Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 100266 |
| Name | oriT_pRL8  |
| Organism | Rhizobium johnstonii 3841 |
| Sequence Completeness | core |
| NCBI accession of oriT (coordinates [strand]) | NC_008383 (126421..126470 [+], 50 nt) |
| oriT length | 50 nt |
| IRs (inverted repeats) | 22..27, 32..37 (CGTCGC..GCGACG) |
| Location of nic site | 11..12 |
| Conserved sequence flanking the nic site |
_ |
| Note | predicted by the oriTfinder |
oriT sequence
Download Length: 50 nt
>oriT_pRL8
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGCTGAAGGG
GGATCCAAGGGCGCAATTATACGTCGCTGACGCGACGCCCTGCTGAAGGG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 337 | GenBank | WP_011654745 |
| Name | TraA_pRL8 |
UniProt ID | Q1M997 |
| Length | 1197 a.a. | PDB ID | |
| Note | putative relaxase | ||
Relaxase protein sequence
Download Length: 1197 a.a. Molecular weight: 131887.62 Da Isoelectric Point: 9.1379
>WP_011654745.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPETAPDWLRSMIADR
SVSGASEAFWNKVEAFEKRADAQLAKDVTIALPVELSNDQNIALVRDFVERHITAKGMVADWVYHDALGN
PHIHLMTTLRPLTEDGFGAKKVAVLAPAGKPVRNDAGKIVYELWAGSTDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKGDNKTGWGEEKVALERLELQEERRAENARRIQRNPEI
VLDLITREKSVFDERDIAKILYRYIDDAALFQNLMARILQSPQTLRLDRERMDLVTGVRAPSKYTTRELI
RLEAQMANQAIWLSQRSSHGVRHAVLSGVFSRHDRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKA
ARQAWEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSAWELRWDQERDRLDEKSVFVLDEAGMVSSRQMA
RFVEAVTVSGAKLVLVGDPEQLQPIEAGAAFRAISGRIGYAELETIYRQREQWMRDASLDLARGNVSAAL
DAYAQRDMVRTGWTRDEAITALIADWDHEYDPAKSTLILAHRRIDVRLLNEMARSKLVERGLIEAGHAFK
TEDGTRQLAAGDQIVFLKNEGSLGVKNGMLARVVDAQPGRIVAEIGNGEDRRRVVVEQRFYANVDHGYAT
TVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPGNRD
SYYVTLGFADGQERTVWGVDLARAMDASGARIGDRIGLKHVGSQRVTLPDGTEVDRNSWKVVPVEELAMA
RLHERLSRPGSKETTLDYQDASHYRAALRFAEARSLHLMNVARTIAHDQLQWTIRQSSKLAELGARLVAV
AAKLGLGGAKSTVSTTSAIKEAKPMVSGTTTFPRSIGQAAEDKLSADPGLKASWQEVSARFHHVFADPQA
AFKTVNVDAMLANGTVAATTIVQIAEQPESFGALKGKTGLFAGSAEKRAHDTALVNAPALARDLQGFIAK
RAEAASRYEDEERAVRTKLSLDIPALSASAKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAV
SERFGERTFLPLAAKTADGKAFEVASAGMQPAQKNELRSAWDTIRTVQQLAAHERTAVALKQAEAIRQTQ
TKGLSLK
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEFEREARTIDYSRKQGLLHEEFVIPETAPDWLRSMIADR
SVSGASEAFWNKVEAFEKRADAQLAKDVTIALPVELSNDQNIALVRDFVERHITAKGMVADWVYHDALGN
PHIHLMTTLRPLTEDGFGAKKVAVLAPAGKPVRNDAGKIVYELWAGSTDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKGDNKTGWGEEKVALERLELQEERRAENARRIQRNPEI
VLDLITREKSVFDERDIAKILYRYIDDAALFQNLMARILQSPQTLRLDRERMDLVTGVRAPSKYTTRELI
RLEAQMANQAIWLSQRSSHGVRHAVLSGVFSRHDRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKA
ARQAWEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSAWELRWDQERDRLDEKSVFVLDEAGMVSSRQMA
RFVEAVTVSGAKLVLVGDPEQLQPIEAGAAFRAISGRIGYAELETIYRQREQWMRDASLDLARGNVSAAL
DAYAQRDMVRTGWTRDEAITALIADWDHEYDPAKSTLILAHRRIDVRLLNEMARSKLVERGLIEAGHAFK
TEDGTRQLAAGDQIVFLKNEGSLGVKNGMLARVVDAQPGRIVAEIGNGEDRRRVVVEQRFYANVDHGYAT
TVHKSQGATVDRVKVLASSTLDRHLSYVAMTRHRETAELYVGLEEFAQRRGGVLIAHGEAPYEHKPGNRD
SYYVTLGFADGQERTVWGVDLARAMDASGARIGDRIGLKHVGSQRVTLPDGTEVDRNSWKVVPVEELAMA
RLHERLSRPGSKETTLDYQDASHYRAALRFAEARSLHLMNVARTIAHDQLQWTIRQSSKLAELGARLVAV
AAKLGLGGAKSTVSTTSAIKEAKPMVSGTTTFPRSIGQAAEDKLSADPGLKASWQEVSARFHHVFADPQA
AFKTVNVDAMLANGTVAATTIVQIAEQPESFGALKGKTGLFAGSAEKRAHDTALVNAPALARDLQGFIAK
RAEAASRYEDEERAVRTKLSLDIPALSASAKQVLERVRDAIDRNDIPAGLEFALADKMVKAELEGFAKAV
SERFGERTFLPLAAKTADGKAFEVASAGMQPAQKNELRSAWDTIRTVQQLAAHERTAVALKQAEAIRQTQ
TKGLSLK
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | Q1M997 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 131867..147095
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RL_RS25775 (pRL80123) | 130132..130695 | + | 564 | WP_122330904 | conjugative transfer signal peptidase TraF | - |
| RL_RS25780 (pRL80124) | 130685..131851 | + | 1167 | WP_011654747 | conjugal transfer protein TraB | - |
| RL_RS25785 (pRL80125) | 131867..132484 | + | 618 | WP_011654748 | TraH family protein | virB1 |
| RL_RS25790 (pRL80126) | 132508..133125 | - | 618 | WP_011654749 | hypothetical protein | - |
| RL_RS25795 | 133122..133301 | - | 180 | WP_018010295 | hypothetical protein | - |
| RL_RS25800 (pRL80128) | 133444..134439 | - | 996 | WP_011654750 | alpha/beta hydrolase | - |
| RL_RS25805 (pRL80130) | 134429..136048 | - | 1620 | WP_041936710 | hypothetical protein | - |
| RL_RS25810 (pRL80131) | 136336..137040 | + | 705 | WP_011654752 | autoinducer binding domain-containing protein | - |
| RL_RS25815 (pRL80132) | 137041..137340 | - | 300 | WP_011654753 | transcriptional repressor TraM | - |
| RL_RS25820 (pRL80133) | 137542..138840 | - | 1299 | WP_011654754 | IncP-type conjugal transfer protein TrbI | virB10 |
| RL_RS25825 (pRL80134) | 138856..139302 | - | 447 | WP_011654755 | conjugal transfer protein TrbH | - |
| RL_RS25830 (pRL80135) | 139306..140100 | - | 795 | WP_244432395 | P-type conjugative transfer protein TrbG | virB9 |
| RL_RS25835 (pRL80136) | 140152..140814 | - | 663 | WP_011654757 | conjugal transfer protein TrbF | virB8 |
| RL_RS25840 (pRL80137) | 140836..142017 | - | 1182 | WP_011654758 | P-type conjugative transfer protein TrbL | virB6 |
| RL_RS25845 | 142011..142211 | - | 201 | WP_028744197 | entry exclusion protein TrbK | - |
| RL_RS25850 (pRL80138) | 142208..143017 | - | 810 | WP_011654759 | P-type conjugative transfer protein TrbJ | virB5 |
| RL_RS25855 (pRL80139) | 143010..145445 | - | 2436 | WP_011654760 | conjugal transfer protein TrbE | virb4 |
| RL_RS25860 (pRL80140) | 145456..145755 | - | 300 | WP_011654761 | conjugal transfer protein TrbD | virB3 |
| RL_RS25865 (pRL80141) | 145748..146140 | - | 393 | WP_011654762 | TrbC/VirB2 family protein | virB2 |
| RL_RS25870 (pRL80142) | 146130..147095 | - | 966 | WP_011654763 | P-type conjugative transfer ATPase TrbB | virB11 |
Host bacterium
| ID | 728 | GenBank | NC_008383 |
| Plasmid name | pRL8 | Incompatibility group | _ |
| Plasmid size | 147463 bp | Coordinate of oriT [Strand] | 126421..126470 [+] |
| Host baterium | Rhizobium johnstonii 3841 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |