Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101188
Name   oriT_pSM153C_Rh08_Rh04 in_silico
Organism   Rhizobium ruizarguesonis strain SM153C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_SIPY01000005 (91075..91115 [+], 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_pSM153C_Rh08_Rh04
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACGTCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1185 GenBank   WP_130714113
Name   traA_ELI25_RS32025_pSM153C_Rh08_Rh04 insolico UniProt ID   _
Length   1108 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1108 a.a.        Molecular weight: 123097.40 Da        Isoelectric Point: 9.7427

>WP_130714113.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREARTIDYTRKQGLLHEEFVIPADAPEWVRSMIADS
SVAGASEAFWNKVETFEKRSDAQLAKDVTIALPLELTVEQNIALMRDFVAGHITAQGMIADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDDKPIRNDAGKIVYQLWAGSTEDFNAFRDGWFACQNKHLALAG
LEIHIDGRSFEKQGIDLEPTIHLGVGAKAIERKAEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVLLFQSLMVRILQSPEALRLERERINFATGIRTPAKYTTREM
VRLEAEMANRAIWLSGRASHGVREEVLQATFARHSRLSDEQRTAIEHVARATRIAAIIGRAGAGKTTMMK
AAREAWEAAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTRVGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDLSKTSLILAHLRRDVRMLNDMARAKLVERGVVADGFAF
KTEDGTRMFAAGDQIVFLKNEGSLGVKNGMLAKVIEAAAGGIIAEIGEGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDKHLTYVAMTRHREDLAVYYGRRSFAKSGGLIPILSRRNAKETTLDYE
KSALYRQAFRFAEARGLHLMNVARTIAHDRLQWAVRQKQKLADLGARLAAIGKAIGLVRGSNKQTAPNTI
KEAKPMVSGITTFPKSLDQAVEDKLAGDPGLKKQWEDVSTRFQLVYAQPEAAFKAINVDAMVKDQSVAQS
TLARIAGEPESFGALKGKAGVLASRGDKQDREKALANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADKMVKAELEGFAKAVSERFGERTFLPLAAKDTDG
KTFETVTAGMTAGQKAEVRNAWDAMRAVQQMAAHERTTEALKQAETLRQTRSQGLSLK

  Protein domains


Predicted by InterproScan.

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

(864-960)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(696-740)

MobA/MobL family (MobA_MobL)

(17-243)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   788 GenBank   WP_130714111
Name   traG_ELI25_RS32010_pSM153C_Rh08_Rh04 insolico UniProt ID   _
Length   644 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 644 a.a.        Molecular weight: 69549.58 Da        Isoelectric Point: 9.5666

>WP_130714111.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVIVPTALMIPVVIGMTGIEQWLSGFGKTESARLAWGRTGIALPYVASAAIGVLWLFSSAGSI
NIKQAGWGVVAGSSGTILVAAVRETVRLSGFMKTVPADKTVLAYLDPATSIGASTALLGACFALRVALIG
KAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSEHRGGAGRDVFILD
PRKPDTGFNVLDWVGRFGGTKEEDIASVASWIMSDSGGARGVRDDFFRASALQLLTALIADVCLSGHTEE
NGQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGRKFSTSDIAAGKTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQARGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMIGDAPKPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   789 GenBank   WP_130747474
Name   t4cp2_ELI25_RS32105_pSM153C_Rh08_Rh04 insolico UniProt ID   _
Length   816 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 816 a.a.        Molecular weight: 91495.22 Da        Isoelectric Point: 6.0219

>WP_130747474.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLLAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIQTVNYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTYRPLESKKTALSK
YTYSDEVSRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELMQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKIENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVVETEDAIAQASSQLVAYGYYTPVVVL
FDSDRVALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGGDNAEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVGLMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLKLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLCHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQIEIVATATPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSENGHDWPIHWLETRGVHDAASLLK

  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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 96243..110007

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ELI25_RS32030 (ELI25_32010) 94510..95073 + 564 WP_130714114 conjugative transfer signal peptidase TraF -
ELI25_RS32035 (ELI25_32015) 95063..96226 + 1164 WP_130714115 conjugal transfer protein TraB -
ELI25_RS32040 (ELI25_32020) 96243..96860 + 618 WP_130714116 TraH family protein virB1
ELI25_RS32045 (ELI25_32025) 96967..97832 - 866 Protein_91 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
ELI25_RS32050 (ELI25_32030) 97825..98442 - 618 WP_130714117 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
ELI25_RS32055 (ELI25_32035) 98684..98932 - 249 WP_130714118 helix-turn-helix transcriptional regulator -
ELI25_RS32060 (ELI25_32040) 99192..99482 + 291 WP_130714119 transcriptional repressor TraM -
ELI25_RS32065 (ELI25_32045) 99486..100190 - 705 WP_130714120 autoinducer binding domain-containing protein -
ELI25_RS32070 (ELI25_32050) 100502..101800 - 1299 WP_130747468 IncP-type conjugal transfer protein TrbI virB10
ELI25_RS32075 (ELI25_32055) 101812..102252 - 441 WP_130747469 conjugal transfer protein TrbH -
ELI25_RS32080 (ELI25_32060) 102256..103068 - 813 WP_130747470 P-type conjugative transfer protein TrbG virB9
ELI25_RS32085 (ELI25_32065) 103086..103748 - 663 WP_130747471 conjugal transfer protein TrbF virB8
ELI25_RS32090 (ELI25_32070) 103769..104938 - 1170 WP_130747472 P-type conjugative transfer protein TrbL virB6
ELI25_RS32095 (ELI25_32075) 104932..105132 - 201 WP_130747477 entry exclusion protein TrbK -
ELI25_RS32100 (ELI25_32080) 105129..105926 - 798 WP_130747473 P-type conjugative transfer protein TrbJ virB5
ELI25_RS32105 (ELI25_32085) 105904..108354 - 2451 WP_130747474 conjugal transfer protein TrbE virb4
ELI25_RS32110 (ELI25_32090) 108365..108664 - 300 WP_130714129 conjugal transfer protein TrbD virB3
ELI25_RS32115 (ELI25_32095) 108657..109040 - 384 WP_130714130 TrbC/VirB2 family protein virB2
ELI25_RS32120 (ELI25_32100) 109030..110007 - 978 WP_130746550 P-type conjugative transfer ATPase TrbB virB11
ELI25_RS32125 (ELI25_32105) 110004..110642 - 639 WP_130714132 acyl-homoserine-lactone synthase -
ELI25_RS32130 (ELI25_32110) 111019..112242 + 1224 WP_165411169 plasmid partitioning protein RepA -
ELI25_RS32135 (ELI25_32115) 112239..113276 + 1038 WP_130714134 plasmid partitioning protein RepB -
ELI25_RS32140 (ELI25_32120) 113466..114680 + 1215 WP_130714135 plasmid replication protein RepC -

Host bacterium

ID   1632 GenBank   NZ_SIPY01000005
Plasmid name   pSM153C_Rh08_Rh04 Incompatibility group   -
Plasmid size   131997 bp Coordinate of oriT [Strand]   91075..91115 [+]
Host baterium   Rhizobium ruizarguesonis strain SM153C

Cargo genes

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