Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   102917
Name   oriT_pSymA in_silico
Organism   Sinorhizobium meliloti strain CCMM B554 (FSM-MA)
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP019585 (637766..637794 [+], 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_pSymA
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2189 GenBank   WP_088896044
Name   traA_SMB554_RS21280_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: 169887.45 Da        Isoelectric Point: 9.5460

>WP_088896044.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLRAAIDG
RSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEEGFGPKKVPVLGEGGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDDLVLLKPQQIDAETGKAKQPAVFTTREMLRLE
YAMAQSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGREQLQRGDVLVIDEAGMVS
SQQMARILKAVEDTGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQQGRIVETETRAEIVDRIVADWANARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRQVMIGEGALAGAREFQTARGPREFAAGDRIIFLENARFIEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISQDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARQERIERESHRP
QLFKQLVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLADDLGKAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVREQGGDDAYRTAFTY
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
SADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAAGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRVAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPRIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLQVLQQAVRVQSSEKIVSERQRRVIDRARGVTR

  Protein domains


Predicted by InterproScan.

MobA/MobL family (MobA_MobL)

(17-249)

AAA domain (AAA_30)

(391-578)

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

(1047-1125)

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

(1309-1400)


  Protein structure



No available structure.




T4CP

ID   1861 GenBank   WP_088896042
Name   traG_SMB554_RS21265_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: 70255.17 Da        Isoelectric Point: 9.2490

>WP_088896042.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKPHPSLLLILLPVAVTAFAIYVVGWRWPGLAAGMSGKTAYWFLRASPVPALLFGPLAGLLAVWAL
PLHRRRPVAMASLACFLTVAGFYALREFGRLSPSVESGLLSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMSAAGKLFPPDGEIVVGERYRVDKDIVHELPFDPDDPATWGKGGKAP
LLTYGQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVLEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSSGAYFQNQAHNLLTGLLAHVMLSPEYAGRRN
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFRSTGIVTGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTNNSASRRSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVTAIP

  Protein domains


Predicted by InterproScan.

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

(165-637)

  Protein structure



No available structure.



ID   1862 GenBank   WP_088896193
Name   virD4_SMB554_RS24525_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: 62971.28 Da        Isoelectric Point: 9.1751

>WP_088896193.1 type IV secretion system ATPase VirD4 [Sinorhizobium meliloti]
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILLVQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILAMPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QNSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPTPLMIADERF
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: 745852..755431

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SMB554_RS21820 (SMB554_21715) 741469..742491 - 1023 WP_010967682 alcohol dehydrogenase AdhP -
SMB554_RS21825 (SMB554_21720) 742739..743416 - 678 WP_017264167 YoaK family protein -
SMB554_RS21830 (SMB554_21725) 743668..744279 + 612 WP_017264166 TetR/AcrR family transcriptional regulator -
SMB554_RS21835 (SMB554_21730) 744314..745540 + 1227 WP_010967685 MFS transporter -
SMB554_RS21840 (SMB554_21735) 745852..746841 - 990 WP_010967686 P-type DNA transfer ATPase VirB11 virB11
SMB554_RS21845 (SMB554_21740) 746852..748024 - 1173 WP_088896053 type IV secretion system protein VirB10 virB10
SMB554_RS21850 (SMB554_21745) 748034..748888 - 855 WP_014528658 P-type conjugative transfer protein VirB9 virB9
SMB554_RS21855 (SMB554_21750) 748888..749559 - 672 WP_010967689 virB8 family protein virB8
SMB554_RS21860 (SMB554_21755) 749564..749878 - 315 WP_017264165 hypothetical protein -
SMB554_RS21865 (SMB554_21760) 749875..750810 - 936 WP_013845459 type IV secretion system protein virB6
SMB554_RS21870 (SMB554_21765) 750816..751049 - 234 WP_013845460 EexN family lipoprotein -
SMB554_RS21875 (SMB554_21770) 751046..751747 - 702 WP_088896054 P-type DNA transfer protein VirB5 virB5
SMB554_RS21880 (SMB554_21775) 751747..754143 - 2397 WP_198389621 VirB4 family type IV secretion system protein virb4
SMB554_RS21885 (SMB554_21780) 754118..754459 - 342 WP_088896055 type IV secretion system protein VirB3 virB3
SMB554_RS21890 (SMB554_21785) 754464..754763 - 300 WP_010967695 TrbC/VirB2 family protein virB2
SMB554_RS21895 (SMB554_21790) 754760..755431 - 672 WP_010967696 lytic transglycosylase domain-containing protein virB1
SMB554_RS21900 (SMB554_21795) 755435..755953 - 519 WP_088896056 hypothetical protein -
SMB554_RS21905 (SMB554_21800) 756050..756418 + 369 WP_010967698 transcriptional regulator -
SMB554_RS21910 (SMB554_21805) 756679..756882 - 204 WP_088896057 hypothetical protein -
SMB554_RS21915 (SMB554_21810) 757003..757650 - 648 WP_088896058 dihydrofolate reductase family protein -
SMB554_RS21920 (SMB554_21815) 757700..758548 - 849 WP_088896059 alpha/beta fold hydrolase -

Region 2: 1271206..1280619

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SMB554_RS24525 (SMB554_24400) 1267166..1268857 + 1692 WP_088896193 type IV secretion system ATPase VirD4 -
SMB554_RS24530 (SMB554_24405) 1269263..1269988 - 726 WP_088896194 response regulator -
SMB554_RS24545 (SMB554_24415) 1271206..1272246 - 1041 WP_088896195 P-type DNA transfer ATPase VirB11 virB11
SMB554_RS24550 (SMB554_24420) 1272286..1273404 - 1119 WP_088896196 type IV secretion system protein VirB10 virB10
SMB554_RS24555 (SMB554_24425) 1273401..1274282 - 882 WP_088896197 P-type conjugative transfer protein VirB9 virB9
SMB554_RS24560 (SMB554_24430) 1274279..1274992 - 714 WP_088896198 type IV secretion system protein VirB8 virB8
SMB554_RS24565 (SMB554_24435) 1274979..1275146 - 168 WP_088896199 type IV secretion system lipoprotein VirB7 -
SMB554_RS24570 (SMB554_24440) 1275179..1276066 - 888 WP_088896200 type IV secretion system protein virB6
SMB554_RS24575 (SMB554_24445) 1276147..1276830 - 684 WP_088896201 pilin minor subunit VirB5 traI
SMB554_RS24580 (SMB554_24450) 1276844..1279213 - 2370 WP_088896202 VirB4 family type IV secretion/conjugal transfer ATPase virb4
SMB554_RS24585 (SMB554_24455) 1279213..1279539 - 327 WP_003537077 type IV secretion system protein VirB3 virB3
SMB554_RS24590 (SMB554_24460) 1279536..1279898 - 363 WP_014528518 pilin major subunit VirB2 virB2
SMB554_RS24595 (SMB554_24465) 1279912..1280619 - 708 WP_088896203 type IV secretion system lytic transglycosylase VirB1 virB1
SMB554_RS24600 1281050..1281346 - 297 WP_164834811 hypothetical protein -
SMB554_RS24610 (SMB554_24475) 1281629..1282134 + 506 Protein_1241 type IV secretory system conjugative DNA transfer family protein -
SMB554_RS24615 (SMB554_24480) 1282227..1283423 + 1197 WP_010969783 IS256-like element ISRm5 family transposase -
SMB554_RS24625 (SMB554_24490) 1284691..1285416 + 726 WP_003535579 class I SAM-dependent methyltransferase -

Host bacterium

ID   3360 GenBank   NZ_CP019585
Plasmid name   pSymA Incompatibility group   -
Plasmid size   1422736 bp Coordinate of oriT [Strand]   637766..637794 [+]
Host baterium   Sinorhizobium meliloti strain CCMM B554 (FSM-MA)

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   AcrIIA9, NA