Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120354 |
| Name | oriT_pSkuCIP108026a  |
| Organism | Sinorhizobium kummerowiae strain CIP 108026 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP140299 (728816..728844 [-], 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_pSkuCIP108026a
AGGGCGCAATATACGTCGCTGGCGCGACG
AGGGCGCAATATACGTCGCTGGCGCGACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12806 | GenBank | WP_284718752 |
| Name | traA_VPK21_RS03605_pSkuCIP108026a |
UniProt ID | _ |
| Length | 1539 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1539 a.a. Molecular weight: 170001.88 Da Isoelectric Point: 9.5526
>WP_284718752.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium kummerowiae]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
RSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEEGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIAMYFAPADLARRHEMADRLLAEPGLLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDELVLLKPQQIDAETGKAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSDARAAAAVRSIETADTEKPFRLDLEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGRDLLQRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRNVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGREVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPKWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGAAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARRERIERESHRP
QLFKQLVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVAYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPERLGRLRGSELVVDGRAARDERTAATA
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFAF
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDIAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKETFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLQVLQQAVRIQSSEKIVSERQRRVIDRARGVTR
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
RSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEEGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIAMYFAPADLARRHEMADRLLAEPGLLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDELVLLKPQQIDAETGKAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSDARAAAAVRSIETADTEKPFRLDLEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGRDLLQRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRNVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGREVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPKWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGAAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARRERIERESHRP
QLFKQLVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVAYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPERLGRLRGSELVVDGRAARDERTAATA
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFAF
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDIAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKETFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLQVLQQAVRIQSSEKIVSERQRRVIDRARGVTR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 15046 | GenBank | WP_127701843 |
| Name | virD4_VPK21_RS00670_pSkuCIP108026a |
UniProt ID | _ |
| Length | 563 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 563 a.a. Molecular weight: 62957.23 Da Isoelectric Point: 9.1751
>WP_127701843.1 MULTISPECIES: type IV secretion system ATPase VirD4 [Sinorhizobium]
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILFVQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDIVALPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYEESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QNSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPAPLMIADERF
SHV
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILFVQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDIVALPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYEESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QNSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPAPLMIADERF
SHV
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 15047 | GenBank | WP_122102935 |
| Name | traG_VPK21_RS03620_pSkuCIP108026a |
UniProt ID | _ |
| Length | 639 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 639 a.a. Molecular weight: 70239.23 Da Isoelectric Point: 9.3854
>WP_122102935.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Sinorhizobium]
MALKAKPHPSLLVILFPVAVTTAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVVGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERCRVDKDIVHELPFDPNDPATWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEEIVGIAHMLLSESVRFESSTGSYFQNQAHNLLTGLLAHVMLSPDYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAIP
MALKAKPHPSLLVILFPVAVTTAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVVGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERCRVDKDIVHELPFDPNDPATWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEEIVGIAHMLLSESVRFESSTGSYFQNQAHNLLTGLLAHVMLSPDYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAIP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 615456..625031
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| VPK21_RS03050 (VPK21_000608) | 612351..613199 | + | 849 | WP_127525409 | alpha/beta fold hydrolase | - |
| VPK21_RS03055 (VPK21_000609) | 613249..613896 | + | 648 | WP_088196216 | dihydrofolate reductase family protein | - |
| VPK21_RS03060 (VPK21_000610) | 613971..614354 | + | 384 | WP_234837683 | hypothetical protein | - |
| VPK21_RS03065 (VPK21_000611) | 614469..614837 | - | 369 | WP_017264159 | transcriptional regulator | - |
| VPK21_RS03070 (VPK21_000612) | 614934..615452 | + | 519 | WP_088196214 | hypothetical protein | - |
| VPK21_RS03075 (VPK21_000613) | 615456..616127 | + | 672 | WP_127525410 | lytic transglycosylase domain-containing protein | virB1 |
| VPK21_RS03080 (VPK21_000614) | 616124..616423 | + | 300 | WP_088196212 | TrbC/VirB2 family protein | virB2 |
| VPK21_RS03085 (VPK21_000615) | 616428..616769 | + | 342 | WP_017264162 | type IV secretion system protein VirB3 | virB3 |
| VPK21_RS03090 (VPK21_000616) | 616744..619140 | + | 2397 | WP_192925931 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| VPK21_RS03095 (VPK21_000617) | 619140..619838 | + | 699 | WP_127634297 | P-type DNA transfer protein VirB5 | virB5 |
| VPK21_RS03100 (VPK21_000618) | 619835..620050 | + | 216 | WP_014531545 | EexN family lipoprotein | - |
| VPK21_RS03105 (VPK21_000619) | 620073..621008 | + | 936 | WP_127525411 | type IV secretion system protein | virB6 |
| VPK21_RS03110 (VPK21_000620) | 621005..621319 | + | 315 | WP_013845458 | hypothetical protein | - |
| VPK21_RS03115 (VPK21_000621) | 621324..621995 | + | 672 | WP_013845457 | virB8 family protein | virB8 |
| VPK21_RS03120 (VPK21_000622) | 621995..622849 | + | 855 | WP_014531548 | P-type conjugative transfer protein VirB9 | virB9 |
| VPK21_RS03125 (VPK21_000623) | 622859..624031 | + | 1173 | WP_013845455 | type IV secretion system protein VirB10 | virB10 |
| VPK21_RS03130 (VPK21_000624) | 624042..625031 | + | 990 | WP_127525413 | P-type DNA transfer ATPase VirB11 | virB11 |
| VPK21_RS03135 (VPK21_000625) | 625342..626568 | - | 1227 | WP_127634296 | MFS transporter | - |
| VPK21_RS03140 (VPK21_000626) | 626607..627218 | - | 612 | WP_127525415 | TetR/AcrR family transcriptional regulator | - |
| VPK21_RS03145 (VPK21_000627) | 627749..627934 | + | 186 | WP_088198221 | periplasmic nitrate reductase, NapE protein | - |
| VPK21_RS03150 (VPK21_000628) | 627934..628434 | + | 501 | WP_088201148 | ferredoxin-type protein NapF | - |
| VPK21_RS03155 (VPK21_000629) | 628427..628714 | + | 288 | WP_013845449 | chaperone NapD | - |
Host bacterium
| ID | 20783 | GenBank | NZ_CP140299 |
| Plasmid name | pSkuCIP108026a | Incompatibility group | - |
| Plasmid size | 1418903 bp | Coordinate of oriT [Strand] | 728816..728844 [-] |
| Host baterium | Sinorhizobium kummerowiae strain CIP 108026 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | htpB |
| Metal resistance gene | ncrA |
| Degradation gene | - |
| Symbiosis gene | fixA, fixB, nodM, nifN, nodD, nodA, nodB, nodC, nodI, nodJ, nodE, nodF, nodH, nifX, nifE, nifK, nifD, nifH, fixC, fixX, nifB, fixU, fixO, fixN, fixS, fixG |
| Anti-CRISPR | AcrIIA9 |