Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103808
Name   oriT_pSINMEB01 in_silico
Organism   Sinorhizobium meliloti BL225C
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_017324 (1009430..1009458 [+], 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_pSINMEB01
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2827 GenBank   WP_014528600
Name   traA_SINMEB_RS22225_pSINMEB01 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: 169942.77 Da        Isoelectric Point: 9.6192

>WP_014528600.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
QSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEQGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGIAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIAKALHRYVDDPVDFANIRARLMASDDLVLLKPQQVDAETGEAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGRKQLNRADVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQHGRIVETETRAKIVDRIVADWADARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
ASLRQVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTIVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
HAAKEDFEAKPEWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDEQTGEKRFEERQVDRNVWSASQLETAAARRERIERESHRP
QLFKQLVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAAIAEKREQVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVADDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRERGGDDAYRTAFAF
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERKIAERMPEDLAPERREKLTRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAAVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRE
PADAIGKIEDLIVKGFAAERIAAAVTNDPAAYGALRGSDRIMDKLLAVGRERKGALQAVPEAASRIRSLG
ASYASALDAETRGITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPRIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLTILQQAVRVQSSQEIISERQRRVIDRARSVTR

  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   2650 GenBank   WP_014528528
Name   virD4_SINMEB_RS21615_pSINMEB01 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: 63018.38 Da        Isoelectric Point: 9.3803

>WP_014528528.1 type IV secretion system ATPase VirD4 [Sinorhizobium meliloti]
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILLFQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILAMPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QNSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPTPLMIADKRF
SHV

  Protein domains


Predicted by InterproScan.

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

(97-537)

  Protein structure



No available structure.



ID   2651 GenBank   WP_014528597
Name   traG_SINMEB_RS22210_pSINMEB01 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: 70213.22 Da        Isoelectric Point: 9.3518

>WP_014528597.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKPHPSLLVILFPVAVTAAAVYVVGWRWPGLAAGMSGKTAYWFLRAAPVPALLFGPLAGLLAVWAL
PLHRRKPVAMASLACFLTVAGFYALREFGRLSPSVESGALSWDRALSYLDMVAVVGAVVGFMAVAVSARI
STVVPEPVKRAKRGTFGDADWLPMAAAGKLFPPDGEIVIGERYRVDKDIVHELPFDPNDPATWGQGGKVP
LLTYRQDFDSTHMLFFAGSGGYKTTSNVVPTALRYTGPLICLDPSTEVAPMVVEHRTRVLGREVMVLDPT
NPIMGFNVLDGIEHSRQKEEDIVGIAHMLLSESVRFESSIGSYFQNQAHNLLTGLLAHVMLSPEYAGRRT
LRSLRQIVSEPEPSVLAMLRDIQEHSASAFIRETLGVFTNMTEQTFSGVYSTASKDTQWLSLDSYAALVC
GNAFKSSDIVSGKKDVFLNIPASILRSYPGIGRVIIGSLINAMIEADGSFKRRALFMLDEVDLLGYMRLL
EEARDRGRKYGISMMLLYQSLGQLERHFGRDGAVSWIDGCAFASYAAVKALDTARSISAQCGEMTVEVKG
SSRNIGWDTKNSASRKSENVNYQRRPLIMPHEITQSMRKDEQIIIVQGHSPIRCGRAIYFRRKDMNEAAK
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: 872276..881689

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SINMEB_RS21515 (SinmeB_5949) 867737..869194 + 1458 WP_014528515 PLP-dependent aminotransferase family protein -
SINMEB_RS21520 869526..869794 - 269 Protein_871 hypothetical protein -
SINMEB_RS21525 (SinmeB_5951) 869814..870926 - 1113 Protein_872 IS256-like element ISRm5 family transposase -
SINMEB_RS21530 871016..871582 - 567 WP_041867817 type IV secretory system conjugative DNA transfer family protein -
SINMEB_RS21535 (SinmeB_5952) 871566..871757 + 192 Protein_874 Lrp/AsnC ligand binding domain-containing protein -
SINMEB_RS37590 871909..872067 - 159 WP_170849885 hypothetical protein -
SINMEB_RS21540 (SinmeB_5954) 872276..872983 + 708 WP_014528517 type IV secretion system lytic transglycosylase VirB1 virB1
SINMEB_RS21545 (SinmeB_5955) 872997..873359 + 363 WP_014528518 pilin major subunit VirB2 virB2
SINMEB_RS21550 (SinmeB_5956) 873356..873682 + 327 WP_003537077 type IV secretion system protein VirB3 virB3
SINMEB_RS21555 (SinmeB_5957) 873682..876051 + 2370 WP_014528519 VirB4 family type IV secretion/conjugal transfer ATPase virb4
SINMEB_RS21560 (SinmeB_5958) 876065..876748 + 684 WP_014528520 pilin minor subunit VirB5 traI
SINMEB_RS21565 (SinmeB_5959) 876829..877716 + 888 WP_014528521 type IV secretion system protein virB6
SINMEB_RS34555 (SinmeB_5960) 877749..877916 + 168 WP_011970875 type IV secretion system lipoprotein VirB7 -
SINMEB_RS21570 (SinmeB_5961) 877903..878616 + 714 WP_014528522 type IV secretion system protein VirB8 virB8
SINMEB_RS21575 (SinmeB_5962) 878613..879494 + 882 WP_014528523 TrbG/VirB9 family P-type conjugative transfer protein virB9
SINMEB_RS21580 (SinmeB_5963) 879491..880609 + 1119 WP_014528524 type IV secretion system protein VirB10 virB10
SINMEB_RS21585 (SinmeB_5964) 880649..881689 + 1041 WP_014528525 P-type DNA transfer ATPase VirB11 virB11
SINMEB_RS21590 (SinmeB_5965) 882033..882416 + 384 WP_011971017 transposase -
SINMEB_RS21595 (SinmeB_5966) 882413..882760 + 348 WP_011971016 IS66 family insertion sequence element accessory protein TnpB -
SINMEB_RS21600 (SinmeB_5967) 882832..884397 + 1566 WP_011971015 IS66 family transposase -
SINMEB_RS38315 (SinmeB_5968) 884397..884702 + 306 WP_011971014 hypothetical protein -
SINMEB_RS21610 (SinmeB_5970) 885721..886446 + 726 WP_014528527 response regulator -

Region 2: 1124433..1134012

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SINMEB_RS22780 (SinmeB_6211) 1120050..1121072 - 1023 WP_010967682 alcohol dehydrogenase AdhP -
SINMEB_RS22785 (SinmeB_6212) 1121320..1121997 - 678 WP_010967683 YoaK family protein -
SINMEB_RS22790 (SinmeB_6213) 1122249..1122860 + 612 WP_010967684 TetR/AcrR family transcriptional regulator -
SINMEB_RS22795 (SinmeB_6214) 1122895..1124121 + 1227 WP_010967685 MFS transporter -
SINMEB_RS22800 (SinmeB_6215) 1124433..1125422 - 990 WP_010967686 P-type DNA transfer ATPase VirB11 virB11
SINMEB_RS22805 (SinmeB_6216) 1125433..1126605 - 1173 WP_014528657 type IV secretion system protein VirB10 virB10
SINMEB_RS22810 (SinmeB_6217) 1126615..1127469 - 855 WP_014528658 P-type conjugative transfer protein VirB9 virB9
SINMEB_RS22815 (SinmeB_6218) 1127469..1128140 - 672 WP_010967689 virB8 family protein virB8
SINMEB_RS22820 (SinmeB_6219) 1128145..1128459 - 315 WP_010967690 hypothetical protein -
SINMEB_RS22825 (SinmeB_6220) 1128456..1129391 - 936 WP_014528659 type IV secretion system protein virB6
SINMEB_RS22830 (SinmeB_6221) 1129397..1129630 - 234 WP_013845460 EexN family lipoprotein -
SINMEB_RS22835 (SinmeB_6222) 1129627..1130328 - 702 WP_010967692 P-type DNA transfer protein VirB5 virB5
SINMEB_RS22840 (SinmeB_6223) 1130328..1132724 - 2397 WP_014528660 VirB4 family type IV secretion system protein virb4
SINMEB_RS22845 (SinmeB_6224) 1132699..1133040 - 342 WP_014528661 type IV secretion system protein VirB3 virB3
SINMEB_RS22850 (SinmeB_6225) 1133045..1133344 - 300 WP_010967695 TrbC/VirB2 family protein virB2
SINMEB_RS22855 (SinmeB_6226) 1133341..1134012 - 672 WP_010967696 lytic transglycosylase domain-containing protein virB1
SINMEB_RS34840 (SinmeB_6227) 1134016..1134534 - 519 WP_010967697 hypothetical protein -
SINMEB_RS22860 (SinmeB_6228) 1134631..1134999 + 369 WP_010967698 transcriptional regulator -
SINMEB_RS22865 (SinmeB_6229) 1135260..1135511 - 252 WP_010967699 hypothetical protein -
SINMEB_RS22870 (SinmeB_6230) 1135585..1136232 - 648 WP_010967700 dihydrofolate reductase family protein -
SINMEB_RS22875 (SinmeB_6231) 1136282..1137130 - 849 WP_010967701 alpha/beta fold hydrolase -

Host bacterium

ID   4248 GenBank   NC_017324
Plasmid name   pSINMEB01 Incompatibility group   -
Plasmid size   1616209 bp Coordinate of oriT [Strand]   1009430..1009458 [+]
Host baterium   Sinorhizobium meliloti BL225C

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   ncrA
Degradation gene   -
Symbiosis gene   nifT, 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   -