Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 102470
• Name: oriT_pECOS88like
• Organism: Escherichia coli PMV-1
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CBTO010000001 (26980..27332 [+], 353 nt)
• oriT length: 353 nt
• IRs (inverted repeats): 256..263, 272..279 (ACCGCTAG..CTAGCGGT) 192..198, 206..212 (TATAAAA..TTTTATA) 134..141, 152..159 (TCGGCGCG..CGCGCCGA) 40..47, 50..57 (GCAAAAAC..GTTTTTGC)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 353 nt

>oriT_pECOS88like
AGGTTGGTTGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTATCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGGGGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_ECOPMV1_RS23615_pECOS88like

• ID: 1842
• GenBank: WP_024259549
• Name: traI_ECOPMV1_RS23615_pECOS88like
• UniProt ID: _
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 191842.67 Da
• Isoelectric Point: 6.0533

>WP_024259549.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLSSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQVILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ESGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESGRPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSGGQQTRVIRPAQVRAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGSRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDTPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DSKTEQAVREIAGQERDRSAISEREAALPESVLRESQREREAVREVARENLLQERLQQMEQDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

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

• TrwC relaxase (TrwC) (10-283)

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

• AAA domain (AAA_30) (969-1156)

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

Protein structure

No available structure.

Auxiliary protein

WP_001151524_pECOS88like

• ID: 758
• GenBank: WP_001151524
• Name: WP_001151524_pECOS88like
• 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_pECOS88like

• ID: 759
• GenBank: WP_001369361
• Name: WP_001369361_pECOS88like
• 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_ECOPMV1_RS23700_pECOS88like

• ID: 1432
• GenBank: WP_001064252
• Name: traC_ECOPMV1_RS23700_pECOS88like
• UniProt ID: _
• Length: 875 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 875 a.a.
• Molecular weight: 99164.84 Da
• Isoelectric Point: 5.8486

>WP_001064252.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRESGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

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

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

• TraC protein (TraC_F_IV) (38-276)

Protein structure

No available structure.

traD_ECOPMV1_RS23620_pECOS88like

• ID: 1433
• GenBank: WP_001589502
• Name: traD_ECOPMV1_RS23620_pECOS88like
• UniProt ID: _
• Length: 723 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 723 a.a.
• Molecular weight: 82153.71 Da
• Isoelectric Point: 5.0524

>WP_001589502.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQQMQ
RREEVNINVHRERGEDVEPGDDF

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: 26409..52181

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
ECOPMV1_RS23785 (ECOPMV1_pECOS88LIKE00025)	22448..22882	+	435	WP_000845922	conjugation system SOS inhibitor PsiB	-
ECOPMV1_RS23930	22879..23640	+	762	Protein_29	plasmid SOS inhibition protein A	-
ECOPMV1_RS29930	23830..23943	+	114	Protein_30	DUF5431 family protein	-
ECOPMV1_RS23940	23888..24010	+	123	WP_223195199	Hok/Gef family protein	-
ECOPMV1_RS29845	24310..24585	-	276	Protein_32	hypothetical protein	-
ECOPMV1_RS23780 (ECOPMV1_pECOS88LIKE00030)	24886..25173	+	288	WP_000107520	hypothetical protein	-
ECOPMV1_RS23775 (ECOPMV1_pECOS88LIKE00031)	25292..26113	+	822	WP_001234468	DUF932 domain-containing protein	-
ECOPMV1_RS23770 (ECOPMV1_pECOS88LIKE00032)	26409..26918	-	510	WP_000759163	transglycosylase SLT domain-containing protein	virB1
ECOPMV1_RS23765 (ECOPMV1_pECOS88LIKE00033)	27333..27716	+	384	WP_001151524	conjugal transfer relaxosome DNA-binding protein TraM	-
ECOPMV1_RS23760 (ECOPMV1_pECOS88LIKE00034)	27903..28592	+	690	WP_000283385	conjugal transfer transcriptional regulator TraJ	-
ECOPMV1_RS23755 (ECOPMV1_pECOS88LIKE00035)	28691..29086	+	396	WP_001309237	conjugal transfer relaxosome DNA-bindin protein TraY	-
ECOPMV1_RS23750 (ECOPMV1_pECOS88LIKE00036)	29119..29484	+	366	WP_000994779	type IV conjugative transfer system pilin TraA	-
ECOPMV1_RS23745 (ECOPMV1_pECOS88LIKE00037)	29499..29810	+	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
ECOPMV1_RS23740 (ECOPMV1_pECOS88LIKE00038)	29832..30398	+	567	WP_000399785	type IV conjugative transfer system protein TraE	traE
ECOPMV1_RS23735 (ECOPMV1_pECOS88LIKE00039)	30385..31113	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
ECOPMV1_RS23730 (ECOPMV1_pECOS88LIKE00040)	31113..32540	+	1428	WP_000146685	F-type conjugal transfer pilus assembly protein TraB	traB
ECOPMV1_RS23725 (ECOPMV1_pECOS88LIKE00041)	32530..33120	+	591	WP_000002792	conjugal transfer pilus-stabilizing protein TraP	-
ECOPMV1_RS23720 (ECOPMV1_pECOS88LIKE00042)	33107..33304	+	198	WP_001324648	conjugal transfer protein TrbD	-
ECOPMV1_RS23715 (ECOPMV1_pECOS88LIKE00043)	33316..33567	+	252	WP_001038342	conjugal transfer protein TrbG	-
ECOPMV1_RS23710 (ECOPMV1_pECOS88LIKE00044)	33564..34079	+	516	WP_000809841	type IV conjugative transfer system lipoprotein TraV	traV
ECOPMV1_RS26400 (ECOPMV1_pECOS88LIKE00045)	34214..34435	+	222	WP_001278689	conjugal transfer protein TraR	-
ECOPMV1_RS23700 (ECOPMV1_pECOS88LIKE00046)	34595..37222	+	2628	WP_001064252	type IV secretion system protein TraC	virb4
ECOPMV1_RS23695 (ECOPMV1_pECOS88LIKE00047)	37219..37605	+	387	WP_000214082	type-F conjugative transfer system protein TrbI	-
ECOPMV1_RS23690 (ECOPMV1_pECOS88LIKE00048)	37602..38234	+	633	WP_001203720	type-F conjugative transfer system protein TraW	traW
ECOPMV1_RS23685 (ECOPMV1_pECOS88LIKE00049)	38231..39223	+	993	WP_000830839	conjugal transfer pilus assembly protein TraU	traU
ECOPMV1_RS23680 (ECOPMV1_pECOS88LIKE00050)	39232..39870	+	639	WP_000777693	type-F conjugative transfer system pilin assembly protein TrbC	trbC
ECOPMV1_RS23675 (ECOPMV1_pECOS88LIKE00051)	39867..41675	+	1809	WP_000821846	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
ECOPMV1_RS23670 (ECOPMV1_pECOS88LIKE00052)	41702..41959	+	258	WP_000864325	conjugal transfer protein TrbE	-
ECOPMV1_RS23665 (ECOPMV1_pECOS88LIKE00053)	41952..42695	+	744	WP_001030389	type-F conjugative transfer system pilin assembly protein TraF	traF
ECOPMV1_RS23660 (ECOPMV1_pECOS88LIKE00054)	42711..43058	+	348	WP_024259548	conjugal transfer protein TrbA	-
ECOPMV1_RS23655 (ECOPMV1_pECOS88LIKE00055)	43177..43461	+	285	WP_000624110	type-F conjugative transfer system pilin chaperone TraQ	-
ECOPMV1_RS23650 (ECOPMV1_pECOS88LIKE00056)	43448..43993	+	546	WP_000052618	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
ECOPMV1_RS23645 (ECOPMV1_pECOS88LIKE00057)	43923..44285	+	363	WP_002430925	P-type conjugative transfer protein TrbJ	-
ECOPMV1_RS23640 (ECOPMV1_pECOS88LIKE00058)	44285..45658	+	1374	WP_001137358	conjugal transfer pilus assembly protein TraH	traH
ECOPMV1_RS23635 (ECOPMV1_pECOS88LIKE00059)	45655..48477	+	2823	WP_001007012	conjugal transfer mating-pair stabilization protein TraG	traG
ECOPMV1_RS23630 (ECOPMV1_pECOS88LIKE00060)	48492..48995	+	504	WP_000605510	hypothetical protein	-
ECOPMV1_RS23625 (ECOPMV1_pECOS88LIKE00061)	49027..49758	+	732	WP_001447147	conjugal transfer complement resistance protein TraT	-
ECOPMV1_RS23620 (ECOPMV1_pECOS88LIKE00062)	50010..52181	+	2172	WP_001589502	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 2914
• GenBank: NZ_CBTO010000001
• Plasmid name: pECOS88like
• Incompatibility group: -
• Plasmid size: 83288 bp
• Coordinate of oriT [Strand]: 26980..27332 [+]
• Host baterium: Escherichia coli PMV-1

Cargo genes

• Drug resistance gene: -
• Virulence gene: iroN, iroE, iroD
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -