Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100753 |
| Name | oriT_pCCGM7-B  |
| Organism | Sinorhizobium americanum CCGM7 |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP013053 (40338..40371 [-], 34 nt) |
| oriT length | 34 nt |
| IRs (inverted repeats) | 17..23, 28..34 (ACGTCGC..GCGACGT) |
| Location of nic site | 7..8 |
| Conserved sequence flanking the nic site |
AGGG|CGCA |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 34 nt
>oriT_pCCGM7-B
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGT
CCAAGGGCGCAATTATACGTCGCTGGCGCGACGT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 825 | GenBank | WP_037390291 |
| Name | TraA_pCCGM7-B |
UniProt ID | A0A1L3L9H9 |
| Length | 1103 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 1103 a.a. Molecular weight: 122055.48 Da Isoelectric Point: 10.2168
>WP_037390291.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium americanum]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMGFEREARTIDYTRKQGLLHEEFVVPADAPEWLRAMIADH
SVSGASEAFWNKVEGFEKRADAQLAKDITIALPIELSTEQNIVLIRDFIDRHVTSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKIAVLGPDGTPIRNNSGKILYELWAGSAADFNAFRDGWFACQNKHLSLAG
LDIRIDGRSFEKQGIELTPTIHLGVGAKAIERKPAEAGRDISLERLELQEERRGENARRIQRRPEIVLDL
ITREKSVFDERDVAKILHRYFDDAGRFHSLMARILQSPETLRLERERIDFASGLRAPAKYTTRELIRLEA
EMADRANWLSLQSSHGIRDAVLEATFARHTRLSEEQKAAIAHVVAGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGILSRTLSSWELRWSEGRDLIHDRTVFVLDEAGMVSSRQMALFVE
TATKAGAKLVLIGDPQQLQPIEAGAAFRAIADRIGYAELGTIYRQREQWMRDASLDLARGNVGKAVEAYR
AHGHVTGSALKTEAMQALITDWNRDYDPTRTSLILAHLRRDVRMLNEMARAKLVERGIVDEGFAFRTEDG
SRKFATGDQIVFLKNEGALGVKNGMLAKVVDAAPGRIVAEVGEAEHRRRVTVESRFYNNVDLGYATTIHK
SQGVTVDRVKVLASLSLDRHLAYVAMTRHREDLAIYYGRRSFAKAGGLIPILSRKNAKETTLDYANGRLY
RQALRFARARGFHLVSVARTLVRDRLEWTVRQKSRFAELGARLSAIAGKLGLSAAAAGTSQPRTVKELKP
MVSGITTFAKSLEQAVEDRLAADPGLMKQWQEVSARFHLVYAQPEAAFKAADVDAMLKDGAAAKTTISRI
GSEPKAFGPLKGKTGMLVSRAEKQTRETAIANAPALARNLERYLRQRTVAARKYVIEERAMRLKVAFHIP
ALSPAAKQTLERVRDAIDRNDLPAGLEYAVADKMVKAELEGFSRAVSERFGERTFLPLAAKDTGGQAFQS
VSDGMSEAQKAELQSAWNSMRTVQQLAAHERTAEALKQAETMRQTKSQGLSLK
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMGFEREARTIDYTRKQGLLHEEFVVPADAPEWLRAMIADH
SVSGASEAFWNKVEGFEKRADAQLAKDITIALPIELSTEQNIVLIRDFIDRHVTSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKIAVLGPDGTPIRNNSGKILYELWAGSAADFNAFRDGWFACQNKHLSLAG
LDIRIDGRSFEKQGIELTPTIHLGVGAKAIERKPAEAGRDISLERLELQEERRGENARRIQRRPEIVLDL
ITREKSVFDERDVAKILHRYFDDAGRFHSLMARILQSPETLRLERERIDFASGLRAPAKYTTRELIRLEA
EMADRANWLSLQSSHGIRDAVLEATFARHTRLSEEQKAAIAHVVAGERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGILSRTLSSWELRWSEGRDLIHDRTVFVLDEAGMVSSRQMALFVE
TATKAGAKLVLIGDPQQLQPIEAGAAFRAIADRIGYAELGTIYRQREQWMRDASLDLARGNVGKAVEAYR
AHGHVTGSALKTEAMQALITDWNRDYDPTRTSLILAHLRRDVRMLNEMARAKLVERGIVDEGFAFRTEDG
SRKFATGDQIVFLKNEGALGVKNGMLAKVVDAAPGRIVAEVGEAEHRRRVTVESRFYNNVDLGYATTIHK
SQGVTVDRVKVLASLSLDRHLAYVAMTRHREDLAIYYGRRSFAKAGGLIPILSRKNAKETTLDYANGRLY
RQALRFARARGFHLVSVARTLVRDRLEWTVRQKSRFAELGARLSAIAGKLGLSAAAAGTSQPRTVKELKP
MVSGITTFAKSLEQAVEDRLAADPGLMKQWQEVSARFHLVYAQPEAAFKAADVDAMLKDGAAAKTTISRI
GSEPKAFGPLKGKTGMLVSRAEKQTRETAIANAPALARNLERYLRQRTVAARKYVIEERAMRLKVAFHIP
ALSPAAKQTLERVRDAIDRNDLPAGLEYAVADKMVKAELEGFSRAVSERFGERTFLPLAAKDTGGQAFQS
VSDGMSEAQKAELQSAWNSMRTVQQLAAHERTAEALKQAETMRQTKSQGLSLK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A1L3L9H9 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 536962..546474
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SAMCCGM7_RS21505 | 532468..533445 | - | 978 | WP_153045161 | hypothetical protein | - |
| SAMCCGM7_RS21510 (SAMCCGM7_pB0477) | 533740..534879 | - | 1140 | WP_037385408 | RHE_PE00001 family protein | - |
| SAMCCGM7_RS21515 (SAMCCGM7_pB0478) | 535306..535518 | - | 213 | WP_018097600 | helix-turn-helix transcriptional regulator | - |
| SAMCCGM7_RS21520 (SAMCCGM7_pB0479) | 535725..536048 | + | 324 | WP_037385819 | transcriptional repressor TraM | - |
| SAMCCGM7_RS21525 (SAMCCGM7_pB0480) | 536052..536756 | - | 705 | WP_037385415 | autoinducer binding domain-containing protein | - |
| SAMCCGM7_RS21530 (SAMCCGM7_pB0481) | 536962..538263 | - | 1302 | WP_037385418 | IncP-type conjugal transfer protein TrbI | virB10 |
| SAMCCGM7_RS21535 (SAMCCGM7_pB0482) | 538276..538713 | - | 438 | WP_037385421 | conjugal transfer protein TrbH | - |
| SAMCCGM7_RS21540 (SAMCCGM7_pB0483) | 538716..539528 | - | 813 | WP_037385424 | P-type conjugative transfer protein TrbG | virB9 |
| SAMCCGM7_RS21545 (SAMCCGM7_pB0484) | 539543..540205 | - | 663 | WP_037385426 | conjugal transfer protein TrbF | virB8 |
| SAMCCGM7_RS21550 (SAMCCGM7_pB0485) | 540230..541405 | - | 1176 | WP_037385428 | P-type conjugative transfer protein TrbL | virB6 |
| SAMCCGM7_RS21555 (SAMCCGM7_pB0486) | 541399..541599 | - | 201 | WP_037385430 | entry exclusion protein TrbK | - |
| SAMCCGM7_RS21560 (SAMCCGM7_pB0487) | 541596..542396 | - | 801 | WP_037385433 | P-type conjugative transfer protein TrbJ | virB5 |
| SAMCCGM7_RS21565 (SAMCCGM7_pB0488) | 542368..544824 | - | 2457 | WP_037385436 | conjugal transfer protein TrbE | virb4 |
| SAMCCGM7_RS21570 (SAMCCGM7_pB0489) | 544835..545134 | - | 300 | WP_037385439 | conjugal transfer protein TrbD | virB3 |
| SAMCCGM7_RS21575 (SAMCCGM7_pB0490) | 545127..545507 | - | 381 | WP_037385442 | TrbC/VirB2 family protein | virB2 |
| SAMCCGM7_RS21580 (SAMCCGM7_pB0491) | 545497..546474 | - | 978 | WP_037385445 | P-type conjugative transfer ATPase TrbB | virB11 |
| SAMCCGM7_RS21585 (SAMCCGM7_pB0492) | 546486..547106 | - | 621 | WP_037385448 | acyl-homoserine-lactone synthase | - |
Host bacterium
| ID | 1213 | GenBank | NZ_CP013053 |
| Plasmid name | pCCGM7-B | Incompatibility group | _ |
| Plasmid size | 547106 bp | Coordinate of oriT [Strand] | 40338..40371 [-] |
| Host baterium | Sinorhizobium americanum CCGM7 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |