Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 106967 |
| Name | oriT_pRetMIM1f  |
| Organism | Rhizobium etli bv. mimosae str. Mim1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NC_021911 (841705..841733 [+], 29 nt) |
| oriT length | 29 nt |
| IRs (inverted repeats) | 14..19, 24..29 (CGTCGC..GCGACG) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 29 nt
>oriT_pRetMIM1f
AGGGCGCAATATACGTCGCTGGCGCGACG
AGGGCGCAATATACGTCGCTGGCGCGACG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 4602 | GenBank | WP_020919790 |
| Name | traA_REMIM1_RS33340_pRetMIM1f |
UniProt ID | S5S8T3 |
| Length | 1543 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 1543 a.a. Molecular weight: 171256.64 Da Isoelectric Point: 9.1995
>WP_020919790.1 Ti-type conjugative transfer relaxase TraA [Rhizobium etli]
MAIMFVRAQVISRGAGRSIVSAAAYRHRTRMMDEQAGTSFSYRGGAGELMHEELALPDEIPDWLRSAISG
QSVSNASEVFWNAVDAFETRGDAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEDGFGRKKVPVLGGDGKPLRVVTPDRPNGKIVYKVWAGDKETLKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLADPERLLTQ
LVNERSTFDERDIAKALHRYVDDPSDFANIRARLMASTELVMLKPQEIDTQTGKASEPAVFTTRDMLRIE
YEMAQSARVLSGRHDFGVSERHVSAAIESIETRDPQKRFRLDPEQVDAIRHVTGDDGIAAVVGLAGAGKS
TLLAAARLAWESQGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVVVIDEAGMVS
SPQMARVLDIVEQAEAKVVLVGDAMQLQPIQAGAAFRAISERIGFAELAGVRRQRHEWARDASRLFARGE
IDKGLDAYAGHGHLVEAETRQEIVDRIVADWREARRQAIGRSVSEGRDGSLGGDELLVLAHTNADVKRLN
EALRSVMTGEGALGESRSFRTERGAREFAAGDRIIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDVK
GEVLLSVRLDNGSKVVFGEDSYRNVDHGYAATIHKSQGATVERTFVLASGMMDRHLTYVSMTRHRDRADL
YAAKEDFAAKPEWGRKPRVDHAAGVTGELVETGEAKFRPDDEDADDSPYADLRTDDGVVHRLWGVSLPKA
LEDAGILEGDTVTLRKDGIERVKVEVPVIDEKTGQKRYEEREVDRNVWTAKQLETATERQERIERESHRP
DVFKQLVERLSRSGAKTTTLDFDSEAGYRAHAQDFARRRGIEHLSLVAAEMEESLLRRWAWIAEKREQVE
KLWERASVALGFAIERERRISYNEQRAETRAEVRSPDTRYLIPPATAFARSVDEDARLAQLSTPAWKERE
AILRPLLEKIYRDPDAALVALNALASNTSIAPRALASNLAAAPDRLGRLRGSDLIVDGRAARDERNVAMA
ALQELLPLARAHATGFRRNAERFELREQTRRASMSLSVPALSERAMTRLMEIEAVRAQGGGDAYKTAFAL
AAQDRTVVREIKAVSEAITARFGWSAFTSKADAIADRNMVERMPEDLTAGRREELTRLLEAVRRFAEEQH
LAERQDRSKVVAGASADLSKEPGKEKVTMPPTFAAVTEFKVLVEEEARSRALASPLYRQQRAAMADAART
IWRDPAGAVGRIEELLAKGFAADRIAAAVTNDPAAYGALRGSSRLMDRMLASGRERKAAIEAVPETAARL
RSFGAAYANIFDAGRHAITEERRRMAVAIPALSKSAEEALTRLTAEARKDSRRLSVSAASLDPNIRREFA
AVSRALDDRFGRNAIVRGDKDLINRVPPPQRRVFEAMQEKLKVLQQTVRLQSSEQIIVERRQRTSSRARG
INL
MAIMFVRAQVISRGAGRSIVSAAAYRHRTRMMDEQAGTSFSYRGGAGELMHEELALPDEIPDWLRSAISG
QSVSNASEVFWNAVDAFETRGDAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEDGFGRKKVPVLGGDGKPLRVVTPDRPNGKIVYKVWAGDKETLKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLADPERLLTQ
LVNERSTFDERDIAKALHRYVDDPSDFANIRARLMASTELVMLKPQEIDTQTGKASEPAVFTTRDMLRIE
YEMAQSARVLSGRHDFGVSERHVSAAIESIETRDPQKRFRLDPEQVDAIRHVTGDDGIAAVVGLAGAGKS
TLLAAARLAWESQGRRVIGAALAGKAAEGLEDSSGIKSRTLASWELTWANGRDTLHRGDVVVIDEAGMVS
SPQMARVLDIVEQAEAKVVLVGDAMQLQPIQAGAAFRAISERIGFAELAGVRRQRHEWARDASRLFARGE
IDKGLDAYAGHGHLVEAETRQEIVDRIVADWREARRQAIGRSVSEGRDGSLGGDELLVLAHTNADVKRLN
EALRSVMTGEGALGESRSFRTERGAREFAAGDRIIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDVK
GEVLLSVRLDNGSKVVFGEDSYRNVDHGYAATIHKSQGATVERTFVLASGMMDRHLTYVSMTRHRDRADL
YAAKEDFAAKPEWGRKPRVDHAAGVTGELVETGEAKFRPDDEDADDSPYADLRTDDGVVHRLWGVSLPKA
LEDAGILEGDTVTLRKDGIERVKVEVPVIDEKTGQKRYEEREVDRNVWTAKQLETATERQERIERESHRP
DVFKQLVERLSRSGAKTTTLDFDSEAGYRAHAQDFARRRGIEHLSLVAAEMEESLLRRWAWIAEKREQVE
KLWERASVALGFAIERERRISYNEQRAETRAEVRSPDTRYLIPPATAFARSVDEDARLAQLSTPAWKERE
AILRPLLEKIYRDPDAALVALNALASNTSIAPRALASNLAAAPDRLGRLRGSDLIVDGRAARDERNVAMA
ALQELLPLARAHATGFRRNAERFELREQTRRASMSLSVPALSERAMTRLMEIEAVRAQGGGDAYKTAFAL
AAQDRTVVREIKAVSEAITARFGWSAFTSKADAIADRNMVERMPEDLTAGRREELTRLLEAVRRFAEEQH
LAERQDRSKVVAGASADLSKEPGKEKVTMPPTFAAVTEFKVLVEEEARSRALASPLYRQQRAAMADAART
IWRDPAGAVGRIEELLAKGFAADRIAAAVTNDPAAYGALRGSSRLMDRMLASGRERKAAIEAVPETAARL
RSFGAAYANIFDAGRHAITEERRRMAVAIPALSKSAEEALTRLTAEARKDSRRLSVSAASLDPNIRREFA
AVSRALDDRFGRNAIVRGDKDLINRVPPPQRRVFEAMQEKLKVLQQTVRLQSSEQIIVERRQRTSSRARG
INL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 4697 | GenBank | WP_020919787 |
| Name | traG_REMIM1_RS33325_pRetMIM1f |
UniProt ID | _ |
| Length | 639 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 639 a.a. Molecular weight: 70353.54 Da Isoelectric Point: 9.5793
>WP_020919787.1 Ti-type conjugative transfer system protein TraG [Rhizobium etli]
MGLRGKPHPSLLLVLVPIAVTTVTIYVVGWRWPGLAAGMSRKMGYSFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLCFLGVAAFYALREFGRLAPAVQARVVPWDRALSYVDMVAVIAAVAGFMAVAVSARI
SVVVPDEIKRARRGIFGDADWLPMAAAGKLFPPDGEIVVGERYRVDREIVHALPFDASDRSTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALKYTGPLICLDPSTEVAPMVVEHRTNALRREVMVLDPT
NPTMGFNVLDGIETSSQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFTRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAIKALDTARSVSAQCGEMTVEVKG
SLRNLGWDKRAAGPRKSESISFQRRPLIMPHEITQSMRKDEQIIVVQGHSPIRCGRAIYFRRKEMDAVAK
ANRFVKSIT
MGLRGKPHPSLLLVLVPIAVTTVTIYVVGWRWPGLAAGMSRKMGYSFLRAAPVPPLLFGPLAGLLTVWAL
PLHRRRPVAMASLLCFLGVAAFYALREFGRLAPAVQARVVPWDRALSYVDMVAVIAAVAGFMAVAVSARI
SVVVPDEIKRARRGIFGDADWLPMAAAGKLFPPDGEIVVGERYRVDREIVHALPFDASDRSTWGQGGKAP
LLTYKQDFDSTHMLFFAGSGGYKTTSNVVPTALKYTGPLICLDPSTEVAPMVVEHRTNALRREVMVLDPT
NPTMGFNVLDGIETSSQKEEDIVGIAHMLLSESVRFESSTGSYFQSQAHNLLTGLLAHVMLSPEYAGRRN
LRSLREIVSEPEPSVLAMLRDIQENSQSDFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKPSDIVSGRKDVFLNIPASILRSYPGIGRVIIGSLINAMMQADGAFTRRALFMLDEVDLLGYMRVL
EEARDRGRKYGISMMLMYQSVGQLERHFGKDGATSWIEGCAFASYAAIKALDTARSVSAQCGEMTVEVKG
SLRNLGWDKRAAGPRKSESISFQRRPLIMPHEITQSMRKDEQIIVVQGHSPIRCGRAIYFRRKEMDAVAK
ANRFVKSIT
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 818615..833147
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| REMIM1_RS33165 (REMIM1_PF00759) | 813627..815744 | + | 2118 | WP_020919756 | ParB/RepB/Spo0J family partition protein | - |
| REMIM1_RS33170 (REMIM1_PF00760) | 815817..816473 | + | 657 | WP_020919757 | hypothetical protein | - |
| REMIM1_RS33175 (REMIM1_PF00761) | 816550..817740 | + | 1191 | WP_020919758 | hypothetical protein | - |
| REMIM1_RS38135 (REMIM1_PF00762) | 817829..818602 | + | 774 | WP_020919759 | DUF6117 family protein | - |
| REMIM1_RS33185 (REMIM1_PF00763) | 818615..819649 | + | 1035 | WP_020919760 | toprim domain-containing protein | traP |
| REMIM1_RS33190 (REMIM1_PF00764) | 819963..820898 | + | 936 | WP_020919761 | DUF2493 domain-containing protein | - |
| REMIM1_RS36925 | 820895..821380 | - | 486 | WP_155249495 | hypothetical protein | - |
| REMIM1_RS37890 (REMIM1_PF00766) | 821703..821867 | + | 165 | WP_245294264 | hypothetical protein | - |
| REMIM1_RS33205 | 821922..822204 | - | 283 | Protein_769 | HU family DNA-binding protein | - |
| REMIM1_RS33210 (REMIM1_PF00768) | 822557..822922 | - | 366 | WP_020919765 | MarR family transcriptional regulator | - |
| REMIM1_RS33215 (REMIM1_PF00769) | 823021..823557 | + | 537 | WP_020919766 | hypothetical protein | - |
| REMIM1_RS33220 (REMIM1_PF00770) | 823561..824220 | + | 660 | WP_020919767 | lytic transglycosylase domain-containing protein | virB1 |
| REMIM1_RS33225 (REMIM1_PF00771) | 824217..824516 | + | 300 | WP_020919768 | TrbC/VirB2 family protein | virB2 |
| REMIM1_RS33230 (REMIM1_PF00772) | 824522..824863 | + | 342 | WP_020919769 | type IV secretion system protein VirB3 | virB3 |
| REMIM1_RS33235 (REMIM1_PF00773) | 824848..827214 | + | 2367 | WP_041679330 | VirB4 family type IV secretion system protein | virb4 |
| REMIM1_RS33240 (REMIM1_PF00774) | 827211..827912 | + | 702 | WP_020919771 | P-type DNA transfer protein VirB5 | virB5 |
| REMIM1_RS33245 (REMIM1_PF00775) | 827909..828142 | + | 234 | WP_020919772 | EexN family lipoprotein | - |
| REMIM1_RS33250 (REMIM1_PF00776) | 828145..829077 | + | 933 | WP_020919773 | type IV secretion system protein | virB6 |
| REMIM1_RS37895 (REMIM1_PF00777) | 829112..829396 | + | 285 | WP_020919774 | hypothetical protein | - |
| REMIM1_RS33260 (REMIM1_PF00778) | 829398..830069 | + | 672 | WP_020919775 | virB8 family protein | virB8 |
| REMIM1_RS33265 (REMIM1_PF00779) | 830066..830923 | + | 858 | WP_020919776 | P-type conjugative transfer protein VirB9 | virB9 |
| REMIM1_RS33270 (REMIM1_PF00780) | 830932..832107 | + | 1176 | WP_020919777 | type IV secretion system protein VirB10 | virB10 |
| REMIM1_RS33275 (REMIM1_PF00781) | 832116..833147 | + | 1032 | WP_020919778 | P-type DNA transfer ATPase VirB11 | virB11 |
| REMIM1_RS33280 (REMIM1_PF00782) | 833300..834508 | - | 1209 | WP_041679331 | DUF1173 domain-containing protein | - |
| REMIM1_RS33285 (REMIM1_PF00783) | 835095..835331 | + | 237 | WP_020919780 | type II toxin-antitoxin system VapB family antitoxin | - |
| REMIM1_RS33290 (REMIM1_PF00784) | 835331..835732 | + | 402 | WP_020919781 | type II toxin-antitoxin system VapC family toxin | - |
| REMIM1_RS33295 (REMIM1_PF00785) | 835867..836199 | - | 333 | WP_020919782 | WGR domain-containing protein | - |
| REMIM1_RS33300 (REMIM1_PF00786) | 836662..836985 | + | 324 | WP_008530485 | DUF736 family protein | - |
| REMIM1_RS37335 (REMIM1_PF00787) | 837300..837467 | + | 168 | WP_196232147 | hypothetical protein | - |
Host bacterium
| ID | 7404 | GenBank | NC_021911 |
| Plasmid name | pRetMIM1f | Incompatibility group | - |
| Plasmid size | 1082659 bp | Coordinate of oriT [Strand] | 841705..841733 [+] |
| Host baterium | Rhizobium etli bv. mimosae str. Mim1 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | dxnH, LinG, bphB |
| Symbiosis gene | fixN, fixO, fixQ, fixG, fixA, fixB |
| Anti-CRISPR | - |