Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101144 |
| Name | oriT_pSM85_Rh04  |
| Organism | Rhizobium ruizarguesonis strain SM85 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_SIMK01000005 (28325..28365 [+], 41 nt) |
| oriT length | 41 nt |
| IRs (inverted repeats) | 19..24, 29..34 (CGTCGC..GCGACG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 41 nt
>oriT_pSM85_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1142 | GenBank | WP_130674195 |
| Name | traA_ELH33_RS31070_pSM85_Rh04 |
UniProt ID | _ |
| Length | 1107 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1107 a.a. Molecular weight: 122861.94 Da Isoelectric Point: 10.2104
>WP_130674195.1 Ti-type conjugative transfer relaxase TraA [Rhizobium ruizarguesonis]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPTGAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDSQLAKDLTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGAKKIAVASPDGNPMRNDAGKIVYELWAGSADDFNAVRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIDRKAEQANARTSAWSPKLERVELQQDRRAENARRIQRRPD
IVLDLITREKSVFDDRDVGKILHRYIDDAALFQNLMMRILQSPQALRLERDRIDFATGVRTPAKYTTREM
IKLEAEMVNRAIWLSDRASHGVREAALEVTFARHARLSDEQRTAIERVAGGERIAAVMGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNRIDARTVFVLDEAGMVSSRQM
AHFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRAQWMRDASLDLARGNVGKA
VDAYRAHGQVRGLDLKAQAVENLIADWNHDYDPSKSSLILAHLRRDVRMLNDMARAKLVERGIVADGFAF
KSEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRLVVALGEGDHRRVVTIEQRFYNKLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLVPILARRNAKETTLDYE
KSSFYGQALRFAEARGLHLMNVARTLARDRLEWTVRQKQKLADLGARLAAIGVKLGRAANAKTSPNLNAK
ESKPMVSGISTFSKSIDQSVEDKLAADPGLKKQWEDVSARFHLVYAQPESAFKAANVEAMLKDQAIAKTT
LAKLAGEPERFGALRGKTGVFANRGDKQDRERAIANVPALARNLERYLRQRAEVERKHETEERAVRRQVS
VDIPALSASAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELDGFAKAVSERFGERTFLGIASKDPSGE
TFKSVTAGMNPAQKAEVEIAWNSMRSIQQLSAHEKTTEALKQAETLRQTRSQGFSLK
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKRGLLHEEFVIPTGAPTWLRAMIADR
SVSGASEAFWNKVEAFEKRSDSQLAKDLTIALPIELSAEQNVALVRDFVERHITSKGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGAKKIAVASPDGNPMRNDAGKIVYELWAGSADDFNAVRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIELTPTIHLGVGTKAIDRKAEQANARTSAWSPKLERVELQQDRRAENARRIQRRPD
IVLDLITREKSVFDDRDVGKILHRYIDDAALFQNLMMRILQSPQALRLERDRIDFATGVRTPAKYTTREM
IKLEAEMVNRAIWLSDRASHGVREAALEVTFARHARLSDEQRTAIERVAGGERIAAVMGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIQSRTLSSWELRWNQGRNRIDARTVFVLDEAGMVSSRQM
AHFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRAQWMRDASLDLARGNVGKA
VDAYRAHGQVRGLDLKAQAVENLIADWNHDYDPSKSSLILAHLRRDVRMLNDMARAKLVERGIVADGFAF
KSEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAPGRLVVALGEGDHRRVVTIEQRFYNKLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKSGGLVPILARRNAKETTLDYE
KSSFYGQALRFAEARGLHLMNVARTLARDRLEWTVRQKQKLADLGARLAAIGVKLGRAANAKTSPNLNAK
ESKPMVSGISTFSKSIDQSVEDKLAADPGLKKQWEDVSARFHLVYAQPESAFKAANVEAMLKDQAIAKTT
LAKLAGEPERFGALRGKTGVFANRGDKQDRERAIANVPALARNLERYLRQRAEVERKHETEERAVRRQVS
VDIPALSASAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELDGFAKAVSERFGERTFLGIASKDPSGE
TFKSVTAGMNPAQKAEVEIAWNSMRSIQQLSAHEKTTEALKQAETLRQTRSQGFSLK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 705 | GenBank | WP_024323836 |
| Name | traG_ELH33_RS31055_pSM85_Rh04 |
UniProt ID | _ |
| Length | 655 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 655 a.a. Molecular weight: 71050.85 Da Isoelectric Point: 8.7825
>WP_024323836.1 Ti-type conjugative transfer system protein TraG [Rhizobium ruizarguesonis]
MTANKIALFSVPIALMILVTIGMTGTEQWFSEFGKTETGRLILGRTGIALPYIASAATGIIFLFASAGST
NIKLAGWGVVGGSSATVVIAALRETVRLAAIFDHFPAVRSALSYADPATMIGAGAALMSAGFALRVALVG
NAAFARSEPRRIRGRRALHGEAEWMKSTEAGKLFPDTGGIVIGERYRVDKDIAAKQSFRADSVETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVLLDPSNEVAPMVIGHRTNAGRDVHILD
PRTPDTGFNALDWIGLHGRTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDRTEE
DDQTLRQVRKNLSEPEPKLRARLQSIYDNSRSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSESTFSTNDISAGNADVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
ENRFHSPARGDESAMDPETPMKLRG
MTANKIALFSVPIALMILVTIGMTGTEQWFSEFGKTETGRLILGRTGIALPYIASAATGIIFLFASAGST
NIKLAGWGVVGGSSATVVIAALRETVRLAAIFDHFPAVRSALSYADPATMIGAGAALMSAGFALRVALVG
NAAFARSEPRRIRGRRALHGEAEWMKSTEAGKLFPDTGGIVIGERYRVDKDIAAKQSFRADSVETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLVLLDPSNEVAPMVIGHRTNAGRDVHILD
PRTPDTGFNALDWIGLHGRTKEEDIAAVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSDRTEE
DDQTLRQVRKNLSEPEPKLRARLQSIYDNSRSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSESTFSTNDISAGNADVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGALKGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSVQSKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVG
ENRFHSPARGDESAMDPETPMKLRG
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 706 | GenBank | WP_024323902 |
| Name | t4cp2_ELH33_RS31260_pSM85_Rh04 |
UniProt ID | _ |
| Length | 815 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 815 a.a. Molecular weight: 91549.04 Da Isoelectric Point: 6.2219
>WP_024323902.1 conjugal transfer protein TrbE [Rhizobium ruizarguesonis]
MVSLRAFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEVSRQINAILSRLG
SGWMIQVEAVRLATVDYASAGKSHFPDRVTQAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YIYSDEDSRKQSYADTVLFIFRNAIREVEQYLANIISIRRMLTRETVERGGARVAHYDELLQFIRFCVTG
ENHPVRVPDIPMYLDWIATAELRHGLAPKVENRFLGVVAIDGLPSESWPGILNSLDAMPLGYRWSSRFIF
LDAEEARVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDALSMVAETEDAIAQASSQLVAYGYYTPVVVL
FESDSERLNEKTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GNPRAPCPFYSPDSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLACGGDHYEIGGDEDTGLSFCPLSELSSEGDRAWASEWIESLVGMQGITITPDHRNAIS
RQIGLMDGASGRSISDFVSGVQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQTFEIEQVMNMGERN
LVPVLTYLFRRIEKRLTGAPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREPGTRDFYERIGFNERQIEIVATAIPKREYYVASPEGRRLFDMALGPLTL
SFVGASSKDDLKHIRALHGEHGPQWPLHWLQKRGIKDAASLLKDA
MVSLRAFRHTAPSFADLVPYAGLVDNGIILLKDGSLMAGWYFAGPDSESSTDFERNEVSRQINAILSRLG
SGWMIQVEAVRLATVDYASAGKSHFPDRVTQAIDEERRAHFEREQGHFESRHAIIATYRPTEQRRSRLSK
YIYSDEDSRKQSYADTVLFIFRNAIREVEQYLANIISIRRMLTRETVERGGARVAHYDELLQFIRFCVTG
ENHPVRVPDIPMYLDWIATAELRHGLAPKVENRFLGVVAIDGLPSESWPGILNSLDAMPLGYRWSSRFIF
LDAEEARVRLERTRKKWQQKVRPFFDQLFQTQSRSVDQDALSMVAETEDAIAQASSQLVAYGYYTPVVVL
FESDSERLNEKTEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTRNLSDLIPLNSVWS
GNPRAPCPFYSPDSPPLMQVATGSTPFRLNLHVDDVGHTLVFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGRSMLPLTLACGGDHYEIGGDEDTGLSFCPLSELSSEGDRAWASEWIESLVGMQGITITPDHRNAIS
RQIGLMDGASGRSISDFVSGVQMREIKDALHHYTVDGPMGQLLDAETDGLALGLFQTFEIEQVMNMGERN
LVPVLTYLFRRIEKRLTGAPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAERSGI
IDVLKESCPTKICLPNGAAREPGTRDFYERIGFNERQIEIVATAIPKREYYVASPEGRRLFDMALGPLTL
SFVGASSKDDLKHIRALHGEHGPQWPLHWLQKRGIKDAASLLKDA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 707 | GenBank | WP_130826827 |
| Name | t4cp2_ELH33_RS32885_pSM85_Rh04 |
UniProt ID | _ |
| Length | 560 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 560 a.a. Molecular weight: 60844.10 Da Isoelectric Point: 7.3488
>WP_130826827.1 type IV secretory system conjugative DNA transfer family protein [Rhizobium ruizarguesonis]
MIHASQIKIAFANMMRMAARDPLWAIVALITFPLRYAKSFVMGAFGYLLVVFTVYFGIDYLRRVILGGHR
GDVIWHIGDWVVMAFAIVLLIRLLSTPLITHFGSAMDDTHGSARFAGGREIAPLTKTSSGLLIGRAPGSA
RLLRYDGPAHLLTMAPTRGGKGVGTIIPNLLTADRSIICIDPKGENAQIAGDAREKFGPVHILDPFGITG
RPSAAFNPMDGVDPGSVDVAEDATTLADALVFDEPGLSGDAHWNEEAKALIAGLLLHVIASQPDDKRTLT
TLRHLLTMAPAAFQNLLHEMQGNDAISGLIARAANRHLGKSDREASGVLSAAQRHTHFLDSPRMTGVLSG
SDFRFADLKANKATVFLVLPPDRLAAYSRWLRLLVAQSLTEMARTPPSPHPSTPPVLYLLDEFTALGHLA
PIERAMGLMAGYGVQLWPIIQDIHQLRATYRQRAGTFLSNAGVLQVFGVNDHDSARLVSDLLGQETVVFN
TAARALDSEKSGLSFAEQHVGRPLLTPDEVRNMHAETELLFIAGQRPIIATKLRYYADPEFAGLFGNQER
MIHASQIKIAFANMMRMAARDPLWAIVALITFPLRYAKSFVMGAFGYLLVVFTVYFGIDYLRRVILGGHR
GDVIWHIGDWVVMAFAIVLLIRLLSTPLITHFGSAMDDTHGSARFAGGREIAPLTKTSSGLLIGRAPGSA
RLLRYDGPAHLLTMAPTRGGKGVGTIIPNLLTADRSIICIDPKGENAQIAGDAREKFGPVHILDPFGITG
RPSAAFNPMDGVDPGSVDVAEDATTLADALVFDEPGLSGDAHWNEEAKALIAGLLLHVIASQPDDKRTLT
TLRHLLTMAPAAFQNLLHEMQGNDAISGLIARAANRHLGKSDREASGVLSAAQRHTHFLDSPRMTGVLSG
SDFRFADLKANKATVFLVLPPDRLAAYSRWLRLLVAQSLTEMARTPPSPHPSTPPVLYLLDEFTALGHLA
PIERAMGLMAGYGVQLWPIIQDIHQLRATYRQRAGTFLSNAGVLQVFGVNDHDSARLVSDLLGQETVVFN
TAARALDSEKSGLSFAEQHVGRPLLTPDEVRNMHAETELLFIAGQRPIIATKLRYYADPEFAGLFGNQER
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 58083..67552
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| ELH33_RS31200 (ELH33_31195) | 53547..53753 | + | 207 | WP_080642907 | hypothetical protein | - |
| ELH33_RS31205 (ELH33_31200) | 53873..54025 | - | 153 | Protein_53 | aminoglycoside phosphotransferase | - |
| ELH33_RS31210 (ELH33_31205) | 54077..56038 | - | 1962 | WP_130720409 | elongation factor G | - |
| ELH33_RS31215 (ELH33_31210) | 56878..57081 | - | 204 | Protein_55 | IS6 family transposase | - |
| ELH33_RS31220 (ELH33_31215) | 57347..58057 | + | 711 | WP_024323909 | autoinducer binding domain-containing protein | - |
| ELH33_RS31225 (ELH33_31220) | 58083..59363 | - | 1281 | WP_130674183 | IncP-type conjugal transfer protein TrbI | virB10 |
| ELH33_RS31230 (ELH33_31225) | 59378..59806 | - | 429 | WP_018068569 | conjugal transfer protein TrbH | - |
| ELH33_RS31235 (ELH33_31230) | 59809..60630 | - | 822 | WP_018068568 | P-type conjugative transfer protein TrbG | virB9 |
| ELH33_RS31240 (ELH33_31235) | 60647..61309 | - | 663 | WP_024323906 | conjugal transfer protein TrbF | virB8 |
| ELH33_RS31245 (ELH33_31240) | 61330..62478 | - | 1149 | WP_050574296 | P-type conjugative transfer protein TrbL | virB6 |
| ELH33_RS31250 (ELH33_31245) | 62505..62702 | - | 198 | WP_130674182 | entry exclusion protein TrbK | - |
| ELH33_RS31255 (ELH33_31250) | 62699..63499 | - | 801 | WP_130674181 | P-type conjugative transfer protein TrbJ | virB5 |
| ELH33_RS31260 (ELH33_31255) | 63471..65918 | - | 2448 | WP_024323902 | conjugal transfer protein TrbE | virb4 |
| ELH33_RS31265 (ELH33_31260) | 65928..66227 | - | 300 | WP_024323901 | conjugal transfer protein TrbD | virB3 |
| ELH33_RS31270 (ELH33_31265) | 66217..66597 | - | 381 | WP_018068562 | TrbC/VirB2 family protein | virB2 |
| ELH33_RS31275 (ELH33_31270) | 66587..67552 | - | 966 | WP_024323900 | P-type conjugative transfer ATPase TrbB | virB11 |
| ELH33_RS31280 (ELH33_31275) | 67566..68192 | - | 627 | WP_130674180 | acyl-homoserine-lactone synthase TraI | - |
| ELH33_RS31285 (ELH33_31280) | 68557..69774 | + | 1218 | WP_075225817 | plasmid partitioning protein RepA | - |
| ELH33_RS31290 (ELH33_31285) | 69759..70799 | + | 1041 | WP_027689819 | plasmid partitioning protein RepB | - |
| ELH33_RS31295 (ELH33_31290) | 71038..72303 | + | 1266 | WP_130676474 | plasmid replication protein RepC | - |
Host bacterium
| ID | 1588 | GenBank | NZ_SIMK01000005 |
| Plasmid name | pSM85_Rh04 | Incompatibility group | - |
| Plasmid size | 490868 bp | Coordinate of oriT [Strand] | 28325..28365 [+] |
| Host baterium | Rhizobium ruizarguesonis strain SM85 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | gmd |
| Metal resistance gene | hupE2 |
| Degradation gene | - |
| Symbiosis gene | noeL |
| Anti-CRISPR | - |