Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 121132 |
| Name | oriT_pSymA  |
| Organism | Sinorhizobium meliloti strain L6-AK89 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP085527 (471814..471842 [+], 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_pSymA
AGGGCGCAATATACGTCGCTGGCGCGACG
AGGGCGCAATATACGTCGCTGGCGCGACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 13340 | GenBank | WP_227692188 |
| Name | traA_LJD24_RS21265_pSymA |
UniProt ID | _ |
| Length | 1539 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1539 a.a. Molecular weight: 169848.40 Da Isoelectric Point: 9.2786
>WP_227692188.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
QSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEQGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVAMYFAPADLARRQEMADRLLAEPELLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDDLVLLKPQQIDAETGKAKQPAVFTTREMLRLE
YAMAQSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGREQLQRGDVLVIDEAGMVS
SQQMARVLKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRNVMIGEGALAGAQEFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRRPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVHRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARQERIERESHRP
QLFAALVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFAF
AVEDRLLIQEVKAVNEALTSRFGWSAFTAKADVIAERNMSERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAAVTEFKTTVAEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFTSERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPRIAREFAKVSR
ALDERFGRNAILRGDTDVINRVSPAQRRAFEAMRDRLQVLQQAVRVQSSQEIISERQRRVIDRARGVTR
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
QSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEQGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVAMYFAPADLARRQEMADRLLAEPELLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDDLVLLKPQQIDAETGKAKQPAVFTTREMLRLE
YAMAQSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGREQLQRGDVLVIDEAGMVS
SQQMARVLKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRNVMIGEGALAGAQEFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRRPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVHRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARQERIERESHRP
QLFAALVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFAF
AVEDRLLIQEVKAVNEALTSRFGWSAFTAKADVIAERNMSERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAAVTEFKTTVAEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFTSERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPRIAREFAKVSR
ALDERFGRNAILRGDTDVINRVSPAQRRAFEAMRDRLQVLQQAVRVQSSQEIISERQRRVIDRARGVTR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 15630 | GenBank | WP_028005199 |
| Name | traG_LJD24_RS21250_pSymA |
UniProt ID | _ |
| Length | 639 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 639 a.a. Molecular weight: 70259.22 Da Isoelectric Point: 9.4585
>WP_028005199.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKPHPSLLVILFPVAVTAAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVAGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVLGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERYRVDKDIVHELPFDPNDPATWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFMNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAVP
MALKAKPHPSLLVILFPVAVTAAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVAGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVLGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERYRVDKDIVHELPFDPNDPATWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSTGSYFQNQAHNLLTGLLAHVMLSPEYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFMNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAVP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 556502..566069
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| LJD24_RS21670 (LJD24_21670) | 552825..553112 | - | 288 | WP_013845449 | chaperone NapD | - |
| LJD24_RS21675 (LJD24_21675) | 553105..553605 | - | 501 | WP_013845450 | ferredoxin-type protein NapF | - |
| LJD24_RS21680 (LJD24_21680) | 553605..553790 | - | 186 | WP_013845451 | periplasmic nitrate reductase, NapE protein | - |
| LJD24_RS21685 (LJD24_21685) | 554317..554928 | + | 612 | WP_013845452 | TetR/AcrR family transcriptional regulator | - |
| LJD24_RS21690 (LJD24_21690) | 554965..556191 | + | 1227 | WP_013845453 | MFS transporter | - |
| LJD24_RS21695 (LJD24_21695) | 556502..557491 | - | 990 | WP_013845454 | P-type DNA transfer ATPase VirB11 | virB11 |
| LJD24_RS21700 (LJD24_21700) | 557502..558674 | - | 1173 | WP_017271456 | type IV secretion system protein VirB10 | virB10 |
| LJD24_RS21705 (LJD24_21705) | 558684..559538 | - | 855 | WP_013845456 | P-type conjugative transfer protein VirB9 | virB9 |
| LJD24_RS21710 (LJD24_21710) | 559538..560209 | - | 672 | WP_013845457 | virB8 family protein | virB8 |
| LJD24_RS21715 (LJD24_21715) | 560214..560528 | - | 315 | WP_013845458 | hypothetical protein | - |
| LJD24_RS21720 (LJD24_21720) | 560525..561460 | - | 936 | WP_013845459 | type IV secretion system protein | virB6 |
| LJD24_RS21725 (LJD24_21725) | 561466..561699 | - | 234 | WP_013845460 | EexN family lipoprotein | - |
| LJD24_RS21730 (LJD24_21730) | 561696..562397 | - | 702 | WP_017269092 | P-type DNA transfer protein VirB5 | virB5 |
| LJD24_RS21735 (LJD24_21735) | 562397..564793 | - | 2397 | WP_017271457 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| LJD24_RS21740 (LJD24_21740) | 564768..565109 | - | 342 | WP_013845463 | type IV secretion system protein VirB3 | virB3 |
| LJD24_RS21745 (LJD24_21745) | 565114..565413 | - | 300 | WP_017269093 | TrbC/VirB2 family protein | virB2 |
| LJD24_RS21750 (LJD24_21750) | 565410..566069 | - | 660 | WP_013845465 | lytic transglycosylase domain-containing protein | virB1 |
| LJD24_RS21755 (LJD24_21755) | 566073..566591 | - | 519 | WP_017269094 | hypothetical protein | - |
| LJD24_RS21760 (LJD24_21760) | 566688..567056 | + | 369 | WP_013845467 | hypothetical protein | - |
| LJD24_RS21765 (LJD24_21765) | 567317..567568 | - | 252 | WP_017269095 | hypothetical protein | - |
| LJD24_RS21770 (LJD24_21770) | 567642..568289 | - | 648 | WP_010967700 | dihydrofolate reductase family protein | - |
| LJD24_RS21775 (LJD24_21775) | 568339..569187 | - | 849 | WP_017269096 | alpha/beta fold hydrolase | - |
Host bacterium
| ID | 21560 | GenBank | NZ_CP085527 |
| Plasmid name | pSymA | Incompatibility group | - |
| Plasmid size | 1217792 bp | Coordinate of oriT [Strand] | 471814..471842 [+] |
| Host baterium | Sinorhizobium meliloti strain L6-AK89 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | htpB |
| Metal resistance gene | ncrA |
| 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 |