Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   108135
Name   oriT_NLR16a|p4 in_silico
Organism   Rhizobium sp. NLR16a
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP072869 (262633..262673 [+], 41 nt)
oriT length   41 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: 41 nt

>oriT_NLR16a|p4
TCCAAGGGCGCAATTATACGTCGCTGATGCGACGCCCTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5452 GenBank   WP_210633084
Name   traA_J7U39_RS28230_NLR16a|p4 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: 123277.88 Da        Isoelectric Point: 10.0476

>WP_210633084.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Rhizobium]
MAVPHFSVSVVARGAGRSAILSAAYRHCAKMEFEREARVIDYTRKQGLLHEEFVIPVDSPEWLRSMVADR
SVAGASEAFWNKVEGFEKRSDAQLAKDITIALPLELTAAQNIALMRDFVERHITAKGMVADWVYHDAPGN
PHVHLMTTLRPLTEDGFGSKKVAVLGPDGKPIRNDAGKIVYELWAGSTKDFNAFRDGWFACQNKHLALAG
LDIRIDGRSFEKQGIDLEPTIHLGVGAKAIEHKIEQSDHKSETSTPKLERIELQEERRSENARRIQRRPE
IVLDLITREKSVFDERDVAKVLYRYIDDVALFQSLMDRILQSPEALRLERERINFATGIRTPAKYTTREM
IRLEAEMANRAIWLSGRASLGVREAVLEATFARHSRLSDEQRTAIEHVAGATRIAAVIGRAGAGKTTMMK
AAREAWETAGYRVVGGALAGKAAEGLEKEAGIVSRTLSSWELRWNQGRNQLDDKTVFVLDEAGMVSSRQM
ALLVETATKAGAKLVLVGDPEQLQPIEAGAAFRAIVDRIGYAELETIYRQRQQWMRDASLDLARGKVRKA
VDAYTAHGRMIGLRLKDEAVESLIAAWDRDYDPSKTSLILAHLRRDVRKLNDMARAKLVERGVVAHGFAF
KTEDGTRMFATGDQIVFLKNEGSLGVKNGMLAKVLEAVAGRIVAEIGDGEHRRQVTIEQRFYNNLDHGYA
TTIHKSQGATVDRVKVLASLSLDRHLTYVAMTRHREDLAVYYGSRSFAKSGGLIPILSRRNAKETTLDYE
KASFYQQALRFAEARGLHLMNVARTVARDRLEWTIRQKQKLVDLGARLAAIATKLGFVGNFKNSPIQNPI
KEAKPMVSGITTFPKSFEQAVEDKLAADPGLKKQWEGVSTRFHLVYAQPEAAFKAINVDAMLKDQSAAQT
TLARIAGDPESFGALKGKTGLLVSRTDKQDRARAIANVPALARNLERYLRERAEAELKHETEERAARRKV
SVDIPALSPAAKQTLERVRDAIDRNDLPAGLEYALADRMVKAELEGFAKAVAERFGERTFLPLAAKDTDG
KTFETVTAGMTAGQKAEVQTAWNSMRTVQQLAAHERTTKALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

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)

AAA domain (AAA_30)

(387-570)


  Protein structure



No available structure.




T4CP

ID   5799 GenBank   WP_210633081
Name   traG_J7U39_RS28215_NLR16a|p4 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: 69295.51 Da        Isoelectric Point: 9.4898

>WP_210633081.1 MULTISPECIES: Ti-type conjugative transfer system protein TraG [Rhizobium]
MTINRIALVVVPGTLMILVVIGMTGIEQWLSGIGKTEAARLAWGRAGIALPYLASAAVGILSLFATAGSI
NIKQAGWGVVAGSSGTILIAAVRETMRLSSFMKSVPADKTVLAFLDPATAIGAGVALMCACFALRVVLIG
NAAFARAEPKRIQGKRALHGEADWMKLTEAAKLFPDAGGIVIGERYRVDKDSVGSQAFRADSAETWGVGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGTLIVLDPSNEVAPMVSGHRGGAGRDVFILD
PRKPATGFNVLDWVGRFGGTKEEDIASVASWIMSDSGSARGVRDDFFRASALQLLTALIADVCLSGHTDE
KEQTLRQVRMNLSEPEPTLRKRLQDIYDNSGSDFVKENVAAFVNMTQETFSGVYANAVKETHWLSYPNYA
ALVSGKKFSTSDIAAGNTDVFINIDLKTLETHSGLARVIIGSFLNAIYNRDGQIKGRALFLLDEVARLGY
MRIIETARDAGRKYGITLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTPGNAPLRCGRAIWFRRGDMKACVG
TNRFHMIGDTPTA

  Protein domains


Predicted by InterproScan.

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

(163-634)

  Protein structure



No available structure.



ID   5800 GenBank   WP_210633095
Name   t4cp2_J7U39_RS28310_NLR16a|p4 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: 91501.12 Da        Isoelectric Point: 5.6893

>WP_210633095.1 MULTISPECIES: conjugal transfer protein TrbE [Rhizobium]
MVALKRFRVTGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAVLSRLG
SGWMIQVEAIRIPTVDYPSEDRCHFPDPVTRAIDAERRSHFAREQGHFESKHALILTNRPLESKKTALSK
YIYSDEQSRKKSYADTVLFVFKNAVRELEQYFANTLSIRRMETRETVERGGERIARYDELLQFARFCTTG
ESHPIRLPDVPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQIFQTQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVVL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATDAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTAFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYENAQIFA
FDKGSSLLPLTLAAGGDHYEIGDDNVEEGRALAFCPLSELKSDADRAWATEWIEMLVGLQGVTITPDHRN
AISRQVALMASASGRSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLGALQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLIVLDEAWLMLSHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAARESGTREFYERIGLNERQIEIVSSSIPKREYYVATPDGRRLFDMSLGP
IALSFVGASGKEDLKRIRALKSEHGHEWPIHWLETRGVHDAASLLK

  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: 267805..281790

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J7U39_RS28235 (J7U39_28235) 266069..266635 + 567 WP_210633085 conjugative transfer signal peptidase TraF -
J7U39_RS28240 (J7U39_28240) 266625..267788 + 1164 WP_210633086 conjugal transfer protein TraB -
J7U39_RS28245 (J7U39_28245) 267805..268410 + 606 WP_210633087 TraH family protein virB1
J7U39_RS28250 (J7U39_28250) 268637..269506 - 870 WP_210633088 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
J7U39_RS28255 (J7U39_28255) 269499..270116 - 618 WP_127431473 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
J7U39_RS32030 270163..270374 - 212 Protein_259 hypothetical protein -
J7U39_RS28260 (J7U39_28260) 270464..270706 - 243 WP_087002841 helix-turn-helix transcriptional regulator -
J7U39_RS28265 (J7U39_28265) 270930..271253 + 324 WP_210633218 transcriptional repressor TraM -
J7U39_RS28270 (J7U39_28270) 271257..271961 - 705 WP_210633089 autoinducer binding domain-containing protein -
J7U39_RS28275 (J7U39_28275) 272273..273571 - 1299 WP_210633090 IncP-type conjugal transfer protein TrbI virB10
J7U39_RS28280 (J7U39_28280) 273583..274023 - 441 WP_210633091 conjugal transfer protein TrbH -
J7U39_RS28285 (J7U39_28285) 274027..274839 - 813 WP_210633092 P-type conjugative transfer protein TrbG virB9
J7U39_RS28290 (J7U39_28290) 274857..275519 - 663 WP_210633093 conjugal transfer protein TrbF virB8
J7U39_RS28295 (J7U39_28295) 275540..276721 - 1182 WP_087002828 P-type conjugative transfer protein TrbL virB6
J7U39_RS28300 (J7U39_28300) 276715..276915 - 201 WP_087002826 entry exclusion protein TrbK -
J7U39_RS28305 (J7U39_28305) 276912..277709 - 798 WP_210633094 P-type conjugative transfer protein TrbJ virB5
J7U39_RS28310 (J7U39_28310) 277687..280137 - 2451 WP_210633095 conjugal transfer protein TrbE virb4
J7U39_RS28315 (J7U39_28315) 280148..280447 - 300 WP_168301555 conjugal transfer protein TrbD virB3
J7U39_RS28320 (J7U39_28320) 280440..280823 - 384 WP_168301556 TrbC/VirB2 family protein virB2
J7U39_RS28325 (J7U39_28325) 280813..281790 - 978 WP_210633096 P-type conjugative transfer ATPase TrbB virB11
J7U39_RS28330 (J7U39_28330) 281787..282425 - 639 WP_210633097 acyl-homoserine-lactone synthase -
J7U39_RS28335 (J7U39_28335) 282630..283067 + 438 WP_168301559 hypothetical protein -
J7U39_RS28340 (J7U39_28340) 283064..283252 + 189 WP_168301560 IS66 family insertion sequence element accessory protein TnpB -
J7U39_RS28345 (J7U39_28345) 284047..285261 + 1215 WP_168301561 plasmid partitioning protein RepA -
J7U39_RS28350 (J7U39_28350) 285258..286280 + 1023 WP_168301562 plasmid partitioning protein RepB -

Host bacterium

ID   8570 GenBank   NZ_CP072869
Plasmid name   NLR16a|p4 Incompatibility group   -
Plasmid size   404135 bp Coordinate of oriT [Strand]   262633..262673 [+]
Host baterium   Rhizobium sp. NLR16a

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixA, fixB, fixQ, fixO, fixN, nifN, nifE, nifK, nifD, nifH, fixC, fixX, nifB, nodJ, nodI, nodC, nodA, nodD, nodF, nodE, nodM
Anti-CRISPR   -