Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105536
Name   oriT_pSmeSM11c in_silico
Organism   Sinorhizobium meliloti SM11
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_017327 (192294..192350 [-], 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_pSmeSM11c
GCAGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTAAGGGGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   3769 GenBank   WP_014531067
Name   t4cp2_SM11_RS20015_pSmeSM11c 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.



ID   3770 GenBank   WP_014531614
Name   traG_SM11_RS23670_pSmeSM11c 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 204961..214884

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SM11_RS20005 (SM11_pC0237) 200233..202077 - 1845 Protein_211 DUF3604 domain-containing protein -
SM11_RS20015 (SM11_pC0239) 202865..204964 - 2100 WP_014531067 type IV secretory system conjugative DNA transfer family protein -
SM11_RS20020 (SM11_pC0240) 204961..205989 - 1029 WP_014531068 P-type DNA transfer ATPase VirB11 virB11
SM11_RS20025 (SM11_pC0241) 205970..207181 - 1212 WP_014531069 type IV secretion system protein VirB10 virB10
SM11_RS20030 (SM11_pC0242) 207181..207990 - 810 WP_014531070 TrbG/VirB9 family P-type conjugative transfer protein virB9
SM11_RS20035 (SM11_pC0243) 207987..208682 - 696 WP_014531071 type IV secretion system protein virB8
SM11_RS20040 (SM11_pC0244) 208722..209750 - 1029 WP_014531072 type IV secretion system protein virB6
SM11_RS20045 (SM11_pC0245) 209766..209993 - 228 WP_014531073 hypothetical protein -
SM11_RS20050 (SM11_pC0246) 209983..210684 - 702 WP_014531074 type IV secretion system protein -
SM11_RS20055 (SM11_pC0247) 210696..211784 - 1089 WP_014531075 lytic transglycosylase domain-containing protein -
SM11_RS20060 (SM11_pC0248) 211781..214240 - 2460 WP_014531076 VirB4 family type IV secretion/conjugal transfer ATPase virb4
SM11_RS20065 (SM11_pC0249) 214243..214542 - 300 WP_014531077 VirB3 family type IV secretion system protein virB3
SM11_RS20070 (SM11_pC0250) 214546..214884 - 339 WP_014531078 TrbC/VirB2 family protein virB2
SM11_RS20075 (SM11_pC0251) 214896..215798 - 903 WP_014531079 lytic transglycosylase domain-containing protein -
SM11_RS20080 (SM11_pC0252) 216021..216629 + 609 WP_014531080 hypothetical protein -
SM11_RS20085 (SM11_pC0253) 216626..217162 + 537 WP_014531081 succinoglycan biosynthesis protein exoi -
SM11_RS20090 (SM11_pC0254) 217159..217860 + 702 WP_014531082 thermonuclease family protein -
SM11_RS20095 (SM11_pC0255) 218265..218858 + 594 WP_026029870 hypothetical protein -
SM11_RS20100 (SM11_pC0256) 218882..219298 + 417 WP_014531084 hypothetical protein -
SM11_RS20105 (SM11_pC0257) 219380..219715 - 336 WP_013845322 hypothetical protein -

Region 2: 861523..871101

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SM11_RS23175 (SM11_pC0934) 858416..859264 + 849 WP_014531539 alpha/beta fold hydrolase -
SM11_RS23180 (SM11_pC0935) 859314..859961 + 648 WP_010967700 dihydrofolate reductase family protein -
SM11_RS23185 (SM11_pC0936) 860082..860285 + 204 WP_017266272 hypothetical protein -
SM11_RS23190 (SM11_pC0937) 860546..860914 - 369 WP_010967698 transcriptional regulator -
SM11_RS40255 861011..861519 + 509 Protein_872 hypothetical protein -
SM11_RS23200 (SM11_pC0940) 861523..862194 + 672 WP_010967696 lytic transglycosylase domain-containing protein virB1
SM11_RS23205 (SM11_pC0941) 862191..862490 + 300 WP_003526741 TrbC/VirB2 family protein virB2
SM11_RS23210 (SM11_pC0942) 862495..862836 + 342 WP_003526740 type IV secretion system protein VirB3 virB3
SM11_RS23215 (SM11_pC0943) 862811..865207 + 2397 WP_017266273 VirB4 family type IV secretion system protein virb4
SM11_RS23220 (SM11_pC0944) 865207..865908 + 702 WP_014531544 P-type DNA transfer protein VirB5 virB5
SM11_RS23225 (SM11_pC0945) 865905..866120 + 216 WP_014531545 EexN family lipoprotein -
SM11_RS23230 (SM11_pC0946) 866143..867078 + 936 WP_014531546 type IV secretion system protein virB6
SM11_RS23235 (SM11_pC0947) 867075..867389 + 315 WP_013845458 hypothetical protein -
SM11_RS23240 (SM11_pC0948) 867394..868065 + 672 WP_014531547 virB8 family protein virB8
SM11_RS23245 (SM11_pC0949) 868065..868919 + 855 WP_014531548 P-type conjugative transfer protein VirB9 virB9
SM11_RS23250 (SM11_pC0950) 868929..870101 + 1173 WP_014531549 type IV secretion system protein VirB10 virB10
SM11_RS23255 (SM11_pC0951) 870112..871101 + 990 WP_013845454 P-type DNA transfer ATPase VirB11 virB11
SM11_RS23260 (SM11_pC0952) 871412..872638 - 1227 WP_013845453 MFS transporter -
SM11_RS23265 (SM11_pC0953) 872675..873286 - 612 WP_014531550 TetR/AcrR family transcriptional regulator -
SM11_RS23270 (SM11_pC0954) 873813..873998 + 186 WP_013845451 periplasmic nitrate reductase, NapE protein -
SM11_RS36135 (SM11_pC0955) 873998..874498 + 501 WP_013845450 ferredoxin-type protein NapF -
SM11_RS23280 (SM11_pC0956) 874491..874778 + 288 WP_013845449 chaperone NapD -

Host bacterium

ID   5974 GenBank   NC_017327
Plasmid name   pSmeSM11c Incompatibility group   -
Plasmid size   1633319 bp Coordinate of oriT [Strand]   192294..192350 [-]
Host baterium   Sinorhizobium meliloti SM11

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