (2008) Identification of the origin of transfer (oriT) and a new gene required for mobilization of the SXT/R391 family of integrating conjugative elements. J Bacteriol. 190(15):5328-38. [PMID:18539733]
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 34540..59357
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_32 | 32341..34491 | + | 2151 | AAM08003 | TraI | - |
| Locus_33 | 34540..36360 | + | 1821 | AAM08004 | TraD | virb4 |
| Locus_34 | 36370..36930 | + | 561 | AAM08047 | hypothetical protein | - |
| Locus_35 | 36908..37552 | + | 645 | AAM08039 | hypothetical protein | tfc7 |
| Locus_36 | 37579..38166 | - | 588 | AAM08045 | hypothetical protein | - |
| Locus_37 | 38180..38419 | - | 240 | AAM08075 | hypothetical protein | - |
| Locus_38 | 38455..38736 | + | 282 | AAM08076 | TraL | traL |
| Locus_39 | 38967..39359 | + | 393 | AAM08060 | TraE | traE |
| Locus_40 | 39340..40242 | + | 903 | AAM08021 | TraK | traK |
| Locus_41 | 40242..41531 | + | 1290 | AAM08009 | TraB | traB |
| Locus_42 | 41528..42178 | + | 651 | AAM08037 | HtdD | traV |
| Locus_43 | 42175..42561 | + | 387 | AAM08062 | TraA | - |
| Locus_44 | 42602..42922 | - | 321 | AAM08077 | unknown | - |
| Locus_45 | 43099..43365 | - | 267 | AAM08078 | unknown | - |
| Locus_46 | 43543..43920 | - | 378 | AAM08063 | hypothetical protein | - |
| Locus_47 | 44406..45323 | + | 918 | AAM08079 | putative transposase tnpR391B | - |
| Locus_48 | 45687..46010 | - | 324 | AAM08066 | hypothetical protein | - |
| Locus_49 | 45742..47268 | + | 1527 | AAM08007 | putative sulfate permease | - |
| Locus_50 | 46452..46700 | - | 249 | AAM08080 | hypothetical protein | - |
| Locus_51 | 47280..48131 | + | 852 | AAM08025 | hypothetical protein | - |
| Locus_52 | 48155..48604 | - | 450 | AAM08056 | hypothetical protein | - |
| Locus_53 | 48635..49144 | - | 510 | AAM08052 | hypothetical protein | - |
| Locus_54 | 49249..49425 | - | 177 | AAM08087 | hypothetical protein | - |
| Locus_55 | 49588..50280 | + | 693 | AAM08034 | DsbC | trbB |
| Locus_56 | 50280..52679 | + | 2400 | AAM08001 | TraC | virb4 |
| Locus_57 | 53024..53515 | + | 492 | AAM08054 | TrhF | - |
| Locus_58 | 53523..54650 | + | 1128 | AAM08011 | TraW | traW |
| Locus_59 | 54634..55662 | + | 1029 | AAM08014 | TraU | traU |
| Locus_60 | 55665..59357 | + | 3693 | AAM07995 | TraN | traN |
| Locus_61 | 59951..60613 | + | 663 | AAM08036 | hypothetical protein | - |
| Locus_62 | 60704..61306 | - | 603 | AAM08043 | hypothetical protein | - |
| Locus_63 | 61662..62000 | + | 339 | AAM08064 | hypothetical protein | - |
| Locus_64 | 62016..62435 | + | 420 | AAM08058 | hypothetical protein | - |
| Locus_65 | 62515..63333 | + | 819 | AAM08027 | hypothetical protein | - |
Host bacterium
| ID | 65 | Element type | |
| Element name | R391 | GenBank | AY090559 |
| Element size | 88532 bp | Coordinate of oriT [Strand] | 5428..5726 [+] |
| Host bacterium | Providencia rettgeri |
Cargo genes
| Drug resistance gene | aph(3')-Ia |
| Virulence gene | - |
| Metal resistance gene | mercury resistance |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |