Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103948
Name   oriT_pSmeAK21b in_silico
Organism   Sinorhizobium meliloti strain AK21
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026529 (114831..114887 [-], 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_pSmeAK21b
GCAGGAAAAGGGCGTAGCACATTTTTCCGTATCCTGCCTCTCCAAATTGTGAGGGGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


T4CP

ID   2794 GenBank   WP_127591188
Name   virD4_C3L21_RS35295_pSmeAK21b 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: 62953.24 Da        Isoelectric Point: 9.1751

>WP_127591188.1 type IV secretion system ATPase VirD4 [Sinorhizobium meliloti]
MISSKTRPLSIAGSIMCSLAVGFCGASAYSTFRFGFDGRALMTFDILAFWYETPFYLGYTTLFFYRGLAV
VVLTSGAILLVQQMVSVRDRQHHGTARWARVDEMRRAGYLQRYSRISGPVFGKTSGPFWSDYYLTNSEQP
HSLIVAPTRAGKGVGIVIPTLLTYEGSVIALDVKGELFDLTSRARKARGDSVFKLAPLDPERRTNCYNPL
LDILALPSERQFTEARRLAANLIATKGQSAEGFINGARDLFVAGILACIERGTPTIGAVYDLFAQPGEKY
SLFARLAQETQNKEAQRIFDEMASNDTKILTSYTSVLGDGGLNLWADPLIKAATSRSDFSIYDLRRRRTC
IYLCVSPNDLEVVAPLMRLLFQQVVSILQRSLPGKDEKHEVLFLLDEFKHLGKLEAIETAITTIAGYKGR
FMFIIQSLSALTGTYDESGKQNFLSNTGVQVFMATADDETPVYISKAIGEYTFQARSTSYTQSLTFDRNI
QNSDQGAPLLRPEQVRLLPDKYQIVLIKGQPPLQLRKVRYYSDRALKRIFDSQTGRLPEPTPLMIADERF
SHV

  Protein domains


Predicted by InterproScan.

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

(97-537)

  Protein structure



No available structure.



ID   2795 GenBank   WP_158528845
Name   t4cp2_C3L21_RS35400_pSmeAK21b 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: 77761.58 Da        Isoelectric Point: 9.5348

>WP_158528845.1 type IV secretory system conjugative DNA transfer family protein [Sinorhizobium meliloti]
MTKQLQAFYLLFCVGIAFVVWMLGYGLGLQLFYKDGRILETTITSNPFAPIQQFWHYKTSPALQKVALGS
LVPAMLVAGLVAYIGLKPTSSPLGDAAFQDMASLRRGKWFRKQGHIFGRVGRNILRTRDDRHHLIIGPTR
SGKGAGYVIPNALMHEGSMIVTDLKGEVFKATAGYRRENGSQVFLFAPGSEKTSSYNPLDFIRPERGNRT
TDIQNIASILVPENTASENSVWQATAQQVLAGAISYITESPFYKDRRNLAEVNSFFNSGVDLQALMKYIK
EKEPYLSKFTVESFNSYIALSERAAASALLDIQKAMRPFKNERIVAATNVTDMDLRAMKRRPISIYLAPN
ITDISLLRPLLTLFVQQVMDILTLEHDPNSLPVYFLLDEFRQLKRMDEIMTKLPYVAGYNIKLAFIIQDL
KNLDEIYGETSRHSLLGNCGYQLVLGANDQATAEYASRALGKRTIRYQSESRTIELMGLPRRTKVEQIRE
RDLMMPQEVRQMPENKMILLIEGQRPIFGEKLRFFQTQPFKSAEAFSQANIPRVPEVDYLSPKPVPATTP
EYAKGGEPSVEIPSPAIEKEEEPVAAAAIQSAAVKEEPAADDMPSTPAKRTVNRKALRPSAKATAANTGG
AEASPSLDAMEARIKAIEEGLKPKAAQLKEVVETKAEKLGDKSPTKRRNIMDIFGATVPDPVEVGVTAE

  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: 83677..93090

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C3L21_RS35170 (C3L21_36270) 78768..80225 + 1458 WP_158528840 PLP-dependent aminotransferase family protein -
C3L21_RS37815 80553..80824 - 272 Protein_76 hypothetical protein -
C3L21_RS35175 (C3L21_36275) 80874..82070 - 1197 WP_010969296 IS256-like element ISRm5 family transposase -
C3L21_RS35180 (C3L21_36280) 82152..82718 - 567 WP_127591194 type IV secretory system conjugative DNA transfer family protein -
C3L21_RS35185 (C3L21_36285) 82702..82893 + 192 Protein_79 Lrp/AsnC ligand binding domain-containing protein -
C3L21_RS36425 83048..83206 - 159 WP_194966990 hypothetical protein -
C3L21_RS35195 (C3L21_36295) 83677..84384 + 708 WP_033049347 type IV secretion system lytic transglycosylase VirB1 virB1
C3L21_RS35200 (C3L21_36300) 84398..84760 + 363 WP_014528518 pilin major subunit VirB2 virB2
C3L21_RS35205 (C3L21_36305) 84757..85083 + 327 WP_003537077 type IV secretion system protein VirB3 virB3
C3L21_RS35210 (C3L21_36310) 85083..87452 + 2370 WP_127610437 VirB4 family type IV secretion/conjugal transfer ATPase virb4
C3L21_RS35215 (C3L21_36315) 87466..88149 + 684 WP_003537081 pilin minor subunit VirB5 traI
C3L21_RS35220 (C3L21_36320) 88230..89117 + 888 WP_003537089 type IV secretion system protein virB6
C3L21_RS35225 (C3L21_36325) 89150..89317 + 168 WP_003537091 type IV secretion system lipoprotein VirB7 -
C3L21_RS35230 (C3L21_36330) 89304..90017 + 714 WP_003537093 type IV secretion system protein VirB8 virB8
C3L21_RS35235 (C3L21_36335) 90014..90895 + 882 WP_003537095 P-type conjugative transfer protein VirB9 virB9
C3L21_RS35240 (C3L21_36340) 90892..92010 + 1119 WP_033049349 type IV secretion system protein VirB10 virB10
C3L21_RS35245 (C3L21_36345) 92050..93090 + 1041 WP_003537101 P-type DNA transfer ATPase VirB11 virB11
C3L21_RS35260 (C3L21_36360) 93931..94305 + 375 WP_012477218 transposase -
C3L21_RS35265 (C3L21_36365) 94302..94649 + 348 WP_012477217 IS66 family insertion sequence element accessory protein TnpB -
C3L21_RS35270 (C3L21_36370) 94713..96334 + 1622 Protein_94 IS66 family transposase -
C3L21_RS35275 (C3L21_36375) 96334..96630 + 297 WP_014531779 hypothetical protein -
C3L21_RS35285 (C3L21_36385) 97118..97843 + 726 WP_003537873 response regulator -

Region 2: 123067..132990

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C3L21_RS35390 (C3L21_36495) 118161..118604 + 444 WP_158528844 ester cyclase -
C3L21_RS35395 (C3L21_36500) 118785..120746 - 1962 WP_102764831 AAA family ATPase -
C3L21_RS35400 (C3L21_36505) 120971..123070 - 2100 WP_158528845 type IV secretory system conjugative DNA transfer family protein -
C3L21_RS35405 (C3L21_36510) 123067..124095 - 1029 WP_158528846 P-type DNA transfer ATPase VirB11 virB11
C3L21_RS35410 (C3L21_36515) 124076..125287 - 1212 WP_014531069 type IV secretion system protein VirB10 virB10
C3L21_RS35415 (C3L21_36520) 125287..126096 - 810 WP_017266188 TrbG/VirB9 family P-type conjugative transfer protein virB9
C3L21_RS35420 (C3L21_36525) 126093..126788 - 696 WP_158528847 type IV secretion system protein virB8
C3L21_RS35425 (C3L21_36530) 126828..127856 - 1029 WP_158528848 type IV secretion system protein virB6
C3L21_RS35430 (C3L21_36535) 127872..128099 - 228 WP_158528849 hypothetical protein -
C3L21_RS35435 (C3L21_36540) 128089..128790 - 702 WP_158528902 type IV secretion system protein -
C3L21_RS35440 (C3L21_36545) 128802..129890 - 1089 WP_158528850 lytic transglycosylase domain-containing protein -
C3L21_RS35445 (C3L21_36550) 129887..132346 - 2460 WP_158528851 VirB4 family type IV secretion/conjugal transfer ATPase virb4
C3L21_RS35450 (C3L21_36555) 132349..132648 - 300 WP_020479309 VirB3 family type IV secretion system protein virB3
C3L21_RS35455 (C3L21_36560) 132652..132990 - 339 WP_017265136 TrbC/VirB2 family protein virB2
C3L21_RS35460 (C3L21_36565) 133002..133913 - 912 WP_194966987 lytic transglycosylase domain-containing protein -
C3L21_RS35465 (C3L21_36570) 134135..134743 + 609 WP_158528852 hypothetical protein -
C3L21_RS35470 (C3L21_36575) 134740..135276 + 537 WP_158528853 thermonuclease family protein -
C3L21_RS35475 (C3L21_36580) 135273..135971 + 699 WP_158528854 thermonuclease family protein -
C3L21_RS35480 (C3L21_36585) 136029..136361 + 333 WP_234913492 hypothetical protein -
C3L21_RS35485 (C3L21_36590) 136373..136966 + 594 WP_158528855 hypothetical protein -
C3L21_RS35490 (C3L21_36595) 136990..137406 + 417 WP_014531084 hypothetical protein -

Host bacterium

ID   4388 GenBank   NZ_CP026529
Plasmid name   pSmeAK21b Incompatibility group   -
Plasmid size   209149 bp Coordinate of oriT [Strand]   114831..114887 [-]
Host baterium   Sinorhizobium meliloti strain AK21

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   actP
Degradation gene   bphC
Symbiosis gene   -
Anti-CRISPR   -