Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 105615 |
| Name | oriT_pSfHH103d  |
| Organism | Sinorhizobium fredii HH103 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NT_187148 (216876..216904 [+], 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_pSfHH103d
AGGGCGCAATATACGTCGCTGGCGCGACG
AGGGCGCAATATACGTCGCTGGCGCGACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3812 | GenBank | WP_015633563 |
| Name | traA_SFHH103_RS23705_pSfHH103d |
UniProt ID | A0A844A347 |
| Length | 1539 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1539 a.a. Molecular weight: 170749.69 Da Isoelectric Point: 8.8055
>WP_015633563.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Sinorhizobium]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGASELVHEELALPDQIPGWLKAAIDR
QSVAKASEALWNAVESHETRADAQLARELIIALPEELTRAENIALVREFIRDNLTSKGMVADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEDGEPLRVVTPDRPNGKIVYQLWAGDKETMKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLHGIAQKHLGPEKAALARKGVEMYFAPADLARRQEMADRLIADPELLLKQ
LGSERSTFEERDIAKALHRYVDDPVDFVNIRARLMASDDLVLLKPQEVDAQTGRASEPAVFTTREILRIE
YDMAQSAQALSERKGFGVSTKQVAAAIRNVETADPEEPFKLHAEQVDAVRHVTGDSGMAAVVGLAGAGKS
TLLAAARVAWESEDRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWAGGREQLDRGDVLVIDEAGMIS
SQQMARVLKIAQEAQAKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREQWARDASRLFARGK
VEEGLDAYAQQGHIVETETRAEIVDRIVSDWTDARRDLLQKSAAGEHPGRLRGEELLVLAHTNQDVRKLN
ESLRKVMIDEGALTAAREFQTARGSREFAAGDRIIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDKR
GCALLTVRLDNGRDVVISEDSYRNIDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRHRADL
YVAKEDFEVRPEWGRKPRVDHAAGVIGELVETGEAKFRPQERQAKESPYADVRTDDGTVHRLWGVSLPKA
LEEGSVSTGDTVTLRKDGVEKVIVKIPVTDEETGEKRLEEREVERNVWTANRVETADARQERIKRERHRL
ELFKQLVERLGRSGAKTTTLDFASEEVYQAHARDFARRRGIDTLAEVAAGMEEGVSRRLAWIAEKRGQVA
KLWERASVALGFAIERERRVSYNEERTASFSAGIPLVGKYLMPPTTKFSRSVEEDARLAQLSSERWKERE
AVLRPVLAKIYLDPDGALSALNALASDTAIEPRKLAENLGSVPDRLGRLRGSNLMVDGRAARDDRTAATA
AVSELLPLARAHSTEFRRQAERFGIREQQRRAHMSLSVPALSKTAMARLVEIEAVCDRGGADAYKTAFAY
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVVAERNMFERMPEDIPPERREKLARLFAVIRRFVEEQH
LAERQDRSKIVAGASVEWGKETMAVLPMLPAVTEFKTTVADEAKERALAAPHYGHHRAALVETATRVWRD
PADAIGNIEELVVKGFASERIAAAVSNDPAAYGALRGSDRIMDKLLTTGRERKEALQAVPEVASRVRSLG
ASYASAVDAETQAIAEERRRMAIAIPGLSQAAEDALKRLAAEIKKKDGKLDVAAGSLDARIRQEFAGVSR
ALDERFGRNAILRGEKDVINRVSPAQRRAFEAMRDRLQVLQQTVRLQSSQEIISERQRRVIDRARGVTR
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGTSFSYRGGASELVHEELALPDQIPGWLKAAIDR
QSVAKASEALWNAVESHETRADAQLARELIIALPEELTRAENIALVREFIRDNLTSKGMVADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEDGEPLRVVTPDRPNGKIVYQLWAGDKETMKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLHGIAQKHLGPEKAALARKGVEMYFAPADLARRQEMADRLIADPELLLKQ
LGSERSTFEERDIAKALHRYVDDPVDFVNIRARLMASDDLVLLKPQEVDAQTGRASEPAVFTTREILRIE
