Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103918
Name   oriT_pAlCFBP5473 in_silico
Organism   Agrobacterium larrymoorei strain CFBP5473
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039693 (199692..199735 [+], 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_pAlCFBP5473
GGATCCGAAGGGCGCAATTATACGTCGCTGATGCGACGCTTTGC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2910 GenBank   WP_027674825
Name   traA_CFBP5473_RS22030_pAlCFBP5473 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   2754 GenBank   WP_027674822
Name   traG_CFBP5473_RS22015_pAlCFBP5473 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   2755 GenBank   WP_027674841
Name   t4cp2_CFBP5473_RS22110_pAlCFBP5473 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: 205116..218011

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CFBP5473_RS22035 (CFBP5473_22035) 203421..203951 + 531 WP_027674826 conjugative transfer signal peptidase TraF -
CFBP5473_RS22040 (CFBP5473_22040) 203941..205101 + 1161 WP_027674827 conjugal transfer protein TraB -
CFBP5473_RS22045 (CFBP5473_22045) 205116..205724 + 609 WP_027674828 TraH family protein virB1
CFBP5473_RS22050 (CFBP5473_22050) 205773..206150 - 378 WP_027674829 DUF5615 family PIN-like protein -
CFBP5473_RS22055 (CFBP5473_22055) 206155..206778 - 624 WP_027674830 DUF433 domain-containing protein -
CFBP5473_RS22060 (CFBP5473_22060) 206895..207113 - 219 WP_027674831 helix-turn-helix transcriptional regulator -
CFBP5473_RS22065 (CFBP5473_22065) 207278..207571 + 294 WP_136954429 transcriptional repressor TraM -
CFBP5473_RS22070 (CFBP5473_22070) 207578..208285 - 708 WP_037170882 autoinducer binding domain-containing protein -
CFBP5473_RS22075 (CFBP5473_22075) 208499..209797 - 1299 WP_027674834 IncP-type conjugal transfer protein TrbI virB10
CFBP5473_RS22080 (CFBP5473_22080) 209813..210250 - 438 WP_027674835 conjugal transfer protein TrbH -
CFBP5473_RS22085 (CFBP5473_22085) 210254..211066 - 813 WP_027674836 P-type conjugative transfer protein TrbG virB9
CFBP5473_RS22090 (CFBP5473_22090) 211083..211745 - 663 WP_027674837 conjugal transfer protein TrbF virB8
CFBP5473_RS22095 (CFBP5473_22095) 211767..212975 - 1209 WP_027674838 P-type conjugative transfer protein TrbL virB6
CFBP5473_RS22100 (CFBP5473_22100) 212980..213156 - 177 WP_027674839 transfer trbK protein -
CFBP5473_RS22105 (CFBP5473_22105) 213150..213908 - 759 WP_234881921 P-type conjugative transfer protein TrbJ virB5
CFBP5473_RS22110 (CFBP5473_22110) 213925..216381 - 2457 WP_027674841 conjugal transfer protein TrbE virb4
CFBP5473_RS22115 (CFBP5473_22115) 216392..216676 - 285 WP_027674842 conjugal transfer protein TrbD virB3
CFBP5473_RS22120 (CFBP5473_22120) 216673..217050 - 378 WP_027674843 TrbC/VirB2 family protein virB2
CFBP5473_RS22125 (CFBP5473_22125) 217040..218011 - 972 WP_027674844 P-type conjugative transfer ATPase TrbB virB11
CFBP5473_RS22130 (CFBP5473_22130) 218014..218640 - 627 WP_027674845 acyl-homoserine-lactone synthase TraI -
CFBP5473_RS22135 (CFBP5473_22135) 218950..220033 - 1084 Protein_212 DNA polymerase Y family protein -
CFBP5473_RS22140 (CFBP5473_22140) 219954..220639 - 686 Protein_213 ImuA family protein -
CFBP5473_RS22145 (CFBP5473_22145) 221020..221796 + 777 WP_210163857 exonuclease domain-containing protein -
CFBP5473_RS22150 (CFBP5473_22150) 221793..222113 + 321 WP_027674848 hypothetical protein -
CFBP5473_RS22155 (CFBP5473_22155) 222168..222569 + 402 Protein_216 DUF1810 domain-containing protein -

Host bacterium

ID   4358 GenBank   NZ_CP039693
Plasmid name   pAlCFBP5473 Incompatibility group   -
Plasmid size   396698 bp Coordinate of oriT [Strand]   199692..199735 [+]
Host baterium   Agrobacterium larrymoorei strain CFBP5473

Cargo genes

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