Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105994
Name   oriT_pRHB30-C05_3 in_silico
Organism   Klebsiella pneumoniae strain RHB30-C05
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP057315 (121325..121374 [+], 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_pRHB30-C05_3
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTCATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4029 GenBank   WP_102000654
Name   traI_HVY73_RS26370_pRHB30-C05_3 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   4041 GenBank   WP_094309621
Name   traD_HVY73_RS26375_pRHB30-C05_3 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..121932

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HVY73_RS26375 (HVY73_26390) 92965..95247 - 2283 WP_094309621 type IV conjugative transfer system coupling protein TraD virb4
HVY73_RS26380 (HVY73_26395) 95374..96063 - 690 WP_181672279 hypothetical protein -
HVY73_RS26385 (HVY73_26400) 96256..96987 - 732 WP_004152629 conjugal transfer complement resistance protein TraT -
HVY73_RS26390 (HVY73_26405) 97175..97702 - 528 WP_040120388 conjugal transfer protein TraS -
HVY73_RS26395 (HVY73_26410) 97708..100557 - 2850 WP_117062995 conjugal transfer mating-pair stabilization protein TraG traG
HVY73_RS26400 (HVY73_26415) 100557..101936 - 1380 WP_072198320 conjugal transfer pilus assembly protein TraH traH
HVY73_RS26405 (HVY73_26420) 101914..102357 - 444 WP_065801492 F-type conjugal transfer protein TrbF -
HVY73_RS26410 (HVY73_26425) 102403..102960 - 558 WP_065801493 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HVY73_RS26415 (HVY73_26430) 102932..103171 - 240 WP_004144400 type-F conjugative transfer system pilin chaperone TraQ -
HVY73_RS26420 (HVY73_26435) 103182..103934 - 753 WP_004152677 type-F conjugative transfer system pilin assembly protein TraF traF
HVY73_RS26425 (HVY73_26440) 103955..104281 - 327 WP_004152676 hypothetical protein -
HVY73_RS26430 (HVY73_26445) 104294..104542 - 249 WP_117062994 hypothetical protein -
HVY73_RS26435 (HVY73_26450) 104520..104774 - 255 WP_004152674 conjugal transfer protein TrbE -
HVY73_RS26440 (HVY73_26455) 104806..106761 - 1956 WP_117062993 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HVY73_RS26445 (HVY73_26460) 106820..107458 - 639 WP_065801495 type-F conjugative transfer system pilin assembly protein TrbC trbC
HVY73_RS26450 (HVY73_26465) 107471..108460 - 990 WP_046664201 conjugal transfer pilus assembly protein TraU traU
HVY73_RS26455 (HVY73_26470) 108457..108858 - 402 WP_004194979 hypothetical protein -
HVY73_RS26460 (HVY73_26475) 108893..109528 - 636 WP_032441885 type-F conjugative transfer system protein TraW traW
HVY73_RS26465 (HVY73_26480) 109528..109917 - 390 WP_004167468 type-F conjugative transfer system protein TrbI -
HVY73_RS26470 (HVY73_26485) 109917..112556 - 2640 WP_087786333 type IV secretion system protein TraC virb4
HVY73_RS26475 (HVY73_26490) 112628..113026 - 399 WP_074188112 hypothetical protein -
HVY73_RS26480 (HVY73_26495) 113034..113333 - 300 WP_055322554 hypothetical protein -
HVY73_RS26485 (HVY73_26500) 113376..113780 - 405 WP_065801498 hypothetical protein -
HVY73_RS26490 (HVY73_26505) 113847..114158 - 312 WP_065801499 hypothetical protein -
HVY73_RS26495 (HVY73_26510) 114159..114377 - 219 WP_004195468 hypothetical protein -
HVY73_RS26500 (HVY73_26515) 114700..115284 - 585 WP_065801500 type IV conjugative transfer system lipoprotein TraV traV
HVY73_RS26505 (HVY73_26520) 115307..115903 - 597 WP_065801501 conjugal transfer pilus-stabilizing protein TraP -
HVY73_RS26510 (HVY73_26525) 115896..117320 - 1425 WP_117062992 F-type conjugal transfer pilus assembly protein TraB traB
HVY73_RS26515 (HVY73_26530) 117320..118060 - 741 WP_004152497 type-F conjugative transfer system secretin TraK traK
HVY73_RS26520 (HVY73_26535) 118047..118613 - 567 WP_004152602 type IV conjugative transfer system protein TraE traE
HVY73_RS26525 (HVY73_26540) 118633..118938 - 306 WP_004178059 type IV conjugative transfer system protein TraL traL
HVY73_RS26530 (HVY73_26545) 118952..119320 - 369 WP_064147976 type IV conjugative transfer system pilin TraA -
HVY73_RS26535 (HVY73_26550) 119382..119588 - 207 WP_172412524 TraY domain-containing protein -
HVY73_RS26540 (HVY73_26555) 119721..120440 - 720 WP_023320098 hypothetical protein -
HVY73_RS26545 (HVY73_26560) 120640..121056 - 417 WP_074181767 conjugal transfer relaxosome DNA-binding protein TraM -
HVY73_RS26550 (HVY73_26565) 121447..121932 + 486 WP_065801502 transglycosylase SLT domain-containing protein virB1
HVY73_RS26555 (HVY73_26570) 121965..122294 - 330 WP_011977736 DUF5983 family protein -
HVY73_RS26560 (HVY73_26575) 122327..123148 - 822 WP_065801503 DUF932 domain-containing protein -
HVY73_RS26565 (HVY73_26580) 123982..124395 - 414 WP_004182074 helix-turn-helix domain-containing protein -
HVY73_RS26570 (HVY73_26585) 124396..124674 - 279 WP_004152721 helix-turn-helix transcriptional regulator -
HVY73_RS26575 (HVY73_26590) 124664..124984 - 321 WP_004152720 type II toxin-antitoxin system RelE/ParE family toxin -
HVY73_RS26580 (HVY73_26595) 125065..125289 - 225 WP_065801604 hypothetical protein -
HVY73_RS26585 (HVY73_26600) 125300..125512 - 213 WP_019706020 hypothetical protein -
HVY73_RS26590 (HVY73_26605) 125573..125929 - 357 WP_019706019 hypothetical protein -

Host bacterium

ID   6431 GenBank   NZ_CP057315
Plasmid name   pRHB30-C05_3 Incompatibility group   IncFIB
Plasmid size   147224 bp Coordinate of oriT [Strand]   121325..121374 [+]
Host baterium   Klebsiella pneumoniae strain RHB30-C05

Cargo genes

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