Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115915
Name   oriT_pIncFII_Silv108 in_silico
Organism   Raoultella ornithinolytica strain MQB_Silv_108
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP104453 (26918..26966 [-], 49 nt)
oriT length   49 nt
IRs (inverted repeats)      6..13, 16..23  (GCAAAATT..AATTTTGC)
Location of nic site      32..33
Conserved sequence flanking the
  nic site    		  TGTGTGGTGA
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 49 nt

>oriT_pIncFII_Silv108
AATCTGCAAAATTTTAATTTTGCGTAGTGTGTGGTGATTTTGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10187 GenBank   WP_040212835
Name   traI_N2J37_RS29905_pIncFII_Silv108 insolico UniProt ID   A0A509A0S3
Length   1752 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 190231.91 Da        Isoelectric Point: 6.2218

>WP_040212835.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Klebsiella/Raoultella group]
MLSFSQVKSAGSAGNYYTDKDNYYVIGSMDERWQGKGAEALGLEGKVDKQVFTELLQGKLPDGSDLTRIQ
DGVNKHRPGYDLTFSAPKSVSMLAMLGGDKRLIDAHNRAVTVALNQVESLASTRVKRDGVSETVLTGNLI
IARFNHDTSRAQDPQIHTHSVVINTTQNGDKWQTLASDTVGKTGFSENILANRIALGKIYQNSLRADVES
MGYKTVDAGKNGMWEMEGVPVESFSTRSQELREAAGPDASLKSRDVAALDTRKSKEAIDPAEKMVEWMNT
LKETGFDIRGYREAADARAAELARAPAAPVNTDGPDITDVVTKAIAGLSDRKVQFTYADLLARTVGQLEA
KDGVFELARAGIDAAIEREQLIPLDREKGLFTSNIHVLDELAVKALSQEVQRQNHVSVTPDASVVRQVPF
SDAVSVLAQDRPVMGIVSGQGGATGQRERVAELTLMAREQGRDVHILAADNRSRDFLAGDVRLAGETVTG
KSALQDGTAFIPGGTLIVDQAEKLSLKETISLLDGAMRHNVQVLLSDSGKRSGTGSALTVLKDSGVNTYR
WQGGHQTTADIISEPDKGARYSRLAQEFAVSVREGQESVAQISGTREQSVLNGLIRDSLRHEGVLGEKDT
TITALTPVWLDSKSRGVRDYYREGMVMERWDPETRTHDRFVIDRVTASSNMLTLKDRDGVRLDLKVSAVD
SQWTLFRAETLPVAEGERLAVLGKIPDTRLKGGESITVMKVEDGQLTVQRPGQKTTQTLAVGAGVFDGIK
IGHGWVESPGRSVSETATVFASVTQRELDNATLNQLAQSGSHLRLYSAQDAARTTEKLSRHTAFSVVSEQ
LKTRSGETDLDAAIAQQKAGLRTPAEQAIHLAIPLLESEKLTFSRPQLLATALETGGGKVPMADIDTTIQ
AQIRSGQLLNVPVAHGHGNDLLISRQTWDAEKSILTHVLEGKDAVAPLMDRVPASLMTDLTAGQRAATRM
ILESTDRFTVVQGYAGVGKTTQFRAVMSAISLLPEETRPRVIGLAPTHRAVGEMQSAGVDARTTASFLHD
TQLLQRNGQTPDFSNTLFLLDESSMVGLADMAKAHSLIVAGGGRAVSSGDNDQLQPIAPGQPFRLMQQRS
AADVAIMKEIVRQVPELRPAVYSLIERDVHRALTTIEQVTPEQVPRKEGVWAPGSSVVEFTPAQEKAIQK
ALSEGETLPAGQPATLYEALVKDYTGRTPEAQSQTLIITHLNKDRRALNSLIHDARRENGETGKEEITLP
VLVTSNIRDGELRKLSTWTAHKEAVALVDNVYHRISKVDKDNQLITLTDSEGKERYISPREASAEGVTLY
RQEKITVSQGDRMRFSKSDLERGYVANSIWEVQSVSGDSVTLSDGKTTRTLTPKADQAQQHIDLAYAITA
HGAQGASEPYAIALEGVAGGREQMASFESAYVALSRMKQHVQVYTDSREGWIKAIKHSPEKATAHDILEP
RNDRAVKSADLLFGRARPLDETAAGRAALQQSGLAQGNSPGKFISPGKKYPQPHVALPAFDKNGKAAGIW
LSPLTDRDGRLEAIGGEGRIMGNDAARFVALQNSRNGESLLAGNMGEGVRMARDNPDTGVVVRLAGDDRP
WNPGAITGGRVWADPAPVGPVPQAGADIILPPEVLAQRAAEEQQRREMEKQAEQTAREVAGEARKAGEPA
DRVKEVIGDVIRGLERDRPGPEKTTLPDDPQFRRQEAAIQQVASESLQRERLQAVERDMVRDLNREKTLG
GD

  Protein domains


Predicted by InterproScan.

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

(576-628)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1432-1554)

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

(634-713)

AAA domain (AAA_30)

(970-1156)


  Protein structure



No available structure.




Auxiliary protein

ID   5987 GenBank   WP_020805752
Name   WP_020805752_pIncFII_Silv108 insolico UniProt ID   A0A377TIM3
Length   130 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 130 a.a.        Molecular weight: 14772.81 Da        Isoelectric Point: 4.5715

>WP_020805752.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKIQVYVNDNVAEKINAIAVQRRAEGAKEKDISYSSIASMLLELGLRVYEAQMERKESGFNQMAFNRAL
LESMVKTQFTVNKVLGIECLSPHVNGNPKWEWSGLIENIRDDVSAVMEKFFPNESEIEDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-125)


  Protein structure


Source ID Structure
AlphaFold DB A0A377TIM3


T4CP

ID   11897 GenBank   WP_023313941
Name   traD_N2J37_RS29900_pIncFII_Silv108 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: 85666.78 Da        Isoelectric Point: 5.2499

>WP_023313941.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacterales]
MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLMLMYRLSWQTFVNGCVYWWCTTLGPMR
DIIRSQPVYTIQYYGQSLEYTSEQILADKYTIWCGEQLWTSFVFAAVVSLVICIVTFFIASWVLGRQGKQ
QSEDENTGGRQLSDKPKEVARQMKRDGMASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVR
ARGDMAIIYDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDPFWQG
SGRTIFAEGAYLMREDKDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WIFADELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIA
EFAAGEIGEKEILKASEQYSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLAL
KYKPRPKIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDAPASGTADTNSHAGEQPEPVSQPA
PAEVTVSPAPVKAPATTKMPAAEPSARTAEPPVLRVTTVPLIKPKAAAAAAAAATASSAGTPAAAAGGTE
QELAQQSAEQGQDMLPAGMNKDGVIEDMQAYDAWADEQTLRDMQRREEVNINHSHRHDEQDDVEIGGNF

  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: 29345..56402

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
N2J37_RS29710 (N2J37_29710) 25798..26328 + 531 WP_020277941 antirestriction protein -
N2J37_RS29715 (N2J37_29715) 26366..26773 - 408 WP_020805750 transglycosylase SLT domain-containing protein -
N2J37_RS29720 (N2J37_29720) 27277..27669 + 393 WP_020805752 conjugal transfer relaxosome DNA-binding protein TraM -
N2J37_RS29725 (N2J37_29725) 27907..28608 + 702 WP_023316396 hypothetical protein -
N2J37_RS29730 (N2J37_29730) 28694..28894 + 201 WP_048289787 TraY domain-containing protein -
N2J37_RS29735 (N2J37_29735) 28963..29331 + 369 WP_020316649 type IV conjugative transfer system pilin TraA -
N2J37_RS29740 (N2J37_29740) 29345..29650 + 306 WP_004178059 type IV conjugative transfer system protein TraL traL
N2J37_RS29745 (N2J37_29745) 29670..30236 + 567 WP_020316627 type IV conjugative transfer system protein TraE traE
N2J37_RS29750 (N2J37_29750) 30223..30963 + 741 WP_020804840 type-F conjugative transfer system secretin TraK traK
N2J37_RS29755 (N2J37_29755) 30963..32387 + 1425 WP_023316397 F-type conjugal transfer pilus assembly protein TraB traB
N2J37_RS29760 (N2J37_29760) 32380..32976 + 597 WP_023316398 conjugal transfer pilus-stabilizing protein TraP -
N2J37_RS29765 (N2J37_29765) 32999..33568 + 570 WP_023316399 type IV conjugative transfer system lipoprotein TraV traV
N2J37_RS29770 (N2J37_29770) 33700..34110 + 411 WP_023316400 hypothetical protein -
N2J37_RS29775 (N2J37_29775) 34115..34399 + 285 WP_023316401 hypothetical protein -
N2J37_RS29780 (N2J37_29780) 34423..34641 + 219 WP_023316402 hypothetical protein -
N2J37_RS29785 (N2J37_29785) 34642..34953 + 312 WP_023316403 hypothetical protein -
N2J37_RS29790 (N2J37_29790) 35020..35424 + 405 WP_023340941 hypothetical protein -
N2J37_RS29795 (N2J37_29795) 35421..35711 + 291 WP_023340940 hypothetical protein -
N2J37_RS29800 (N2J37_29800) 35719..36117 + 399 WP_074186017 hypothetical protein -
N2J37_RS29805 (N2J37_29805) 36189..38828 + 2640 WP_060446930 type IV secretion system protein TraC virb4
N2J37_RS29810 (N2J37_29810) 38828..39217 + 390 WP_020314627 type-F conjugative transfer system protein TrbI -
N2J37_RS29815 (N2J37_29815) 39217..39843 + 627 WP_020314628 type-F conjugative transfer system protein TraW traW
N2J37_RS29820 (N2J37_29820) 39887..40846 + 960 WP_029497356 conjugal transfer pilus assembly protein TraU traU
N2J37_RS29825 (N2J37_29825) 40859..41497 + 639 WP_020321224 type-F conjugative transfer system pilin assembly protein TrbC trbC
N2J37_RS29830 (N2J37_29830) 41556..43511 + 1956 WP_020803160 type-F conjugative transfer system mating-pair stabilization protein TraN traN
N2J37_RS29835 (N2J37_29835) 43544..43825 + 282 WP_022644736 hypothetical protein -
N2J37_RS29840 (N2J37_29840) 43815..44042 + 228 WP_012540032 conjugal transfer protein TrbE -
N2J37_RS29845 (N2J37_29845) 44053..44379 + 327 WP_020323521 hypothetical protein -
N2J37_RS29850 (N2J37_29850) 44400..45152 + 753 WP_023316406 type-F conjugative transfer system pilin assembly protein TraF traF
N2J37_RS29855 (N2J37_29855) 45607..45846 + 240 WP_023316407 type-F conjugative transfer system pilin chaperone TraQ -
N2J37_RS29860 (N2J37_29860) 45818..46375 + 558 WP_020804677 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
N2J37_RS29865 (N2J37_29865) 46421..46864 + 444 WP_020804675 F-type conjugal transfer protein TrbF -
N2J37_RS29870 (N2J37_29870) 46842..48221 + 1380 WP_072198238 conjugal transfer pilus assembly protein TraH traH
N2J37_RS29875 (N2J37_29875) 48221..51064 + 2844 WP_023316409 conjugal transfer mating-pair stabilization protein TraG traG
N2J37_RS29880 (N2J37_29880) 51075..51524 + 450 WP_260990879 hypothetical protein -
N2J37_RS29890 (N2J37_29890) 52351..53082 + 732 WP_004152629 conjugal transfer complement resistance protein TraT -
N2J37_RS29895 (N2J37_29895) 53275..53964 + 690 WP_023316411 hypothetical protein -
N2J37_RS29900 (N2J37_29900) 54093..56402 + 2310 WP_023313941 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   16348 GenBank   NZ_CP104453
Plasmid name   pIncFII_Silv108 Incompatibility group   IncFII
Plasmid size   128787 bp Coordinate of oriT [Strand]   26918..26966 [-]
Host baterium   Raoultella ornithinolytica strain MQB_Silv_108

Cargo genes

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