Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101307
Name   oriT_SCPM-O-B-8045|unnamed in_silico
Organism   Klebsiella pneumoniae strain SCPM-O-B-8045
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_NPII01000022 (26947..26996 [-], 50 nt)
oriT length   50 nt
IRs (inverted repeats)      7..14, 17..24  (GCAAAATT..AATTTTGC)
Location of nic site      33..34
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 50 nt

>oriT_SCPM-O-B-8045|unnamed
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1241 GenBank   WP_065519309
Name   traI_CIT28_RS24455_SCPM-O-B-8045|unnamed insolico UniProt ID   A0A809SXI2
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190492.21 Da        Isoelectric Point: 6.0263

>WP_065519309.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWLTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESVTVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDAAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAPGRGNDLLISRQAWDAEKSILTRVLEGKDAVAPLMDRVPDSLMTELTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIAAGGGRAVPSGDTDQLPPIASGQPFRLTQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKITRTLTPKAEQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDNREGWIKAIKNSPEKATAHDILEP
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)

(969-1156)

TrwC relaxase (TrwC)

(11-283)

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

(634-713)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   852 GenBank   WP_013214038
Name   traD_CIT28_RS24450_SCPM-O-B-8045|unnamed 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: 86010.07 Da        Isoelectric Point: 5.1787

>WP_013214038.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGPADTNSHAGEQPEPVSQPA
PADMTVSPEPVKAPPTIKRPAAEPSVRTTEPSVLRVTTVPLIKPKAAAAAAAASTASSSGAPATAAGGTQ
QELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 26389..55001

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CIT28_RS24215 (CIT28_24195) 21545..21862 + 318 WP_014343505 hypothetical protein -
CIT28_RS24220 (CIT28_24200) 22703..23059 + 357 WP_014343501 hypothetical protein -
CIT28_RS24225 (CIT28_24205) 23120..23332 + 213 WP_014343500 hypothetical protein -
CIT28_RS24230 (CIT28_24210) 23343..23567 + 225 WP_014343499 hypothetical protein -
CIT28_RS24235 (CIT28_24215) 23648..23968 + 321 WP_014343498 type II toxin-antitoxin system RelE/ParE family toxin -
CIT28_RS24240 (CIT28_24220) 23958..24236 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
CIT28_RS30360 (CIT28_24225) 24240..24344 + 105 Protein_37 transcriptional regulator -
CIT28_RS24265 (CIT28_24245) 25173..25994 + 822 WP_004152492 DUF932 domain-containing protein -
CIT28_RS24270 (CIT28_24250) 26027..26356 + 330 WP_013214015 DUF5983 family protein -
CIT28_RS24275 (CIT28_24255) 26389..26874 - 486 WP_014343495 transglycosylase SLT domain-containing protein virB1
CIT28_RS24280 (CIT28_24260) 27265..27681 + 417 WP_014343494 conjugal transfer relaxosome DNA-binding protein TraM -
CIT28_RS24285 (CIT28_24265) 27881..28618 + 738 WP_013214018 conjugal transfer protein TrbJ -
CIT28_RS24290 (CIT28_24270) 28733..28939 + 207 WP_171773970 TraY domain-containing protein -
CIT28_RS24295 (CIT28_24275) 29001..29369 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
CIT28_RS24300 (CIT28_24280) 29383..29688 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
CIT28_RS24305 (CIT28_24285) 29708..30274 + 567 WP_004144423 type IV conjugative transfer system protein TraE traE
CIT28_RS24310 (CIT28_24290) 30261..31001 + 741 WP_013214019 type-F conjugative transfer system secretin TraK traK
CIT28_RS24315 (CIT28_24295) 31001..32425 + 1425 WP_013214020 F-type conjugal transfer pilus assembly protein TraB traB
CIT28_RS24320 (CIT28_24300) 32497..33081 + 585 WP_014343493 type IV conjugative transfer system lipoprotein TraV traV
CIT28_RS24325 (CIT28_24305) 33404..33622 + 219 WP_004195468 hypothetical protein -
CIT28_RS24330 (CIT28_24310) 33623..33934 + 312 WP_013214022 hypothetical protein -
CIT28_RS24335 (CIT28_24315) 34001..34405 + 405 WP_004197817 hypothetical protein -
CIT28_RS24350 (CIT28_24330) 34782..35180 + 399 WP_014343490 hypothetical protein -
CIT28_RS24355 (CIT28_24335) 35252..37891 + 2640 WP_013214024 type IV secretion system protein TraC virb4
CIT28_RS24360 (CIT28_24340) 37891..38280 + 390 WP_013214025 type-F conjugative transfer system protein TrbI -
CIT28_RS24365 (CIT28_24345) 38280..38915 + 636 WP_013214026 type-F conjugative transfer system protein TraW traW
CIT28_RS24370 (CIT28_24350) 38950..39351 + 402 WP_004194979 hypothetical protein -
CIT28_RS24375 (CIT28_24355) 39348..40337 + 990 WP_013214027 conjugal transfer pilus assembly protein TraU traU
CIT28_RS24380 (CIT28_24360) 40350..40988 + 639 WP_004193871 type-F conjugative transfer system pilin assembly protein TrbC trbC
CIT28_RS24385 (CIT28_24365) 41047..43002 + 1956 WP_014343489 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CIT28_RS24390 (CIT28_24370) 43034..43288 + 255 WP_004152674 conjugal transfer protein TrbE -
CIT28_RS24395 (CIT28_24375) 43266..43514 + 249 WP_013214029 hypothetical protein -
CIT28_RS24400 (CIT28_24380) 43527..43853 + 327 WP_013214030 hypothetical protein -
CIT28_RS24405 (CIT28_24385) 43874..44626 + 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
CIT28_RS24410 (CIT28_24390) 44637..44876 + 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
CIT28_RS24415 (CIT28_24395) 44848..45405 + 558 WP_013214031 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CIT28_RS24420 (CIT28_24400) 45451..45894 + 444 WP_013214032 F-type conjugal transfer protein TrbF -
CIT28_RS24425 (CIT28_24405) 45872..47251 + 1380 WP_074160414 conjugal transfer pilus assembly protein TraH traH
CIT28_RS24430 (CIT28_24410) 47251..50073 + 2823 WP_013214034 conjugal transfer mating-pair stabilization protein TraG traG
CIT28_RS24435 (CIT28_24415) 50096..50698 + 603 WP_013214035 conjugal transfer protein TraS -
CIT28_RS24440 (CIT28_24420) 50949..51680 + 732 WP_013214036 conjugal transfer complement resistance protein TraT -
CIT28_RS29990 51873..52562 + 690 WP_014343485 hypothetical protein -
CIT28_RS24450 (CIT28_24430) 52689..55001 + 2313 WP_013214038 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1751 GenBank   NZ_NPII01000022
Plasmid name   SCPM-O-B-8045|unnamed Incompatibility group   IncFIB
Plasmid size   82279 bp Coordinate of oriT [Strand]   26947..26996 [-]
Host baterium   Klebsiella pneumoniae strain SCPM-O-B-8045

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9