Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105016
Name   oriT_pC2601-2 in_silico
Organism   Klebsiella pneumoniae strain C2601
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP039814 (121884..121933 [+], 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_pC2601-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3511 GenBank   WP_162262645
Name   traI_FBF56_RS26775_pC2601-2 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: 190522.07 Da        Isoelectric Point: 6.0386

>WP_162262645.1 conjugative transfer relaxase/helicase TraI [Klebsiella pneumoniae]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTQKQEKEIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKTADLLFGRARPLDETAAGRAALQQSGLAQGSSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAMTGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

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

(634-713)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   3465 GenBank   WP_014386205
Name   traD_FBF56_RS26780_pC2601-2 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: 92812..122491

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FBF56_RS26780 (FBF56_26875) 92812..95121 - 2310 WP_014386205 type IV conjugative transfer system coupling protein TraD virb4
FBF56_RS26785 95248..95937 - 690 WP_014343485 hypothetical protein -
FBF56_RS26790 (FBF56_26885) 96130..96861 - 732 WP_013214036 conjugal transfer complement resistance protein TraT -
FBF56_RS26795 (FBF56_26890) 97112..97714 - 603 WP_013214035 conjugal transfer protein TraS -
FBF56_RS26800 (FBF56_26895) 97737..100559 - 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
FBF56_RS26805 (FBF56_26900) 100559..101938 - 1380 WP_072157884 conjugal transfer pilus assembly protein TraH traH
FBF56_RS26810 (FBF56_26905) 101916..102359 - 444 WP_013214032 F-type conjugal transfer protein TrbF -
FBF56_RS26815 (FBF56_26910) 102405..102962 - 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
FBF56_RS26820 (FBF56_26915) 102934..103173 - 240 WP_032440623 type-F conjugative transfer system pilin chaperone TraQ -
FBF56_RS26825 (FBF56_26920) 103184..103936 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
FBF56_RS26830 (FBF56_26925) 103957..104283 - 327 WP_013214030 hypothetical protein -
FBF56_RS26835 (FBF56_26930) 104296..104544 - 249 WP_013214029 hypothetical protein -
FBF56_RS26840 (FBF56_26935) 104522..104776 - 255 WP_004152674 conjugal transfer protein TrbE -
FBF56_RS26845 (FBF56_26940) 104808..106763 - 1956 WP_014343489 type-F conjugative transfer system mating-pair stabilization protein TraN traN
FBF56_RS26850 (FBF56_26945) 106822..107460 - 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
FBF56_RS26855 (FBF56_26950) 107473..108462 - 990 WP_029497420 conjugal transfer pilus assembly protein TraU traU
FBF56_RS26860 (FBF56_26955) 108459..108860 - 402 WP_004194979 hypothetical protein -
FBF56_RS26865 (FBF56_26960) 108895..109530 - 636 WP_162262138 type-F conjugative transfer system protein TraW traW
FBF56_RS26870 (FBF56_26965) 109530..109919 - 390 WP_013214025 type-F conjugative transfer system protein TrbI -
FBF56_RS26875 (FBF56_26970) 109919..112558 - 2640 WP_013214024 type IV secretion system protein TraC virb4
FBF56_RS26880 (FBF56_26975) 112630..113028 - 399 WP_014343490 hypothetical protein -
FBF56_RS26890 (FBF56_26990) 113393..113809 - 417 WP_032408906 hypothetical protein -
FBF56_RS26895 (FBF56_26995) 113876..114187 - 312 WP_029497417 hypothetical protein -
FBF56_RS26900 (FBF56_27000) 114188..114406 - 219 WP_004195468 hypothetical protein -
FBF56_RS26905 (FBF56_27005) 114430..114720 - 291 WP_014386198 hypothetical protein -
FBF56_RS26910 (FBF56_27010) 114725..115135 - 411 WP_014386197 hypothetical protein -
FBF56_RS26915 (FBF56_27015) 115266..115850 - 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
FBF56_RS26920 (FBF56_27020) 115897..116469 - 573 WP_014386195 conjugal transfer pilus-stabilizing protein TraP -
FBF56_RS26925 (FBF56_27025) 116462..117886 - 1425 WP_014386194 F-type conjugal transfer pilus assembly protein TraB traB
FBF56_RS26930 (FBF56_27030) 117886..118626 - 741 WP_014386193 type-F conjugative transfer system secretin TraK traK
FBF56_RS26935 (FBF56_27035) 118613..119179 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
FBF56_RS26940 (FBF56_27040) 119199..119504 - 306 WP_004144424 type IV conjugative transfer system protein TraL traL
FBF56_RS26945 (FBF56_27045) 119518..119886 - 369 WP_004194426 type IV conjugative transfer system pilin TraA -
FBF56_RS26950 (FBF56_27050) 119948..120154 - 207 WP_171773970 TraY domain-containing protein -
FBF56_RS26955 (FBF56_27055) 120287..121006 - 720 WP_014386192 conjugal transfer protein -
FBF56_RS26960 (FBF56_27060) 121199..121615 - 417 WP_072145360 conjugal transfer relaxosome DNA-binding protein TraM -
FBF56_RS26965 (FBF56_27065) 122006..122491 + 486 WP_162262173 transglycosylase SLT domain-containing protein virB1
FBF56_RS26970 (FBF56_27070) 122524..122853 - 330 WP_011977736 DUF5983 family protein -
FBF56_RS26975 (FBF56_27075) 122886..123707 - 822 WP_004152492 DUF932 domain-containing protein -
FBF56_RS26995 (FBF56_27085) 124536..124949 - 414 WP_069985713 helix-turn-helix domain-containing protein -
FBF56_RS27000 (FBF56_27090) 124950..125228 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
FBF56_RS27005 (FBF56_27095) 125218..125538 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
FBF56_RS27010 (FBF56_27100) 125619..125843 - 225 WP_014343499 hypothetical protein -
FBF56_RS27015 (FBF56_27105) 125854..126066 - 213 WP_019706020 hypothetical protein -
FBF56_RS27020 (FBF56_27110) 126127..126483 - 357 WP_019706019 hypothetical protein -
FBF56_RS27035 (FBF56_27125) 127115..127465 - 351 WP_023287104 hypothetical protein -

Host bacterium

ID   5454 GenBank   NZ_CP039814
Plasmid name   pC2601-2 Incompatibility group   IncFIB
Plasmid size   148657 bp Coordinate of oriT [Strand]   121884..121933 [+]
Host baterium   Klebsiella pneumoniae strain C2601

Cargo genes

Drug resistance gene   blaTEM-1B
Virulence gene   -
Metal resistance gene   pcoD, pcoR, pcoS, pcoE, arsH, arsC, arsB, arsA, arsD, arsR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9