Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 102618
• Name: oriT_pUMNturkey5_IncF
• Organism: Escherichia coli strain UMNturkey5
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_JRQA01000038 (26495..26846 [+], 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_pUMNturkey5_IncF
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATTGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_LS41_RS20330_pUMNturkey5_IncF

• ID: 1951
• GenBank: WP_047402288
• Name: traI_LS41_RS20330_pUMNturkey5_IncF
• UniProt ID: A0A8S7Y2I9
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 192292.94 Da
• Isoelectric Point: 5.9169

>WP_047402288.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHSQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQVVTQAIAGLSERKVQFTYTDVLARTVGILPPE
AGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DTVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENCWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVLESKNLAFSHVDLLTEAKSFAAEGTSFTELGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAVTSERETALPESVLREPQREREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

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

• TrwC relaxase (TrwC) (10-283)

• AAA domain (AAA_30) (969-1156)

• 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_pUMNturkey5_IncF

• ID: 778
• GenBank: WP_001151524
• Name: WP_001151524_pUMNturkey5_IncF
• 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_001369361_pUMNturkey5_IncF

• ID: 779
• GenBank: WP_001369361
• Name: WP_001369361_pUMNturkey5_IncF
• UniProt ID: B7LI64
• Length: 133 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 133 a.a.
• Molecular weight: 15409.70 Da
• Isoelectric Point: 9.9240

>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL

Protein domains

Predicted by InterproScan.

• TraY domain (TraY) (18-61)

• TraY domain (TraY) (72-119)

Protein structure

• AlphaFold DB: B7LI64

T4CP

traC_LS41_RS20240_pUMNturkey5_IncF

• ID: 1579
• GenBank: WP_001064265
• Name: traC_LS41_RS20240_pUMNturkey5_IncF
• 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_LS41_RS20325_pUMNturkey5_IncF

• ID: 1580
• GenBank: WP_047402290
• Name: traD_LS41_RS20325_pUMNturkey5_IncF
• UniProt ID: _
• Length: 717 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 717 a.a.
• Molecular weight: 81547.03 Da
• Isoelectric Point: 5.0541

>WP_047402290.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDRYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDDKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI
NDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDTQQQMQRREEVN
INVHRERGEDVEPGDDF

