Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105037
Name   oriT_pC2974-2 in_silico
Organism   Klebsiella pneumoniae strain C2974
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039796 (142370..142419 [+], 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_pC2974-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3525 GenBank   WP_162262172
Name   traI_FBF58_RS26975_pC2974-2 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190437.95 Da        Isoelectric Point: 6.0893

>WP_162262172.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPAGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

AAA domain (AAA_30)

(970-1156)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)

TrwC relaxase (TrwC)

(10-283)


  Protein structure



No available structure.




T4CP

ID   3488 GenBank   WP_014386205
Name   traD_FBF58_RS26980_pC2974-2 insolico UniProt ID   _
Length   769 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 769 a.a.        Molecular weight: 85924.97 Da        Isoelectric Point: 5.1787

>WP_014386205.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAVAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 113298..142977

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FBF58_RS26980 (FBF58_27055) 113298..115607 - 2310 WP_014386205 type IV conjugative transfer system coupling protein TraD virb4
FBF58_RS26985 115734..116423 - 690 WP_014343485 hypothetical protein -
FBF58_RS26990 (FBF58_27065) 116616..117347 - 732 WP_013214036 conjugal transfer complement resistance protein TraT -
FBF58_RS26995 (FBF58_27070) 117598..118200 - 603 WP_013214035 conjugal transfer protein TraS -
FBF58_RS27000 (FBF58_27075) 118223..121045 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
FBF58_RS27005 (FBF58_27080) 121045..122424 - 1380 WP_072157884 conjugal transfer pilus assembly protein TraH traH
FBF58_RS27010 (FBF58_27085) 122402..122845 - 444 WP_013214032 F-type conjugal transfer protein TrbF -
FBF58_RS27015 (FBF58_27090) 122891..123448 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
FBF58_RS27020 (FBF58_27095) 123420..123659 - 240 WP_032440623 type-F conjugative transfer system pilin chaperone TraQ -
FBF58_RS27025 (FBF58_27100) 123670..124422 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
FBF58_RS27030 (FBF58_27105) 124443..124769 - 327 WP_013214030 hypothetical protein -
FBF58_RS27035 (FBF58_27110) 124782..125030 - 249 WP_013214029 hypothetical protein -
FBF58_RS27040 (FBF58_27115) 125008..125262 - 255 WP_004152674 conjugal transfer protein TrbE -
FBF58_RS27045 (FBF58_27120) 125294..127249 - 1956 WP_014343489 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FBF58_RS27050 (FBF58_27125) 127308..127946 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
FBF58_RS27055 (FBF58_27130) 127959..128948 - 990 WP_029497420 conjugal transfer pilus assembly protein TraU traU
FBF58_RS27060 (FBF58_27135) 128945..129346 - 402 WP_004194979 hypothetical protein -
FBF58_RS27065 (FBF58_27140) 129381..130016 - 636 WP_162262138 type-F conjugative transfer system protein TraW traW
FBF58_RS27070 (FBF58_27145) 130016..130405 - 390 WP_013214025 type-F conjugative transfer system protein TrbI -
FBF58_RS27075 (FBF58_27150) 130405..133044 - 2640 WP_013214024 type IV secretion system protein TraC virb4
FBF58_RS27080 (FBF58_27155) 133116..133514 - 399 WP_014343490 hypothetical protein -
FBF58_RS27090 (FBF58_27170) 133879..134295 - 417 WP_032408906 hypothetical protein -
FBF58_RS27095 (FBF58_27175) 134362..134673 - 312 WP_029497417 hypothetical protein -
FBF58_RS27100 (FBF58_27180) 134674..134892 - 219 WP_004195468 hypothetical protein -
FBF58_RS27105 (FBF58_27185) 134916..135206 - 291 WP_014386198 hypothetical protein -
FBF58_RS27110 (FBF58_27190) 135211..135621 - 411 WP_014386197 hypothetical protein -
FBF58_RS27115 (FBF58_27195) 135752..136336 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
FBF58_RS27120 (FBF58_27200) 136383..136955 - 573 WP_014386195 conjugal transfer pilus-stabilizing protein TraP -
FBF58_RS27125 (FBF58_27205) 136948..138372 - 1425 WP_162262137 F-type conjugal transfer pilus assembly protein TraB traB
FBF58_RS27130 (FBF58_27210) 138372..139112 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
FBF58_RS27135 (FBF58_27215) 139099..139665 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
FBF58_RS27140 (FBF58_27220) 139685..139990 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
FBF58_RS27145 (FBF58_27225) 140004..140372 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
FBF58_RS27150 (FBF58_27230) 140434..140640 - 207 WP_171773970 TraY domain-containing protein -
FBF58_RS27155 (FBF58_27235) 140773..141492 - 720 WP_014386192 conjugal transfer protein -
FBF58_RS27160 (FBF58_27240) 141685..142101 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
FBF58_RS27165 (FBF58_27245) 142492..142977 + 486 WP_162262173 transglycosylase SLT domain-containing protein virB1
FBF58_RS27170 (FBF58_27250) 143010..143339 - 330 WP_071994324 DUF5983 family protein -
FBF58_RS27175 (FBF58_27255) 143372..144193 - 822 WP_004152492 DUF932 domain-containing protein -
FBF58_RS27195 (FBF58_27265) 145022..145435 - 414 WP_069985713 helix-turn-helix domain-containing protein -
FBF58_RS27200 (FBF58_27270) 145436..145714 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
FBF58_RS27205 (FBF58_27275) 145704..146024 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
FBF58_RS27210 (FBF58_27280) 146105..146329 - 225 WP_014343499 hypothetical protein -
FBF58_RS27215 (FBF58_27285) 146340..146552 - 213 WP_019706020 hypothetical protein -
FBF58_RS27220 (FBF58_27290) 146613..146969 - 357 WP_019706019 hypothetical protein -
FBF58_RS27235 (FBF58_27305) 147601..147951 - 351 WP_023287104 hypothetical protein -

Host bacterium

ID   5475 GenBank   NZ_CP039796
Plasmid name   pC2974-2 Incompatibility group   IncFIB
Plasmid size   169144 bp Coordinate of oriT [Strand]   142370..142419 [+]
Host baterium   Klebsiella pneumoniae strain C2974

Cargo genes

Drug resistance gene   blaTEM-1B
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
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9