YDMAQSAQALSERKGFGVSTKQVAAAIRNVETADPEEPFKLHAEQVDAVRHVTGDSGMAAVVGLAGAGKS
TLLAAARVAWESEDRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWAGGREQLDRGDVLVIDEAGMIS
SQQMARVLKIAQEAQAKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREQWARDASRLFARGK
VEEGLDAYAQQGHIVETETRAEIVDRIVSDWTDARRDLLQKSAAGEHPGRLRGEELLVLAHTNQDVRKLN
ESLRKVMIDEGALTAAREFQTARGSREFAAGDRIIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDKR
GCALLTVRLDNGRDVVISEDSYRNIDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRHRADL
YVAKEDFEVRPEWGRKPRVDHAAGVIGELVETGEAKFRPQERQAKESPYADVRTDDGTVHRLWGVSLPKA
LEEGSVSTGDTVTLRKDGVEKVIVKIPVTDEETGEKRLEEREVERNVWTANRVETADARQERIKRERHRL
ELFKQLVERLGRSGAKTTTLDFASEEVYQAHARDFARRRGIDTLAEVAAGMEEGVSRRLAWIAEKRGQVA
KLWERASVALGFAIERERRVSYNEERTASFSAGIPLVGKYLMPPTTKFSRSVEEDARLAQLSSERWKERE
AVLRPVLAKIYLDPDGALSALNALASDTAIEPRKLAENLGSVPDRLGRLRGSNLMVDGRAARDDRTAATA
AVSELLPLARAHSTEFRRQAERFGIREQQRRAHMSLSVPALSKTAMARLVEIEAVCDRGGADAYKTAFAY
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVVAERNMFERMPEDIPPERREKLARLFAVIRRFVEEQH
LAERQDRSKIVAGASVEWGKETMAVLPMLPAVTEFKTTVADEAKERALAAPHYGHHRAALVETATRVWRD
PADAIGNIEELVVKGFASERIAAAVSNDPAAYGALRGSDRIMDKLLTTGRERKEALQAVPEVASRVRSLG
ASYASAVDAETQAIAEERRRMAIAIPGLSQAAEDALKRLAAEIKKKDGKLDVAAGSLDARIRQEFAGVSR
ALDERFGRNAILRGEKDVINRVSPAQRRAFEAMRDRLQVLQQTVRLQSSQEIISERQRRVIDRARGVTR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 3816 | GenBank | WP_014857689 |
| Name | traG_SFHH103_RS23690_pSfHH103d |
UniProt ID | _ |
| Length | 639 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 639 a.a. Molecular weight: 70288.20 Da Isoelectric Point: 9.2510
>WP_014857689.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Sinorhizobium]
MALKAKPHPSLLLVLVPVAVTAFAVYVVGWRWQALAEGMSGKTQYWFLRVSPVPALLFGPLAGLLAVWAL
PLHRRRPVAMAGLACFLTVAGFYAVREFGRLAPSVESGALSWDRALSYLDMVAVVGAVVGFIAVAIAARI
STVVSEPVKRAKLGTFGDADWLPMSAAGKLFPPDGEIVVGERYRVDKDIVHELPFDPNDPAAWGKGGKTP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESIRFESSTGSYFQNQAHNLLTGLLTHVMLSPEYAGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGNKDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGGFKRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKG
SSRNIGWDTKNSASRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKPIP
MALKAKPHPSLLLVLVPVAVTAFAVYVVGWRWQALAEGMSGKTQYWFLRVSPVPALLFGPLAGLLAVWAL
PLHRRRPVAMAGLACFLTVAGFYAVREFGRLAPSVESGALSWDRALSYLDMVAVVGAVVGFIAVAIAARI
STVVSEPVKRAKLGTFGDADWLPMSAAGKLFPPDGEIVVGERYRVDKDIVHELPFDPNDPAAWGKGGKTP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESIRFESSTGSYFQNQAHNLLTGLLTHVMLSPEYAGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGNKDVFLNIPASILRSYPGIGRVIIGSLINAMVQADGGFKRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIDGCAFASYAAIKALDTARNVSAQCGEMTVEVKG
SSRNIGWDTKNSASRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKPIP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 141184..150761
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SFHH103_RS23340 (SFHH103_04680) | 137671..138327 | - | 657 | WP_014857948 | CBS domain-containing protein | - |
| SFHH103_RS23345 (SFHH103_04682) | 138663..138857 | + | 195 | WP_014857951 | hypothetical protein | - |
| SFHH103_RS23350 (SFHH103_04683) | 138866..140464 | + | 1599 | WP_014857952 | AarF/UbiB family protein | - |
| SFHH103_RS39785 | 140527..140703 | + | 177 | Protein_130 | methionine adenosyltransferase | - |
| SFHH103_RS23360 (SFHH103_04685) | 141184..142173 | - | 990 | WP_014857954 | P-type DNA transfer ATPase VirB11 | virB11 |
| SFHH103_RS23365 (SFHH103_04686) | 142184..143356 | - | 1173 | WP_037457198 | type IV secretion system protein VirB10 | virB10 |
| SFHH103_RS23370 (SFHH103_04687) | 143366..144220 | - | 855 | WP_014857956 | P-type conjugative transfer protein VirB9 | virB9 |
| SFHH103_RS23375 (SFHH103_04688) | 144220..144891 | - | 672 | WP_014857957 | virB8 family protein | virB8 |
| SFHH103_RS23380 (SFHH103_04689) | 144896..145171 | - | 276 | WP_014857958 | hypothetical protein | - |
| SFHH103_RS23385 (SFHH103_04690) | 145208..146143 | - | 936 | WP_014857959 | type IV secretion system protein | virB6 |
| SFHH103_RS23390 (SFHH103_04691) | 146149..146379 | - | 231 | WP_014857960 | EexN family lipoprotein | - |
| SFHH103_RS23395 (SFHH103_04692) | 146376..147074 | - | 699 | WP_014857961 | P-type DNA transfer protein VirB5 | virB5 |
| SFHH103_RS23400 (SFHH103_04693) | 147074..149455 | - | 2382 | WP_014857962 | VirB4 family type IV secretion system protein | virb4 |
| SFHH103_RS23405 (SFHH103_04694) | 149448..149789 | - | 342 | WP_014857963 | type IV secretion system protein VirB3 | virB3 |
| SFHH103_RS23410 (SFHH103_04695) | 149794..150093 | - | 300 | WP_014857964 | TrbC/VirB2 family protein | virB2 |
| SFHH103_RS23415 (SFHH103_04696) | 150090..150761 | - | 672 | WP_014857965 | lytic transglycosylase domain-containing protein | virB1 |
| SFHH103_RS23420 (SFHH103_04697) | 150765..151283 | - | 519 | WP_014857966 | hypothetical protein | - |
| SFHH103_RS23425 (SFHH103_04698) | 151380..151748 | + | 369 | WP_014857967 | transcriptional regulator | - |
| SFHH103_RS35875 | 151967..152645 | - | 679 | Protein_145 | acyl-homoserine-lactone synthase TraI | - |
| SFHH103_RS23435 (SFHH103_04700) | 153033..154220 | + | 1188 | WP_014857970 | plasmid partitioning protein RepA | - |
| SFHH103_RS23440 (SFHH103_04701) | 154295..155281 | + | 987 | WP_014857971 | plasmid partitioning protein RepB | - |
Host bacterium
| ID | 6053 | GenBank | NT_187148 |
| Plasmid name | pSfHH103d | Incompatibility group | - |
| Plasmid size | 248150 bp | Coordinate of oriT [Strand] | 216876..216904 [+] |
| Host baterium | Sinorhizobium fredii HH103 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | nia |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |