Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 116512
• Name: oriT_6S41-1|p1-6S41-1
• Organism: Escherichia fergusonii strain 6S41-1
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP079885 (78923..79274 [+], 352 nt)
• oriT length: 352 nt
• IRs (inverted repeats): 255..262, 271..278 (ACCGCTAG..CTAGCGGT) 192..198, 206..212 (TATAAAA..TTTTATA) 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_6S41-1|p1-6S41-1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATTGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_KYC43_RS23705_6S41-1|p1-6S41-1

• ID: 10550
• GenBank: WP_223672105
• Name: traI_KYC43_RS23705_6S41-1|p1-6S41-1
• UniProt ID: _
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 192045.58 Da
• Isoelectric Point: 5.7904

>WP_223672105.1 conjugative transfer relaxase/helicase TraI [Escherichia fergusonii]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQYNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DTVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMIFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMRDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPDCSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQNGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDGVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTATSERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

• AAA domain (AAA_30) (969-1156)

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

• TrwC relaxase (TrwC) (10-283)

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

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

Protein structure

No available structure.

Auxiliary protein

WP_001151524_6S41-1|p1-6S41-1

• ID: 6194
• GenBank: WP_001151524
• Name: WP_001151524_6S41-1|p1-6S41-1
• UniProt ID: A0A5W2DT22
• Length: 127 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 127 a.a.
• Molecular weight: 14517.48 Da
• Isoelectric Point: 5.0516

>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE

Protein domains

Predicted by InterproScan.

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

Protein structure

• AlphaFold DB: A0A5W2DT22

WP_001309237_6S41-1|p1-6S41-1

• ID: 6195
• GenBank: WP_001309237
• Name: WP_001309237_6S41-1|p1-6S41-1
• UniProt ID: A0A5W1N5T0
• Length: 131 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 131 a.a.
• Molecular weight: 15183.38 Da
• Isoelectric Point: 9.9240

>WP_001309237.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVKYL
TMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

Protein domains

Predicted by InterproScan.

• TraY domain (TraY) (70-117)

• TraY domain (TraY) (16-59)

Protein structure

• AlphaFold DB: A0A5W1N5T0

T4CP

traC_KYC43_RS23605_6S41-1|p1-6S41-1

• ID: 12320
• GenBank: WP_001064265
• Name: traC_KYC43_RS23605_6S41-1|p1-6S41-1
• UniProt ID: _
• Length: 875 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 875 a.a.
• Molecular weight: 99296.07 Da
• Isoelectric Point: 6.3032

>WP_001064265.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKNRARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
AGGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

• TraC protein (TraC_F_IV) (38-276)

• TraG P-loop domain (P-loop_TraG) (467-771)

• Family of unknown function (DUF5934) (DUF5934) (289-446)

Protein structure

No available structure.

traD_KYC43_RS23700_6S41-1|p1-6S41-1

• ID: 12321
• GenBank: WP_086210965
• Name: traD_KYC43_RS23700_6S41-1|p1-6S41-1
• UniProt ID: _
• Length: 744 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 744 a.a.
• Molecular weight: 84602.31 Da
• Isoelectric Point: 5.1657

>WP_086210965.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Escherichia]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVV
DMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

Protein domains

Predicted by InterproScan.

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (173-560)

• F sex factor protein N terminal (TraD_N) (32-128)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 78352..105384

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
KYC43_RS23505 (KYC43_23400)	74425..74859	+	435	WP_042634413	conjugation system SOS inhibitor PsiB	-
KYC43_RS23510 (KYC43_23405)	74856..75642	+	787	Protein_92	plasmid SOS inhibition protein A	-
KYC43_RS23515	75792..75944	+	153	Protein_93	DUF5431 family protein	-
KYC43_RS23520 (KYC43_23410)	75889..76011	+	123	WP_223163518	Hok/Gef family protein	-
KYC43_RS23525 (KYC43_23415)	76312..76608	-	297	Protein_95	hypothetical protein	-
KYC43_RS24660	76678..76800	+	123	Protein_96	single-stranded DNA-binding protein	-
KYC43_RS23530 (KYC43_23420)	76832..77128	+	297	WP_001272240	hypothetical protein	-
KYC43_RS23535 (KYC43_23425)	77234..78055	+	822	WP_001234469	DUF932 domain-containing protein	-
KYC43_RS23540 (KYC43_23430)	78352..78954	-	603	WP_112889074	transglycosylase SLT domain-containing protein	virB1
KYC43_RS23545 (KYC43_23435)	79275..79658	+	384	WP_001151524	conjugal transfer relaxosome DNA-binding protein TraM	-
KYC43_RS23550 (KYC43_23440)	79845..80534	+	690	WP_047402313	conjugal transfer transcriptional regulator TraJ	-
KYC43_RS23555 (KYC43_23445)	80633..81028	+	396	WP_001309237	conjugal transfer relaxosome DNA-bindin protein TraY	-
KYC43_RS23560 (KYC43_23450)	81061..81423	+	363	WP_000994784	type IV conjugative transfer system pilin TraA	-
KYC43_RS23565 (KYC43_23455)	81428..81739	+	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
KYC43_RS23570 (KYC43_23460)	81761..82327	+	567	WP_000399792	type IV conjugative transfer system protein TraE	traE
KYC43_RS23575 (KYC43_23465)	82314..83042	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
KYC43_RS23580 (KYC43_23470)	83042..84469	+	1428	WP_047402310	F-type conjugal transfer pilus assembly protein TraB	traB
KYC43_RS23585 (KYC43_23475)	84459..85046	+	588	WP_000002772	conjugal transfer pilus-stabilizing protein TraP	-
KYC43_RS23590 (KYC43_23480)	85033..85353	+	321	WP_001057283	conjugal transfer protein TrbD	-
KYC43_RS23595 (KYC43_23485)	85350..85865	+	516	WP_000724019	type IV conjugative transfer system lipoprotein TraV	traV
KYC43_RS23600 (KYC43_23490)	86000..86221	+	222	WP_001278692	conjugal transfer protein TraR	-
KYC43_RS23605 (KYC43_23495)	86381..89008	+	2628	WP_001064265	type IV secretion system protein TraC	virb4
KYC43_RS23610 (KYC43_23500)	89005..89391	+	387	WP_000099693	type-F conjugative transfer system protein TrbI	-
KYC43_RS23615 (KYC43_23505)	89388..90020	+	633	WP_042047196	type-F conjugative transfer system protein TraW	traW
KYC43_RS23620 (KYC43_23510)	90017..91009	+	993	WP_042047198	conjugal transfer pilus assembly protein TraU	traU
KYC43_RS23625 (KYC43_23515)	91018..91656	+	639	WP_042047200	type-F conjugative transfer system pilin assembly protein TrbC	trbC
KYC43_RS23630 (KYC43_23520)	91653..93461	+	1809	WP_047402305	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
KYC43_RS23635 (KYC43_23525)	93488..93745	+	258	WP_000864320	conjugal transfer protein TrbE	-
KYC43_RS23640 (KYC43_23530)	93738..94481	+	744	WP_001030378	type-F conjugative transfer system pilin assembly protein TraF	traF
KYC43_RS23645 (KYC43_23535)	94495..94836	+	342	WP_047402303	conjugal transfer protein TrbA	-
KYC43_RS23650 (KYC43_23540)	94817..95152	-	336	WP_000415571	hypothetical protein	-
KYC43_RS23655 (KYC43_23545)	95233..95517	+	285	WP_000624108	type-F conjugative transfer system pilin chaperone TraQ	-
KYC43_RS23660 (KYC43_23550)	95504..96049	+	546	WP_000059818	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
KYC43_RS23665 (KYC43_23555)	96039..96353	+	315	WP_001384255	P-type conjugative transfer protein TrbJ	-
KYC43_RS23670 (KYC43_23560)	96307..96699	+	393	WP_000126338	F-type conjugal transfer protein TrbF	-
KYC43_RS23675 (KYC43_23565)	96686..98059	+	1374	WP_000944325	conjugal transfer pilus assembly protein TraH	traH
KYC43_RS23680 (KYC43_23570)	98056..100878	+	2823	WP_062873754	conjugal transfer mating-pair stabilization protein TraG	traG
KYC43_RS23685 (KYC43_23575)	100893..101396	+	504	WP_000605510	hypothetical protein	-
KYC43_RS23690 (KYC43_23580)	101428..102159	+	732	WP_000850424	conjugal transfer complement resistance protein TraT	-
KYC43_RS23695 (KYC43_23585)	102362..103099	+	738	WP_000199900	hypothetical protein	-
KYC43_RS23700 (KYC43_23590)	103150..105384	+	2235	WP_086210965	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 16945
• GenBank: NZ_CP079885
• Plasmid name: 6S41-1|p1-6S41-1
• Incompatibility group: -
• Plasmid size: 118628 bp
• Coordinate of oriT [Strand]: 78923..79274 [+]
• Host baterium: Escherichia fergusonii strain 6S41-1

Cargo genes

• Drug resistance gene: -
• Virulence gene: vat, cseA
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -