Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120996
Name   oriT_AF3.44|unnamed1 in_silico
Organism   Agrobacterium larrymoorei strain AF3.44
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP072170 (89376..89419 [+], 44 nt)
oriT length   44 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: 44 nt

>oriT_AF3.44|unnamed1
GGATCCGAAGGGCGCAATTATACGTCGCTGATGCGACGCTTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13246 GenBank   WP_027674825
Name   traA_J5285_RS24270_AF3.44|unnamed1 insolico UniProt ID   A0A4D7DWF1
Length   1192 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1192 a.a.        Molecular weight: 131905.45 Da        Isoelectric Point: 8.2848

>WP_027674825.1 Ti-type conjugative transfer relaxase TraA [Agrobacterium larrymoorei]
MAVPHFSVSIVARGSGRSAVLSAAYRHCAKMDYEREARTIDYTRKQGLLHEEIAIPADAPEWLQSMIADR
SVSGASEALWNKVEEFEKRSDAQLAKDITIALPIELSAEQNVELVRDFVASHITAHGMVADWVFHDAPGN
PHIHLMTTLRPLADDGFGPKKVAVTGPDGQSLRNDSGKIVYELWAGGLENFNAFRDGWFACQNRHLTLAG
LDIRVDGRSFEKQGIDLKPTIHLGVGTKAIERKAEGGEESAALERLELQEERRAENARRIQRNPEIVLDL
ITREKSVFDERDVAKILHRYIDDAGLFQSLKARILQSPETLRLERERVDFATGTLTSAKYTTRELIRLEA
EMAKRAIWLSHRSSHSVRKAVIEATFARHDRLSDEQKTAIEHVAGDAGIAAVIGRAGAGKTTMMKAAREV
WEAAGYRVVGAALAGKAAEGLEKEGGIVSRTLSSWELRWEKERDHLDDETVFVIDEAGMVSSRQLAFFVE
AVAKAGAKLVLIGDPDQLQPIEAGAAFRAMTDRVGYAELETIYRQKDQWMRDASLDLARGNVSLALNAYE
QAGLVQTGWTRQDAIVGLIESWNRDYDPDKTTLILAHRRRDVRELNELARGRLVERCIVGEGFAFNTQDG
PRRFAAGDQIVFLKNEGSLGVKNGMLAKVLDAAPGRIVAEIGDGENRTQVIVEQRFYANIDHGYATTIHK
SQGATVDRVKVLASSTLDRHLIYVAMTRHREAAELHVGVEEFTSRRGGRLVDHGVAPYEHKPGSRDSYFV
TLEHSDGQQSTIWGVDLKRAIEEARPDIGDRIGLKHDGSETVTLPDGTTAERNTWRIIHVADLAIERLKE
RLARDGSKETTLDYEGASSYRAALRFAGARGLHLMNVARTISKDRLAWTVRQKQKLVNLAARLAAFGAKL
GFATSTANTFPNAAKETKPMVAGITTFPRSIEQAVEDKLAADPALKKQWDEVSMRFKHVYAQPEAAFKAA
NVDAMLIDQAAAKKTIARIVGEPQSFGALKGKTGLLASRADKLDRDRALKNVAPLADSIRDYLRQRGEAE
RRNHAQELAVRRQVALEIPALSANAKSVLERVRDAIDRNDLPSGLEYALADKMVKAELEGFAKAITERFG
DRTLLPLAAKDTNGEAFQRVTAGMNAAQKSEVQQAWTTMRTVQQLSAHERSVTALKQAEALRQTRSQGLT
LK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-568)

MobA/MobL family (MobA_MobL)

(17-243)

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

(948-1044)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-732)


  Protein structure


Source ID Structure
AlphaFold DB A0A4D7DWF1


T4CP

ID   15527 GenBank   WP_027674822
Name   traG_J5285_RS24255_AF3.44|unnamed1 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: 69114.88 Da        Isoelectric Point: 8.9201

>WP_027674822.1 Ti-type conjugative transfer system protein TraG [Agrobacterium larrymoorei]
MKANKIALVILPAAVMGAAVFALTGIETWLAGFGKTDAAKLALGRAGVAAPYVAAAALGLIFLFATAGSA
SVRAAGLGATIGNVAVILTACLREGVRLAAFFSQVPADKSSLSYLDPSTMIGAATALMSGCFAIRVAVIG
NGAFARAAPKRITGKRALHGEADWMKLAEAEKLFPGTGGIVVGELYRVDRDGVAGVSFRADNSETWGAGG
KSPLLCFDGSFGSSHGIIFAGSGGYKTTSVTIPTALKWAGSLILLDPSNEVAPMISKHREDAGRRIRILD
PRKPATGFNALDWVGQYGGTKEEDIASVASWIMSDSGRASGVRDDFFRASGLQLLTAIIADVCLSGHTPT
EKQTLRQVRENLSEPEPKLRQRLQDIYDNSESDFVKENVAAFVNMTPETFSGVYANAIKETHWLSYQNYA
ALVSGSTFRTEDISSGKTDVFINIDLKTLETHAGLARVVIGSFLNAIYNRDGAMEGRALFLLDEVARLGY
MRILETARDAGRKYGITLTMIYQSIGQMRETYGGRDASSKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSSNFQCRGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNPPLRCGRAIWFRRADMKSCVT
QGRFQPAATGAPSE

  Protein domains


Predicted by InterproScan.

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

(163-638)

  Protein structure



No available structure.



ID   15528 GenBank   WP_027674841
Name   t4cp2_J5285_RS24350_AF3.44|unnamed1 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: 91906.56 Da        Isoelectric Point: 5.4002

>WP_027674841.1 conjugal transfer protein TrbE [Agrobacterium larrymoorei]
MASLKRFRTTGPSFADLVPYAGLIDNGVLLLKDGSLMAGWYFAGPDSESATDLERNELSRQINAILSRLG
TGWMIQVEAIRVPTIDYPTPDQCHFPDPVTRAIDAERRAYFGREQGHFESKHAIILTYRPLESKRTSLSK
YIYSDEESRKKSYADTVLFIFRNAIREIEQYLANTLSIGRMQTREVRDRGGERVARYDDLMQFVRFCITG
ESHPVRLPEVPMYLDWLATAELEHGLTPKVENRFLAVVAIDGLPAESWPGILNNLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQIQSRSVDQDAMTMVAETEDAIAQASSQLVAYGYYTPVVIL
FDEDREALQEKAEAIRRLLQAEGFGARVETLNATDAFLGSLPGNWYANIREPLINTSNLADLVPLNSVWS
GNPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYEFAQIFA
FDKGNSLLPLTLAAGGDHYEIGNDQNGEGRALAFCPLFDLSTDGDRAWATEWIEMLVALQGVTITPDHRN
AISRQIGLMATAPGKSLSDFVSGVQLREIKDALHHYTVDGPMGQLLDAEEDGLTLQAFQCFEIEQLMNMG
ERNLVPVLTYLFHRIEKRLDGSPSLILLDEAWLMLGHPVFRDKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSGAIPKREYYVATPDGRRLFDMSLGP
VALSFVGASGKEDLNRIRALKAEHGQDWLSHWLQSRGVHDATSHLNVE

  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: 94800..107695

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
J5285_RS24275 (J5285_24285) 93105..93635 + 531 WP_027674826 conjugative transfer signal peptidase TraF -
J5285_RS24280 (J5285_24290) 93625..94785 + 1161 WP_027674827 conjugal transfer protein TraB -
J5285_RS24285 (J5285_24295) 94800..95408 + 609 WP_027674828 TraH family protein virB1
J5285_RS24290 (J5285_24300) 95457..95834 - 378 WP_027674829 DUF5615 family PIN-like protein -
J5285_RS24295 (J5285_24305) 95839..96462 - 624 WP_027674830 DUF433 domain-containing protein -
J5285_RS24300 (J5285_24310) 96579..96797 - 219 WP_027674831 helix-turn-helix domain-containing protein -
J5285_RS24305 (J5285_24315) 96962..97255 + 294 WP_136954429 transcriptional repressor TraM -
J5285_RS24310 (J5285_24320) 97262..97963 - 702 WP_235695871 autoinducer binding domain-containing protein -
J5285_RS24315 (J5285_24325) 98183..99481 - 1299 WP_027674834 IncP-type conjugal transfer protein TrbI virB10
J5285_RS24320 (J5285_24330) 99497..99934 - 438 WP_027674835 conjugal transfer protein TrbH -
J5285_RS24325 (J5285_24335) 99938..100750 - 813 WP_027674836 P-type conjugative transfer protein TrbG virB9
J5285_RS24330 (J5285_24340) 100767..101429 - 663 WP_027674837 conjugal transfer protein TrbF virB8
J5285_RS24335 (J5285_24345) 101451..102659 - 1209 WP_027674838 P-type conjugative transfer protein TrbL virB6
J5285_RS24340 (J5285_24350) 102664..102840 - 177 WP_027674839 transfer trbK protein -
J5285_RS24345 (J5285_24355) 102834..103592 - 759 WP_234881921 P-type conjugative transfer protein TrbJ virB5
J5285_RS24350 (J5285_24360) 103609..106065 - 2457 WP_027674841 conjugal transfer protein TrbE virb4
J5285_RS24355 (J5285_24365) 106076..106360 - 285 WP_027674842 conjugal transfer protein TrbD virB3
J5285_RS24360 (J5285_24370) 106357..106734 - 378 WP_027674843 TrbC/VirB2 family protein virB2
J5285_RS24365 (J5285_24375) 106724..107695 - 972 WP_027674844 P-type conjugative transfer ATPase TrbB virB11
J5285_RS24370 (J5285_24380) 107698..108324 - 627 WP_027674845 acyl-homoserine-lactone synthase TraI -
J5285_RS24375 (J5285_24385) 108634..109717 - 1084 Protein_109 DNA polymerase Y family protein -
J5285_RS24380 (J5285_24390) 109638..110323 - 686 Protein_110 ImuA family protein -
J5285_RS24385 (J5285_24395) 110704..111480 + 777 WP_210163857 exonuclease domain-containing protein -
J5285_RS24390 (J5285_24400) 111477..111797 + 321 WP_027674848 hypothetical protein -
J5285_RS24395 (J5285_24405) 111852..112253 + 402 Protein_113 DUF1810 domain-containing protein -

Host bacterium

ID   21425 GenBank   NZ_CP072170
Plasmid name   AF3.44|unnamed1 Incompatibility group   -
Plasmid size   396698 bp Coordinate of oriT [Strand]   89376..89419 [+]
Host baterium   Agrobacterium larrymoorei strain AF3.44

Cargo genes

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