Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106572
Name   oriT_pNY1688-2 in_silico
Organism   Klebsiella aerogenes strain NY1688
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP094274 (28533..28582 [-], 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_pNY1688-2
AAATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4365 GenBank   WP_029498346
Name   traI_MQE04_RS26965_pNY1688-2 insolico UniProt ID   A0A2R4NEL5
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190742.66 Da        Isoelectric Point: 6.1403

>WP_029498346.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSQVKSAGSAGNYYTEKDNYYVIGSMEERWQGKGAELLGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKKDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINATQNGDKWQTLASDTVGKTGFSETILANRIAFGKIYQNSLRADVES
MGYKTVDAGRNGMWEMEGVPVESFSTRSQELLEAAGPDASLKSRDVAALDTRKSKEAIDPAENMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFDLARKGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPENRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRADTLPVAEGERLAVLGKIPDTRLKGGESITVMKVEEGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETAMVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGYGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQMPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGAWAPGSSVVEFTPKQEKAIEK
ALSEGKTLLEGQPATLYEALVKDYTGRTPEAQSQTLVITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKLTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNEDARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRIWAEPAPVAPVPQTGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGTEKTTLPDDPQFRRQEEAIQQVASERLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(634-713)

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

(576-628)

AAA domain (AAA_30)

(970-1156)

TrwC relaxase (TrwC)

(11-283)

DNA helicase TraI (TraI_C)

(1432-1554)


  Protein structure



No available structure.




T4CP

ID   4400 GenBank   WP_048255491
Name   traD_MQE04_RS26960_pNY1688-2 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: 84914.98 Da        Isoelectric Point: 5.0560

>WP_048255491.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSREIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPEPGPADTDSHAGEQPEPVSPPA
PAEMTVSPAPVKAPPTTKRPAAEPPVLPVTPIPLLKPKAAAAAATASSAGTPAAAAGGTEQELAQQSAEQ
GQDMLPAGMNEDGVIEDMQAYAAWLADEQTQRDMQRREEVNINHNHRHDEQDDVEIGGNI

  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: 27975..57187

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
MQE04_RS26730 (MQE04_26730) 23512..23868 + 357 WP_014343501 hypothetical protein -
MQE04_RS26735 (MQE04_26735) 23929..24141 + 213 WP_014343500 hypothetical protein -
MQE04_RS26740 (MQE04_26740) 24152..24376 + 225 WP_014343499 hypothetical protein -
MQE04_RS26745 (MQE04_26745) 24457..24777 + 321 WP_014343498 type II toxin-antitoxin system RelE/ParE family toxin -
MQE04_RS26750 (MQE04_26750) 24767..25045 + 279 WP_004152721 helix-turn-helix transcriptional regulator -
MQE04_RS26755 (MQE04_26755) 25049..25153 + 105 Protein_38 transcriptional regulator -
MQE04_RS26760 (MQE04_26760) 25982..26140 + 159 Protein_39 DUF945 domain-containing protein -
MQE04_RS26765 (MQE04_26765) 26196..26893 + 698 WP_095033700 IS1-like element IS1B family transposase -
MQE04_RS26770 (MQE04_26770) 26909..27580 + 672 Protein_41 DUF932 domain-containing protein -
MQE04_RS26775 (MQE04_26775) 27613..27942 + 330 WP_013214015 DUF5983 family protein -
MQE04_RS26780 (MQE04_26780) 27975..28460 - 486 WP_014343495 transglycosylase SLT domain-containing protein virB1
MQE04_RS26785 (MQE04_26785) 28851..29267 + 417 WP_014343494 conjugal transfer relaxosome DNA-binding protein TraM -
MQE04_RS26790 (MQE04_26790) 29467..30204 + 738 WP_013214018 conjugal transfer protein TrbJ -
MQE04_RS26795 (MQE04_26795) 30319..30525 + 207 WP_171773970 TraY domain-containing protein -
MQE04_RS26800 (MQE04_26800) 30587..30955 + 369 WP_004194426 type IV conjugative transfer system pilin TraA -
MQE04_RS26805 (MQE04_26805) 30969..31274 + 306 WP_004144424 type IV conjugative transfer system protein TraL traL
MQE04_RS26810 (MQE04_26810) 31294..31860 + 567 WP_016831035 type IV conjugative transfer system protein TraE traE
MQE04_RS26815 (MQE04_26815) 31847..32587 + 741 WP_047670045 type-F conjugative transfer system secretin TraK traK
MQE04_RS26820 (MQE04_26820) 32587..34011 + 1425 WP_015632498 F-type conjugal transfer pilus assembly protein TraB traB
MQE04_RS26825 (MQE04_26825) 34004..34600 + 597 WP_047670043 conjugal transfer pilus-stabilizing protein TraP -
MQE04_RS26830 (MQE04_26830) 34623..35207 + 585 WP_014386196 type IV conjugative transfer system lipoprotein TraV traV
MQE04_RS26835 (MQE04_26835) 35339..35749 + 411 WP_015632501 hypothetical protein -
MQE04_RS26840 (MQE04_26840) 35754..36023 + 270 WP_032433956 hypothetical protein -
MQE04_RS26845 (MQE04_26845) 36062..36280 + 219 WP_004171484 hypothetical protein -
MQE04_RS26850 (MQE04_26850) 36281..36592 + 312 WP_015632502 hypothetical protein -
MQE04_RS26855 (MQE04_26855) 36659..37063 + 405 WP_032433941 hypothetical protein -
MQE04_RS26860 (MQE04_26860) 37106..37495 + 390 WP_015632504 hypothetical protein -
MQE04_RS26865 (MQE04_26865) 37503..37901 + 399 WP_015632505 hypothetical protein -
MQE04_RS26870 (MQE04_26870) 37973..40612 + 2640 WP_015632506 type IV secretion system protein TraC virb4
MQE04_RS26875 (MQE04_26875) 40612..41001 + 390 WP_015632507 type-F conjugative transfer system protein TrbI -
MQE04_RS26880 (MQE04_26880) 41001..41636 + 636 WP_047670041 type-F conjugative transfer system protein TraW traW
MQE04_RS26885 (MQE04_26885) 41671..42072 + 402 WP_004194979 hypothetical protein -
MQE04_RS26890 (MQE04_26890) 42069..43058 + 990 WP_015632509 conjugal transfer pilus assembly protein TraU traU
MQE04_RS26895 (MQE04_26895) 43334..43981 + 648 WP_015632510 type-F conjugative transfer system pilin assembly protein TrbC trbC
MQE04_RS26900 (MQE04_26900) 44040..45995 + 1956 WP_015065533 type-F conjugative transfer system mating-pair stabilization protein TraN traN
MQE04_RS26905 (MQE04_26905) 46027..46281 + 255 WP_032433943 conjugal transfer protein TrbE -
MQE04_RS26910 (MQE04_26910) 46259..46507 + 249 WP_004152675 hypothetical protein -
MQE04_RS26915 (MQE04_26915) 46520..46846 + 327 WP_015632512 hypothetical protein -
MQE04_RS26920 (MQE04_26920) 46867..47619 + 753 WP_015632513 type-F conjugative transfer system pilin assembly protein TraF traF
MQE04_RS26925 (MQE04_26925) 47630..47869 + 240 WP_048255490 type-F conjugative transfer system pilin chaperone TraQ -
MQE04_RS26930 (MQE04_26930) 47841..48398 + 558 WP_023158002 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
MQE04_RS26935 (MQE04_26935) 48444..48887 + 444 WP_023158001 F-type conjugal transfer protein TrbF -
MQE04_RS26940 (MQE04_26940) 48865..50244 + 1380 WP_023158000 conjugal transfer pilus assembly protein TraH traH
MQE04_RS26945 (MQE04_26945) 50244..53093 + 2850 WP_023329044 conjugal transfer mating-pair stabilization protein TraG traG
MQE04_RS26950 (MQE04_26950) 53099..53626 + 528 WP_029498351 conjugal transfer protein TraS -
MQE04_RS26955 (MQE04_26955) 53816..54547 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
MQE04_RS26960 (MQE04_26960) 54905..57187 + 2283 WP_048255491 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   7009 GenBank   NZ_CP094274
Plasmid name   pNY1688-2 Incompatibility group   IncFII
Plasmid size   112047 bp Coordinate of oriT [Strand]   28533..28582 [-]
Host baterium   Klebsiella aerogenes strain NY1688

Cargo genes

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