Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107797
Name   oriT_pNGR234a in_silico
Organism   Sinorhizobium fredii NGR234
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_000914 (512921..512977 [-], 57 nt)
oriT length   57 nt
IRs (inverted repeats)     _
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_pNGR234a
CCCCGCCAGGGCCGCAAAACAGGATGTCGCGACAGCGACGTATAATTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5235 GenBank   WP_010875410
Name   traA_NGR_RS32090_pNGR234a insolico UniProt ID   P55418
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 123034.13 Da        Isoelectric Point: 9.8696

>WP_010875410.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium fredii]
MAVPHFSVSVVARGSGRSAVLSAAYRHCARMDYEREARTIDYRAKQGLLHEEFVIPAESPEWLRSMIADR
SVASASEAFWNKVEDFEKRSDAQLAKDVTIALPIELTTEQNIVLVRDFVERHVTAKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKLAVVGPDGNSLRNDAGKIVYELWAGSLDDFNAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKATTDDQAVSLERLELQEEKRAENARRIQRRPEIVLDL
ITREKSVFDERDVAKILHRYIDDPGVFHSLMARILQSPKTLRLERERIAFATGIRAPAKYTTRELIRLEA
EMGSRAIWLSRRSSHGVRKEVLEAAFSRHSRLSDEQKTAIEHVAGAERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGIASRTLSSWELRWNEGRKQLDDKTIFVLDEAGMVSSRQMALFVE
TATKAGAKLVLVGDPEQLQPIEAGAAFRAIADRIGYAELETIYRQREQWMCDASLDLARGNVGKVVDTYR
ANGRMMRSELKAEAVQNLIADWDRDYDPTKTTLILAHLRRDVRMLNQMARAKLVERGIVDAGFSFKAEDG
NRRFAPGDQIVFLKNEGALGVKNGMRGKVVEAAQNRIVAEIGEVEHRRQVMVESRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGVYYGARSFAKSGGLIQILSQKNSKETTLDYEKATFY
RQALRFAEARGMHLVNVARTIARDRLEWTVRQKQKLADLTQRLVAIGARFGLAVGAKTTNSQNLKETRPM
VAGIATFPKSMEQAVADRLEVDPGLKKQWEDVSTRFHLVYTQPEVAFKAVNVDAMLKDETVAKSALSNMA
NQPESYGSLKGKTGLLASRADKQDRERAERNVPALAQSLSDYMRQRSRAEQCYQADELAVRRKVAIEIPA
LSPGARQTLERVRDAIDRNDLPAALEFALADRQVKAELEGFARAVTERFGERAFLPLAAKDTNGETFKTI
TAGMNPGPKAEVQSAWNTMRTVQQLNAHERTIEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(382-565)

MobA/MobL family (MobA_MobL)

(17-243)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(692-735)

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

(858-954)


  Protein structure


Source ID Structure
AlphaFold DB P55418


T4CP

ID   5480 GenBank   WP_010875407
Name   traG_NGR_RS32075_pNGR234a insolico UniProt ID   _
Length   640 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 640 a.a.        Molecular weight: 69180.09 Da        Isoelectric Point: 8.7095

>WP_010875407.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium fredii]
MTVNRIALVVAPVVLMVLTVIGMSGIEQCLSTFGKTDAARLALGRIGIAFPYVTAAAIAVIFLFASAGSA
IIKLAGWGALAGSAATMLIATMREASRLAAFAAQVPAGKSIASYLDHATLIGATAALMSGCFSLRVALIG
NAAFARAEPRRIRGKRALHGEADWMNMQDAARLFSDAGGVVIGERYRVDKDSTAARSFRADDPETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVYEHRKAAARFIRILD
PKEPETGFNALDWIGRFGGTKEEDIASVASWIMSDSGGMRGVRDDFFRASALQLLTALIADVCLSGHTDK
ENQTLRQVRANLAEPEPKLRERLQSIYDNSNSDFVKENVAAYVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSTFSTDALAAGETDVFINIDLKTLETHAGLARVIIGSFLNAIYNRDGEVKGRALFFLDEVARLGY
MRILETARDAGRKYGIMLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQTKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACGG
EPVSQGRKDV

  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: 510341..534825

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NGR_RS32055 (NGR234_80) 507813..508121 + 309 WP_037426368 DUF736 domain-containing protein -
NGR_RS32060 (NGR234_79) 508261..508527 + 267 WP_010875404 type II toxin-antitoxin system prevent-host-death family antitoxin -
NGR_RS32065 508524..508940 + 417 WP_164924763 hypothetical protein -
NGR_RS33530 509292..509543 - 252 Protein_487 WGR domain-containing protein -
NGR_RS33535 509740..510119 - 380 Protein_488 thermonuclease family protein -
NGR_RS32075 (NGR234_75) 510341..512263 - 1923 WP_010875407 Ti-type conjugative transfer system protein TraG virb4
NGR_RS32080 (NGR234_74) 512250..512465 - 216 WP_010875408 type IV conjugative transfer system coupling protein TraD -
NGR_RS32085 (NGR234_73) 512470..512778 - 309 WP_010875409 conjugal transfer protein TraC -
NGR_RS32090 (NGR234_72) 513031..516339 + 3309 WP_010875410 Ti-type conjugative transfer relaxase TraA -
NGR_RS32095 (NGR234_71) 516408..516902 + 495 WP_240545256 conjugative transfer signal peptidase TraF -
NGR_RS32100 (NGR234_70) 516892..518055 + 1164 WP_010875412 conjugal transfer protein TraB -
NGR_RS32105 (NGR234_69) 518072..518674 + 603 WP_010875413 TraH family protein virB1
NGR_RS32110 (NGR_a04020) 519146..519547 + 402 WP_240545257 reverse transcriptase -
NGR_RS32115 519671..519964 + 294 WP_164924764 hypothetical protein -
NGR_RS32120 (NGR234_66) 520682..521911 - 1230 WP_010875415 HipA domain-containing protein -
NGR_RS32125 (NGR234_65) 521904..522494 - 591 WP_010875416 helix-turn-helix transcriptional regulator -
NGR_RS33630 522683..522871 - 189 WP_282096858 DUF5372 family protein -
NGR_RS32135 522850..523107 + 258 Protein_501 IS21 family transposase -
NGR_RS32140 (NGR_a04060) 523148..523378 + 231 Protein_502 AAA family ATPase -
NGR_RS32145 (NGR234_62) 523513..523746 - 234 WP_010875417 helix-turn-helix transcriptional regulator -
NGR_RS32150 (NGR234_61) 523964..524287 + 324 WP_010875418 transcriptional repressor TraM -
NGR_RS32155 (NGR234_60) 524291..525001 - 711 WP_010875419 autoinducer binding domain-containing protein -
NGR_RS32160 (NGR234_59) 525304..526599 - 1296 WP_010875420 IncP-type conjugal transfer protein TrbI virB10
NGR_RS32165 (NGR234_58) 526611..527057 - 447 WP_010875421 conjugal transfer protein TrbH -
NGR_RS32170 (NGR234_57) 527061..527873 - 813 WP_010875422 P-type conjugative transfer protein TrbG virB9
NGR_RS32175 (NGR234_56) 527891..528553 - 663 WP_010875423 conjugal transfer protein TrbF virB8
NGR_RS32180 (NGR234_55) 528577..529752 - 1176 WP_010875424 P-type conjugative transfer protein TrbL virB6
NGR_RS32185 (NGR234_54) 529746..529943 - 198 WP_010875425 entry exclusion protein TrbK -
NGR_RS32190 (NGR234_53) 529940..530743 - 804 WP_010875426 P-type conjugative transfer protein TrbJ virB5
NGR_RS32195 (NGR234_52) 530715..533172 - 2458 Protein_513 conjugal transfer protein TrbE -
NGR_RS32200 (NGR234_50) 533183..533482 - 300 WP_010875429 conjugal transfer protein TrbD virB3
NGR_RS32205 (NGR234_49) 533475..533858 - 384 WP_010875430 TrbC/VirB2 family protein virB2
NGR_RS32210 (NGR234_48) 533848..534825 - 978 WP_010875431 P-type conjugative transfer ATPase TrbB virB11
NGR_RS32215 (NGR234_47) 534836..535462 - 627 WP_010875432 acyl-homoserine-lactone synthase -

Host bacterium

ID   8232 GenBank   NC_000914
Plasmid name   pNGR234a Incompatibility group   -
Plasmid size   536165 bp Coordinate of oriT [Strand]   512921..512977 [-]
Host baterium   Sinorhizobium fredii NGR234

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   nodD, nodZ, nolV, nolU, nolT, nopB, nolW, nolX, mLTONO_5203, nifX, nifK, nifD, nifH, nifS, nifE, fixA, fixB, fixC, fixX, nifB, nifZ, nifT, nodS, nodU, nodA, nodB, nodC, nodI, nodJ, eB233_29665
Anti-CRISPR   -