Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107579
Name   oriT_pSymA in_silico
Organism   Sinorhizobium meliloti RU11/001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP021217 (1088650..1088706 [+], 57 nt)
oriT length   57 nt
IRs (inverted repeats)      4..9, 23..28  (GGAAAA..TTTTCC)
Location of nic site      36..37
Conserved sequence flanking the
  nic site    		  TCCTGCCTCT
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 57 nt

>oriT_pSymA
GCAGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   5311 GenBank   WP_014531614
Name   traG_SMRU11_RS05055_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: 70270.30 Da        Isoelectric Point: 9.4769

>WP_014531614.1 Ti-type conjugative transfer system protein TraG [Sinorhizobium meliloti]
MALKAKTHPSLLVILFPVAVTAAAVYVVGWRWPGLAAVMSGKTAYWFLRAAPVPALLFGPLAGLLAVWVL
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.



ID   5312 GenBank   WP_014531067
Name   t4cp2_SMRU11_RS08000_pSymA insolico UniProt ID   _
Length   699 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 699 a.a.        Molecular weight: 77789.72 Da        Isoelectric Point: 9.6861

>WP_014531067.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium meliloti]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
LVPAMLVAGLVACIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRVGRNILRTRDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRENGSQVFLFAPGSEKTSSYNPLDFIRPQRGNRT
TDIQNIASILVPENTASENSVWQATAQQVLAGAISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDITLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPRVPEVDYLSPKPVPATTP
EYAKGGEPSVEIPSSAIEKEEKPVAAAAIQSAAVKEEPAADDMPSTPAKRTVNRKALRPSAKATAANTGG
AEASPSLDAMEARIRAIEEGLKPKAAQLREVVEMKAEKLGDKSPTKRRNIMDIFSATVPDPVEVGVAAE

  Protein domains


Predicted by InterproScan.

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

(103-533)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 451249..460827

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SMRU11_RS04525 (SMRU11_04550) 448142..448990 + 849 WP_014531539 alpha/beta fold hydrolase -
SMRU11_RS04530 (SMRU11_04555) 449040..449687 + 648 WP_010967700 dihydrofolate reductase family protein -
SMRU11_RS04540 (SMRU11_04565) 449808..450011 + 204 WP_017266272 hypothetical protein -
SMRU11_RS04545 (SMRU11_04570) 450272..450640 - 369 WP_010967698 transcriptional regulator -
SMRU11_RS40950 (SMRU11_04575) 450737..451245 + 509 Protein_437 hypothetical protein -
SMRU11_RS04555 (SMRU11_04580) 451249..451920 + 672 WP_010967696 lytic transglycosylase domain-containing protein virB1
SMRU11_RS04560 (SMRU11_04585) 451917..452216 + 300 WP_003526741 TrbC/VirB2 family protein virB2
SMRU11_RS04565 (SMRU11_04590) 452221..452562 + 342 WP_003526740 type IV secretion system protein VirB3 virB3
SMRU11_RS04570 (SMRU11_04595) 452537..454933 + 2397 WP_017266273 VirB4 family type IV secretion system protein virb4
SMRU11_RS04575 (SMRU11_04600) 454933..455634 + 702 WP_014531544 P-type DNA transfer protein VirB5 virB5
SMRU11_RS04580 (SMRU11_04605) 455631..455846 + 216 WP_029727813 EexN family lipoprotein -
SMRU11_RS04585 (SMRU11_04610) 455869..456804 + 936 WP_014531546 type IV secretion system protein virB6
SMRU11_RS04590 (SMRU11_04615) 456801..457115 + 315 WP_013845458 hypothetical protein -
SMRU11_RS04595 (SMRU11_04620) 457120..457791 + 672 WP_014531547 virB8 family protein virB8
SMRU11_RS04600 (SMRU11_04625) 457791..458645 + 855 WP_014531548 P-type conjugative transfer protein VirB9 virB9
SMRU11_RS04605 (SMRU11_04630) 458655..459827 + 1173 WP_014531549 type IV secretion system protein VirB10 virB10
SMRU11_RS04610 (SMRU11_04635) 459838..460827 + 990 WP_013845454 P-type DNA transfer ATPase VirB11 virB11
SMRU11_RS04615 (SMRU11_04640) 461138..462364 - 1227 WP_013845453 MFS transporter -
SMRU11_RS04620 (SMRU11_04645) 462401..463012 - 612 WP_014531550 TetR/AcrR family transcriptional regulator -
SMRU11_RS04625 (SMRU11_04650) 463539..463724 + 186 WP_013845451 periplasmic nitrate reductase, NapE protein -
SMRU11_RS04630 (SMRU11_04655) 463724..464224 + 501 WP_013845450 ferredoxin-type protein NapF -
SMRU11_RS04635 (SMRU11_04660) 464217..464504 + 288 WP_013845449 chaperone NapD -

Region 2: 1066116..1076039

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SMRU11_RS07905 (SMRU11_07930) 1061285..1061620 + 336 WP_013845322 hypothetical protein -
SMRU11_RS07910 (SMRU11_07935) 1061702..1062118 - 417 WP_014531084 hypothetical protein -
SMRU11_RS07915 (SMRU11_07940) 1062142..1062735 - 594 WP_026029870 hypothetical protein -
SMRU11_RS07925 (SMRU11_07950) 1063140..1063841 - 702 WP_014531082 thermonuclease family protein -
SMRU11_RS07930 (SMRU11_07955) 1063838..1064374 - 537 WP_014531081 succinoglycan biosynthesis protein exoi -
SMRU11_RS07935 (SMRU11_07960) 1064371..1064979 - 609 WP_014531080 hypothetical protein -
SMRU11_RS07940 (SMRU11_07965) 1065202..1066104 + 903 WP_029727939 lytic transglycosylase domain-containing protein -
SMRU11_RS07945 (SMRU11_07970) 1066116..1066454 + 339 WP_014531078 TrbC/VirB2 family protein virB2
SMRU11_RS07950 (SMRU11_07975) 1066458..1066757 + 300 WP_014531077 VirB3 family type IV secretion system protein virB3
SMRU11_RS07955 (SMRU11_07980) 1066760..1069219 + 2460 WP_014531076 VirB4 family type IV secretion/conjugal transfer ATPase virb4
SMRU11_RS07960 (SMRU11_07985) 1069216..1070304 + 1089 WP_014531075 lytic transglycosylase domain-containing protein -
SMRU11_RS07965 (SMRU11_07990) 1070316..1071017 + 702 WP_014531074 type IV secretion system protein -
SMRU11_RS07970 (SMRU11_07995) 1071007..1071234 + 228 WP_014531073 hypothetical protein -
SMRU11_RS07975 (SMRU11_08000) 1071250..1072278 + 1029 WP_014531072 type IV secretion system protein virB6
SMRU11_RS07980 (SMRU11_08005) 1072318..1073013 + 696 WP_014531071 type IV secretion system protein virB8
SMRU11_RS07985 (SMRU11_08010) 1073010..1073819 + 810 WP_014531070 TrbG/VirB9 family P-type conjugative transfer protein virB9
SMRU11_RS07990 (SMRU11_08015) 1073819..1075030 + 1212 WP_014531069 type IV secretion system protein VirB10 virB10
SMRU11_RS07995 (SMRU11_08020) 1075011..1076039 + 1029 WP_014531068 P-type DNA transfer ATPase VirB11 virB11
SMRU11_RS08000 (SMRU11_08025) 1076036..1078135 + 2100 WP_014531067 type IV secretory system conjugative DNA transfer family protein -
SMRU11_RS08010 (SMRU11_08035) 1078923..1080767 + 1845 Protein_1076 DUF3604 domain-containing protein -

Host bacterium

ID   8014 GenBank   NZ_CP021217
Plasmid name   pSymA Incompatibility group   -
Plasmid size   1613292 bp Coordinate of oriT [Strand]   1088650..1088706 [+]
Host baterium   Sinorhizobium meliloti RU11/001

Cargo genes

Drug resistance gene   -
Virulence gene   htpB
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
Anti-CRISPR   AcrIIA9