Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115785
Name   oriT_pCB3060_4 in_silico
Organism   Rhizobium sp. CB3060
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP104162 (67261..67300 [+], 40 nt)
oriT length   40 nt
IRs (inverted repeats)      18..25, 27..34  (ACGTCGCA..TGCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 40 nt

>oriT_pCB3060_4
TCCAAGGGCGCAATTATACGTCGCAATGCGACGTGCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10109 GenBank   WP_260306250
Name   traA_N2601_RS33815_pCB3060_4 insolico UniProt ID   _
Length   1100 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1100 a.a.        Molecular weight: 123260.72 Da        Isoelectric Point: 9.8667

>WP_260306250.1 Ti-type conjugative transfer relaxase TraA [Rhizobium sp. CB3060]
MAIAHFSASIVSRGSGRSVVLSAAYRHCAKMEYEREARTIDYTRKQGLLHEEFVLPADAPQWARSLIADR
SVSSAVEAFWNRVEAFEKRTDAQLARDLTIALPFELTPEQNIALVRDFVEKHILSKGMVADWVYHDNPGN
PHIHLMTTLRPLAEDGFGSKKVAVIGDDGQPVRTKSGKILYELWAGSTDDFNVLRDGWFERLNHHLALGG
IDLRIDGRSYEKQGIDLEPTIHLGVGAKAIERKAEQQGVHPELERIALNEERRSENTRRIVKNPAIVLDL
ITREKSVFDERDVAKVLHRYVDNPAVFQQLMLRIILNPEVLRLQRDTIDFATGEKVPARYSTRTMIRLES
TMARQALWLSGKETHAVSASVVDAAFRRHARLSEEQKTAIERIAGHARIAAVVGRAGAGKTTMMKAAREA
WELAGYRVVGGALAGKAAEGLEKEAGIVSRTLASWELRWDRGRDVLDSKTVFVMDEAGMVASKQMAGFID
AVVRAGAKIVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQREDWMRKASLDLARGNVEKALNAYG
ANAKITGERLKDEAVTSLITDWNHSYDPTKTTLILAHLRRDVRMLNVMARDKLVERGIVGEGHSFKTADG
IRQFDAGDQIVFLKNEGSLGVKNGMIGHVVEALPNRIVAVVGDGDQRRQIVVEQRFYSNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLQLYYGTRSFAFNGGLSRVLSRKNAKETTLDYDRGKLY
REALRFAENRGLHIVQVARTLVRDRLDWTLRQKAKLTDLGQRLAAFTERFGLAQSPKTQTMKEAEPMVAG
IKTFSGSVADTVGDQLGADPALKRQWEEVSARFRYVFADPEAAFRAMNFDVVLADKEAAKQVLQKLEAEP
ASIGPLNGKTGILASKADREARRIAEVNAPALKRDLEQYFRMREIATQRLQMDEQALRQRISIDIPALSP
AARAVLERVRDAIDRNDLPAAMAYALSNRETKLEIDRFNQAVTERFGERTLLSNAAREPSGKLYEKLAEG
MRPEQKAQLKQAWPVMRTAQQLAAHERTIQSLRQAEELRLTQLQSPVLKQ

  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)

(689-736)

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

(856-951)


  Protein structure



No available structure.




T4CP

ID   11811 GenBank   WP_260306246
Name   traG_N2601_RS33800_pCB3060_4 insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 68826.91 Da        Isoelectric Point: 9.7811

>WP_260306246.1 Ti-type conjugative transfer system protein TraG [Rhizobium sp. CB3060]
MTANRLLLVIMPAAIMIAAMVLTSGMEHRLAALGTSVPAKLMLGRAGLALPYIAAAAIGVIALFAANGSA
NIKAAGLSVLAGSAAVVIIAIARETIRLNGISSRVPAGQPVLAYVDPATMTGTGIALIGGVFALRVAIRG
NAAFVASAPKRIGGKRAVHGEADWMKMREAEKLFPDAGGIVIGERYRVDRDSVATISFRADEKQSWGVGG
KSRLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGGLVVLDPSSEVAPMVSEHRRQAGRKVIVLD
PTAGGVGFNALDWIGRHGNTKEEDIVAVATWIMTDNPRTASARDDFFRASAMQLLTALIADVCLSGHTEE
KDQTLRQVRANLSEPEPKLRARLTKIYEGSESDFVKENVSVFVNMTPETFSGVYANAVKETHWLSYPNYA
GLVSGSSFSTDDLADGRTDIFIALDLKVLEAHPGLARVVIGSLLNAIYNRNGNVKDRTLFLLDEVARLGY
LRILETARDAGRKYGITLTMIFQSLGQTREAYGGRDATSKWFESASWISFAAINDPDTADYISKRCGDTT
VEVDQTNRSSGMKGSSRSRSKQLSRRPLILPHEVLRMRGDEQIVFTSGNPPLRCGRAIWFRRDDMSACVG
ENRFQPEKKA

  Protein domains


Predicted by InterproScan.

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

(163-636)

  Protein structure



No available structure.



ID   11812 GenBank   WP_260306186
Name   t4cp2_N2601_RS34110_pCB3060_4 insolico UniProt ID   _
Length   820 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 820 a.a.        Molecular weight: 91659.54 Da        Isoelectric Point: 5.9699

>WP_260306186.1 conjugal transfer protein TrbE [Rhizobium sp. CB3060]
MVALKSFRHSGPSFADLVPYAGLVDNGVILLKDGSLMAGWYFAGPDSESSTDAERNEVSRQINAILSRLG
SGWMIQVEAVRVPTADYPHHPDCHFPDLVTRAIDAERRAHFQKERGHFESRHALILTWRPPEPRRSGLTR
YIYSDTASRSATYADKALDSFLSSIREVEQYLANVVSIRRMMTRETSERGGFRTARYDELFQFIRFCVTG
ENHPVRLPEIPMYLDWLVTAELQHGLTPLVENRFLGVVAIDGLPAESWPGILNALDLMPLTYRWSSRFVF
LDAEEARAKLERTRKKWQQKVRPFFDQLFQTQSRSLDQDAMMMVAETEDAIAEASSQLVAYGYYTPVIVL
FEEDQARLQEKSEAIRRLIQAEGFGARIETLNATDAFLGSLPGVSYANIREPLINTRNLADLVPLNSVWS
GSPTAPCPFYPPASPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLSLIAAQFRRYAGAQIFA
FDKGGSMLPLTLGINGDHYQIGGDATAEREGRVLSFCPLAELSTEGDRAFAAEWIEMLVALQGVTITPDY
RNAISRQIGLMAESRGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEEDGLALGTFQCFEIEELMN
MGERNLVPVLTYLFRRIEKRLTGAPSLIILDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDA
ERSGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVATAIPKRDYYVVSPEGRRLFDMAL
GPVALSFVGASGKEDLKRIRALHSEHGAAWPLQWLQQRGIAHADTLFPAD

  Protein domains


Predicted by InterproScan.

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

(186-400)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 128036..137725

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N2601_RS34050 (N2601_34050) 123825..124826 - 1002 WP_260306164 extradiol dioxygenase -
N2601_RS34055 (N2601_34055) 125147..125872 + 726 WP_260306165 GntR family transcriptional regulator -
N2601_RS34060 (N2601_34060) 125969..126616 + 648 WP_260306170 FadR/GntR family transcriptional regulator -
N2601_RS34065 (N2601_34065) 126694..127026 + 333 WP_260306171 cupin domain-containing protein -
N2601_RS34070 (N2601_34070) 127088..127732 + 645 WP_260306174 FAD-dependent oxidoreductase -
N2601_RS34075 (N2601_34075) 128036..129352 - 1317 WP_260306175 IncP-type conjugal transfer protein TrbI virB10
N2601_RS34080 (N2601_34080) 129364..129840 - 477 WP_260306176 conjugal transfer protein TrbH -
N2601_RS34085 (N2601_34085) 129840..130694 - 855 WP_260306178 P-type conjugative transfer protein TrbG virB9
N2601_RS34090 (N2601_34090) 130711..131388 - 678 WP_260306180 conjugal transfer protein TrbF virB8
N2601_RS34095 (N2601_34095) 131406..132596 - 1191 WP_260306182 P-type conjugative transfer protein TrbL virB6
N2601_RS34100 (N2601_34100) 132590..132817 - 228 WP_260306184 entry exclusion protein TrbK -
N2601_RS34105 (N2601_34105) 132814..133578 - 765 WP_260306185 P-type conjugative transfer protein TrbJ virB5
N2601_RS34110 (N2601_34110) 133595..136057 - 2463 WP_260306186 conjugal transfer protein TrbE virb4
N2601_RS34115 (N2601_34115) 136068..136367 - 300 WP_260306187 conjugal transfer protein TrbD virB3
N2601_RS34120 (N2601_34120) 136360..136764 - 405 WP_260306188 conjugal transfer pilin TrbC virB2
N2601_RS34125 (N2601_34125) 136754..137725 - 972 WP_260306189 P-type conjugative transfer ATPase TrbB virB11
N2601_RS34130 (N2601_34130) 137722..138360 - 639 WP_260306190 acyl-homoserine-lactone synthase -

Host bacterium

ID   16218 GenBank   NZ_CP104162
Plasmid name   pCB3060_4 Incompatibility group   -
Plasmid size   138725 bp Coordinate of oriT [Strand]   67261..67300 [+]
Host baterium   Rhizobium sp. CB3060

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -