Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105974
Name   oriT_pRHB16-C24_2 in_silico
Organism   Klebsiella pneumoniae strain RHB16-C24
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP057723 (121326..121375 [+], 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_pRHB16-C24_2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4021 GenBank   WP_102000654
Name   traI_HVX23_RS25290_pRHB16-C24_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: 190481.24 Da        Isoelectric Point: 6.1898

>WP_102000654.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRQEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDREGDRLDLKVSAVD
SQWTLFRADTLPVAEGERLVVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQALAAGAGVFDGIK
VGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKSRSGETDLDTAIAQQKAGLHTPAEQAIHLAIPLLESQDLTFSRPQLLATAMETGGGKVSMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKGAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVEARTTASFLHD
TQLLQRNGQIPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPKQEKAIEK
ALSEGKTLPEGQPASLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERFISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDPERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGGAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIQHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGSSPGRFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWAEPAPVAPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPVTEKTTLPDDPQFRRQEAAIQQVASVRLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

TrwC relaxase (TrwC)

(11-283)

DNA helicase TraI (TraI_C)

(1432-1554)

AAA domain (AAA_30)

(970-1156)

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

(634-713)


  Protein structure



No available structure.




T4CP

ID   4032 GenBank   WP_094309621
Name   traD_HVX23_RS25295_pRHB16-C24_2 insolico UniProt ID   _
Length   760 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 760 a.a.        Molecular weight: 84847.80 Da        Isoelectric Point: 5.0065

>WP_094309621.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTAWCGEQLWTGFVFAATVSIVICIVTFFVASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYDAWLADEQTQRDMQRREEVNINHSHRHDEQDDVEIGGNI

  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: 92965..121933

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVX23_RS25295 (HVX23_25295) 92965..95247 - 2283 WP_094309621 type IV conjugative transfer system coupling protein TraD virb4
HVX23_RS25300 (HVX23_25300) 95374..96063 - 690 WP_181672279 hypothetical protein -
HVX23_RS25305 (HVX23_25305) 96256..96987 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
HVX23_RS25310 (HVX23_25310) 97175..97702 - 528 WP_040120388 conjugal transfer protein TraS -
HVX23_RS25315 (HVX23_25315) 97708..100557 - 2850 WP_117062995 conjugal transfer mating-pair stabilization protein TraG traG
HVX23_RS25320 (HVX23_25320) 100557..101936 - 1380 WP_072198320 conjugal transfer pilus assembly protein TraH traH
HVX23_RS25325 (HVX23_25325) 101914..102357 - 444 WP_065801492 F-type conjugal transfer protein TrbF -
HVX23_RS25330 (HVX23_25330) 102403..102960 - 558 WP_065801493 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HVX23_RS25335 (HVX23_25335) 102932..103171 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HVX23_RS25340 (HVX23_25340) 103182..103934 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
HVX23_RS25345 (HVX23_25345) 103955..104281 - 327 WP_004152676 hypothetical protein -
HVX23_RS25350 (HVX23_25350) 104294..104542 - 249 WP_117062994 hypothetical protein -
HVX23_RS25355 (HVX23_25355) 104520..104774 - 255 WP_004152674 conjugal transfer protein TrbE -
HVX23_RS25360 (HVX23_25360) 104806..106761 - 1956 WP_117062993 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HVX23_RS25365 (HVX23_25365) 106820..107458 - 639 WP_065801495 type-F conjugative transfer system pilin assembly protein TrbC trbC
HVX23_RS25370 (HVX23_25370) 107471..108460 - 990 WP_046664201 conjugal transfer pilus assembly protein TraU traU
HVX23_RS25375 (HVX23_25375) 108457..108858 - 402 WP_004194979 hypothetical protein -
HVX23_RS25380 (HVX23_25380) 108893..109528 - 636 WP_032441885 type-F conjugative transfer system protein TraW traW
HVX23_RS25385 (HVX23_25385) 109528..109917 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
HVX23_RS25390 (HVX23_25390) 109917..112556 - 2640 WP_087786333 type IV secretion system protein TraC virb4
HVX23_RS25395 (HVX23_25395) 112628..113026 - 399 WP_074188112 hypothetical protein -
HVX23_RS25400 (HVX23_25400) 113034..113333 - 300 WP_055322554 hypothetical protein -
HVX23_RS25405 (HVX23_25405) 113376..113780 - 405 WP_065801498 hypothetical protein -
HVX23_RS25410 (HVX23_25410) 113847..114158 - 312 WP_065801499 hypothetical protein -
HVX23_RS25415 (HVX23_25415) 114159..114377 - 219 WP_004195468 hypothetical protein -
HVX23_RS25420 (HVX23_25420) 114700..115284 - 585 WP_065801500 type IV conjugative transfer system lipoprotein TraV traV
HVX23_RS25425 (HVX23_25425) 115307..115903 - 597 WP_065801501 conjugal transfer pilus-stabilizing protein TraP -
HVX23_RS25430 (HVX23_25430) 115896..117320 - 1425 WP_016529134 F-type conjugal transfer pilus assembly protein TraB traB
HVX23_RS25435 (HVX23_25435) 117320..118060 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
HVX23_RS25440 (HVX23_25440) 118047..118613 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
HVX23_RS25445 (HVX23_25445) 118633..118938 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HVX23_RS25450 (HVX23_25450) 118952..119320 - 369 WP_064147976 type IV conjugative transfer system pilin TraA -
HVX23_RS25455 (HVX23_25455) 119382..119588 - 207 WP_172412524 TraY domain-containing protein -
HVX23_RS25460 (HVX23_25460) 119721..120440 - 720 WP_023320098 hypothetical protein -
HVX23_RS25465 (HVX23_25465) 120640..121057 - 418 Protein_139 conjugal transfer relaxosome DNA-binding protein TraM -
HVX23_RS25470 (HVX23_25470) 121448..121933 + 486 WP_065801502 transglycosylase SLT domain-containing protein virB1
HVX23_RS25475 (HVX23_25475) 121966..122295 - 330 WP_011977736 DUF5983 family protein -
HVX23_RS25480 (HVX23_25480) 122328..123149 - 822 WP_065801503 DUF932 domain-containing protein -
HVX23_RS25485 (HVX23_25485) 123983..124396 - 414 WP_004182074 helix-turn-helix domain-containing protein -
HVX23_RS25490 (HVX23_25490) 124397..124675 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HVX23_RS25495 (HVX23_25495) 124665..124985 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HVX23_RS25500 (HVX23_25500) 125066..125290 - 225 WP_065801604 hypothetical protein -
HVX23_RS25505 (HVX23_25505) 125301..125513 - 213 WP_019706020 hypothetical protein -
HVX23_RS25510 (HVX23_25510) 125574..125930 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   6411 GenBank   NZ_CP057723
Plasmid name   pRHB16-C24_2 Incompatibility group   IncFIB
Plasmid size   147522 bp Coordinate of oriT [Strand]   121326..121375 [+]
Host baterium   Klebsiella pneumoniae strain RHB16-C24

Cargo genes

Drug resistance gene   -
Virulence gene   iutA, iucD, iucC, iucB, iucA, cseA
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIE9