Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101183 |
| Name | oriT_pSM96_Rh04  |
| Organism | Rhizobium ruizarguesonis strain SM96 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_SIMV01000005 (99054..99094 [+], 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_pSM96_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1180 | GenBank | WP_130674195 |
| Name | traA_ELH44_RS31400_pSM96_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 | 779 | GenBank | WP_024323836 |
| Name | traG_ELH44_RS31385_pSM96_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.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 128812..138283
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| ELH44_RS31530 (ELH44_31530) | 124276..124482 | + | 207 | WP_080642907 | hypothetical protein | - |
| ELH44_RS31535 (ELH44_31535) | 124602..124754 | - | 153 | Protein_134 | aminoglycoside phosphotransferase | - |
| ELH44_RS31540 (ELH44_31540) | 124806..126767 | - | 1962 | WP_130720409 | elongation factor G | - |
| ELH44_RS31545 (ELH44_31545) | 127607..127810 | - | 204 | Protein_136 | IS6 family transposase | - |
| ELH44_RS31550 (ELH44_31550) | 128076..128786 | + | 711 | WP_024323909 | autoinducer binding domain-containing protein | - |
| ELH44_RS31555 (ELH44_31555) | 128812..130092 | - | 1281 | WP_130674183 | IncP-type conjugal transfer protein TrbI | virB10 |
| ELH44_RS31560 (ELH44_31560) | 130107..130535 | - | 429 | WP_018068569 | conjugal transfer protein TrbH | - |
| ELH44_RS31565 (ELH44_31565) | 130538..131359 | - | 822 | WP_018068568 | P-type conjugative transfer protein TrbG | virB9 |
| ELH44_RS31570 (ELH44_31570) | 131376..132038 | - | 663 | WP_024323906 | conjugal transfer protein TrbF | virB8 |
| ELH44_RS31575 (ELH44_31575) | 132059..133207 | - | 1149 | WP_050574296 | P-type conjugative transfer protein TrbL | virB6 |
| ELH44_RS31580 (ELH44_31580) | 133234..133431 | - | 198 | WP_130674182 | entry exclusion protein TrbK | - |
| ELH44_RS31585 (ELH44_31585) | 133428..134228 | - | 801 | WP_130674181 | P-type conjugative transfer protein TrbJ | virB5 |
| ELH44_RS31590 (ELH44_31590) | 134200..136649 | - | 2450 | Protein_145 | conjugal transfer protein TrbE | - |
| ELH44_RS31595 (ELH44_31595) | 136659..136958 | - | 300 | WP_024323901 | conjugal transfer protein TrbD | virB3 |
| ELH44_RS31600 (ELH44_31600) | 136948..137328 | - | 381 | WP_018068562 | TrbC/VirB2 family protein | virB2 |
| ELH44_RS31605 (ELH44_31605) | 137318..138283 | - | 966 | WP_024323900 | P-type conjugative transfer ATPase TrbB | virB11 |
| ELH44_RS31610 (ELH44_31610) | 138297..138923 | - | 627 | WP_130674180 | acyl-homoserine-lactone synthase TraI | - |
| ELH44_RS31615 (ELH44_31615) | 139288..140505 | + | 1218 | WP_075225817 | plasmid partitioning protein RepA | - |
| ELH44_RS31620 (ELH44_31620) | 140490..141530 | + | 1041 | WP_027689819 | plasmid partitioning protein RepB | - |
| ELH44_RS31625 (ELH44_31625) | 141769..143034 | + | 1266 | WP_130676474 | plasmid replication protein RepC | - |
Host bacterium
| ID | 1627 | GenBank | NZ_SIMV01000005 |
| Plasmid name | pSM96_Rh04 | Incompatibility group | - |
| Plasmid size | 171135 bp | Coordinate of oriT [Strand] | 99054..99094 [+] |
| Host baterium | Rhizobium ruizarguesonis strain SM96 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | nodD, nodA |
| Anti-CRISPR | - |