Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106966
Name   oriT_pRetNIM1c in_silico
Organism   Rhizobium etli bv. mimosae str. Mim1
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_021910 (245840..245883 [+], 44 nt)
oriT length   44 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 44 nt

>oriT_pRetNIM1c
GGATCCGAAGGGCGCAATTATACGTCGCTGCCGCGACGCCCTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4601 GenBank   WP_020919038
Name   traA_REMIM1_RS24110_pRetNIM1c insolico UniProt ID   S5S3Y8
Length   1103 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1103 a.a.        Molecular weight: 122358.82 Da        Isoelectric Point: 9.8995

>WP_020919038.1 Ti-type conjugative transfer relaxase TraA [Rhizobium etli]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVIPADAPEWLRSMIADR
SVAGASEAFWNKVEDFEKRSDAQLAKDVTIALPLELTPEQNITLLRDFVAQHITAKGMVVDWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKVPVTGPDGNPIRNDAGKIVYELWAGSIDDFNVFRDGWFACQNRHLALAG
LDIRVDGRSFEKQGIDLEPTIHLGVGTKAIERKSDGASEPVELERLELQEARRSENVRRIDRNPELVLAL
IMREKSVFDERDVAKILHRYVDDAALFQSLMVRILLCPETFRIERERIDLANGIRVPAKYTTRDMIRLEA
EMANRAVWLSQRSSHGVRDVVLAATFARHKRLSDEQKTAIEHVAGPERIAAVIGRAGAGKTTMMKAAREA
WEAAGYHVVGGALAGKAAEGLEQEAGIVSRTLASWELRWNQGRDQLDSKTVFVLDEAGMVSSRQMALFVE
AVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGKVGKAVDAYR
ANGKVIGLDLKADAVDNLIAAWDRDYDPAKTSLILAHLRRDVRMLNQMARIKLIERGILGQGTVFKTADG
ERNFAVGDQIVFLKNEGSLGVKNGMLAKVMGVGAGRIIARIGDGENARQVLVEQRFYQHLDHGYATTIHK
SQGATVDQVKVLASLSLDRHLTYVAMTRHREDLAVYYGRRSFAKNGGLVAILSRRNAKETTLDYEKSAFY
RQALRFAEARGLNLVNVARTLVRDRLEWVVSQKQKLAKLGVRLAAIAGKLGLVRGAAQSPTQNRTKEAKP
MVSGITTFAKSVEQAIEDKVAADPGLKKQWEEVSTRFHLVYAQPESAFKAVNVDAMLKDETAQKSTLAKI
GSEPERFGTLKGKTGILASRSDREEREKAQTNAPALARNLERYLRQRAEAERKFEAEERAVRLKVSIDIP
ALSANAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVAERFGERTFLSLAAKEPNGQTFNT
VTSGMTAGQKAEVQSAWNMMRTVQQLAAHERTTEALKQAETMRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(382-566)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(689-735)

BID domain of Bartonella effector protein (Bep) (Bep_C_terminal)

(859-955)


  Protein structure


Source ID Structure
AlphaFold DB S5S3Y8


T4CP

ID   4695 GenBank   WP_041679005
Name   traG_REMIM1_RS24095_pRetNIM1c insolico UniProt ID   _
Length   657 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 657 a.a.        Molecular weight: 71389.54 Da        Isoelectric Point: 8.9869

>WP_041679005.1 Ti-type conjugative transfer system protein TraG [Rhizobium etli]
MIRILLYVAPCALMLLTAIGMAGVEHWLAAFGKSDAAKQMLGRTGIALPYVVASFVGIVFLFASAGSARI
RSAGWSVFTGAIATLVVAILREAIRLSAFRAEVPAGKSILNYLDPATTIGAAAVLMSALFGLRVAIAGNA
AFARSEPKRIYGKRALHGEADWMKLSQAEKLFAADGGIVIGERYRVDRDSVAAYAFRADSAETWGAGGTS
PLLCFDGAFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALIVLDPSNEVAPMVSKHRGDADRDVFVLDPK
RSEIGFNALDWIGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTPEND
QTLRQVRKNLSEPEPKLRERLQSIYDNSDSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAAL
VSGSTFTTQDLGEGKTDIFINVDLKTLETHSGLARVIIGSFLNAIYNRNGQMEGRALFLLDEVARLGYMR
ILETARDAGRKYGITLLMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETAEYISRRCGMTTVE
IDQVSRSSQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMRACVGMN
KFHQLKDRPDAHPIEPARSATSKADRG

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(161-633)

  Protein structure



No available structure.



ID   4696 GenBank   WP_020919054
Name   t4cp2_REMIM1_RS24190_pRetNIM1c insolico UniProt ID   _
Length   818 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 818 a.a.        Molecular weight: 91969.67 Da        Isoelectric Point: 5.8562

>WP_020919054.1 conjugal transfer protein TrbE [Rhizobium etli]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINTILSRLG
SGWMIQVEAVRIPTFDYPSDDRCHFPDPVTRAIDAERRAHFAREQGHFESKHALVLTYRPLESKKTALSK
YIYSDEESRKKTYADTVLFIFRNAVREIEQYLGNTLSIRRMETREVVERGGEREARYDELLQFVRFCITG
ENHPIRLPDAPMYLDWIATAELEHGLTPKVESRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAQEARQKLERTRKKWQQKVRPFFDQLFQTQSRSIDQDAMSMVAETEDAIAQASSQLVAYGYYTPVIVL
FDYDREALQEKAEAIRRLIQAEGFGARIETLNATDAFLGSLPGNWYCNIREPLINSSNLADLIPLNSVWS
GSPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYERAQIFA
FDKGNSLLPLTLAAGGDHYEIGGDTHEEGRALAFCPLSELASDGDRAWATEWIEMLVALQGVAITPDHRN
AISRQIGLMARAGGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVLLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSNATPKREYYVVTPDGRRLFDMALGP
VALSFVGASGKEDLKRIRALHSEHGHDWPIHWLQTRGVHDAASLLNFE

  Protein domains


Predicted by InterproScan.

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(191-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 251003..264797

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
REMIM1_RS24115 (REMIM1_PC00243) 249266..249832 + 567 WP_020919039 conjugative transfer signal peptidase TraF -
REMIM1_RS24120 (REMIM1_PC00244) 249822..250985 + 1164 WP_020919040 conjugal transfer protein TraB -
REMIM1_RS24125 (REMIM1_PC00245) 251003..251620 + 618 WP_020919041 TraH family protein virB1
REMIM1_RS38075 251738..252382 - 645 WP_342452336 hypothetical protein -
REMIM1_RS38080 252353..253000 + 648 WP_342452337 ImmA/IrrE family metallo-endopeptidase -
REMIM1_RS24135 (REMIM1_PC00247) 253010..253504 + 495 WP_020919043 DUF4411 family protein -
REMIM1_RS24140 (REMIM1_PC00248) 253521..253739 - 219 WP_020919044 helix-turn-helix transcriptional regulator -
REMIM1_RS24145 (REMIM1_PC00249) 253925..254245 + 321 WP_020919045 transcriptional repressor TraM -
REMIM1_RS24150 (REMIM1_PC00250) 254242..254994 - 753 WP_080655841 autoinducer binding domain-containing protein -
REMIM1_RS24155 (REMIM1_PC00251) 255278..256573 - 1296 WP_020919047 IncP-type conjugal transfer protein TrbI virB10
REMIM1_RS24160 (REMIM1_PC00252) 256587..257027 - 441 WP_020919048 conjugal transfer protein TrbH -
REMIM1_RS24165 (REMIM1_PC00253) 257031..257843 - 813 WP_020919049 P-type conjugative transfer protein TrbG virB9
REMIM1_RS24170 (REMIM1_PC00254) 257861..258523 - 663 WP_020919050 conjugal transfer protein TrbF virB8
REMIM1_RS24175 (REMIM1_PC00255) 258548..259723 - 1176 WP_020919051 P-type conjugative transfer protein TrbL virB6
REMIM1_RS24180 (REMIM1_PC00256) 259717..259917 - 201 WP_020919052 entry exclusion protein TrbK -
REMIM1_RS24185 (REMIM1_PC00257) 259914..260717 - 804 WP_020919053 P-type conjugative transfer protein TrbJ virB5
REMIM1_RS24190 (REMIM1_PC00258) 260689..263145 - 2457 WP_020919054 conjugal transfer protein TrbE virb4
REMIM1_RS24195 (REMIM1_PC00259) 263155..263454 - 300 WP_020919055 conjugal transfer protein TrbD virB3
REMIM1_RS24200 (REMIM1_PC00260) 263447..263830 - 384 WP_020919056 TrbC/VirB2 family protein virB2
REMIM1_RS24205 (REMIM1_PC00261) 263820..264797 - 978 WP_020919057 P-type conjugative transfer ATPase TrbB virB11
REMIM1_RS24210 (REMIM1_PC00262) 264808..265434 - 627 WP_020919058 acyl-homoserine-lactone synthase TraI -
REMIM1_RS24215 (REMIM1_PC00263) 265823..267037 + 1215 WP_020919059 plasmid partitioning protein RepA -
REMIM1_RS24220 (REMIM1_PC00264) 267034..268059 + 1026 WP_020919060 plasmid partitioning protein RepB -
REMIM1_RS24225 (REMIM1_PC00266) 268215..269426 + 1212 WP_020919061 plasmid replication protein RepC -

Host bacterium

ID   7403 GenBank   NC_021910
Plasmid name   pRetNIM1c Incompatibility group   -
Plasmid size   269426 bp Coordinate of oriT [Strand]   245840..245883 [+]
Host baterium   Rhizobium etli bv. mimosae str. Mim1

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   dxnH, linJ
Symbiosis gene   -
Anti-CRISPR   -