Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 120263 |
| Name | oriT_LMB1|pB  |
| Organism | Sinorhizobium meliloti strain LMB1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP141214 (131124..131164 [-], 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_LMB1|pB
TCCAAGGGCGCAATTATACGTCGCTAACGCGACGCCCTTGC
TCCAAGGGCGCAATTATACGTCGCTAACGCGACGCCCTTGC
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 12742 | GenBank | WP_324765413 |
| Name | traA_SO078_RS25360_LMB1|pB |
UniProt ID | _ |
| Length | 1103 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1103 a.a. Molecular weight: 122156.53 Da Isoelectric Point: 9.8644
>WP_324765413.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPADAPEWLRAMIADR
SVAGASEAFWNKVEDFEKRSDAQLAKDVTIELPIELSAQQNIALVRDFVERHITSKGMVVDWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKVAVLGPDGNPIRNDAGKIVYKLWAGGIDDFNAFRDGWFACQNRHLALAG
LDLRVDGRSFEKQGIDLEPTIHLGVGTRAIERKTDVATKPVELELIELQDARKAENARRIDRNPKLVIDL
ITREKSVFDERDVAKVLHRYIDDSALFQSLMVRIILHPDTLRLERERIDFATGIRVPVKYTSRDMIRLEA
EMANRAVWLSQRTSHGVRDAVLAATFARHERLSDEQKTAIEHASGSERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWHGGRNQLDSKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVGRAVAAYR
TNGKVIGWDLKADAVDNLIAAWDRDYDPAKTSLILAHLRRDVRMLNQMARIKLIERGVLDEGTVFKTADG
DRNFAIGDQIVFLKNEGSLGVKNGMLAKVVETGPGRIIAKVGDGELARQVLVEQRFYNNLDYGYATTIHK
SQGATVDRVKVLGSLSLDRHLTYVAMTRHREDLAVYYGRRSFAKAGGLIPVLSRRNTKETTLDYEKGSFS
RQTLCFAEARGLNLVNVARTLLRDRLEWTVGQKQKLIDLGARLAAVAAKLGLIISSVKSPLQDTVRKVKP
MVSGITTFAKSVDQAVEDKVAADRGLKKQWEEVSTRFHLVYAQPERAFKAINVDALLKDGAVADATISRI
RDQPESFGALKGKTGLLASGTDKQARSTALTNAPALARNLERYLRQRAEAERKFEVEERAVRLKMSIDIP
ALSANAKETLERVRDAIDRNDLPAGLEYALADRQVKAEFEGFAKAVAERFGERTFLPLAAKDSSGQTFNA
ITGAMTAGQKAEVQSAWNSMRTVQQLAAHERTTEALKQAESLCQKKSQGISLK
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEFVIPADAPEWLRAMIADR
SVAGASEAFWNKVEDFEKRSDAQLAKDVTIELPIELSAQQNIALVRDFVERHITSKGMVVDWVYHDAPGN
PHVHLMTTLRPLTEDGFGAKKVAVLGPDGNPIRNDAGKIVYKLWAGGIDDFNAFRDGWFACQNRHLALAG
LDLRVDGRSFEKQGIDLEPTIHLGVGTRAIERKTDVATKPVELELIELQDARKAENARRIDRNPKLVIDL
ITREKSVFDERDVAKVLHRYIDDSALFQSLMVRIILHPDTLRLERERIDFATGIRVPVKYTSRDMIRLEA
EMANRAVWLSQRTSHGVRDAVLAATFARHERLSDEQKTAIEHASGSERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWHGGRNQLDSKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLIGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVGRAVAAYR
TNGKVIGWDLKADAVDNLIAAWDRDYDPAKTSLILAHLRRDVRMLNQMARIKLIERGVLDEGTVFKTADG
DRNFAIGDQIVFLKNEGSLGVKNGMLAKVVETGPGRIIAKVGDGELARQVLVEQRFYNNLDYGYATTIHK
SQGATVDRVKVLGSLSLDRHLTYVAMTRHREDLAVYYGRRSFAKAGGLIPVLSRRNTKETTLDYEKGSFS
RQTLCFAEARGLNLVNVARTLLRDRLEWTVGQKQKLIDLGARLAAVAAKLGLIISSVKSPLQDTVRKVKP
MVSGITTFAKSVDQAVEDKVAADRGLKKQWEEVSTRFHLVYAQPERAFKAINVDALLKDGAVADATISRI
RDQPESFGALKGKTGLLASGTDKQARSTALTNAPALARNLERYLRQRAEAERKFEVEERAVRLKMSIDIP
ALSANAKETLERVRDAIDRNDLPAGLEYALADRQVKAEFEGFAKAVAERFGERTFLPLAAKDSSGQTFNA
ITGAMTAGQKAEVQSAWNSMRTVQQLAAHERTTEALKQAESLCQKKSQGISLK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 14960 | GenBank | WP_324765104 |
| Name | t4cp2_SO078_RS25275_LMB1|pB |
UniProt ID | _ |
| Length | 818 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 818 a.a. Molecular weight: 91976.87 Da Isoelectric Point: 5.7915
>WP_324765104.1 conjugal transfer protein TrbE [Sinorhizobium meliloti]
MVALKRFRATGPSFADLVPYAGLVDDGVLLLKDGSLMAGWYFAGPDTESATDLERNELSRQINAILSRLG
NGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFARDQRHFESKHALILTYRPLEPKKTALSR
YIYSDEESRKKTYADTVLFIFKNAVREIEQYFANTLSIRRMGTREVVERGGERVARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELKHGLTPKVESRYLGVVAIDGLPAESWPGILHSLDLMPLSYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSIDQDAMSMVAETEDAIAQASSQLVAYGYYTPVIVL
FDGDREALQEEAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYANVREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPDSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLATGGDHYEIGGGSEEKGKALAFCPLSDLSSETDRAWATEWIEMLVDLQGVTITPDHRN
AISRQIGLMVSAPGRSLSDFASGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGAPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYDRIGFNERQIEIVSNAIPKREYYVVTPEGRRLFDMALGP
LALSFVGASGKEDLKRIRALYSEHGRDWPIHWLQMKGVHDAASLLNFE
MVALKRFRATGPSFADLVPYAGLVDDGVLLLKDGSLMAGWYFAGPDTESATDLERNELSRQINAILSRLG
NGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRAHFARDQRHFESKHALILTYRPLEPKKTALSR
YIYSDEESRKKTYADTVLFIFKNAVREIEQYFANTLSIRRMGTREVVERGGERVARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELKHGLTPKVESRYLGVVAIDGLPAESWPGILHSLDLMPLSYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSIDQDAMSMVAETEDAIAQASSQLVAYGYYTPVIVL
FDGDREALQEEAEAVRRLIQAEGFGARIETLNATDAYLGSLPGNWYANVREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPDSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLATGGDHYEIGGGSEEKGKALAFCPLSDLSSETDRAWATEWIEMLVDLQGVTITPDHRN
AISRQIGLMVSAPGRSLSDFASGVQMREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGAPSLIVLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYDRIGFNERQIEIVSNAIPKREYYVVTPEGRRLFDMALGP
LALSFVGASGKEDLKRIRALYSEHGRDWPIHWLQMKGVHDAASLLNFE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 111791..126008
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| SO078_RS25240 (SO078_25240) | 106952..108274 | + | 1323 | WP_324765097 | FAD-binding oxidoreductase | - |
| SO078_RS25245 (SO078_25245) | 108493..109131 | - | 639 | WP_324765098 | SGNH/GDSL hydrolase family protein | - |
| SO078_RS25250 (SO078_25250) | 109621..110949 | + | 1329 | WP_324765099 | MFS transporter | - |
| SO078_RS25255 (SO078_25255) | 111157..111780 | + | 624 | WP_324765100 | acyl-homoserine-lactone synthase | - |
| SO078_RS25260 (SO078_25260) | 111791..112768 | + | 978 | WP_324765101 | P-type conjugative transfer ATPase TrbB | virB11 |
| SO078_RS25265 (SO078_25265) | 112758..113141 | + | 384 | WP_324765102 | TrbC/VirB2 family protein | virB2 |
| SO078_RS25270 (SO078_25270) | 113134..113433 | + | 300 | WP_324765103 | conjugal transfer protein TrbD | virB3 |
| SO078_RS25275 (SO078_25275) | 113444..115900 | + | 2457 | WP_324765104 | conjugal transfer protein TrbE | virb4 |
| SO078_RS25280 (SO078_25280) | 115872..116675 | + | 804 | WP_324765105 | P-type conjugative transfer protein TrbJ | virB5 |
| SO078_RS25285 (SO078_25285) | 116669..116845 | + | 177 | WP_324765106 | entry exclusion protein TrbK | - |
| SO078_RS25290 (SO078_25290) | 116850..118028 | + | 1179 | WP_324765107 | P-type conjugative transfer protein TrbL | virB6 |
| SO078_RS25295 (SO078_25295) | 118053..118715 | + | 663 | WP_324765108 | conjugal transfer protein TrbF | virB8 |
| SO078_RS25300 (SO078_25300) | 118732..119544 | + | 813 | WP_324765109 | P-type conjugative transfer protein TrbG | virB9 |
| SO078_RS25305 (SO078_25305) | 119548..119985 | + | 438 | WP_324765110 | conjugal transfer protein TrbH | - |
| SO078_RS25310 (SO078_25310) | 119998..121299 | + | 1302 | WP_324765111 | IncP-type conjugal transfer protein TrbI | virB10 |
| SO078_RS25315 (SO078_25315) | 121618..122322 | + | 705 | WP_324765112 | autoinducer binding domain-containing protein | - |
| SO078_RS25320 (SO078_25320) | 122326..122646 | - | 321 | WP_324765113 | transcriptional repressor TraM | - |
| SO078_RS25325 (SO078_25325) | 122890..123111 | + | 222 | WP_324765114 | helix-turn-helix transcriptional regulator | - |
| SO078_RS25330 (SO078_25330) | 123210..123842 | + | 633 | WP_324765115 | DUF433 domain-containing protein | - |
| SO078_RS25335 (SO078_25335) | 123839..124025 | + | 187 | Protein_119 | DUF5615 family PIN-like protein | - |
| SO078_RS25340 (SO078_25340) | 124092..125294 | - | 1203 | WP_324765411 | ATP-binding protein | - |
| SO078_RS25345 (SO078_25345) | 125310..126008 | - | 699 | WP_324765116 | TraH family protein | virB1 |
| SO078_RS25350 (SO078_25350) | 126026..127189 | - | 1164 | WP_324765117 | conjugal transfer protein TraB | - |
| SO078_RS25355 (SO078_25355) | 127179..127718 | - | 540 | WP_324765412 | conjugative transfer signal peptidase TraF | - |
Host bacterium
| ID | 20692 | GenBank | NZ_CP141214 |
| Plasmid name | LMB1|pB | Incompatibility group | - |
| Plasmid size | 997266 bp | Coordinate of oriT [Strand] | 131124..131164 [-] |
| Host baterium | Sinorhizobium meliloti strain LMB1 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | nia, silP, actP, arsC |
| Degradation gene | RPYSC3_16500 |
| Symbiosis gene | fixN, fixO, fixG |
| Anti-CRISPR | - |