Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103488 |
| Name | oriT_pBS3d  |
| Organism | Rhizobium phaseoli strain S3 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP064935 (971462..971490 [-], 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_pBS3d
AGGGCGCAATATACGTCGCTGCCGCGACG
AGGGCGCAATATACGTCGCTGCCGCGACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2610 | GenBank | WP_064820496 |
| Name | traA_HER27_RS31995_pBS3d |
UniProt ID | A0A7X6J0B9 |
| Length | 1543 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1543 a.a. Molecular weight: 171090.63 Da Isoelectric Point: 7.0921
>WP_064820496.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGISFSYRGGASELMHEELALPDQIPAWLKMAMDG
RSIAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVSGNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEHGKPLRVVTPDRPNGRIVYKVWAGDKETMKAWKVAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELFFAPADLARRQEMADRLLAEPELLLKQ
LGNESSTFDEKDIAKALHRYVDDPVEFANIRARLMASDELVMLKPQEMDADTGKVSEPALFTTRDMLRIE
YYMADSARRLSNRSGYAVSRKHVAAAIERIESDDPKNLFRLDAEQGDAIRHVTGDSGIAAVVGLAGAGKS
TLLAAARLAWESEGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVLVIDEAGMVS
SQQMARVLKIAEEAEIKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQEWARDASRLFARGE
VERGLDAYAQQGHLVEAGTREEAINRIVVDWTEARKQAIDRSTSEGRDGHLRGDELLVLAHTNADVKRLN
EALREVMKAEQALSDSRTFQTARGAREFAVGDRIIFLENARFLEPRARHSGPQYVKNGMLGTVVATGDKR
GDPLMSVLLDNGRNVVFSEDSYRNVDHGYASTIHKSQGATVDRTFVLATGMMDRHLTYVSMTRHRDRADL
YAVKEDFQVRSEWGRRLRADHAAGVTGELVETGEAKFRPDDEDADDSHYADIRTGDGTVHRLWGVSLPKA
LEEAGISEGDTITLRKDGVERVKVQIAVVDEATGQKRYDEREVDRNVWRAKQIETADARQERIERERHRP
DVFGRLVERLARSGAKTTTLDFESEAGYRAHADDFARRRGLDHLSLAAAEMEEGVSRRLAWIAEKRGQIA
KLWERASVALGLAIERERRVAYNEERSETMIGAISSEERYLIPPATDFRRSLDEDARLAQLSSPAWKERE
AILRPLLETIYRDPDAALVRLNALASYTGTEPRGLADNLAVAPDRLGRLRGSELIVEGRAARDERDVAMA
ALEELLPLVRGHATEFRRNAERFELREQARRASMSLSVPALSEQAMARLMEIEAVRTQGGDDAYKTAFAL
AAEDRSVVQEVKAVSEALTARFGWSAFTAKADAMAERNMVERMPEDLSAGRREELIRLFEAVKRFAEEQH
LAERRDRSKIVAAASAVPGAAPGKQTVTVLPMLAAVTEFKTSVDDEARSRAIAAPLYRQQRAALAEAARM
IWRDPAATVDNIESLLEKGFAADRIAAAVTNDPAAYGALRGSDRLMDRMLASGRERKDAVQAVPEAAARL
RSLGSAYVNVLDAERQAIAEERRRMAVAIPGLSKAAEGVLMRLTTEVKNNGRTRNAAAGSLDPSIHREFD
AVSRALDERFGRSAIVRGEKDLLNRMPPAQRAAFAAMQEKLKVLQQTVRWESSEKIVSELRNRTVNRGRG
IEL
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMMDEQAGISFSYRGGASELMHEELALPDQIPAWLKMAMDG
RSIAKASEALWNAVDAFEKRADAQLARELIIALPEELTRAENIALVREFVSGNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGPKKVAVLGEHGKPLRVVTPDRPNGRIVYKVWAGDKETMKAWKVAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELFFAPADLARRQEMADRLLAEPELLLKQ
LGNESSTFDEKDIAKALHRYVDDPVEFANIRARLMASDELVMLKPQEMDADTGKVSEPALFTTRDMLRIE
YYMADSARRLSNRSGYAVSRKHVAAAIERIESDDPKNLFRLDAEQGDAIRHVTGDSGIAAVVGLAGAGKS
TLLAAARLAWESEGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVLVIDEAGMVS
SQQMARVLKIAEEAEIKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQRQEWARDASRLFARGE
VERGLDAYAQQGHLVEAGTREEAINRIVVDWTEARKQAIDRSTSEGRDGHLRGDELLVLAHTNADVKRLN
EALREVMKAEQALSDSRTFQTARGAREFAVGDRIIFLENARFLEPRARHSGPQYVKNGMLGTVVATGDKR
GDPLMSVLLDNGRNVVFSEDSYRNVDHGYASTIHKSQGATVDRTFVLATGMMDRHLTYVSMTRHRDRADL
YAVKEDFQVRSEWGRRLRADHAAGVTGELVETGEAKFRPDDEDADDSHYADIRTGDGTVHRLWGVSLPKA
LEEAGISEGDTITLRKDGVERVKVQIAVVDEATGQKRYDEREVDRNVWRAKQIETADARQERIERERHRP
DVFGRLVERLARSGAKTTTLDFESEAGYRAHADDFARRRGLDHLSLAAAEMEEGVSRRLAWIAEKRGQIA
KLWERASVALGLAIERERRVAYNEERSETMIGAISSEERYLIPPATDFRRSLDEDARLAQLSSPAWKERE
AILRPLLETIYRDPDAALVRLNALASYTGTEPRGLADNLAVAPDRLGRLRGSELIVEGRAARDERDVAMA
ALEELLPLVRGHATEFRRNAERFELREQARRASMSLSVPALSEQAMARLMEIEAVRTQGGDDAYKTAFAL
AAEDRSVVQEVKAVSEALTARFGWSAFTAKADAMAERNMVERMPEDLSAGRREELIRLFEAVKRFAEEQH
LAERRDRSKIVAAASAVPGAAPGKQTVTVLPMLAAVTEFKTSVDDEARSRAIAAPLYRQQRAALAEAARM
IWRDPAATVDNIESLLEKGFAADRIAAAVTNDPAAYGALRGSDRLMDRMLASGRERKDAVQAVPEAAARL
RSLGSAYVNVLDAERQAIAEERRRMAVAIPGLSKAAEGVLMRLTTEVKNNGRTRNAAAGSLDPSIHREFD
AVSRALDERFGRSAIVRGEKDLLNRMPPAQRAAFAAMQEKLKVLQQTVRWESSEKIVSELRNRTVNRGRG
IEL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 2411 | GenBank | WP_064820498 |
| Name | traG_HER27_RS32010_pBS3d |
UniProt ID | _ |
| Length | 639 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 639 a.a. Molecular weight: 70447.36 Da Isoelectric Point: 9.3885
>WP_064820498.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MIARGKPHPSLLFVFAPVVVTAIAVYIAGWRWPGLAAGMPGRMEYWFLRAAPVPALLFGPLAGLLTVWAL
PLHRRRPVAMTSLLCYLGVSASFAMREFARLGPSVQTGVITWDRALSYLDMVAVLGAVAGFLAVALSARI
SVVVPDEINRARRGTFGDADWLSMAAAAKLFPPDGEIVVGERYRVDKEIVHQLPFDANDRGTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHTLGREVMVLDPT
NPIMGFNVLDGIETSRQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GKAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFRRRALFMLDEVDLLGYMRVL
EEARDRGRKYGVSMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAVKALDTARTVSAQCGEMTVEVKG
SSRNLGWNSRNGGTRKSESVSFQRRPLIMPHEITQSMRKDEQVIIVQGHSPIRCGRAIYFRRKEMDGVAK
ANRFVKPVP
MIARGKPHPSLLFVFAPVVVTAIAVYIAGWRWPGLAAGMPGRMEYWFLRAAPVPALLFGPLAGLLTVWAL
PLHRRRPVAMTSLLCYLGVSASFAMREFARLGPSVQTGVITWDRALSYLDMVAVLGAVAGFLAVALSARI
SVVVPDEINRARRGTFGDADWLSMAAAAKLFPPDGEIVVGERYRVDKEIVHQLPFDANDRGTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTHTLGREVMVLDPT
NPIMGFNVLDGIETSRQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GKAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFRRRALFMLDEVDLLGYMRVL
EEARDRGRKYGVSMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAVKALDTARTVSAQCGEMTVEVKG
SSRNLGWNSRNGGTRKSESVSFQRRPLIMPHEITQSMRKDEQVIIVQGHSPIRCGRAIYFRRKEMDGVAK
ANRFVKPVP
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 983369..992925
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HER27_RS32055 (HER27_032055) | 978944..979126 | + | 183 | WP_012490320 | hypothetical protein | - |
| HER27_RS32060 (HER27_032060) | 979259..980296 | - | 1038 | WP_064820506 | toprim domain-containing protein | - |
| HER27_RS32065 (HER27_032065) | 980659..981849 | + | 1191 | WP_064820507 | DUF1173 domain-containing protein | - |
| HER27_RS32070 (HER27_032070) | 982292..982885 | + | 594 | WP_037146723 | DUF433 domain-containing protein | - |
| HER27_RS32075 (HER27_032075) | 982900..983325 | + | 426 | WP_237357452 | PIN domain-containing protein | - |
| HER27_RS32080 (HER27_032080) | 983369..984364 | - | 996 | WP_064820508 | P-type DNA transfer ATPase VirB11 | virB11 |
| HER27_RS32085 (HER27_032085) | 984373..985548 | - | 1176 | WP_064820509 | type IV secretion system protein VirB10 | virB10 |
| HER27_RS32090 (HER27_032090) | 985557..986411 | - | 855 | WP_037146719 | P-type conjugative transfer protein VirB9 | virB9 |
| HER27_RS32095 (HER27_032095) | 986408..987079 | - | 672 | WP_037146717 | virB8 family protein | virB8 |
| HER27_RS32100 (HER27_032100) | 987073..987360 | - | 288 | WP_016737562 | hypothetical protein | - |
| HER27_RS32105 (HER27_032105) | 987401..988333 | - | 933 | WP_046977230 | type IV secretion system protein | virB6 |
| HER27_RS32110 (HER27_032110) | 988336..988569 | - | 234 | WP_016735278 | EexN family lipoprotein | - |
| HER27_RS32115 (HER27_032115) | 988566..989267 | - | 702 | WP_016735279 | P-type DNA transfer protein VirB5 | virB5 |
| HER27_RS32120 (HER27_032120) | 989264..991630 | - | 2367 | WP_046977231 | VirB4 family type IV secretion system protein | virb4 |
| HER27_RS32125 (HER27_032125) | 991623..991961 | - | 339 | WP_064820510 | type IV secretion system protein VirB3 | virB3 |
| HER27_RS32130 (HER27_032130) | 991967..992266 | - | 300 | WP_064820511 | TrbC/VirB2 family protein | virB2 |
| HER27_RS32135 (HER27_032135) | 992263..992925 | - | 663 | WP_064820512 | transglycosylase SLT domain-containing protein | virB1 |
| HER27_RS32140 (HER27_032140) | 992929..993465 | - | 537 | WP_064820513 | hypothetical protein | - |
| HER27_RS32145 (HER27_032145) | 993564..993935 | + | 372 | WP_041684118 | hypothetical protein | - |
| HER27_RS32150 (HER27_032150) | 994288..995478 | - | 1191 | WP_064820514 | hypothetical protein | - |
| HER27_RS32155 (HER27_032155) | 995553..996209 | - | 657 | WP_064820515 | hypothetical protein | - |
Host bacterium
| ID | 3931 | GenBank | NZ_CP064935 |
| Plasmid name | pBS3d | Incompatibility group | - |
| Plasmid size | 1111454 bp | Coordinate of oriT [Strand] | 971462..971490 [-] |
| Host baterium | Rhizobium phaseoli strain S3 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | gmd |
| Metal resistance gene | hupE2 |
| Degradation gene | dxnH, LinG |
| Symbiosis gene | noeL, fixB, fixA |
| Anti-CRISPR | AcrIIA8 |