Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   117179
Name   oriT_LMG 23571|unnamed in_silico
Organism   Klebsiella variicola strain LMG 23571
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP013986 (347..395 [+], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_LMG 23571|unnamed
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Auxiliary protein

ID   6421 GenBank   WP_020805752
Name   WP_020805752_LMG 23571|unnamed insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   12778 GenBank   WP_119867257
Name   traD_AWN63_RS28470_LMG 23571|unnamed insolico UniProt ID   _
Length   775 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 775 a.a.        Molecular weight: 86435.56 Da        Isoelectric Point: 5.0101

>WP_119867257.1 type IV conjugative transfer system coupling protein TraD [Klebsiella variicola]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSDQILADKYTVWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIQRRLDTRVDARLSALLEAREAEGSLARVLFTPDAPASGPADTNSHAGEQPEPISQPA
PAEVTVSPAPVKAPPPTKMPAEEPSARAPASPPPEAPVLRVTTVPLIKPKAAAAAAAASTASSAVTPAAA
AGGTEQELAQQSAEQGPDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVE
IGGNF

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(172-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 135650..161220

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AWN63_RS28470 (AWN63_26870) 135650..137977 - 2328 WP_119867257 type IV conjugative transfer system coupling protein TraD virb4
AWN63_RS28475 (AWN63_26875) 138339..139070 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
AWN63_RS28480 (AWN63_26880) 139483..140016 - 534 WP_114501468 hypothetical protein -
AWN63_RS28485 (AWN63_26885) 140027..142870 - 2844 WP_119867258 conjugal transfer mating-pair stabilization protein TraG traG
AWN63_RS28490 (AWN63_26890) 142870..144249 - 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
AWN63_RS28495 (AWN63_26895) 144227..144670 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
AWN63_RS28500 (AWN63_26900) 144716..145273 - 558 WP_032441889 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AWN63_RS28505 (AWN63_26905) 145245..145484 - 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
AWN63_RS28510 (AWN63_26910) 145495..146247 - 753 WP_042934721 type-F conjugative transfer system pilin assembly protein TraF traF
AWN63_RS28515 (AWN63_26915) 146268..146594 - 327 WP_064144773 hypothetical protein -
AWN63_RS28520 (AWN63_26920) 146605..146832 - 228 WP_065808180 conjugal transfer protein TrbE -
AWN63_RS28525 (AWN63_26925) 146822..147103 - 282 WP_064144771 hypothetical protein -
AWN63_RS28530 (AWN63_26930) 147136..149091 - 1956 WP_119867267 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AWN63_RS28535 (AWN63_26935) 149088..149471 - 384 WP_065808179 hypothetical protein -
AWN63_RS28540 (AWN63_26940) 149468..150106 - 639 WP_065901066 type-F conjugative transfer system pilin assembly protein TrbC trbC
AWN63_RS28545 (AWN63_26945) 150119..151078 - 960 WP_168712236 conjugal transfer pilus assembly protein TraU traU
AWN63_RS28550 (AWN63_26950) 151122..151748 - 627 WP_065808176 type-F conjugative transfer system protein TraW traW
AWN63_RS28555 (AWN63_26955) 151748..152137 - 390 WP_020326931 type-F conjugative transfer system protein TrbI -
AWN63_RS28560 (AWN63_26960) 152137..154776 - 2640 WP_119867259 type IV secretion system protein TraC virb4
AWN63_RS28565 (AWN63_26965) 154847..155245 - 399 WP_164078962 hypothetical protein -
AWN63_RS28570 (AWN63_26970) 155253..155543 - 291 WP_119867261 hypothetical protein -
AWN63_RS28575 (AWN63_26975) 155540..155944 - 405 WP_119867262 hypothetical protein -
AWN63_RS28580 (AWN63_26980) 156011..156328 - 318 WP_023307544 hypothetical protein -
AWN63_RS28585 156329..156547 - 219 WP_004171484 hypothetical protein -
AWN63_RS29640 (AWN63_26985) 156571..156861 - 291 WP_032429299 hypothetical protein -
AWN63_RS28595 (AWN63_26990) 156866..157276 - 411 WP_023292154 hypothetical protein -
AWN63_RS28600 157408..157977 - 570 WP_032429300 type IV conjugative transfer system lipoprotein TraV traV
AWN63_RS28605 (AWN63_26995) 157996..158181 - 186 WP_038990989 hypothetical protein -
AWN63_RS28610 (AWN63_27000) 158178..159602 - 1425 WP_071080849 F-type conjugal transfer pilus assembly protein TraB traB
AWN63_RS28615 (AWN63_27005) 159602..160342 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
AWN63_RS28620 (AWN63_27010) 160329..160895 - 567 WP_020316627 type IV conjugative transfer system protein TraE traE
AWN63_RS28625 (AWN63_27015) 160915..161220 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
AWN63_RS28630 (AWN63_27020) 161234..161602 - 369 WP_049155512 type IV conjugative transfer system pilin TraA -
AWN63_RS28635 161671..161871 - 201 WP_071080869 TraY domain-containing protein -

Host bacterium

ID   17612 GenBank   NZ_CP013986
Plasmid name   LMG 23571|unnamed Incompatibility group   IncFIB
Plasmid size   163254 bp Coordinate of oriT [Strand]   347..395 [+]
Host baterium   Klebsiella variicola strain LMG 23571

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   arsC, arsB, arsR, arsH
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -