Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101009 |
| Name | oriT_pRETCFN42d  |
| Organism | Rhizobium etli CFN 42 |
| Sequence Completeness | intact |
| NCBI accession of oriT (coordinates [strand]) | NC_004041 (182609..182628 [-], 20 nt) |
| oriT length | 20 nt |
| IRs (inverted repeats) | _ |
| Location of nic site | 12..13 |
| Conserved sequence flanking the nic site |
TATTGCG|C |
| Note | (1) The relaxase TraA_pRETCFN42d has a nic site cis-acting preference [PMID:16916896]. (2) Overexpression of the yp028 gene promotes the conjugation pRetCFN42d, and this promotion effect is relaxase TraA_pRetCFN42d-dependent [PMID:15317780]. (3) Mobilization of pSymB is pSymA-dependent: pSymB carries a functional oriT and an adjacent relaxase gene, traA2, that is transcriptionally repressed by rctA. In trans mobilization of pSymB requires the T4SS of pSymA [PMID:20889746]. (4) Conjugation of pSymA is regulated by the transcriptional repressor RctA [PMID:20889746]. |
oriT sequence
Download Length: 20 nt
>oriT_pRETCFN42d
ACGTATATTGCGCCCTCAAA
ACGTATATTGCGCCCTCAAA
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 1077 | GenBank | WP_011053391 |
| Name | TraA_pRETCFN42d |
UniProt ID | Q8KIN6 |
| Length | 1552 a.a. | PDB ID | |
| Note | (1) The relaxase TraA_pRETCFN42d has a nic site cis-acting preference [PMID:16916896]. (2) Overexpression of the yp028 gene promotes the conjugation pRetCFN42d, and this promotion effect is relaxase TraA_pRetCFN42d-dependent [PMID:15317780]. |
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Relaxase protein sequence
Download Length: 1552 a.a. Molecular weight: 171898.01 Da Isoelectric Point: 7.3779
>WP_011053391.1 Ti-type conjugative transfer relaxase TraA [Rhizobium etli]
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETMKAWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLSEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPQEIEAETGKVSEPAVFTTREMLRIE
YDMAQSARVLSERRGFGVSERNVTVAIERVESIESGDPKTPFRLDAEQVDAVRHVTGDGGIAAIVGLAGA
GKSTLLAAARLAWESEGHRVIGAALAGKAAEGLQDSSGIKSRTLASWELAWANGRDTLHRGDVLVIDEAG
MVASQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREAWARNASRLFA
RGEVEKGLDAYARHGHLVEAGTREETIDRIVSDWAAARREAIERSTSEGRDGRLRGDELLVLAHTNDDVR
KLNEALREVMAGDNALGESRSFRTERGARKFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVTATG
DKRGDPLLSVLLDNGNKVVFGEDSYDNVDHGYAATIHKSQGSTVDRTFVLATGMMDRHLTYVSMTRHRDR
VDLYAAKEDFEPRPEWGRKPRVDHAAGVTGELVETGEAKFRPEDEDADDSPYADVRTDDGTAHRLWGVSL
PKALDDAGISDGDTITLRKDGVERVKVQIAIVDEETGQKRYEEREVDRNVWTARQIETAEARQERIERES
HRPDVFSRLVERLSRSGAKTTTLDFESEAGYRAQAQDFARRRGLDHLSLAAAEMEESLSRRWTWITAKRE
QVEKLWERASVALGFAIERERRFAYNEARTESHTIASASAGEPQYLIPPSTSFVRSVEADARLAQRSSPA
WTERETMLRPLLTKIYRDPDAALVALNALASDTGTEPRRLTADLAAAPDRLGRLRGSELIVDGGAALSER
KVAKAALEELLPLARAHATGFRRNAERFEMREQTRRSYMSLSIPALSERAMPRLMEIEAVRNRDGDDAYK
SAFALAAEDRSVVQEIKAVSEALTARFGWSAFTAKADAVAERNMTERLPEDLTAGRREELARLFEAVKRF
AEAQHLAERQDRSKIVMAASVVRGQETENGPGKENVAVPPMLAAVIAFKTSVDDEARLRALSNPFYRQQR
GALANAATMIWRDPSGAVGKIEELLRKGFAADRIAAAVTNDPAAYGALRGSNRLLDRMLASGRERKEAMR
AVPETAARLRALGAAHLNALDAERQAITDERRRMAVAIPALSKAAEEALAHLTVEVRKDSRKLSVSAASL
EQGIAREFAAVSRALDERFGRNALVRGDKDLVNRVPPAQRRAFEAMQERLKVLQQTVRLQSSEQIIAERR
QRAASRARGINL
MAIMFVRAQVISRGSGRSIVSAAAYRHRARMMDEQAGTSFSYRGGAGELMYEELALPDEIPDWLRSAISG
QSVSKASEVFWNAVDAFETRADAQLARELIIALPEELTRAENITLVREFVRDNLTSKGMIADWVYHDKDG
NPHIHLMTTLRPLTEEGFGAKKVPVLGEGGKPLRVVTPDRPNGKIVYKVWAGDKETMKAWKIAWAETANR
HLALAGHDIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGRELHFAPADLARRQEMADRLLSEPELLLKQ
LGNERSTFDERDIARALHRYVDDPTDFANIRARLMASDQLVILKPQEIEAETGKVSEPAVFTTREMLRIE
YDMAQSARVLSERRGFGVSERNVTVAIERVESIESGDPKTPFRLDAEQVDAVRHVTGDGGIAAIVGLAGA
GKSTLLAAARLAWESEGHRVIGAALAGKAAEGLQDSSGIKSRTLASWELAWANGRDTLHRGDVLVIDEAG
MVASQQMARVLKIAEEAEVKVVLVGDAMQLQPIQAGAAFRAITERIGFAELAGVRRQREAWARNASRLFA
RGEVEKGLDAYARHGHLVEAGTREETIDRIVSDWAAARREAIERSTSEGRDGRLRGDELLVLAHTNDDVR
KLNEALREVMAGDNALGESRSFRTERGARKFAAGDRIIFLENARFLEPRAKHSGPQYVKNGMLGTVTATG
DKRGDPLLSVLLDNGNKVVFGEDSYDNVDHGYAATIHKSQGSTVDRTFVLATGMMDRHLTYVSMTRHRDR
VDLYAAKEDFEPRPEWGRKPRVDHAAGVTGELVETGEAKFRPEDEDADDSPYADVRTDDGTAHRLWGVSL
PKALDDAGISDGDTITLRKDGVERVKVQIAIVDEETGQKRYEEREVDRNVWTARQIETAEARQERIERES
HRPDVFSRLVERLSRSGAKTTTLDFESEAGYRAQAQDFARRRGLDHLSLAAAEMEESLSRRWTWITAKRE
QVEKLWERASVALGFAIERERRFAYNEARTESHTIASASAGEPQYLIPPSTSFVRSVEADARLAQRSSPA
WTERETMLRPLLTKIYRDPDAALVALNALASDTGTEPRRLTADLAAAPDRLGRLRGSELIVDGGAALSER
KVAKAALEELLPLARAHATGFRRNAERFEMREQTRRSYMSLSIPALSERAMPRLMEIEAVRNRDGDDAYK
SAFALAAEDRSVVQEIKAVSEALTARFGWSAFTAKADAVAERNMTERLPEDLTAGRREELARLFEAVKRF
AEAQHLAERQDRSKIVMAASVVRGQETENGPGKENVAVPPMLAAVIAFKTSVDDEARLRALSNPFYRQQR
GALANAATMIWRDPSGAVGKIEELLRKGFAADRIAAAVTNDPAAYGALRGSNRLLDRMLASGRERKEAMR
AVPETAARLRALGAAHLNALDAERQAITDERRRMAVAIPALSKAAEEALAHLTVEVRKDSRKLSVSAASL
EQGIAREFAAVSRALDERFGRNALVRGDKDLVNRVPPAQRRAFEAMQERLKVLQQTVRLQSSEQIIAERR
QRAASRARGINL
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 161901..171502
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| RHE_RS34725 | 158712..158938 | - | 227 | Protein_147 | chaperonin GroEL | - |
| RHE_RS30115 (RHE_PD00139) | 159233..160148 | + | 916 | Protein_148 | zincin-like metallopeptidase domain-containing protein | - |
| RHE_RS30120 (RHE_PD00141) | 160891..161262 | - | 372 | WP_042120136 | hypothetical protein | - |
| RHE_RS30125 (RHE_PD00142) | 161361..161897 | + | 537 | WP_011053366 | hypothetical protein | - |
| RHE_RS30130 (RHE_PD00143) | 161901..162569 | + | 669 | WP_011053367 | lytic transglycosylase domain-containing protein | virB1 |
| RHE_RS30135 (RHE_PD00144) | 162566..162865 | + | 300 | WP_011053368 | TrbC/VirB2 family protein | virB2 |
| RHE_RS30140 (RHE_PD00145) | 162871..163209 | + | 339 | WP_011053369 | type IV secretion system protein VirB3 | virB3 |
| RHE_RS30145 (RHE_PD00146) | 163202..165568 | + | 2367 | WP_042120098 | VirB4 family type IV secretion system protein | virb4 |
| RHE_RS30150 (RHE_PD00147) | 165565..166266 | + | 702 | WP_011053371 | P-type DNA transfer protein VirB5 | virB5 |
| RHE_RS30155 | 166263..166496 | + | 234 | WP_008537008 | EexN family lipoprotein | - |
| RHE_RS30160 (RHE_PD00148) | 166499..167431 | + | 933 | WP_011053372 | type IV secretion system protein | virB6 |
| RHE_RS34730 (RHE_PD00149) | 167473..167754 | + | 282 | WP_011053373 | hypothetical protein | - |
| RHE_RS30165 (RHE_PD00150) | 167756..168427 | + | 672 | WP_011053374 | virB8 family protein | virB8 |
| RHE_RS30170 (RHE_PD00151) | 168424..169281 | + | 858 | WP_011053375 | P-type conjugative transfer protein VirB9 | virB9 |
| RHE_RS30175 (RHE_PD00152) | 169290..170465 | + | 1176 | WP_011053376 | type IV secretion system protein VirB10 | virB10 |
| RHE_RS30180 (RHE_PD00153) | 170474..171502 | + | 1029 | WP_011053377 | P-type DNA transfer ATPase VirB11 | virB11 |
| RHE_RS30185 (RHE_PD00154) | 171539..172051 | - | 513 | WP_244425864 | PIN domain-containing protein | - |
| RHE_RS30190 (RHE_PD00155) | 172105..172551 | - | 447 | WP_244425866 | DNA-binding protein | - |
| RHE_RS30195 (RHE_PD00156) | 173058..174248 | - | 1191 | WP_011053380 | DUF1173 domain-containing protein | - |
| RHE_RS34735 | 174558..174815 | + | 258 | Protein_166 | toprim domain-containing protein | - |
| RHE_RS30205 (RHE_PD00157) | 175140..176080 | + | 941 | Protein_167 | DUF2493 domain-containing protein | - |
| RHE_RS30210 (RHE_PD00158) | 176165..176431 | + | 267 | WP_004676093 | hypothetical protein | - |
Host bacterium
| ID | 1470 | GenBank | NC_004041 |
| Plasmid name | pRETCFN42d | Incompatibility group | - |
| Plasmid size | 371254 bp | Coordinate of oriT [Strand] | 182609..182628 [-] |
| Host baterium | Rhizobium etli CFN 42 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | nifX, nifN, nifE, nifK, nifD, nifH, nifS, nifW, fixA, fixB, fixC, fixX, nifA, nifB, nifZ, nifT, a9174_31165, nodD, nodJ, nodI, nodS, nodC, nodB, nodZ, fixG, fixO, fixN, mLTONO_5203, nodA |
| Anti-CRISPR | - |