Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114582
Name   oriT_punanmed2 in_silico
Organism   Agrobacterium sp. MA01
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP045856 (277269..277306 [+], 38 nt)
oriT length   38 nt
IRs (inverted repeats)      23..28, 33..38  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 38 nt

>oriT_punanmed2
GGTTCCGAAGGGCGCAATTATACGTCGCTGACGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9344 GenBank   WP_153763887
Name   traA_GH983_RS23930_punanmed2 insolico UniProt ID   _
Length   1134 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1134 a.a.        Molecular weight: 126180.88 Da        Isoelectric Point: 10.0822

>WP_153763887.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium sp. MA01]
MAVPHFSVSIVARGSGRSAVMSAAYRHCAQMDFEREARRIDYTRKQGLRHEEFVIPADAPDWLCKMIGDR
SVAGASEAFWNHVEIFEKRVDAQLAKDATIALPVELSSAQNIQLMREFVEGFITSKGMVADWVYHDVPGN
PHVHLMTTLRPLTEDGFGAKKRTVLLPDGRPLRNDAGKIVYEVWAGGTEDFNVLRDGWFSCLNRHLMLAG
LDLHVDGRSFKKQGIELQPTLHIGVGATAVDRKSQAVHARETVALPAGLPVPGSASAPLSAPIKAAGSPA
HRRELERIALQEEVRAHNLRRIEENPRIVLDLVTREKSVFDERDIAKVLHRYVDDAGRFQCLMTRIMQHP
DILRLDQERIDFSSGIKRPARLTTRQMIRLEAQMANQAIWLSEKSAFDVCRARLEKALSHFPRLSDEQKA
AISHVTTASRIALVIGRAGAGKTTMMKAAREVWEAAGYQVVGAALAGKAAEGLEKEAGIVSRTLSSWELR
WDGGKNHLDEKTIMVLDEAGMVSSKQMALLVKEATLRGGKLVLIGDPEQLQPIEAGAAFRAIADRIGYAE
LETIYRQYQPWMREASLDLAHGHVEQAVASYAKQGRVLGSETKAEAVRRLIADWDRDYDPGCSSLILAHL
RRDVRLLNQLARERLVERGIVEPGYRFKTEEGIRLFAAGDQIVFLKNDAVLGVKNGLLAKVIAAGPGVVT
AEIGAGADRRLVRIDERLYGNLDHGYATTIHKSQGATVEQVKVLASLSLDRHLTYVAMTRHRQELSVYYG
RRSFKKAGGLGRVLSRKNAKETTLDYEENSFYRAALRFAEARGLHLLDVARMLVRDRLEWTCRQKERLTK
LGSRLIAIAGRLRQKQSVMAAVQTPSDPVKPMVSGMTAFAKSISQAVEEKLAVDPGLKRQWQEVLARFAK
VYRDPETAFRALQIDAMMKDPQTAPLKLDRVAKAPESFGELNGMPGLIASARQKQARDVALTNAPALARH
LERYLKARAEAELRFKQDEHAIRQHASFEIPRLSPAAMETLSRLEARLDRQQSPGGLDTPEIDGMVRDEL
RRFAEAVATRFGERTLLSLAAKNADGEVFHKLTAGMNQAQKSEVQAAWMAMRTSQQLSVAERLTKGQRQV
EGLRQTQSKGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(414-598)

MobA/MobL family (MobA_MobL)

(17-243)

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

(890-986)


  Protein structure



No available structure.




T4CP

ID   10840 GenBank   WP_153763793
Name   t4cp2_GH983_RS22860_punanmed2 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: 91088.71 Da        Isoelectric Point: 6.3195

>WP_153763793.1 VirB4 family type IV secretion/conjugal transfer ATPase [Agrobacterium sp. MA01]
MVGLSRFRHHGPSFADLMPYAALIEDGTLLLKDGSLLAGWYFFGPDTESATAYERNIISHEINSIISKFG
SGWMLQVDSLRVPSAGYHDRDRSHFPDPVSRAIDEERRRHFAVQDRHFESRQSLVLTYKPGHQTGEGLSQ
FVFSSDSAAKAGPADRALAAFSNAIREIEQYLSATISLQRMQAHRLNEAFGLREARFDSLLQFVRFCISG
ENMPVRLPDVGMYLDCILTAQMEHGTTPKLDDRHIGVVAIDGFPSQSWPGILNSLDQMPLSYRWSSRFIF
LDAHDARRRLEQKRRRWQQKVRPFLDQLFQTQGRSLDQDAAAMVAETETAIAQANSGLVAFGYYTSVIIL
FDDDPDRLLENAELVRRMIQAEGFGARIETLNATEAYLGSLPGNWYANVRDPLINTSNLSDLLPVNSVWT
GETTAPCPFYPSDAPALIQVASGSTPFHFNLHHEDVGHTLIFGPTGSGKSTLLALIAAQFRRYRDAQVFA
FDKGMSLMPLTRAVGGDHHEIGAEEDGRASLSFCPLADLESDADQAFAAEFIEMLLVFQGVTVTPLHRNA
IAHQITLMAASSGRSLSDFVSGVQLRDIKDGLKHYTIDGPMGHLMDAEMDTLAFQSFQCIELEALMSMGE
RNLVPVLVHLFRRIEKRLTGAPSLIILDEAWLMLGHQVFREKIREWLKVLRKANCAVILATQSISDAERS
GIVDVLIESCPTKICLANPAAQTTSMASFYERLGFNQRQIEIIATARPKRDYYCVTPKGRRLFEMALGPL
TLAFTGVSDAEQIRTIKRLFQAHGSDWPRHWLSLKGETDALSLLAC

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(592-743)

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

(186-400)

  Protein structure



No available structure.



ID   10841 GenBank   WP_153763884
Name   traG_GH983_RS23915_punanmed2 insolico UniProt ID   _
Length   645 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 645 a.a.        Molecular weight: 70190.39 Da        Isoelectric Point: 9.2144

>WP_153763884.1 Ti-type conjugative transfer system protein TraG [Agrobacterium sp. MA01]
MTPTKILIATAAAAIMGLCALVLPLVIFPWHLSFGVSDKTRIILDHVSAILPHAAAAASGLILLFAARGA
LSIKATGWGVAAGAILVLLFEVSSKSSRNFSSSGADVFDASGFFRLDVATAIGPVLLALCGGFALRVAVR
GNAAFQRREPKRIRGRRALHGDADWMSLTKAAKLFGEGGGIVIGECYRVDHDSAASIAFRTDNEATWGAG
GRSKLLCFDASFGSTHGIAFAGSGGFKTTSVTIPTALKWNGTLIVLDPSNEVAPMVEEHRMTDGRDVFVL
NPKDPTVGFNALDWIGCHGTSKEEDIAAVASWIMSESGRASSHRDDFFRASALQLLTAVIADVCLSGHTD
KRNQNLRTVRANLSEPEPKLRARLERIHESSQSDFVKENVATFVNMTPETFSGVYANAIKETHWLSYPNY
AALVSGSTFATDDLANGKTDIFIALDLKTLEMHAGLARVMIGTFLNAIYGRDGAMPGRALFLLDEVARLG
FMRILETARDAGRKYGISLILLYQSIGQMRESFGGRDAASKWFESASWISFSAINDPETADYISRRCGMT
TVEIDKISRSFQARGMSKTRSTQLASRPLILPHEVLQMRADEQIIFTSGNPPLRCGRALWFRRSEMRACL
NQSRFRQAREHQNIR

  Protein domains


Predicted by InterproScan.

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

(165-638)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 33582..43136

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GH983_RS24415 28620..28952 - 333 WP_246727651 hypothetical protein -
GH983_RS22805 (GH983_22805) 28951..29160 + 210 WP_153763785 hypothetical protein -
GH983_RS22810 (GH983_22810) 29219..30610 - 1392 WP_153763913 amidohydrolase family protein -
GH983_RS22815 (GH983_22815) 30622..31356 - 735 WP_153763786 response regulator transcription factor -
GH983_RS22820 (GH983_22820) 31521..32441 + 921 WP_194842865 response regulator transcription factor -
GH983_RS22825 (GH983_22825) 32761..33477 + 717 WP_153763788 autoinducer binding domain-containing protein -
GH983_RS22830 (GH983_22830) 33582..34916 - 1335 WP_153763789 IncP-type conjugal transfer protein TrbI virB10
GH983_RS22835 (GH983_22835) 34913..35449 - 537 WP_153763790 hypothetical protein -
GH983_RS22840 (GH983_22840) 35451..36275 - 825 WP_246727653 P-type conjugative transfer protein TrbG virB9
GH983_RS22845 (GH983_22845) 36334..36999 - 666 WP_069044336 conjugal transfer protein TrbF virB8
GH983_RS22850 (GH983_22850) 36999..38177 - 1179 WP_153763914 P-type conjugative transfer protein TrbL virB6
GH983_RS22855 (GH983_22855) 38237..39055 - 819 WP_153763792 P-type conjugative transfer protein TrbJ virB5
GH983_RS22860 (GH983_22860) 39030..41480 - 2451 WP_153763793 VirB4 family type IV secretion/conjugal transfer ATPase virb4
GH983_RS22865 (GH983_22865) 41495..41791 - 297 WP_153763915 conjugal transfer protein TrbD virB3
GH983_RS22870 (GH983_22870) 41791..42183 - 393 WP_153763794 TrbC/VirB2 family protein virB2
GH983_RS22875 (GH983_22875) 42201..43136 - 936 WP_069044339 P-type conjugative transfer ATPase TrbB virB11
GH983_RS22880 (GH983_22880) 43133..44008 - 876 WP_246727654 acyl-homoserine-lactone synthase -
GH983_RS22885 (GH983_22885) 44220..45407 + 1188 WP_069044341 plasmid partitioning protein RepA -
GH983_RS22890 (GH983_22890) 45482..46459 + 978 WP_153763917 plasmid partitioning protein RepB -
GH983_RS22895 (GH983_22895) 46624..47838 + 1215 WP_153763795 plasmid replication protein RepC -

Host bacterium

ID   15017 GenBank   NZ_CP045856
Plasmid name   punanmed2 Incompatibility group   -
Plasmid size   310891 bp Coordinate of oriT [Strand]   277269..277306 [+]
Host baterium   Agrobacterium sp. MA01

Cargo genes

Drug resistance gene   -
Virulence gene   tviB, bplB, bplC
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -