Detailed information of oriT
oriT
The information of the oriT region
oriTDB ID | 101187 |
Name | oriT_pSM109_Rh04 |
Organism | Rhizobium ruizarguesonis strain SM109 |
Sequence Completeness | - |
NCBI accession of oriT (coordinates [strand]) | NZ_SINI01000005 (28346..28386 [+], 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_pSM109_Rh04
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC
TCCAATGGCGCAATTATACGTCGCTGACGCGACGCCCTTGC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure fileRelaxase
ID | 1184 | GenBank | WP_130674195 |
Name | traA_ELH57_RS35905_pSM109_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 | 786 | GenBank | WP_024323836 |
Name | traG_ELH57_RS35890_pSM109_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 | 787 | GenBank | WP_024323902 |
Name | t4cp2_ELH57_RS36095_pSM109_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.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 58104..67573
Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
---|---|---|---|---|---|---|
ELH57_RS36035 (ELH57_36030) | 53568..53774 | + | 207 | WP_080642907 | hypothetical protein | - |
ELH57_RS36040 (ELH57_36035) | 53894..54046 | - | 153 | Protein_53 | aminoglycoside phosphotransferase | - |
ELH57_RS36045 (ELH57_36040) | 54098..56059 | - | 1962 | WP_130720409 | elongation factor G | - |
ELH57_RS36050 (ELH57_36045) | 56899..57102 | - | 204 | Protein_55 | IS6 family transposase | - |
ELH57_RS36055 (ELH57_36050) | 57368..58078 | + | 711 | WP_024323909 | autoinducer binding domain-containing protein | - |
ELH57_RS36060 (ELH57_36055) | 58104..59384 | - | 1281 | WP_130674183 | IncP-type conjugal transfer protein TrbI | virB10 |
ELH57_RS36065 (ELH57_36060) | 59399..59827 | - | 429 | WP_018068569 | conjugal transfer protein TrbH | - |
ELH57_RS36070 (ELH57_36065) | 59830..60651 | - | 822 | WP_018068568 | P-type conjugative transfer protein TrbG | virB9 |
ELH57_RS36075 (ELH57_36070) | 60668..61330 | - | 663 | WP_024323906 | conjugal transfer protein TrbF | virB8 |
ELH57_RS36080 (ELH57_36075) | 61351..62499 | - | 1149 | WP_050574296 | P-type conjugative transfer protein TrbL | virB6 |
ELH57_RS36085 (ELH57_36080) | 62526..62723 | - | 198 | WP_130674182 | entry exclusion protein TrbK | - |
ELH57_RS36090 (ELH57_36085) | 62720..63520 | - | 801 | WP_130674181 | P-type conjugative transfer protein TrbJ | virB5 |
ELH57_RS36095 (ELH57_36090) | 63492..65939 | - | 2448 | WP_024323902 | conjugal transfer protein TrbE | virb4 |
ELH57_RS36100 (ELH57_36095) | 65949..66248 | - | 300 | WP_024323901 | conjugal transfer protein TrbD | virB3 |
ELH57_RS36105 (ELH57_36100) | 66238..66618 | - | 381 | WP_018068562 | TrbC/VirB2 family protein | virB2 |
ELH57_RS36110 (ELH57_36105) | 66608..67573 | - | 966 | WP_024323900 | P-type conjugative transfer ATPase TrbB | virB11 |
ELH57_RS36115 (ELH57_36110) | 67587..68213 | - | 627 | WP_130674180 | acyl-homoserine-lactone synthase TraI | - |
ELH57_RS36120 (ELH57_36115) | 68578..69795 | + | 1218 | WP_075225817 | plasmid partitioning protein RepA | - |
ELH57_RS36125 (ELH57_36120) | 69780..70820 | + | 1041 | WP_027689819 | plasmid partitioning protein RepB | - |
ELH57_RS36130 (ELH57_36125) | 71059..72324 | + | 1266 | WP_130676474 | plasmid replication protein RepC | - |
Host bacterium
ID | 1631 | GenBank | NZ_SINI01000005 |
Plasmid name | pSM109_Rh04 | Incompatibility group | - |
Plasmid size | 100244 bp | Coordinate of oriT [Strand] | 28346..28386 [+] |
Host baterium | Rhizobium ruizarguesonis strain SM109 |
Cargo genes
Drug resistance gene | - |
Virulence gene | - |
Metal resistance gene | - |
Degradation gene | - |
Symbiosis gene | nodD, nodA |
Anti-CRISPR | - |