Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 119089
• Name: oriT_p202000562-4
• Organism: Shigella sonnei strain 202000562
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_OP038284 (37417..37768 [+], 352 nt)
• oriT length: 352 nt
• IRs (inverted repeats): 192..198, 206..212 (TATAAAA..TTTTATA) 104..109, 119..124 (TTTAAA..TTTAAA) 93..98, 106..111 (GATTTA..TAAATC) 40..47, 50..57 (GCAAAAAC..GTTTTTGC) 4..11, 16..23 (TTGGTGGT..ACCACCAA)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 352 nt

>oriT_p202000562-4
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTTTTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCTAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_OVP42_RS00455_p202000562-4

• ID: 12055
• GenBank: WP_033807965
• Name: traI_OVP42_RS00455_p202000562-4
• UniProt ID: A0A8B4LAZ2
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 191666.38 Da
• Isoelectric Point: 5.9043

>WP_033807965.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDSVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTATSEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

• DNA helicase TraI (TraI_C) (1434-1557)

• AAA domain (AAA_30) (968-1156)

• TrwC relaxase (TrwC) (10-283)

• single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N) (575-626)

• DNA relaxase TraI 2B/2B-like domain (TraI_2B) (633-712)

Protein structure

No available structure.

Auxiliary protein

WP_001151529_p202000562-4

• ID: 6890
• GenBank: WP_001151529
• Name: WP_001151529_p202000562-4
• UniProt ID: A0A7I0L277
• Length: 127 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 127 a.a.
• Molecular weight: 14497.49 Da
• Isoelectric Point: 4.8662

>WP_001151529.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSAEMERFFPKNDDE

Protein domains

Predicted by InterproScan.

• TraM protein, DNA-binding (Tra_M) (1-126)

Protein structure

• AlphaFold DB: A0A7I0L277

T4CP

traC_OVP42_RS00345_p202000562-4

• ID: 14117
• GenBank: WP_000069772
• Name: traC_OVP42_RS00345_p202000562-4
• UniProt ID: _
• Length: 876 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 876 a.a.
• Molecular weight: 99344.15 Da
• Isoelectric Point: 6.4096

>WP_000069772.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

• Family of unknown function (DUF5934) (DUF5934) (291-447)

• TraG P-loop domain (P-loop_TraG) (468-764)

• TraC protein (TraC_F_IV) (39-277)

Protein structure

No available structure.

traD_OVP42_RS00450_p202000562-4

• ID: 14118
• GenBank: WP_113328784
• Name: traD_OVP42_RS00450_p202000562-4
• UniProt ID: _
• Length: 741 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 741 a.a.
• Molecular weight: 84372.17 Da
• Isoelectric Point: 5.2345

>WP_113328784.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGVSTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQSQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA
AYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

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) (173-560)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 36846..61782

