Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102519
Name   oriT_pSM159_Rh07 in_silico
Organism   Rhizobium leguminosarum strain SM159
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIQK01000005 (37768..37808 [-], 41 nt)
oriT length   41 nt
IRs (inverted repeats)      18..24, 29..35  (ACGTCGC..GCGACGT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 41 nt

>oriT_pSM159_Rh07
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1870 GenBank   WP_130759159
Name   traA_ELI37_RS33265_pSM159_Rh07 insolico UniProt ID   _
Length   1107 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1107 a.a.        Molecular weight: 122958.22 Da        Isoelectric Point: 9.6155

>WP_130759159.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADS
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTAEQNIALMRDFVAGHITAQGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
VRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRVGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAAGGIIAEIGEGEHRQVTIEQRFYNNLDHGYAT
TIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYEK
SALCRQAFRFAEARGLHLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGKALGLVRGSNKHSIPDTIK
EARPMVSGITTFPKSLDQAVEDKLAADPGLKKQWEDVSTRFQLVYAQPEAAFKAINVDAMVKDQSVAQST
LARIAGEPESFGALKGKTGVLASRGDKHDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKVS
VDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDGK
TFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(695-739)

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

(863-959)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   1469 GenBank   WP_130759152
Name   t4cp2_ELI37_RS33180_pSM159_Rh07 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: 91786.31 Da        Isoelectric Point: 5.5010

>WP_130759152.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNEQSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLIPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPSNSPPLVQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRVLAFCPLSDLNSDVDRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEELMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATAIPKREYYVATPEGRRLFNMSLGP
VALSFVGASGKEDLKRIRALKSEHGHDWPIHWLETRGVHDAASLLRFE

  Protein domains


Predicted by InterproScan.

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

(192-400)

  Protein structure



No available structure.



ID   1470 GenBank   WP_130692298
Name   traG_ELI37_RS33280_pSM159_Rh07 insolico UniProt ID   _
Length   643 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 643 a.a.        Molecular weight: 69483.71 Da        Isoelectric Point: 9.1051

>WP_130692298.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVMPGTLMILVVIGMTGVEQWLSGFGKTEAARLAWGRAGIALPYVASAAIGILLLFSSAGSI
NIKQAGWGVVAGCSGTILIAAIRETMRLSAFMTVPADKTVWAFLDPATSIGASAALLCACFALRVALIGN
AAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGGK
SPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSVHRGGAGRDVFVLDP
RKPDIGFNVLDWVGRFGGTKEEDIASIASWIMSDSGGVRGVRDDFFRASALQLLTALIADVCLSGHTDEK
DQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYAA
LVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGYM
RIIETARDAGRKYGIALTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTTV
EIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVGT
NRFHMVGDTPRPA

  Protein domains


Predicted by InterproScan.

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

(162-633)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 18355..40382

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI37_RS33140 (ELI37_33140) 13885..14907 - 1023 WP_130759149 plasmid partitioning protein RepB -
ELI37_RS33145 (ELI37_33145) 14904..16118 - 1215 WP_027691186 plasmid partitioning protein RepA -
ELI37_RS33150 (ELI37_33150) 16735..16989 - 255 WP_130759150 IS66 family insertion sequence element accessory protein TnpB -
ELI37_RS38075 17030..17242 - 213 WP_245458276 hypothetical protein -
ELI37_RS33160 (ELI37_33160) 17720..18358 + 639 WP_130759151 acyl-homoserine-lactone synthase -
ELI37_RS33165 (ELI37_33165) 18355..19332 + 978 WP_130692274 P-type conjugative transfer ATPase TrbB virB11
ELI37_RS33170 (ELI37_33170) 19322..19705 + 384 WP_063473648 TrbC/VirB2 family protein virB2
ELI37_RS33175 (ELI37_33175) 19698..19997 + 300 WP_027681723 conjugal transfer protein TrbD virB3
ELI37_RS33180 (ELI37_33180) 20008..22464 + 2457 WP_130759152 conjugal transfer protein TrbE virb4
ELI37_RS33185 (ELI37_33185) 22436..23239 + 804 WP_130759153 P-type conjugative transfer protein TrbJ virB5
ELI37_RS33190 (ELI37_33190) 23236..23436 + 201 WP_130759154 entry exclusion protein TrbK -
ELI37_RS33195 (ELI37_33195) 23430..24611 + 1182 WP_130759155 P-type conjugative transfer protein TrbL virB6
ELI37_RS33200 (ELI37_33200) 24632..25294 + 663 WP_130692280 conjugal transfer protein TrbF virB8
ELI37_RS33205 (ELI37_33205) 25312..26124 + 813 WP_130759156 P-type conjugative transfer protein TrbG virB9
ELI37_RS33210 (ELI37_33210) 26128..26568 + 441 WP_130692284 conjugal transfer protein TrbH -
ELI37_RS33215 (ELI37_33215) 26580..27878 + 1299 WP_130692286 IncP-type conjugal transfer protein TrbI virB10
ELI37_RS33220 (ELI37_33220) 28187..28891 + 705 WP_128408806 autoinducer binding domain-containing protein -
ELI37_RS33225 (ELI37_33225) 28876..29217 - 342 WP_130759157 transcriptional repressor TraM -
ELI37_RS33230 (ELI37_33230) 29443..29685 + 243 WP_128408808 helix-turn-helix transcriptional regulator -
ELI37_RS33235 (ELI37_33235) 29799..30431 + 633 WP_128408809 DUF433 domain-containing protein -
ELI37_RS33240 (ELI37_33240) 30428..30802 + 375 WP_130692288 DUF5615 family PIN-like protein -
ELI37_RS33245 (ELI37_33245) 31159..31874 + 716 Protein_30 Crp/Fnr family transcriptional regulator -
ELI37_RS33250 (ELI37_33250) 32019..32639 - 621 WP_130692290 TraH family protein virB1
ELI37_RS33255 (ELI37_33255) 32657..33823 - 1167 WP_130759158 conjugal transfer protein TraB -
ELI37_RS33260 (ELI37_33260) 33813..34376 - 564 WP_130692294 conjugative transfer signal peptidase TraF -
ELI37_RS33265 (ELI37_33265) 34373..37696 - 3324 WP_130759159 Ti-type conjugative transfer relaxase TraA -
ELI37_RS33270 (ELI37_33270) 37951..38244 + 294 WP_128409207 conjugal transfer protein TraC -
ELI37_RS33275 (ELI37_33275) 38249..38464 + 216 WP_011654561 type IV conjugative transfer system coupling protein TraD -
ELI37_RS33280 (ELI37_33280) 38451..40382 + 1932 WP_130692298 Ti-type conjugative transfer system protein TraG virb4
ELI37_RS33285 (ELI37_33285) 40820..41269 + 450 WP_130692300 thermonuclease family protein -
ELI37_RS33290 (ELI37_33290) 41511..41825 - 315 WP_130692302 hypothetical protein -
ELI37_RS33295 (ELI37_33295) 42269..42577 + 309 WP_063473655 WGR domain-containing protein -
ELI37_RS37415 42645..42818 - 174 WP_165403408 hypothetical protein -
ELI37_RS37420 43113..43262 - 150 WP_165403406 hypothetical protein -
ELI37_RS33300 (ELI37_33300) 43563..43874 - 312 WP_027691174 DUF736 domain-containing protein -
ELI37_RS37425 44331..44507 + 177 WP_018482051 hypothetical protein -

Host bacterium

ID   2963 GenBank   NZ_SIQK01000005
Plasmid name   pSM159_Rh07 Incompatibility group   -
Plasmid size   50953 bp Coordinate of oriT [Strand]   37768..37808 [-]
Host baterium   Rhizobium leguminosarum strain SM159

Cargo genes

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