Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104010
Name   oriT_pA in_silico
Organism   Sinorhizobium meliloti WSM1022
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP054392 (947549..947577 [-], 29 nt)
oriT length   29 nt
IRs (inverted repeats)      14..19, 24..29  (CGTCGC..GCGACG)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 29 nt

>oriT_pA
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2973 GenBank   WP_174167964
Name   traA_HR059_RS29635_pA insolico UniProt ID   _
Length   1539 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1539 a.a.        Molecular weight: 170141.90 Da        Isoelectric Point: 9.3645

>WP_174167964.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVISRGAGRSIVSAAAYRHRARMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLRAAIDG
RSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEEGFGPKKVPVLGEDGEPLRVITPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMTSDELVLLKPQQVDAETGKAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWEMAWESGREQLQRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRNVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARRERIERESHRP
QLFKQLVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPLSGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMTLSVPALSKTAMARLVEIEAVREQGGDDAYRTAFAF
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKETFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLTILQQAVRIQSSQEIISERQRRVIDRARGVTR

  Protein domains


Predicted by InterproScan.

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

(1047-1125)

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

(1309-1400)

AAA domain (AAA_30)

(391-578)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   2834 GenBank   WP_028011681
Name   virD4_HR059_RS26780_pA insolico UniProt ID   _
Length   563 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 563 a.a.        Molecular weight: 62923.22 Da        Isoelectric Point: 9.1751

>WP_028011681.1 type IV secretion system ATPase VirD4 [Sinorhizobium meliloti]
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILLVQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILALPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QNSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPAPLMIADERF
SHV

  Protein domains


Predicted by InterproScan.

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

(97-537)

  Protein structure



No available structure.



ID   2835 GenBank   WP_028011664
Name   traG_HR059_RS29650_pA insolico UniProt ID   _
Length   639 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 639 a.a.        Molecular weight: 70413.41 Da        Isoelectric Point: 9.3555

>WP_028011664.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKPHPSLLLILLPVAVTAFAIYVVGWRWPGLAAGMSGKTAYWFLRASPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVAGFYALREFGRLSPSVESGLLSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMSAAGKLFPPDGEIVVGERYRVDKDIVHELPFDPDDPATWGKGGKAP
LLTYSQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVLEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSSGAYFQNQAHNLLTGLLAHVMLSPEYAGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSQSAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFRSTDIVTGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAIP

  Protein domains


Predicted by InterproScan.

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

(165-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 335426..344839

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HR059_RS26685 (HR059_26685) 330507..331964 + 1458 WP_028011837 PLP-dependent aminotransferase family protein -
HR059_RS26690 (HR059_26690) 332291..332562 - 272 Protein_320 hypothetical protein -
HR059_RS26695 (HR059_26695) 332612..333808 - 1197 WP_174167946 IS256-like element ISRm5 family transposase -
HR059_RS26700 (HR059_26700) 333900..334466 - 567 WP_028011686 type IV secretory system conjugative DNA transfer family protein -
HR059_RS26705 (HR059_26705) 334450..334641 + 192 Protein_323 Lrp/AsnC ligand binding domain-containing protein -
HR059_RS26710 (HR059_26710) 334700..335098 + 399 WP_164820336 hypothetical protein -
HR059_RS26715 (HR059_26715) 335426..336133 + 708 WP_028011685 type IV secretion system lytic transglycosylase VirB1 virB1
HR059_RS26720 (HR059_26720) 336147..336509 + 363 WP_014528518 pilin major subunit VirB2 virB2
HR059_RS26725 (HR059_26725) 336506..336832 + 327 WP_003537077 type IV secretion system protein VirB3 virB3
HR059_RS26730 (HR059_26730) 336832..339201 + 2370 WP_028011684 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HR059_RS26735 (HR059_26735) 339215..339898 + 684 WP_003537081 pilin minor subunit VirB5 traI
HR059_RS26740 (HR059_26740) 339979..340866 + 888 WP_003537089 type IV secretion system protein virB6
HR059_RS26745 (HR059_26745) 340899..341066 + 168 WP_003537091 type IV secretion system lipoprotein VirB7 -
HR059_RS26750 (HR059_26750) 341053..341766 + 714 WP_003537093 type IV secretion system protein VirB8 virB8
HR059_RS26755 (HR059_26755) 341763..342644 + 882 WP_028011683 P-type conjugative transfer protein VirB9 virB9
HR059_RS26760 (HR059_26760) 342641..343759 + 1119 WP_028011682 type IV secretion system protein VirB10 virB10
HR059_RS26765 (HR059_26765) 343799..344839 + 1041 WP_017263499 P-type DNA transfer ATPase VirB11 virB11
HR059_RS26770 (HR059_26770) 346077..346802 + 726 WP_017263500 response regulator -
HR059_RS26775 (HR059_26775) 347001..347177 + 177 WP_153323329 hypothetical protein -
HR059_RS26780 (HR059_26780) 347219..348910 - 1692 WP_028011681 type IV secretion system ATPase VirD4 -

Region 2: 822940..832519

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HR059_RS28995 (HR059_28995) 819827..820675 + 849 WP_017264156 alpha/beta fold hydrolase -
HR059_RS29000 (HR059_29000) 820725..821372 + 648 WP_017264157 dihydrofolate reductase family protein -
HR059_RS29005 (HR059_29005) 821491..821694 + 204 WP_033052013 hypothetical protein -
HR059_RS29010 (HR059_29010) 821953..822321 - 369 WP_017264159 transcriptional regulator -
HR059_RS32185 822418..822936 + 519 WP_017264160 hypothetical protein -
HR059_RS29015 (HR059_29015) 822940..823611 + 672 WP_017264161 lytic transglycosylase domain-containing protein virB1
HR059_RS29020 (HR059_29020) 823608..823907 + 300 WP_003526741 TrbC/VirB2 family protein virB2
HR059_RS29025 (HR059_29025) 823912..824253 + 342 WP_017264162 type IV secretion system protein VirB3 virB3
HR059_RS29030 (HR059_29030) 824228..826624 + 2397 WP_174167962 VirB4 family type IV secretion system protein virb4
HR059_RS29035 (HR059_29035) 826624..827325 + 702 WP_010967692 P-type DNA transfer protein VirB5 virB5
HR059_RS29040 (HR059_29040) 827322..827555 + 234 WP_013845460 EexN family lipoprotein -
HR059_RS29045 (HR059_29045) 827561..828496 + 936 WP_013845459 type IV secretion system protein virB6
HR059_RS29050 (HR059_29050) 828493..828807 + 315 WP_028010966 hypothetical protein -
HR059_RS29055 (HR059_29055) 828812..829483 + 672 WP_010967689 virB8 family protein virB8
HR059_RS29060 (HR059_29060) 829483..830337 + 855 WP_014528658 P-type conjugative transfer protein VirB9 virB9
HR059_RS29065 (HR059_29065) 830347..831519 + 1173 WP_010967687 type IV secretion system protein VirB10 virB10
HR059_RS29070 (HR059_29070) 831530..832519 + 990 WP_010967686 P-type DNA transfer ATPase VirB11 virB11
HR059_RS29075 (HR059_29075) 832831..834057 - 1227 WP_010967685 MFS transporter -
HR059_RS29080 (HR059_29080) 834092..834703 - 612 WP_010967684 TetR/AcrR family transcriptional regulator -
HR059_RS29085 (HR059_29085) 834955..835632 + 678 WP_010967683 YoaK family protein -
HR059_RS29090 (HR059_29090) 835879..836901 + 1023 WP_028010967 alcohol dehydrogenase AdhP -

Host bacterium

ID   4450 GenBank   NZ_CP054392
Plasmid name   pA Incompatibility group   -
Plasmid size   1383549 bp Coordinate of oriT [Strand]   947549..947577 [-]
Host baterium   Sinorhizobium meliloti WSM1022

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   fixN, fixO, fixG, fixS, nodM, nifN, nodD, nodA, nodB, nodC, nodI, nodJ, nodE, nodF, nodH, nifX, nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifB, fixU
Anti-CRISPR   -