Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104885
Name   oriT_pGN4549-1 in_silico
Organism   Klebsiella pneumoniae strain GN4549
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP101836 (194363..194412 [+], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_pGN4549-1
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3456 GenBank   WP_015065542
Name   traI_NPH93_RS27125_pGN4549-1 insolico UniProt ID   K7R3U7
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190318.03 Da        Isoelectric Point: 6.2890

>WP_015065542.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacterales]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMSREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALAVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDREGGRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGGGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEAAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(576-628)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(11-283)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




T4CP

ID   3403 GenBank   WP_015065541
Name   traD_NPH93_RS27130_pGN4549-1 insolico UniProt ID   _
Length   770 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 770 a.a.        Molecular weight: 86025.00 Da        Isoelectric Point: 5.0577

>WP_015065541.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

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

(172-560)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 164956..194970

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
NPH93_RS27130 (NPH93_27120) 164956..167268 - 2313 WP_015065541 type IV conjugative transfer system coupling protein TraD virb4
NPH93_RS27135 (NPH93_27125) 167397..168086 - 690 Protein_179 hypothetical protein -
NPH93_RS27140 (NPH93_27130) 168278..169009 - 732 WP_032329926 conjugal transfer complement resistance protein TraT -
NPH93_RS27145 (NPH93_27135) 169318..169842 - 525 WP_015065538 hypothetical protein -
NPH93_RS27150 (NPH93_27140) 169853..172696 - 2844 WP_023157999 conjugal transfer mating-pair stabilization protein TraG traG
NPH93_RS27155 (NPH93_27145) 172696..174075 - 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
NPH93_RS27160 (NPH93_27150) 174053..174496 - 444 WP_023158001 F-type conjugal transfer protein TrbF -
NPH93_RS27165 (NPH93_27155) 174542..175099 - 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
NPH93_RS27170 (NPH93_27160) 175071..175310 - 240 WP_023158003 type-F conjugative transfer system pilin chaperone TraQ -
NPH93_RS27175 (NPH93_27165) 175321..176073 - 753 WP_015065535 type-F conjugative transfer system pilin assembly protein TraF traF
NPH93_RS27180 (NPH93_27170) 176094..176420 - 327 WP_015065534 hypothetical protein -
NPH93_RS27185 (NPH93_27175) 176433..176681 - 249 WP_004152675 hypothetical protein -
NPH93_RS27190 (NPH93_27180) 176659..176913 - 255 WP_015065558 conjugal transfer protein TrbE -
NPH93_RS27195 (NPH93_27185) 176945..178900 - 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
NPH93_RS27200 (NPH93_27190) 178959..179606 - 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
NPH93_RS27205 (NPH93_27195) 179685..179861 - 177 WP_162866177 hypothetical protein -
NPH93_RS27210 (NPH93_27200) 179882..180871 - 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
NPH93_RS27215 (NPH93_27205) 180868..181269 - 402 WP_023158005 hypothetical protein -
NPH93_RS27220 (NPH93_27210) 181304..181939 - 636 WP_023158006 type-F conjugative transfer system protein TraW traW
NPH93_RS27225 (NPH93_27215) 181939..182328 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
NPH93_RS27230 (NPH93_27220) 182328..184967 - 2640 WP_023158007 type IV secretion system protein TraC virb4
NPH93_RS27235 (NPH93_27225) 185039..185437 - 399 WP_023158008 hypothetical protein -
NPH93_RS27240 (NPH93_27230) 185445..185834 - 390 WP_023158009 hypothetical protein -
NPH93_RS27245 (NPH93_27235) 185877..186281 - 405 WP_016831042 hypothetical protein -
NPH93_RS27250 (NPH93_27240) 186348..186659 - 312 WP_014386200 hypothetical protein -
NPH93_RS27255 (NPH93_27245) 186660..186878 - 219 WP_014386199 hypothetical protein -
NPH93_RS27260 (NPH93_27250) 186902..187191 - 290 Protein_204 hypothetical protein -
NPH93_RS27265 (NPH93_27255) 187196..187606 - 411 WP_016831039 hypothetical protein -
NPH93_RS27270 (NPH93_27260) 187738..188322 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
NPH93_RS27275 (NPH93_27265) 188345..188941 - 597 Protein_207 conjugal transfer pilus-stabilizing protein TraP -
NPH93_RS27280 (NPH93_27270) 188934..190358 - 1425 WP_023158013 F-type conjugal transfer pilus assembly protein TraB traB
NPH93_RS27285 (NPH93_27275) 190358..191098 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
NPH93_RS27290 (NPH93_27280) 191085..191651 - 567 WP_016831035 type IV conjugative transfer system protein TraE traE
NPH93_RS27295 (NPH93_27285) 191671..191976 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
NPH93_RS27300 (NPH93_27290) 191990..192358 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
NPH93_RS27305 (NPH93_27295) 192420..192626 - 207 WP_171773970 TraY domain-containing protein -
NPH93_RS27310 (NPH93_27300) 192759..193478 - 720 WP_016831034 conjugal transfer protein TrbJ -
NPH93_RS27315 (NPH93_27305) 193678..194094 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
NPH93_RS27320 (NPH93_27310) 194485..194970 + 486 WP_004178063 transglycosylase SLT domain-containing protein virB1
NPH93_RS27325 (NPH93_27315) 195003..195332 - 330 WP_011977736 DUF5983 family protein -
NPH93_RS27330 (NPH93_27320) 195365..196186 - 822 WP_004182076 DUF932 domain-containing protein -
NPH93_RS27335 (NPH93_27325) 197014..197577 - 564 WP_004182054 methyltransferase -
NPH93_RS27340 (NPH93_27330) 197625..198980 - 1356 WP_004182052 DUF3560 domain-containing protein -
NPH93_RS27345 (NPH93_27335) 199032..199262 - 231 WP_001568051 hypothetical protein -
NPH93_RS27350 (NPH93_27340) 199354..199581 - 228 WP_004182050 hypothetical protein -

Host bacterium

ID   5323 GenBank   NZ_CP101836
Plasmid name   pGN4549-1 Incompatibility group   IncFIB
Plasmid size   217547 bp Coordinate of oriT [Strand]   194363..194412 [+]
Host baterium   Klebsiella pneumoniae strain GN4549

Cargo genes

Drug resistance gene   blaCTX-M-15, dfrA14, qnrB1, tet(A), aac(6')-Ib-cr, blaOXA-1
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP, pcoA, pcoB, pcoC, pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR, fecE, fecD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -