Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 104878 |
| Name | oriT_pRSpC104f  |
| Organism | Rhizobium sp. C104 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP092353 (371344..371383 [+], 40 nt) |
| oriT length | 40 nt |
| IRs (inverted repeats) | 20..26, 31..37 (ACGTCGC..GCGACGT) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 40 nt
>oriT_pRSpC104f
ATCCGAAGGGCGCAATTATACGTCGCTGACGCGACGTCCT
ATCCGAAGGGCGCAATTATACGTCGCTGACGCGACGTCCT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 3450 | GenBank | WP_096771934 |
| Name | traA_MF410_RS33885_pRSpC104f |
UniProt ID | _ |
| Length | 1103 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1103 a.a. Molecular weight: 121859.71 Da Isoelectric Point: 9.8572
>WP_096771934.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARAIDYTRKQGLLHEEFVVPVDAPQWLRAMITDR
SVSGASEAFWNSVETFEKRVDAQLAKDVTIALPVELSTAQNIGLVRDFVERYIRSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDSFGAKKVALTGPDGNPLRNDAGKIVYEVWAGSLDDFNAFRDGWFACQNRHLALAG
LDLRVDGRSFEKQGIELAPTVHLGVGAKAIERKSKEAERDISLERLELLEERRAENSRRIQLRPELVLDL
ITREKSVFDERDVAKILHRNIDDAGLFQNLLARILQSPETLRLERERIELSSGRREPARYTTRDLIRLEA
EMANRAIWLAQRSSHGIAEAVREATFARHLRLSDEQKTAIAHITGGERIAAVIGRAGAGKTTTMKAGREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRSQLDDKTVFVLDEAGMVSSRQMALFVE
AATQSGAKLVLVGDPEQLQPIEAGAALRAIVDRIGYAELETIYRQRLQWMRDASLDLARGNIGRAVEAYR
AQGRVHGAELKADALQALIADWNRDYDPAKTAIILAHLRRDVRMLNEMARATLVERGLVAEGFAFRTDDG
HRKFAAGDQIVFLKNEGSLGVKNGMLAKVLEAGPGRIVAEVGEGEHRRPVTVEQRFYANLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGLYYGRRSFAKAGGLSPILSRRQAKETTLDYASGRFY
AQALRFAEARGLHLVNVARTVVRDRLAWTVRQKSKLAELGARLAAIAGRLGLSAGAAKTTQPRSIKKAKP
MVSGITTFPKSLEQAVEDRLAADPGLKKQWEEVSGRFHLVYAQPEEAFKAVNVEAMLKDEAAAKSTIARI
GSEPESFGALKGKTGLLAGRADKQAREMAVTNAPALARNLERYLLQRTEAEHKYEAEEHAARLKVSLDIP
ALSPAAKQTLECVRDAIDRNDLPAGLEYALADNLVKAELEGFARAVSERFGERTFLQLAAKDTSGQTFQS
VTSSMSAGQKAEVQTAWSAMRTLQQLSAHERTTEALKQTVTLRQTRSQGLSLK
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMEYEREARAIDYTRKQGLLHEEFVVPVDAPQWLRAMITDR
SVSGASEAFWNSVETFEKRVDAQLAKDVTIALPVELSTAQNIGLVRDFVERYIRSKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDSFGAKKVALTGPDGNPLRNDAGKIVYEVWAGSLDDFNAFRDGWFACQNRHLALAG
LDLRVDGRSFEKQGIELAPTVHLGVGAKAIERKSKEAERDISLERLELLEERRAENSRRIQLRPELVLDL
ITREKSVFDERDVAKILHRNIDDAGLFQNLLARILQSPETLRLERERIELSSGRREPARYTTRDLIRLEA
EMANRAIWLAQRSSHGIAEAVREATFARHLRLSDEQKTAIAHITGGERIAAVIGRAGAGKTTTMKAGREA
WEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRSQLDDKTVFVLDEAGMVSSRQMALFVE
AATQSGAKLVLVGDPEQLQPIEAGAALRAIVDRIGYAELETIYRQRLQWMRDASLDLARGNIGRAVEAYR
AQGRVHGAELKADALQALIADWNRDYDPAKTAIILAHLRRDVRMLNEMARATLVERGLVAEGFAFRTDDG
HRKFAAGDQIVFLKNEGSLGVKNGMLAKVLEAGPGRIVAEVGEGEHRRPVTVEQRFYANLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGLYYGRRSFAKAGGLSPILSRRQAKETTLDYASGRFY
AQALRFAEARGLHLVNVARTVVRDRLAWTVRQKSKLAELGARLAAIAGRLGLSAGAAKTTQPRSIKKAKP
MVSGITTFPKSLEQAVEDRLAADPGLKKQWEEVSGRFHLVYAQPEEAFKAVNVEAMLKDEAAAKSTIARI
GSEPESFGALKGKTGLLAGRADKQAREMAVTNAPALARNLERYLLQRTEAEHKYEAEEHAARLKVSLDIP
ALSPAAKQTLECVRDAIDRNDLPAGLEYALADNLVKAELEGFARAVSERFGERTFLQLAAKDTSGQTFQS
VTSSMSAGQKAEVQTAWSAMRTLQQLSAHERTTEALKQTVTLRQTRSQGLSLK
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 3395 | GenBank | WP_096771941 |
| Name | t4cp2_MF410_RS33950_pRSpC104f |
UniProt ID | _ |
| Length | 818 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 818 a.a. Molecular weight: 91491.23 Da Isoelectric Point: 6.1914
>WP_096771941.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRLRTTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATALERNELSRQINSILSRLG
SGWMIQVEAIRIPTMDYPSDDRCHFPDPVTRAIDAERRAHFAREQGHFESKHAIVLTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFEFKNAIREIEQYLANNLSIRRMETRVVRERGGTRNARYDELLQFVRFCITG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIESQFLGIVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQRVAYGYYTPVIVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTNNLADLIPLNAVWS
GSPIAPCPFYPPNSAPLMQVASGSTPFRLNLHVGDVGHTLVFGPTGSGKSTLLALIVAQFRRYENAQVFA
FDKGNSLLPLTLAGGGDHYEIGGDTEGEGKALAFCPLSELGSNADRAWASEWIEMLIALQGITVSPDYRN
AISRQVGLMASAPGRSLSDFVSGVQIREIKDALHHYTVDGPMGQLLDAEQDGLSLGALQTFEIDHLMNLG
ERNLVPVLTYLFRRIEKRLDGSPSLILLDEAWLMLGHPVFRAKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIDIVAGAAQKREYYVATPEGRRLFDMTLGP
VALSFVGASGKDDLKRIRALIAEHGRDWPIHWLNTRGVHDAASQLNFE
MVALKRLRTTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATALERNELSRQINSILSRLG
SGWMIQVEAIRIPTMDYPSDDRCHFPDPVTRAIDAERRAHFAREQGHFESKHAIVLTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFEFKNAIREIEQYLANNLSIRRMETRVVRERGGTRNARYDELLQFVRFCITG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIESQFLGIVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDQDAMTMVAETEDAIAQASSQRVAYGYYTPVIVL
FDHDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTNNLADLIPLNAVWS
GSPIAPCPFYPPNSAPLMQVASGSTPFRLNLHVGDVGHTLVFGPTGSGKSTLLALIVAQFRRYENAQVFA
FDKGNSLLPLTLAGGGDHYEIGGDTEGEGKALAFCPLSELGSNADRAWASEWIEMLIALQGITVSPDYRN
AISRQVGLMASAPGRSLSDFVSGVQIREIKDALHHYTVDGPMGQLLDAEQDGLSLGALQTFEIDHLMNLG
ERNLVPVLTYLFRRIEKRLDGSPSLILLDEAWLMLGHPVFRAKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIDIVAGAAQKREYYVATPEGRRLFDMTLGP
VALSFVGASGKDDLKRIRALIAEHGRDWPIHWLNTRGVHDAASQLNFE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 376501..388820
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| MF410_RS33890 (MF410_33875) | 374767..375333 | + | 567 | WP_096771935 | conjugative transfer signal peptidase TraF | - |
| MF410_RS33895 (MF410_33880) | 375323..376485 | + | 1163 | Protein_369 | conjugal transfer protein TraB | - |
| MF410_RS33900 (MF410_33885) | 376501..377124 | + | 624 | WP_088396708 | TraH family protein | virB1 |
| MF410_RS33905 (MF410_33890) | 377561..377824 | - | 264 | WP_088396709 | helix-turn-helix transcriptional regulator | - |
| MF410_RS33910 (MF410_33895) | 378031..378351 | + | 321 | WP_096771936 | transcriptional repressor TraM | - |
| MF410_RS33915 (MF410_33900) | 378355..379059 | - | 705 | WP_088396711 | autoinducer binding domain-containing protein | - |
| MF410_RS33920 (MF410_33905) | 379331..380626 | - | 1296 | WP_096771937 | IncP-type conjugal transfer protein TrbI | virB10 |
| MF410_RS33925 (MF410_33910) | 380637..381074 | - | 438 | WP_096771938 | conjugal transfer protein TrbH | - |
| MF410_RS33930 (MF410_33915) | 381077..381889 | - | 813 | WP_088396714 | P-type conjugative transfer protein TrbG | virB9 |
| MF410_RS33935 (MF410_33920) | 381904..382566 | - | 663 | WP_096771947 | conjugal transfer protein TrbF | virB8 |
| MF410_RS33940 (MF410_33925) | 382591..383784 | - | 1194 | WP_239621092 | P-type conjugative transfer protein TrbL | virB6 |
| MF410_RS33945 (MF410_33930) | 383942..384745 | - | 804 | WP_096771940 | P-type conjugative transfer protein TrbJ | virB5 |
| MF410_RS33950 (MF410_33935) | 384717..387173 | - | 2457 | WP_096771941 | conjugal transfer protein TrbE | virb4 |
| MF410_RS33955 (MF410_33940) | 387184..387483 | - | 300 | WP_088396717 | conjugal transfer protein TrbD | virB3 |
| MF410_RS33960 (MF410_33945) | 387476..387853 | - | 378 | WP_088396718 | TrbC/VirB2 family protein | virB2 |
| MF410_RS33965 (MF410_33950) | 387843..388820 | - | 978 | WP_096771942 | P-type conjugative transfer ATPase TrbB | virB11 |
| MF410_RS33970 (MF410_33955) | 388832..389455 | - | 624 | WP_088396720 | acyl-homoserine-lactone synthase TraI | - |
| MF410_RS33975 (MF410_33960) | 389845..391055 | + | 1211 | Protein_385 | plasmid partitioning protein RepA | - |
| MF410_RS33980 (MF410_33965) | 391029..392081 | + | 1053 | WP_239621170 | plasmid partitioning protein RepB | - |
| MF410_RS33985 (MF410_33970) | 392237..393445 | + | 1209 | WP_096771944 | plasmid replication protein RepC | - |
Host bacterium
| ID | 5316 | GenBank | NZ_CP092353 |
| Plasmid name | pRSpC104f | Incompatibility group | - |
| Plasmid size | 399699 bp | Coordinate of oriT [Strand] | 371344..371383 [+] |
| Host baterium | Rhizobium sp. C104 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | hsiC1/vipB |
| Metal resistance gene | - |
| Degradation gene | dxnH, linJ |
| Symbiosis gene | nodD, nodA, nifH, nifD, nifK, nifX, mLTONO_5203, fixN, fixO, fixG, nodC, nodS, nodJ, nifT, nifZ, fixX, fixC, fixB, fixA, nifW, nifE, nifN |
| Anti-CRISPR | - |