Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103844
Name   oriT_USDA1157|psymA in_silico
Organism   Sinorhizobium meliloti strain USDA1157
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021794 (41612..41640 [-], 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_USDA1157|psymA
AGGGCGCAATATACGTCGCTGGCGCGACG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2854 GenBank   WP_088194634
Name   traA_CDO31_RS19280_USDA1157|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: 169864.47 Da        Isoelectric Point: 9.2615

>WP_088194634.1 Ti-type conjugative transfer relaxase TraA [Sinorhizobium meliloti]
MAIMFVRAQVIGRGAGRSIVSAAAYRHRTRMIDEQAGTSFSYRGGASELVHEELALPDDIPAWLKAAIDG
QSVAKASEALWNAVEAHETRADAQLARELIIALPEELTRAENIALVREFVRDNLTSKGMVADWVYHDKDG
NPHIHLMTALRPLTEQGFGPKKVPVLGEDGEPLRVVTPDRPNGKIVYKLWAGDKETIKAWKIAWAETANR
HLALAGHEIRLDGRSYAEQGLDGIAQKHLGPEKAALARKGVAMYFAPADLARRQEMADRLLAEPGLLLKQ
LGNERSTFDERDIAKALHRYVDDPVDFANIRARLMASDDLVLLKPQQVDAETGEAKQPAVFTTREMLRLE
YAMARSAEVLSRRKGFGVSNARAAAAVRSIETADTEKPFRLDPEQVDAVRHVTRDNAIAAVVGLAGAGKS
TLLAAARVAWEGEGRRVIGAALAGKAAEGLEDSSGIRSRTLASWELAWESGRKQLNRGDVLVIDEAGMVS
SQQMARILKAVEDAGAKAVLVGDAMQLQPIEAGAAFRAITERIGFAELAGVRRQRDAWARDASRLFARGK
VEEGLDAYAQHGRIVETETRAEIVDRIVADWGNARRDLLQKSADGEHPGRLRGDELLVLAHTNDDVRKLN
EALRQVMIGEGALAGAREFQTARGLREFAAGDRIIFLENARFVEPRARRLGPQYVKNGMLGTVVSTGDRR
GDTLLSVRLDSGRDVVISEDSYRNVDHGYAATIHKSQGSTVDRTFVLATGMMDQHLTYVAMTRHRDRADL
YAAKEDFEAKPEWGRKPRVDHAAGVTGELVKEGMAKFRPNDEDADESPYADIRTDDGTVQRLWGVSLPKA
LKDAGVAEGDTITLRKDGVERVKVQVPIVDEQTGEKRFEERQVDRNVWSASQLETAAARQERIERESHRP
QLFAALVERLSRSGAKTTTLDFEDEAGYQAQARDFARRRGLYHLSLVAAGMEAEVLRRWAGIAEKRELVA
KLWERASVALGFAIERERRVSYNEERTETLSTGIPSDGKYLVPPTTTFSRSVAEDARLAQLSSQRWKERE
AIVHPVLAKIYRDPDGALSALNALASDAAIEPRKLAEDLGLAPDRLGRLRGSELVVDGRAARDERTAATV
ALSELLPLARAHATEFRRNAERFGIREQQRRAHMALSVPALSKTAMARLVEIEAVRKQGGDDAYRTAFAY
AVEDRLLVQEVKAVNEALTARFGWSAFTAKADVIAERNIAERMPEDLARERREKLPRLFAVIRRFAEEQH
LAERQDRSKIVAGASVELGKGTFAVLPMLAPVTEFKTTVDEEARERALAAPHYAHHRAALVETATRVWRD
PADAIGKIEDLIVKGFAGERIAAAVTNDPAAYGALRGSDRIMDKLLAAGRERKDALQAVPEAASRIRSLG
ASYASALDAETRSITEERRRMAVAIPGLSPAAEDALKRLAAQIKNKDGKLDVAAGSLDPHIAREFAKVSR
ALDERFGRNAILRGETDVINRVSPAQRRAFEAMRDRLTILQQAVRVQSSQEIISERQRRVIDRARSVTR

  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   2685 GenBank   WP_014528597
Name   traG_CDO31_RS19295_USDA1157|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: 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: 1374514..1385398

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CDO31_RS26525 (CDO31_26530) 1371397..1372244 + 848 Protein_1364 alpha/beta fold hydrolase -
CDO31_RS26530 (CDO31_26535) 1372294..1372941 + 648 WP_010967700 dihydrofolate reductase family protein -
CDO31_RS26535 (CDO31_26540) 1373015..1373266 + 252 WP_010967699 hypothetical protein -
CDO31_RS26540 (CDO31_26545) 1373527..1373895 - 369 WP_010967698 transcriptional regulator -
CDO31_RS26545 (CDO31_26550) 1373992..1374510 + 519 WP_017277528 hypothetical protein -
CDO31_RS26550 (CDO31_26555) 1374514..1375185 + 672 WP_010967696 lytic transglycosylase domain-containing protein virB1
CDO31_RS26555 (CDO31_26560) 1375182..1375481 + 300 WP_003526741 TrbC/VirB2 family protein virB2
CDO31_RS26560 (CDO31_26565) 1375486..1375827 + 342 WP_003526740 type IV secretion system protein VirB3 virB3
CDO31_RS26565 (CDO31_26570) 1375802..1378198 + 2397 WP_017266273 VirB4 family type IV secretion system protein virb4
CDO31_RS26570 (CDO31_26575) 1378198..1378899 + 702 WP_014531544 P-type DNA transfer protein VirB5 virB5
CDO31_RS26575 (CDO31_26580) 1378896..1379111 + 216 WP_014531545 EexN family lipoprotein -
CDO31_RS26580 (CDO31_26585) 1379134..1379697 + 564 Protein_1375 type IV secretion system protein -
CDO31_RS26585 (CDO31_26590) 1379735..1380937 - 1203 WP_010967204 IS256-like element ISRm3 family transposase -
CDO31_RS26595 (CDO31_26600) 1380989..1381375 + 387 Protein_1377 type IV secretion system protein -
CDO31_RS38615 (CDO31_26605) 1381372..1381686 + 315 WP_013845458 hypothetical protein -
CDO31_RS26605 (CDO31_26610) 1381691..1382362 + 672 WP_013845457 virB8 family protein virB8
CDO31_RS26610 (CDO31_26615) 1382362..1383216 + 855 WP_014531548 P-type conjugative transfer protein VirB9 virB9
CDO31_RS26615 (CDO31_26620) 1383226..1384398 + 1173 WP_088194881 type IV secretion system protein VirB10 virB10
CDO31_RS26620 (CDO31_26625) 1384409..1385398 + 990 WP_088194882 P-type DNA transfer ATPase VirB11 virB11
CDO31_RS26625 (CDO31_26630) 1385709..1386935 - 1227 WP_013845453 MFS transporter -
CDO31_RS26630 (CDO31_26635) 1386972..1387583 - 612 WP_014531550 TetR/AcrR family transcriptional regulator -
CDO31_RS26635 (CDO31_26640) 1388110..1388295 + 186 WP_013845451 periplasmic nitrate reductase, NapE protein -
CDO31_RS26640 (CDO31_26645) 1388295..1388795 + 501 WP_088194883 ferredoxin-type protein NapF -
CDO31_RS26645 (CDO31_26650) 1388788..1389075 + 288 WP_088194884 chaperone NapD -

Host bacterium

ID   4284 GenBank   NZ_CP021794
Plasmid name   USDA1157|psymA Incompatibility group   -
Plasmid size   1433621 bp Coordinate of oriT [Strand]   41612..41640 [-]
Host baterium   Sinorhizobium meliloti strain USDA1157

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
Metal resistance gene   ncrA
Degradation gene   -
Symbiosis gene   nodM, nifN, nodD, nodA, nodB, nodC, nodI, nodJ, nodE, nodF, nodH, nifX, nifE, nifK, nifD, nifH, fixA, fixB, fixC, fixX, nifB, fixU, fixO, fixN, fixG, fixS
Anti-CRISPR   AcrIIA7