Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103837
Name   oriT_KH35c|psymA in_silico
Organism   Sinorhizobium meliloti strain KH35c
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021827 (704238..704266 [+], 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_KH35c|psymA
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2847 GenBank   WP_088218274
Name   traA_CDO23_RS22545_KH35c|psymA 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: 169846.39 Da        Isoelectric Point: 9.3523

>WP_088218274.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
RSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEEGFGPKKVPVVGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDELVLLKPQQVDAETGKAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARAAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWEMAWESGREQLQRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRQVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRRPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRSDDGTVQRLWGVSLPKA
LKDAGAAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARQERIERESHRP
QLFAALVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVAYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AILHPVLAKIYRDPDGALSALNALASDAANEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMTLSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFTY
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAAVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAGERIAAAVSNDPAAYGALRGSERIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLQILQQAVRIQSSQEIISERQRRVIDRARGVTR

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-578)

MobA/MobL family (MobA_MobL)

(17-249)

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

(1309-1400)


  Protein structure



No available structure.




T4CP

ID   2677 GenBank   WP_088218122
Name   traG_CDO23_RS22530_KH35c|psymA 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: 70295.28 Da        Isoelectric Point: 9.4585

>WP_088218122.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKPHPSLLVILFPVAVTTAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVAGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERYRVDKDIVHELPFDPNDPATWGQGGKAP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSTGSYFQNQAHNLLTGLLAHVMLSPDYVGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSAPRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAIP

  Protein domains


Predicted by InterproScan.

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

(169-635)

  Protein structure



No available structure.



ID   2678 GenBank   WP_028011681
Name   virD4_CDO23_RS25170_KH35c|psymA 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 812759..822339

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CDO23_RS23095 (CDO23_23115) 808376..809398 - 1023 Protein_776 zinc-dependent alcohol dehydrogenase -
CDO23_RS23100 (CDO23_23120) 809646..810323 - 678 WP_010967683 YoaK family protein -
CDO23_RS23105 (CDO23_23125) 810575..811186 + 612 WP_010967684 TetR/AcrR family transcriptional regulator -
CDO23_RS23110 (CDO23_23130) 811221..812447 + 1227 WP_010967685 MFS transporter -
CDO23_RS23115 (CDO23_23135) 812759..813748 - 990 WP_010967686 P-type DNA transfer ATPase VirB11 virB11
CDO23_RS23120 (CDO23_23140) 813759..814931 - 1173 WP_010967687 type IV secretion system protein VirB10 virB10
CDO23_RS23125 (CDO23_23145) 814941..815795 - 855 WP_014528658 P-type conjugative transfer protein VirB9 virB9
CDO23_RS23130 (CDO23_23150) 815795..816466 - 672 WP_010967689 virB8 family protein virB8
CDO23_RS23135 (CDO23_23155) 816471..816785 - 315 WP_010967690 hypothetical protein -
CDO23_RS23140 (CDO23_23160) 816782..817717 - 936 WP_013845459 type IV secretion system protein virB6
CDO23_RS23145 (CDO23_23165) 817723..817956 - 234 WP_013845460 EexN family lipoprotein -
CDO23_RS23150 (CDO23_23170) 817953..818655 - 703 Protein_787 P-type DNA transfer protein VirB5 -
CDO23_RS23155 (CDO23_23175) 818655..821051 - 2397 WP_014528660 VirB4 family type IV secretion system protein virb4
CDO23_RS23160 (CDO23_23180) 821026..821367 - 342 WP_014528661 type IV secretion system protein VirB3 virB3
CDO23_RS23165 (CDO23_23185) 821372..821671 - 300 WP_088196212 TrbC/VirB2 family protein virB2
CDO23_RS23170 (CDO23_23190) 821668..822339 - 672 WP_010967696 lytic transglycosylase domain-containing protein virB1
CDO23_RS23175 (CDO23_23195) 822343..822861 - 519 WP_010967697 hypothetical protein -
CDO23_RS23180 (CDO23_23200) 822958..823326 + 369 WP_010967698 transcriptional regulator -
CDO23_RS23185 (CDO23_23205) 823587..823838 - 252 WP_010967699 hypothetical protein -
CDO23_RS23190 (CDO23_23210) 823912..824559 - 648 WP_010967700 dihydrofolate reductase family protein -
CDO23_RS23195 (CDO23_23215) 824609..825457 - 849 WP_088218151 alpha/beta fold hydrolase -

Region 2: 1218159..1227572

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CDO23_RS25170 (CDO23_25195) 1214088..1215779 + 1692 WP_028011681 type IV secretion system ATPase VirD4 -
CDO23_RS34025 1215821..1215997 - 177 WP_153323329 hypothetical protein -
CDO23_RS25175 (CDO23_25200) 1216196..1216921 - 726 WP_017263500 response regulator -
CDO23_RS25190 (CDO23_25215) 1218159..1219199 - 1041 WP_017263499 P-type DNA transfer ATPase VirB11 virB11
CDO23_RS25195 (CDO23_25220) 1219239..1220357 - 1119 WP_026030558 type IV secretion system protein VirB10 virB10
CDO23_RS25200 (CDO23_25225) 1220354..1221235 - 882 WP_028011683 P-type conjugative transfer protein VirB9 virB9
CDO23_RS25205 (CDO23_25230) 1221232..1221945 - 714 WP_003537093 type IV secretion system protein VirB8 virB8
CDO23_RS25210 (CDO23_25235) 1221932..1222099 - 168 WP_003537091 type IV secretion system lipoprotein VirB7 -
CDO23_RS25215 (CDO23_25240) 1222132..1223019 - 888 WP_003537089 type IV secretion system protein virB6
CDO23_RS25220 (CDO23_25245) 1223100..1223783 - 684 WP_003537081 pilin minor subunit VirB5 traI
CDO23_RS25225 (CDO23_25250) 1223797..1226166 - 2370 WP_028011684 VirB4 family type IV secretion/conjugal transfer ATPase virb4
CDO23_RS25230 (CDO23_25255) 1226166..1226492 - 327 WP_003537077 type IV secretion system protein VirB3 virB3
CDO23_RS25235 (CDO23_25260) 1226489..1226851 - 363 WP_014528518 pilin major subunit VirB2 virB2
CDO23_RS25240 (CDO23_25265) 1226865..1227572 - 708 WP_028011685 type IV secretion system lytic transglycosylase VirB1 virB1
CDO23_RS25245 (CDO23_25270) 1227900..1228298 - 399 WP_164820336 hypothetical protein -
CDO23_RS25250 (CDO23_25275) 1228357..1228548 - 192 Protein_1181 Lrp/AsnC ligand binding domain-containing protein -
CDO23_RS25255 (CDO23_25280) 1228571..1229098 + 528 WP_157718085 type IV secretory system conjugative DNA transfer family protein -
CDO23_RS25260 (CDO23_25285) 1229190..1230386 + 1197 WP_015241349 IS256-like element ISRm5 family transposase -
CDO23_RS25265 (CDO23_25290) 1230436..1230707 + 272 Protein_1184 hypothetical protein -
CDO23_RS25270 (CDO23_25295) 1231034..1232491 - 1458 WP_088218245 PLP-dependent aminotransferase family protein -

Host bacterium

ID   4277 GenBank   NZ_CP021827
Plasmid name   KH35c|psymA Incompatibility group   -
Plasmid size   1279723 bp Coordinate of oriT [Strand]   704238..704266 [+]
Host baterium   Sinorhizobium meliloti strain KH35c

Cargo genes

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