Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107605
Name   oriT_pSF83666a in_silico
Organism   Sinorhizobium fredii CCBAU 83666
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP023072 (716448..716504 [-], 57 nt)
oriT length   57 nt
IRs (inverted repeats)      25..30, 35..40  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_pSF83666a
CCCCGCCAGGGCCGAAAGCCAAGTCGTCGCGCCAGCGACGTATAATTGCGCCCTTGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5113 GenBank   WP_037426333
Name   traA_SF83666_RS34095_pSF83666a insolico UniProt ID   A0A249P5Y1
Length   1102 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1102 a.a.        Molecular weight: 122803.91 Da        Isoelectric Point: 9.9325

>WP_037426333.1 MULTISPECIES: Ti-type conjugative transfer relaxase TraA [Sinorhizobium]
MAVPHFSVSVVARGSGRSAVLSAAYRHCAKMDYEREARTIDYRAKQGLLHEEFVIPADSPEWLRSMIADR
SVASASEAFWNKVEDFEKRADAQLAKDVTIALPIELTVEQNIALVRDFVERHVTAKGMVADWVYHDAPGN
PHVHLMTTLRPLTADGFGAKKIGVLGPDGSPLRNDAGKIVYDLWAGSLHDFSAFRDGWFACQNRHLALAG
LDIRIDGRSFEKQGIELTPTIHLGVGTKAIERKATADDQAVSLERLEMQEEKRAENARRIQRRPEIVLDL
ITREKSVFDECDVAKILHRYIDDPGVFQSLMARILQSSETLRLERERIAFATGIRVPTKYTTRELIRLEA
EMGSRAIWLSRRSSHGVRKEVLEATFTRHSRLSAEQKAAIEHVAGAERIAAVIGRAGAGKTTMMKAAREA
WEAAGYRVVGGALAGKAAEGLEKEAGITSRTLSSWELRWNEGQNQLDDKTIFVLDEAGMVSSRQMALFVE
TATKAGAKLVLVGDPEQLQPIKAGAAFRAIADRIGYAELETIYRQREQWMRDASLDLARGNVGKVVDTYR
ANGRMMRSKLKAEAVQNLIADWDRDYDPTKTTLILAHLRRDVRMLNEMARAKLVERGIVDAGFSFKTEDG
NRRFAPGDQIVFLKNDGALGVKNGMLGKVVEAARNRIVAEIGEGEHRRQVTVEQRFYNNLDHGYATTIHK
SQGATVDRVKVLASLSLDRHLTYVAMTRHREDLGVYYGARSFAKSGGLVQILSRKNSKETTLDYEKATFY
RQALRFAEARGMHLVNVARTIARDRLEWTVRQKQKLADLTQRLVAIGARFGLAVGAKTTNSQNLKETRPM
VAGIATFPKSMEQAVADRLEVDPGLKKQWEDVSTRFHLVYTQPEVAFKAVNVDAMLKDESAAKSTLSNMA
NQPESYGSLKGKAGLLASRADKQDRERAEHNVPALAQSLSDYMRQRSQAEQRYQADELAVRRKVAIDIPA
LSPGARQTLERVRDAIDRNDLPAALEFALADKMVKAELEGFARAVTERFGERAFLPLAAKDTNGETFKTI
TAGMNPGPKAEVQSAWNTMRTVQQLNAHERTIEALKQAETLRQTKSQGLSLK

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-243)

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

(858-954)

AAA domain (AAA_30)

(382-565)

Viral (Superfamily 1) RNA helicase (Viral_helicase1)

(690-735)


  Protein structure


Source ID Structure
AlphaFold DB A0A249P5Y1


T4CP

ID   5338 GenBank   WP_100209488
Name   traG_SF83666_RS34080_pSF83666a insolico UniProt ID   _
Length   660 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 660 a.a.        Molecular weight: 71201.52 Da        Isoelectric Point: 9.2881

>WP_100209488.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium fredii]
MRVNRITLAVAPVVLMVLAVIGMNSVEQWLSTFGETDAARLTLGRIGVALPYVTAAAIGVIVLFASAGSA
NIKFAGWSALAGAAATILIAGIREAARLAAFARQVPADKSIASYLDPATMLGAAGALMAACFALRVALIG
NAAFAHAEPKRIRGKRALHGEADWMKMQEAAKLFADTGGIVIGERYRVDKDSTAALSFRAGDPETWGAGG
KSPLLCFDGSFGSSHGIVFAGSGGFKTTSVTIPTALKWGGALVVLDPSNEVAPMVYEHRKAAARFIRILD
PKEPETGFNALDWIGRFGGSKEEDIASVASWIMSDSGGMRGVRDDFFRASALQLLTALIADVCLSGHTDK
ENQTLRQVRANLAEPEPKLRERLQSIYDNSNSDFVKENVAAYVNMTPETFSGVYANAVKETHWLSYPNYA
ALVSGSTFSTDALAAGETDVFINIDLKTLETHAGLARVIIGSFLNAIYNRDGEVKGRALFFLDEVARLGY
MRILETARDAGRKYGIMLTMIYQSIGQMRETYGGRDAASKWFESASWISFAAINDPETADYISRRCGMTT
VEIDQVSRSFQAKGSSRTRSKQLAARPLIQPHEVLRMRADEQIVFTAGNAPLRCGRAIWFRREDMKACGG
AKRFPKVGKMSEARVIQPARSATSKADPGE

  Protein domains


Predicted by InterproScan.

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

(163-632)

  Protein structure



No available structure.



ID   5339 GenBank   WP_037435689
Name   t4cp2_SF83666_RS34230_pSF83666a 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: 92074.97 Da        Isoelectric Point: 6.0494

>WP_037435689.1 conjugal transfer protein TrbE [Sinorhizobium fredii]
MVALKRFRATGPSFADLVPYAGLVDNGVLLLKDGSLMAGWYFAGPDSDSATDFERNELSRQINAILSRLG
TGWMIQVEAARIPTYDYPSEVRCHFPDAVTRAIDAERRAHFARERGHFESKHALILTYRPSEAKKTALSK
YIYSDEESRRKTYADTVLFIFKNAIREIEQYFANTLSIRRMETREAAERGGERVARYDELLQFIRFCITG
ENHPIRLPAAPMYLDWIATAELEHGLTPKVENRFLGVVAIDGLPAESWPGILNSLDLMPLTYRWSSRFIF
LDAEEARQKLERTRKKWQQKVRPFFDQLFQTQSRSVDRDAMTMVAETEDAIAQASSQLVAYGYYTPVIIL
FDSDREALQEKAEAIRRLIQAEGFGARIETLNATEAYLGSLPGNWYCNIREPLINTSNLADLIPLNSVWS
GSPVAPCPFYPPNSPPLMQVASGSTPFRLNLHVDDVGHTLIFGPTGSGKSTLLALIAAQFRRYDRSQIFA
FDKGSALLPLTLAAGGDHYEIGGDNAEGRKALAFCPLSDLESDADRAWAAEWIEMLVALQGVTITPDHRN
AMSRQVTLMASAPGRSLSDFVSGVQMREIKDALHHYTVDGPMGQLLDAEQDGLTLGAFQTFEIEQLMNMG
ERNLVPVLTYLFRRIEKRLDGSPSLILLDEAWLMLGHPVFRSKIREWLKVLRKANCAVVLATQSISDAER
SGIIDVLKESCPTKICLPNGAAREPGTREFYERIGFNERQIEIVSNATPKREYYVVTPEGRRLFDMVLGP
VALSFVGASGKEDLKRIRTLHSEYDRDWPVYWLQMRGVHDAASLFNVE

  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: 713820..741507

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SF83666_RS34055 710669..710977 + 309 WP_037426368 DUF736 domain-containing protein -
SF83666_RS34060 (SF83666_a46870) 711117..711383 + 267 WP_010875404 type II toxin-antitoxin system prevent-host-death family antitoxin -
SF83666_RS35740 (SF83666_a46880) 711380..711796 + 417 WP_037426343 hypothetical protein -
SF83666_RS36740 (SF83666_a46900) 712838..713089 - 252 Protein_690 WGR domain-containing protein -
SF83666_RS36745 713286..713663 - 378 Protein_691 thermonuclease family protein -
SF83666_RS34080 (SF83666_a46910) 713820..715802 - 1983 WP_100209488 Ti-type conjugative transfer system protein TraG virb4
SF83666_RS34085 (SF83666_a46920) 715789..716004 - 216 WP_037426337 type IV conjugative transfer system coupling protein TraD -
SF83666_RS34090 (SF83666_a46930) 716009..716305 - 297 WP_037426336 conjugal transfer protein TraC -
SF83666_RS34095 (SF83666_a46940) 716558..719866 + 3309 WP_037426333 Ti-type conjugative transfer relaxase TraA -
SF83666_RS34100 (SF83666_a46950) 719863..720429 + 567 WP_037434798 conjugative transfer signal peptidase TraF -
SF83666_RS34105 (SF83666_a46960) 720419..721582 + 1164 WP_037434797 conjugal transfer protein TraB -
SF83666_RS34110 (SF83666_a46970) 721599..722198 + 600 WP_037434795 TraH family protein virB1
SF83666_RS36750 (SF83666_a46980) 722694..723095 + 402 WP_240533494 hypothetical protein -
SF83666_RS36755 (SF83666_a46990) 723092..723295 + 204 WP_234818732 reverse transcriptase domain-containing protein -
SF83666_RS36760 (SF83666_a47000) 723295..723759 + 465 WP_240533493 group II intron maturase-specific domain-containing protein -
SF83666_RS34120 723988..724332 + 345 Protein_702 transposase -
SF83666_RS36765 (SF83666_a47030) 724490..724636 + 147 WP_158499789 hypothetical protein -
SF83666_RS34135 (SF83666_a47060) 725392..726621 - 1230 WP_014857525 HipA domain-containing protein -
SF83666_RS34140 (SF83666_a47070) 726614..727204 - 591 WP_037426312 helix-turn-helix transcriptional regulator -
SF83666_RS34145 (SF83666_a47080) 727357..727782 - 426 WP_240533492 hypothetical protein -
SF83666_RS34150 (SF83666_a47090) 727972..728265 + 294 Protein_707 helix-turn-helix domain-containing protein -
SF83666_RS34155 (SF83666_a47100) 728288..728501 - 214 Protein_708 DUF5372 family protein -
SF83666_RS34160 728597..728854 + 258 Protein_709 IS21 family transposase -
SF83666_RS34165 728895..729125 + 231 Protein_710 AAA family ATPase -
SF83666_RS34170 729261..729494 - 234 WP_010875417 helix-turn-helix transcriptional regulator -
SF83666_RS34175 (SF83666_a47130) 729713..730036 + 324 WP_014858045 transcriptional repressor TraM -
SF83666_RS34180 730040..730699 - 660 WP_095689848 autoinducer binding domain-containing protein -
SF83666_RS34185 (SF83666_a47150) 730692..731525 - 834 WP_014327878 IS5 family transposase -
SF83666_RS34195 (SF83666_a47160) 731987..733282 - 1296 WP_037426308 IncP-type conjugal transfer protein TrbI virB10
SF83666_RS34200 (SF83666_a47170) 733294..733740 - 447 WP_014858040 conjugal transfer protein TrbH -
SF83666_RS34205 (SF83666_a47180) 733744..734556 - 813 WP_014858039 P-type conjugative transfer protein TrbG virB9
SF83666_RS34210 (SF83666_a47190) 734574..735236 - 663 WP_014858038 conjugal transfer protein TrbF virB8
SF83666_RS34215 (SF83666_a47200) 735260..736435 - 1176 WP_037426305 P-type conjugative transfer protein TrbL virB6
SF83666_RS34220 (SF83666_a47210) 736429..736626 - 198 WP_037426303 entry exclusion protein TrbK -
SF83666_RS34225 (SF83666_a47220) 736623..737426 - 804 WP_037426300 P-type conjugative transfer protein TrbJ virB5
SF83666_RS34230 (SF83666_a47230) 737398..739854 - 2457 WP_037435689 conjugal transfer protein TrbE virb4
SF83666_RS34235 (SF83666_a47240) 739865..740164 - 300 WP_037435687 conjugal transfer protein TrbD virB3
SF83666_RS34240 (SF83666_a47250) 740157..740540 - 384 WP_034859524 TrbC/VirB2 family protein virB2
SF83666_RS34245 (SF83666_a47260) 740530..741507 - 978 WP_015633597 P-type conjugative transfer ATPase TrbB virB11
SF83666_RS34250 (SF83666_a47290) 741518..742144 - 627 WP_037427079 acyl-homoserine-lactone synthase -

Host bacterium

ID   8040 GenBank   NZ_CP023072
Plasmid name   pSF83666a Incompatibility group   -
Plasmid size   742947 bp Coordinate of oriT [Strand]   716448..716504 [-]
Host baterium   Sinorhizobium fredii CCBAU 83666

Cargo genes

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