Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104036
Name   oriT_pSymA in_silico
Organism   Sinorhizobium meliloti strain AK76
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP066361 (856213..856241 [-], 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   2991 GenBank   WP_198868964
Name   traA_JFX10_RS29660_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: 170140.81 Da        Isoelectric Point: 9.4868

>WP_198868964.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
QSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEQGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVAMYFAPADLARRQEMADRLLAEPELLLKQ
LGNERSTFDERDIARALHRYVDDPVDFANIRARLMASDDLVLLKPQQIDAETGEAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARAAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGREQLNRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQHGRIVETETRAKIVDRIVADWADARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRNVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISQDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWDRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDAQTGEKRFEERQVDRNVWSASQLETAAARRERIERESHRP
QLFKQLVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKREQVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSIPALSKTAMARLVEIEAVRKQGGDDAYRTAFTY
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAGERIAAAVSNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDRKLDVAAGSLDPRIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLTILQQAVRVQSSQEIISERQRRVIDRARGVTR

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(391-578)

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

(1309-1400)

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

(1047-1125)

MobA/MobL family (MobA_MobL)

(17-249)


  Protein structure



No available structure.




T4CP

ID   2857 GenBank   WP_198868965
Name   traG_JFX10_RS29675_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: 70228.22 Da        Isoelectric Point: 9.4769

>WP_198868965.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKTHPSLLVILFPVAVTAAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWVL
PLHRRRPVAIASLACFLTVAGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERYRVDKDIVHELPFEPNDPATWGQGGKAL
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVIEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSTGSYFQNQAHNLLTGLLAHVMLSPDYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIQADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARNISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSESVNFQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
ANRFVKAVP

  Protein domains


Predicted by InterproScan.

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

(169-635)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 774451..784029

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JFX10_RS29230 (JFX10_29215) 771333..772181 + 849 WP_017269096 alpha/beta fold hydrolase -
JFX10_RS29235 (JFX10_29220) 772231..772878 + 648 WP_010967700 dihydrofolate reductase family protein -
JFX10_RS29240 (JFX10_29225) 772952..773203 + 252 WP_017269095 hypothetical protein -
JFX10_RS29245 (JFX10_29230) 773464..773832 - 369 WP_013845467 hypothetical protein -
JFX10_RS33715 773929..774447 + 519 WP_013845466 hypothetical protein -
JFX10_RS29250 (JFX10_29235) 774451..775122 + 672 WP_198869109 lytic transglycosylase domain-containing protein virB1
JFX10_RS29255 (JFX10_29240) 775119..775418 + 300 WP_003526741 TrbC/VirB2 family protein virB2
JFX10_RS29260 (JFX10_29245) 775423..775764 + 342 WP_003526740 type IV secretion system protein VirB3 virB3
JFX10_RS29265 (JFX10_29250) 775739..778135 + 2397 WP_198869110 VirB4 family type IV secretion system protein virb4
JFX10_RS29270 (JFX10_29255) 778135..778836 + 702 WP_014531544 P-type DNA transfer protein VirB5 virB5
JFX10_RS29275 (JFX10_29260) 778833..779048 + 216 WP_014531545 EexN family lipoprotein -
JFX10_RS29280 (JFX10_29265) 779071..780006 + 936 WP_014531546 type IV secretion system protein virB6
JFX10_RS33720 780003..780317 + 315 WP_013845458 hypothetical protein -
JFX10_RS29285 (JFX10_29270) 780322..780993 + 672 WP_127514435 virB8 family protein virB8
JFX10_RS29290 (JFX10_29275) 780993..781847 + 855 WP_014531548 P-type conjugative transfer protein VirB9 virB9
JFX10_RS29295 (JFX10_29280) 781857..783029 + 1173 WP_198869111 type IV secretion system protein VirB10 virB10
JFX10_RS29300 (JFX10_29285) 783040..784029 + 990 WP_198869112 P-type DNA transfer ATPase VirB11 virB11
JFX10_RS29305 (JFX10_29290) 784340..785566 - 1227 WP_013845453 MFS transporter -
JFX10_RS29310 (JFX10_29295) 785603..786214 - 612 WP_013845452 TetR/AcrR family transcriptional regulator -
JFX10_RS29315 (JFX10_29300) 786741..786926 + 186 WP_013845451 periplasmic nitrate reductase, NapE protein -
JFX10_RS29320 (JFX10_29305) 786926..787426 + 501 WP_013845450 ferredoxin-type protein NapF -
JFX10_RS29325 (JFX10_29310) 787419..787706 + 288 WP_013845449 chaperone NapD -

Host bacterium

ID   4475 GenBank   NZ_CP066361
Plasmid name   pSymA Incompatibility group   -
Plasmid size   1580177 bp Coordinate of oriT [Strand]   856213..856241 [-]
Host baterium   Sinorhizobium meliloti strain AK76

Cargo genes

Drug resistance gene   aac(3)-IIc
Virulence gene   htpB, katA
Metal resistance gene   ncrA
Degradation gene   -
Symbiosis gene   fixA, fixB, fixN, fixO, fixG, fixS, nodM, nifN, nodD, nodA, nodB, nodC, nodI, nodJ, nodE, nodF, nodH, nifX, nifE, nifK, nifD, nifH, fixC, fixX, nifB, fixU, nifT
Anti-CRISPR   -