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
OVP42_RS00225 (p202000562-4__00040)	33093..33527	+	435	WP_000845953	conjugation system SOS inhibitor PsiB	-
OVP42_RS00230 (p202000562-4__00041)	33524..34286	+	763	Protein_45	plasmid SOS inhibition protein A	-
OVP42_RS00235 (p202000562-4__00042)	34465..34614	+	150	Protein_46	plasmid maintenance protein Mok	-
OVP42_RS00240	34556..34681	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
OVP42_RS00245	35000..35266	-	267	Protein_48	hypothetical protein	-
OVP42_RS00250 (p202000562-4__00043)	35321..35617	+	297	WP_001272251	hypothetical protein	-
OVP42_RS00255 (p202000562-4__00044)	35728..36549	+	822	WP_001234445	DUF932 domain-containing protein	-
OVP42_RS00260 (p202000562-4__00045)	36846..37448	-	603	WP_000243713	transglycosylase SLT domain-containing protein	virB1
OVP42_RS00265 (p202000562-4__00046)	37769..38152	+	384	WP_001151529	conjugal transfer relaxosome DNA-binding protein TraM	-
OVP42_RS00270 (p202000562-4__00047)	38344..38991	+	648	WP_000332523	transcriptional regulator TraJ family protein	-
OVP42_RS00275 (p202000562-4__00048)	39111..39338	+	228	WP_000589556	conjugal transfer relaxosome protein TraY	-
OVP42_RS00280 (p202000562-4__00049)	39372..39731	+	360	WP_001098994	type IV conjugative transfer system pilin TraA	-
OVP42_RS00285 (p202000562-4__00050)	39746..40057	+	312	WP_000012113	type IV conjugative transfer system protein TraL	traL
OVP42_RS00290 (p202000562-4__00051)	40079..40645	+	567	WP_000399780	type IV conjugative transfer system protein TraE	traE
OVP42_RS00295 (p202000562-4__00052)	40632..41360	+	729	WP_001230769	type-F conjugative transfer system secretin TraK	traK
OVP42_RS00300 (p202000562-4__00053)	41360..42787	+	1428	WP_033807957	F-type conjugal transfer pilus assembly protein TraB	traB
OVP42_RS00305 (p202000562-4__00054)	42777..43367	+	591	WP_000002784	conjugal transfer pilus-stabilizing protein TraP	-
OVP42_RS00310 (p202000562-4__00055)	43354..43674	+	321	WP_012881128	conjugal transfer protein TrbD	-
OVP42_RS00315 (p202000562-4__00056)	43671..44186	+	516	WP_000809881	type IV conjugative transfer system lipoprotein TraV	traV
OVP42_RS00320	44321..44542	+	222	WP_001278683	conjugal transfer protein TraR	-
OVP42_RS00325 (p202000562-4__00057)	44535..44948	+	414	WP_000549589	hypothetical protein	-
OVP42_RS00330 (p202000562-4__00058)	44941..45414	+	474	WP_033807958	hypothetical protein	-
OVP42_RS00335 (p202000562-4__00059)	45513..45731	+	219	WP_033807959	hypothetical protein	-
OVP42_RS00340 (p202000562-4__00060)	45759..46106	+	348	WP_000836682	hypothetical protein	-
OVP42_RS00345 (p202000562-4__00061)	46232..48862	+	2631	WP_000069772	type IV secretion system protein TraC	virb4
OVP42_RS00350 (p202000562-4__00062)	48859..49245	+	387	WP_000214084	type-F conjugative transfer system protein TrbI	-
OVP42_RS00355 (p202000562-4__00063)	49242..49874	+	633	WP_001203720	type-F conjugative transfer system protein TraW	traW
OVP42_RS00360 (p202000562-4__00064)	49871..50863	+	993	WP_000830849	conjugal transfer pilus assembly protein TraU	traU
OVP42_RS00365 (p202000562-4__00065)	50893..51198	+	306	WP_000224418	hypothetical protein	-
OVP42_RS00370 (p202000562-4__00066)	51207..51845	+	639	WP_033807960	type-F conjugative transfer system pilin assembly protein TrbC	trbC
OVP42_RS00375 (p202000562-4__00067)	51842..52222	+	381	WP_001462111	hypothetical protein	-
OVP42_RS00380 (p202000562-4__00069)	52458..54362	+	1905	WP_225620370	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
OVP42_RS00385 (p202000562-4__00070)	54389..54646	+	258	WP_033807961	conjugal transfer protein TrbE	-
OVP42_RS00390 (p202000562-4__00071)	54639..55382	+	744	WP_001030371	type-F conjugative transfer system pilin assembly protein TraF	traF
OVP42_RS00395 (p202000562-4__00072)	55396..55737	+	342	WP_000556795	conjugal transfer protein TrbA	-
OVP42_RS00400 (p202000562-4__00073)	55718..56053	-	336	WP_001620807	hypothetical protein	-
OVP42_RS00405 (p202000562-4__00074)	56134..56418	+	285	WP_000624107	type-F conjugative transfer system pilin chaperone TraQ	-
OVP42_RS00410 (p202000562-4__00075)	56405..56950	+	546	WP_000059829	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
OVP42_RS00415 (p202000562-4__00076)	56880..57227	+	348	WP_071571857	P-type conjugative transfer protein TrbJ	-
OVP42_RS00420 (p202000562-4__00077)	57208..57600	+	393	WP_000659962	F-type conjugal transfer protein TrbF	-
OVP42_RS00425 (p202000562-4__00078)	57587..58960	+	1374	WP_033807962	conjugal transfer pilus assembly protein TraH	traH
OVP42_RS00430 (p202000562-4__00079)	58957..61782	+	2826	WP_033807963	conjugal transfer mating-pair stabilization protein TraG	traG
OVP42_RS00435 (p202000562-4__00080)	61779..62288	+	510	WP_000628111	conjugal transfer entry exclusion protein TraS	-
OVP42_RS00440 (p202000562-4__00081)	62302..63033	+	732	WP_012881123	conjugal transfer complement resistance protein TraT	-
OVP42_RS00445 (p202000562-4__00082)	63236..63973	+	738	WP_012881122	hypothetical protein	-
OVP42_RS00450 (p202000562-4__00083)	64024..66249	+	2226	WP_113328784	type IV conjugative transfer system coupling protein TraD	-

Host bacterium

• ID: 19521
• GenBank: NZ_OP038284
• Plasmid name: p202000562-4
• Incompatibility group: -
• Plasmid size: 76702 bp
• Coordinate of oriT [Strand]: 37417..37768 [+]
• Host baterium: Shigella sonnei strain 202000562

Cargo genes

• Drug resistance gene: blaCTX-M-134, aph(3'')-Ib, sul2, mph(A)
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -