Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106817 |
| Name | oriT_pSme442-SymA  |
| Organism | Sinorhizobium meliloti strain BIM B-442D |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP123005 (520715..520743 [+], 29 nt) |
| oriT length | 29 nt |
| IRs (inverted repeats) | 14..19, 24..29 (CGTCGC..GCGACG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 29 nt
>oriT_pSme442-SymA
AGGGCGCAATATACGTCGCTGGCGCGACG
AGGGCGCAATATACGTCGCTGGCGCGACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4493 | GenBank | WP_280097662 |
| Name | traA_QC756_RS21980_pSme442-SymA |
UniProt ID | _ |
| Length | 1539 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1539 a.a. Molecular weight: 169781.44 Da Isoelectric Point: 9.2735
>WP_280097662.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
QSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEQGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIAKALHRYVDDPVDFANIRARLMASDDLVLLKPQQVDAETGEAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGRKQLNRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQHGRIVETETRAEIVDRIVADWGNARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRQVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDEQTGEKRFEERQVDRNVWSASQLETAAARQERIERESHRP
QLFAALVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKRELVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFAF
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNMSERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRGITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLTILQQAVRVQSSQEIISERQRRVIDRARSVTR
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
QSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEQGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIAKALHRYVDDPVDFANIRARLMASDDLVLLKPQQVDAETGEAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGRKQLNRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQHGRIVETETRAEIVDRIVADWGNARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRQVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDEQTGEKRFEERQVDRNVWSASQLETAAARQERIERESHRP
QLFAALVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKRELVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFAF
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNMSERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRGITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLTILQQAVRVQSSQEIISERQRRVIDRARSVTR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 4549 | GenBank | WP_014528597 |
| Name | traG_QC756_RS21965_pSme442-SymA |
UniProt ID | _ |
| Length | 639 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 639 a.a. Molecular weight: 70213.22 Da Isoelectric Point: 9.3518
>WP_014528597.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKPHPSLLVILFPVAVTAAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRKPVAMASLACFLTVAGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERYRVDKDIVHELPFDPNDPATWGQGGKVP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSIGSYFQNQAHNLLTGLLAHVMLSPEYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIEADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARSISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAVP
MALKAKPHPSLLVILFPVAVTAAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRKPVAMASLACFLTVAGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERYRVDKDIVHELPFDPNDPATWGQGGKVP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSIGSYFQNQAHNLLTGLLAHVMLSPEYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIEADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARSISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAVP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 724659..734237
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| QC756_RS22955 (QC756_22955) | 720278..721300 | - | 1023 | WP_280097667 | zinc-dependent alcohol dehydrogenase | - |
| QC756_RS22960 (QC756_22960) | 721548..722225 | - | 678 | WP_127514439 | YoaK family protein | - |
| QC756_RS22965 (QC756_22965) | 722477..723088 | + | 612 | WP_017276198 | TetR/AcrR family transcriptional regulator | - |
| QC756_RS22970 (QC756_22970) | 723125..724348 | + | 1224 | WP_127514437 | MFS transporter | - |
| QC756_RS22975 (QC756_22975) | 724659..725648 | - | 990 | WP_013845454 | P-type DNA transfer ATPase VirB11 | virB11 |
| QC756_RS22980 (QC756_22980) | 725659..726831 | - | 1173 | WP_013845455 | type IV secretion system protein VirB10 | virB10 |
| QC756_RS22985 (QC756_22985) | 726841..727695 | - | 855 | WP_280097668 | P-type conjugative transfer protein VirB9 | virB9 |
| QC756_RS22990 (QC756_22990) | 727695..728366 | - | 672 | WP_280097669 | virB8 family protein | virB8 |
| QC756_RS22995 (QC756_22995) | 728371..728685 | - | 315 | WP_280097670 | hypothetical protein | - |
| QC756_RS23000 (QC756_23000) | 728682..729617 | - | 936 | WP_014531546 | type IV secretion system protein | virB6 |
| QC756_RS23005 (QC756_23005) | 729640..729855 | - | 216 | WP_014531545 | EexN family lipoprotein | - |
| QC756_RS23010 (QC756_23010) | 729852..730553 | - | 702 | WP_014531544 | P-type DNA transfer protein VirB5 | virB5 |
| QC756_RS23015 (QC756_23015) | 730553..732949 | - | 2397 | WP_194966945 | VirB4 family type IV secretion system protein | virb4 |
| QC756_RS23020 (QC756_23020) | 732924..733265 | - | 342 | WP_003526740 | type IV secretion system protein VirB3 | virB3 |
| QC756_RS23025 (QC756_23025) | 733270..733569 | - | 300 | WP_003526741 | TrbC/VirB2 family protein | virB2 |
| QC756_RS23030 (QC756_23030) | 733566..734237 | - | 672 | WP_010967696 | lytic transglycosylase domain-containing protein | virB1 |
| QC756_RS23035 (QC756_23035) | 734241..734759 | - | 519 | WP_017277528 | hypothetical protein | - |
| QC756_RS23040 (QC756_23040) | 734856..735224 | + | 369 | WP_010967698 | transcriptional regulator | - |
| QC756_RS23045 (QC756_23045) | 735485..735736 | - | 252 | WP_127514429 | hypothetical protein | - |
| QC756_RS23050 (QC756_23050) | 735810..736457 | - | 648 | WP_010967700 | dihydrofolate reductase family protein | - |
| QC756_RS23055 (QC756_23055) | 736507..737355 | - | 849 | WP_127514427 | alpha/beta fold hydrolase | - |
Host bacterium
| ID | 7254 | GenBank | NZ_CP123005 |
| Plasmid name | pSme442-SymA | Incompatibility group | - |
| Plasmid size | 1592319 bp | Coordinate of oriT [Strand] | 520715..520743 [+] |
| Host baterium | Sinorhizobium meliloti strain BIM B-442D |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | htpB |
| Metal resistance gene | actP, nia, ncrA, arsH, arsC |
| Degradation gene | - |
| Symbiosis gene | nodD, fixN, fixO, fixU, nifB, fixX, fixC, fixB, fixA, nifH, nifD, nifK, nifE, nifX, nodH, nodF, nodE, nodJ, nodI, nodC, nodB, nodA, nifN, nodM, fixS, fixG |
| Anti-CRISPR | AcrIIA9 |