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: 25924..52118

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LS41_RS20135 (LS41_20135)	20943..21705	+	763	Protein_33	plasmid SOS inhibition protein A	-
LS41_RS28295 (LS41_20140)	21674..21862	-	189	WP_001299721	hypothetical protein	-
LS41_RS28675	21884..22033	+	150	Protein_35	plasmid maintenance protein Mok	-
LS41_RS20145 (LS41_20145)	21975..22100	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
LS41_RS28680	22320..22550	+	231	WP_113707887	hypothetical protein	-
LS41_RS28685 (LS41_20150)	22548..22721	-	174	Protein_38	hypothetical protein	-
LS41_RS28690 (LS41_20155)	22791..23051	+	261	WP_042046747	hypothetical protein	-
LS41_RS20160 (LS41_20160)	23145..24149	-	1005	WP_047402339	IS110 family transposase	-
LS41_RS20165 (LS41_20165)	24400..24687	+	288	WP_000107548	hypothetical protein	-
LS41_RS20170 (LS41_20170)	24806..25627	+	822	WP_001234469	DUF932 domain-containing protein	-
LS41_RS20175 (LS41_20175)	25924..26514	-	591	WP_001376243	transglycosylase SLT domain-containing protein	virB1
LS41_RS20180 (LS41_20180)	26847..27230	+	384	WP_001151524	conjugal transfer relaxosome DNA-binding protein TraM	-
LS41_RS20185 (LS41_20185)	27417..28106	+	690	WP_047402313	conjugal transfer transcriptional regulator TraJ	-
LS41_RS20190 (LS41_20190)	28205..28600	+	396	WP_001309237	conjugal transfer relaxosome DNA-bindin protein TraY	-
LS41_RS20195 (LS41_20195)	28633..28995	+	363	WP_000994784	type IV conjugative transfer system pilin TraA	-
LS41_RS20200 (LS41_20200)	29000..29311	+	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
LS41_RS20205 (LS41_20205)	29333..29899	+	567	WP_000399792	type IV conjugative transfer system protein TraE	traE
LS41_RS20210 (LS41_20210)	29886..30614	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
LS41_RS20215 (LS41_20215)	30614..32041	+	1428	WP_047402310	F-type conjugal transfer pilus assembly protein TraB	traB
LS41_RS20220 (LS41_20220)	32031..32618	+	588	WP_000002772	conjugal transfer pilus-stabilizing protein TraP	-
LS41_RS20225 (LS41_20225)	32605..32925	+	321	WP_001057283	conjugal transfer protein TrbD	-
LS41_RS20230 (LS41_20230)	32922..33437	+	516	WP_000724019	type IV conjugative transfer system lipoprotein TraV	traV
LS41_RS26400 (LS41_20235)	33572..33793	+	222	WP_001278692	conjugal transfer protein TraR	-
LS41_RS20240 (LS41_20240)	33953..36580	+	2628	WP_001064265	type IV secretion system protein TraC	virb4
LS41_RS20245 (LS41_20245)	36577..36963	+	387	WP_000099693	type-F conjugative transfer system protein TrbI	-
LS41_RS20250 (LS41_20250)	36960..37592	+	633	WP_042047196	type-F conjugative transfer system protein TraW	traW
LS41_RS20255 (LS41_20255)	37589..38581	+	993	WP_042047198	conjugal transfer pilus assembly protein TraU	traU
LS41_RS20260 (LS41_20260)	38590..39228	+	639	WP_042047200	type-F conjugative transfer system pilin assembly protein TrbC	trbC
LS41_RS20265 (LS41_20265)	39225..41033	+	1809	WP_047402305	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
LS41_RS20270 (LS41_20270)	41060..41317	+	258	WP_000864320	conjugal transfer protein TrbE	-
LS41_RS20275 (LS41_20275)	41310..42053	+	744	WP_001030378	type-F conjugative transfer system pilin assembly protein TraF	traF
LS41_RS20280 (LS41_20280)	42067..42408	+	342	WP_047402303	conjugal transfer protein TrbA	-
LS41_RS20285 (LS41_20285)	42389..42724	-	336	WP_000415571	hypothetical protein	-
LS41_RS20290 (LS41_20290)	42805..43089	+	285	WP_000624105	type-F conjugative transfer system pilin chaperone TraQ	-
LS41_RS20295 (LS41_20295)	43076..43630	+	555	WP_047402299	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
LS41_RS26405	43620..43934	+	315	WP_023149603	P-type conjugative transfer protein TrbJ	-
LS41_RS20300 (LS41_20300)	43888..44280	+	393	WP_047402297	F-type conjugal transfer protein TrbF	-
LS41_RS20305 (LS41_20305)	44267..45640	+	1374	WP_113444820	conjugal transfer pilus assembly protein TraH	traH
LS41_RS20310 (LS41_20310)	45637..48462	+	2826	WP_047402292	conjugal transfer mating-pair stabilization protein TraG	traG
LS41_RS20315 (LS41_20315)	48459..48968	+	510	WP_000628100	conjugal transfer entry exclusion protein TraS	-
LS41_RS20320 (LS41_20320)	48982..49713	+	732	WP_000850424	conjugal transfer complement resistance protein TraT	-
LS41_RS20325 (LS41_20325)	49965..52118	+	2154	WP_047402290	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 3062
• GenBank: NZ_JRQA01000038
• Plasmid name: pUMNturkey5_IncF
• Incompatibility group: IncFII
• Plasmid size: 66693 bp
• Coordinate of oriT [Strand]: 26495..26846 [+]
• Host baterium: Escherichia coli strain UMNturkey5

Cargo genes

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