Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120358
Name   oriT_pRinCIP108029a in_silico
Organism   Rhizobium indigoferae strain CIP 108029
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP140639 (137082..137115 [-], 34 nt)
oriT length   34 nt
IRs (inverted repeats)      19..24, 29..34  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 34 nt

>oriT_pRinCIP108029a
TCCAAGGGCGCAATTATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12809 GenBank   WP_193444863
Name   traA_U5G49_RS35930_pRinCIP108029a 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: 123031.33 Da        Isoelectric Point: 9.7853

>WP_193444863.1 Ti-type conjugative transfer relaxase TraA [Rhizobium indigoferae]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMEFEREGRTIDYTRKQGLLHEEFVISADAPEWVRSMIADR
SVAGASEMFWNKVEGFEKRCDAQLAKDVTIALPLELTAEQNIALMRDFVERHITAHGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLSPDGKPIRNDAGKIVYQLWAGGTEDFNAFRDGWFACQNKHLALAD
LDILIDGRSYEKQGIDLEPTIHLGVGVKAIERKAEQFDRMQETSASKLERVELQEQRRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDAVLFQSLMVRILQSPEALRLERERINFATGVRTPAKYTTREM
IRLEAEMANRAIWLSARASHGVRVVVVQATFAHHSRLSDEQRTAIEHVAGATRIAAVVGRAGAGKTTMMK
AAREAWEMAGYRVVGGALAGKAAEGLEKEAGIGSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALFVEAVTKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQRQQWMRDASLDLARGNIRRA
VDAYTAHGRMIGLRLKDDAVESLIAAWDRDYDSSKTSLILAHLRRDVRMLNDMARAKLVERGVVAEGLPF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAAPGRIVAEIGDGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYGQALRFAEARGLHLVNVARTIAHDRLQWAVRQKQKLADLGARLAAIGAALGLVRGSNKHSIPDTI
KEAKPMVSGITTFPKSLDQAVEDKLAADPGLKTQWEDVSTRFHLVYAQPEAAFKAINVDAMVKDQSVAQS
TLAKVAGAPESFGALKGKTGLLASRADRQDRKKAIANVPALARNLERYLRERAEAEFKHETEERAVRLKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADRMVKAELEGFAKAVSERFGERTFLPLVAKDTSG
KTFETVTSGMTAGQKAEVQSAWNSMRTVQQLSSHERTTEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(387-570)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(697-740)

MobA/MobL family (MobA_MobL)

(17-243)

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

(864-960)


  Protein structure



No available structure.




T4CP

ID   15049 GenBank   WP_193444878
Name   t4cp2_U5G49_RS35845_pRinCIP108029a 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: 91585.27 Da        Isoelectric Point: 5.7159

>WP_193444878.1 conjugal transfer protein TrbE [Rhizobium indigoferae]
MVALKRFRVTVPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRTHFAREQGHFESKHALILTYRPLESKKTALSK
YIYSDEESRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQMVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTGNLADLIPLNSVWS
GNPVAPCPFYAPNSPPLMQVVSGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQVFA
FDKGSSLLPLTLAAGGDHYEIGGDNSDQGRTLAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDYRN
AISRQVGLMTSASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGFNERQVEIVATAMPKREYYVATPEGRRLFDMSLGP
VALSFVGASGKEDLKRIRALKSEHGRDWPVHWLETRGVHDAASLLK

  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   15050 GenBank   WP_193444860
Name   traG_U5G49_RS35945_pRinCIP108029a 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: 69352.47 Da        Isoelectric Point: 8.9469

>WP_193444860.1 Ti-type conjugative transfer system protein TraG [Rhizobium indigoferae]
MTINRIALVVVPGTLMILVVIGMIGIEQWLSGFGKTEAARLAWGRAGIALPYIASAAIGILFLFASAGSI
NIKQAGWGVLAGCSGTILIAATRETMRLAAFTKALNADKSVLTYLDPATSIGVGAAFMCACFALRVAFIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAADLFTDAGGIVIGERYRVDKDSVGSQTFRADSAETWGAGG
RSPLLCFDGSFGSSHGIIFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSAHRGGAGRDVFVLD
PKKPGMGFNVLDWVGGFGGTKEEDIASVASWIISDSGGARGVRDDFFRASALQLLTALIADVCLSGHTDE
KDQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKFGITLTMIYQSIGQMRETYGGHDAASKWFESASWISFAAINDPETAAYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRRDDMKACVG
TNRFHMIGDAPKPA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 118390..131952

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
U5G49_RS35810 (U5G49_007161) 113723..114937 - 1215 WP_193444883 plasmid replication protein RepC -
U5G49_RS35815 (U5G49_007162) 115125..116162 - 1038 WP_193444891 plasmid partitioning protein RepB -
U5G49_RS35820 (U5G49_007163) 116159..117421 - 1263 WP_193444890 plasmid partitioning protein RepA -
U5G49_RS35825 (U5G49_007164) 117758..118393 + 636 WP_193444882 acyl-homoserine-lactone synthase -
U5G49_RS35830 (U5G49_007165) 118390..119367 + 978 WP_193444881 P-type conjugative transfer ATPase TrbB virB11
U5G49_RS35835 (U5G49_007166) 119357..119740 + 384 WP_193444880 TrbC/VirB2 family protein virB2
U5G49_RS35840 (U5G49_007167) 119733..120032 + 300 WP_193444879 conjugal transfer protein TrbD virB3
U5G49_RS35845 (U5G49_007168) 120043..122493 + 2451 WP_193444878 conjugal transfer protein TrbE virb4
U5G49_RS35850 (U5G49_007169) 122471..123268 + 798 WP_193444877 P-type conjugative transfer protein TrbJ virB5
U5G49_RS35855 (U5G49_007170) 123265..123465 + 201 WP_193444876 entry exclusion protein TrbK -
U5G49_RS35860 (U5G49_007171) 123459..124640 + 1182 WP_193444875 P-type conjugative transfer protein TrbL virB6
U5G49_RS35865 (U5G49_007172) 124661..125323 + 663 WP_193444874 conjugal transfer protein TrbF virB8
U5G49_RS35870 (U5G49_007173) 125341..126153 + 813 WP_193444873 P-type conjugative transfer protein TrbG virB9
U5G49_RS35875 (U5G49_007174) 126157..126597 + 441 WP_193444872 conjugal transfer protein TrbH -
U5G49_RS35880 (U5G49_007175) 126609..127907 + 1299 WP_193444871 IncP-type conjugal transfer protein TrbI virB10
U5G49_RS35885 (U5G49_007176) 128218..128922 + 705 WP_193444870 autoinducer binding domain-containing protein -
U5G49_RS35890 (U5G49_007177) 128926..129216 - 291 WP_193444869 transcriptional repressor TraM -
U5G49_RS35895 (U5G49_007178) 129472..129720 + 249 WP_193444868 helix-turn-helix domain-containing protein -
U5G49_RS35900 (U5G49_007179) 129997..130167 - 171 Protein_123 transcriptional regulator -
U5G49_RS35905 (U5G49_007180) 130197..130325 + 129 Protein_124 transcriptional regulator -
U5G49_RS35910 (U5G49_007181) 130318..131235 + 918 WP_193444867 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
U5G49_RS35915 (U5G49_007182) 131335..131952 - 618 WP_193444866 TraH family protein virB1
U5G49_RS35920 (U5G49_007183) 131969..133132 - 1164 WP_193444865 conjugal transfer protein TraB -
U5G49_RS35925 (U5G49_007184) 133122..133619 - 498 WP_322790966 conjugative transfer signal peptidase TraF -

Host bacterium

ID   20787 GenBank   NZ_CP140639
Plasmid name   pRinCIP108029a Incompatibility group   -
Plasmid size   354923 bp Coordinate of oriT [Strand]   137082..137115 [-]
Host baterium   Rhizobium indigoferae strain CIP 108029

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   LinG, dxnH, linJ
Symbiosis gene   fixG, fixQ, fixO, fixN, nifN, nifE, nifK, nifD, nifH, nodM, nodD
Anti-CRISPR   -