Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100957 |
| Name | oriT_pSmeRU11d  |
| Organism | Sinorhizobium meliloti RU11/001 |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP021216 (45813..45847 [-], 35 nt) |
| oriT length | 35 nt |
| IRs (inverted repeats) | 16..23, 28..35 (TACGTCGC..GCGACGTG) |
| Location of nic site | 7..8 |
| Conserved sequence flanking the nic site |
AGGG|CGCA |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 35 nt
>oriT_pSmeRU11d
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGTG
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGTG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1027 | GenBank | WP_017273093 |
| Name | TraA_pSmeRU11d |
UniProt ID | _ |
| Length | 1210 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 1210 a.a. Molecular weight: 134157.79 Da Isoelectric Point: 7.3633
>WP_017273093.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDFEREARTIDYTRKQGLLHEEFVIPEDAPEWLRAMISDR
SVSGASEAFWNSVEAFEKRSDAQLAKDVTIALPIELSAEQNIDLVQDFVARHITAQGMVADWVYHDAPGN
PHIHMMTTLRPLTDDGFGSKKVAVLGPDGRPQRNDAGKIVYELWADGADDFNAFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIALEPTIHVGVGATAIERKADTAVETASAAAVKLERIELQEERREENARRIQRDPG
LVLDLITREKSVFDERDIARVLHRYIDDPALFQDLMARVLQHPDALRLDSERISFSTGARSPAKYTTYDL
IRIEAEMAQRALWLGRQHSYHVPTRVLGQVFKRHDRLADEQKSAIQHISRDVGIAAVVGRAGAGKTTMMK
AAREAWEAAGYRVVGAALAGKAAEGLEKEAGIASRTLSAWELRWDQDRDDLDDKTVMVLDEAGMVSSRQM
ARFVEAATISGAKLVLVGDPDQLQPIEAGAAFRAISERIGYAGLETIYRQREQWMRDASLDLARGNVSAA
LAAYEQRDMVRTGWTRDDAITTLIADWDRDYDPAKSSLILAHRRRDVRMLNEMARDKLVERGLIEKGHAF
KTEEGSRQFAVGDQIVFLKNEGSIGVKNGMLARVVEAQPGRLVAEIGSGDDCRQVVVEQRFYANVDHGYA
TTVHKSQGATVDRVKVLASSTLDRHLAYVAMTRHREAAELYVGLEEFAQRRGGVLIAHGEAPFEHKPGNR
SSYYVTLGFANGQEHTLWGVDLARAMDVADARIGDRIGIEHAGSERVRLPDGTEANRNSWKVVPVEDLAM
ARMHERLSRDASKETTLDYQNASSYRAALRFADRRGLHLMSVGRTLLRDRLQWTIRQKEKLTDLMSRLAA
VGERLGLRPSVGGERQVRGASEIRNQTNSIIQEDRKPMVAGITTFAKSIEKSVEDKVSADPALKSQWQEV
SARFHLVYADPQAAFNAVNVDAMVGSSETAKATLATISRQPVTFGPLKGKTGLFAGKADSQARETALVNV
PALARDLDEYLQKRAEAERRYEAEERAVRLKVSIDIPALSGAAKQTLERVRDAIDRNDLPSGLEYALADK
MVKAELEGFAKAVSERFGERTFLPLAAKEADGKVFEKLSAGMAPAQKAELHSAWNTMRTVQRLSAHERTA
TALKQAETMRQAKTTGLSLK
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDFEREARTIDYTRKQGLLHEEFVIPEDAPEWLRAMISDR
SVSGASEAFWNSVEAFEKRSDAQLAKDVTIALPIELSAEQNIDLVQDFVARHITAQGMVADWVYHDAPGN
PHIHMMTTLRPLTDDGFGSKKVAVLGPDGRPQRNDAGKIVYELWADGADDFNAFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIALEPTIHVGVGATAIERKADTAVETASAAAVKLERIELQEERREENARRIQRDPG
LVLDLITREKSVFDERDIARVLHRYIDDPALFQDLMARVLQHPDALRLDSERISFSTGARSPAKYTTYDL
IRIEAEMAQRALWLGRQHSYHVPTRVLGQVFKRHDRLADEQKSAIQHISRDVGIAAVVGRAGAGKTTMMK
AAREAWEAAGYRVVGAALAGKAAEGLEKEAGIASRTLSAWELRWDQDRDDLDDKTVMVLDEAGMVSSRQM
ARFVEAATISGAKLVLVGDPDQLQPIEAGAAFRAISERIGYAGLETIYRQREQWMRDASLDLARGNVSAA
LAAYEQRDMVRTGWTRDDAITTLIADWDRDYDPAKSSLILAHRRRDVRMLNEMARDKLVERGLIEKGHAF
KTEEGSRQFAVGDQIVFLKNEGSIGVKNGMLARVVEAQPGRLVAEIGSGDDCRQVVVEQRFYANVDHGYA
TTVHKSQGATVDRVKVLASSTLDRHLAYVAMTRHREAAELYVGLEEFAQRRGGVLIAHGEAPFEHKPGNR
SSYYVTLGFANGQEHTLWGVDLARAMDVADARIGDRIGIEHAGSERVRLPDGTEANRNSWKVVPVEDLAM
ARMHERLSRDASKETTLDYQNASSYRAALRFADRRGLHLMSVGRTLLRDRLQWTIRQKEKLTDLMSRLAA
VGERLGLRPSVGGERQVRGASEIRNQTNSIIQEDRKPMVAGITTFAKSIEKSVEDKVSADPALKSQWQEV
SARFHLVYADPQAAFNAVNVDAMVGSSETAKATLATISRQPVTFGPLKGKTGLFAGKADSQARETALVNV
PALARDLDEYLQKRAEAERRYEAEERAVRLKVSIDIPALSGAAKQTLERVRDAIDRNDLPSGLEYALADK
MVKAELEGFAKAVSERFGERTFLPLAAKEADGKVFEKLSAGMAPAQKAELHSAWNTMRTVQRLSAHERTA
TALKQAETMRQAKTTGLSLK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 25045..48415
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SMRU11_RS01615 (SMRU11_01630) | 20995..22239 | - | 1245 | WP_029727888 | plasmid replication protein RepC | - |
| SMRU11_RS01620 (SMRU11_01635) | 22397..23389 | - | 993 | WP_012477199 | plasmid partitioning protein RepB | - |
| SMRU11_RS01625 (SMRU11_01640) | 23474..24664 | - | 1191 | WP_012477198 | plasmid partitioning protein RepA | - |
| SMRU11_RS01630 (SMRU11_01645) | 25045..26010 | + | 966 | WP_012477360 | P-type conjugative transfer ATPase TrbB | virB11 |
| SMRU11_RS01635 (SMRU11_01650) | 26000..26392 | + | 393 | WP_017273081 | TrbC/VirB2 family protein | virB2 |
| SMRU11_RS01640 (SMRU11_01655) | 26385..26684 | + | 300 | WP_012477358 | conjugal transfer protein TrbD | virB3 |
| SMRU11_RS01645 (SMRU11_01660) | 26695..29130 | + | 2436 | WP_017273083 | conjugal transfer protein TrbE | virb4 |
| SMRU11_RS01650 (SMRU11_01665) | 29123..29929 | + | 807 | WP_017273084 | P-type conjugative transfer protein TrbJ | virB5 |
| SMRU11_RS01655 (SMRU11_01670) | 29974..30129 | + | 156 | WP_234705592 | entry exclusion protein TrbK | - |
| SMRU11_RS01660 (SMRU11_01675) | 30123..31304 | + | 1182 | WP_017273085 | P-type conjugative transfer protein TrbL | virB6 |
| SMRU11_RS01665 (SMRU11_01680) | 31326..31988 | + | 663 | WP_012477352 | conjugal transfer protein TrbF | virB8 |
| SMRU11_RS01670 (SMRU11_01685) | 32040..32834 | + | 795 | WP_017273087 | P-type conjugative transfer protein TrbG | virB9 |
| SMRU11_RS01675 (SMRU11_01690) | 32838..33284 | + | 447 | WP_012477350 | conjugal transfer protein TrbH | - |
| SMRU11_RS01680 (SMRU11_01695) | 33300..34598 | + | 1299 | WP_012477349 | IncP-type conjugal transfer protein TrbI | virB10 |
| SMRU11_RS01685 (SMRU11_01700) | 34806..35105 | + | 300 | WP_012477348 | transcriptional repressor TraM | - |
| SMRU11_RS01690 (SMRU11_01705) | 35106..35804 | - | 699 | WP_017273089 | autoinducer binding domain-containing protein | - |
| SMRU11_RS01695 (SMRU11_01710) | 36124..37734 | + | 1611 | WP_026030850 | hypothetical protein | - |
| SMRU11_RS01700 (SMRU11_01715) | 37724..38719 | + | 996 | WP_017273092 | alpha/beta hydrolase | - |
| SMRU11_RS01705 (SMRU11_01720) | 38886..39692 | - | 807 | WP_012477341 | DUF3800 domain-containing protein | - |
| SMRU11_RS01710 (SMRU11_01725) | 39752..40369 | - | 618 | WP_012477340 | TraH family protein | virB1 |
| SMRU11_RS01715 (SMRU11_01730) | 40384..41550 | - | 1167 | WP_012477339 | conjugal transfer protein TraB | - |
| SMRU11_RS01720 (SMRU11_01735) | 41540..42106 | - | 567 | WP_080591128 | conjugative transfer signal peptidase TraF | - |
| SMRU11_RS01725 (SMRU11_01740) | 42103..45735 | - | 3633 | WP_017273093 | Ti-type conjugative transfer relaxase TraA | - |
| SMRU11_RS01730 (SMRU11_01745) | 45987..46250 | + | 264 | WP_012477336 | TraC family protein | - |
| SMRU11_RS01735 (SMRU11_01750) | 46255..46470 | + | 216 | WP_017273095 | type IV conjugative transfer system coupling protein TraD | - |
| SMRU11_RS01740 (SMRU11_01755) | 46457..48415 | + | 1959 | WP_012477334 | Ti-type conjugative transfer system protein TraG | virb4 |
| SMRU11_RS01745 (SMRU11_01760) | 48432..48629 | + | 198 | WP_017273096 | hypothetical protein | - |
| SMRU11_RS01750 (SMRU11_01765) | 48844..49110 | + | 267 | WP_012477331 | WGR domain-containing protein | - |
| SMRU11_RS01755 (SMRU11_01770) | 49146..49634 | + | 489 | WP_017273097 | thermonuclease family protein | - |
| SMRU11_RS40010 | 49672..49845 | - | 174 | WP_012477329 | hypothetical protein | - |
| SMRU11_RS40015 | 50108..50278 | - | 171 | WP_017273098 | hypothetical protein | - |
| SMRU11_RS01760 (SMRU11_01775) | 50599..50907 | - | 309 | WP_012477327 | DUF736 domain-containing protein | - |
| SMRU11_RS40020 | 51365..51538 | + | 174 | WP_017273099 | hypothetical protein | - |
| SMRU11_RS01765 (SMRU11_01780) | 51542..51754 | - | 213 | Protein_53 | zincin-like metallopeptidase domain-containing protein | - |
| SMRU11_RS01770 (SMRU11_01785) | 51907..53139 | + | 1233 | WP_017273100 | hypothetical protein | - |
Host bacterium
| ID | 1415 | GenBank | NZ_CP021216 |
| Plasmid name | pSmeRU11d | Incompatibility group | _ |
| Plasmid size | 166875 bp | Coordinate of oriT [Strand] | 45813..45847 [-] |
| Host baterium | Sinorhizobium meliloti RU11/001 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |