oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	101057
Name	oriT_pUnk_2670
Organism	Escherichia coli strain PH-2670-18
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_WLVN01000005 (95065..95150 [+], 86 nt)
oriT length	86 nt
IRs (inverted repeats)	61..68, 73..80 (TTGGTGGT..ACCACCAA) 27..34, 37..44 (GCAAAAAC..GTTTTTGC) 8..13, 21..26 (TGATTT..AAATCA)
*Location of nic* site**	53..54
Conserved sequence flanking the nic site	GGTGTGGTGC
Note	Predicted by oriTfinder 2.0

oriT sequence

Download Length: 86 nt

                        >oriT_pUnk_2670
AATTACATGATTTAAAACACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_GKM64_RS20795_pUnk_2670

ID	1104	GenBank	WP_021518366
Name	traI_GKM64_RS20795_pUnk_2670	UniProt ID	_
Length	1756 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1756 a.a. Molecular weight: 192172.86 Da Isoelectric Point: 6.1609

          >WP_021518366.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]

MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA

LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIRETVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT

LKETGFDIRAYRDAAEQRAYTRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

AGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW

QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL

ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KARAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFTELGREIDA

QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI

LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVAIMKEIVRQTPELREAVYSLINRDVEKALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM

VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT

LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL

EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG

IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTELAVRDIAGQERDRTATSERETALPESVLRESQREREAVREVARENLLQRLLQQMERDMVRDLQKE

KTLGGD

Protein domains

Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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.

ID	400	GenBank	WP_001352842
Name	WP_001352842_pUnk_2670	UniProt ID	A0A6Y3H4U0
Length	71 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 71 a.a. Molecular weight: 8117.19 Da Isoelectric Point: 9.9216

                        >WP_001352842.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacteriaceae]

MSRGRTRAAPGNKVLLILDETTNQKLLAARDRSGRTKTNEVFIRLKDHLNRFPDFYNASLVKEEAESIDD

I

Protein domains

Predicted by InterproScan.

TraY domain (TraY)

(14-60)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A6Y3H4U0

ID	401	GenBank	WP_001063020
Name	WP_001063020_pUnk_2670	UniProt ID	A0A6Y3HD60
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 127 a.a. Molecular weight: 14442.54 Da Isoelectric Point: 5.3125

                        >WP_001063020.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Bacteria]

MAKIQVYVNDHVSEKINAIAVQRRAEGAKEKDVSYSSIASMLLELGLRVYEAQMERKESAFNQAEFNKLL

LECVVKTQSTVAKILGIESLSPHVSGKPKFEYANMVEDIREKVSVEMERFFPKNDDE

Protein domains

Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A6Y3HD60

T4CP

traD_GKM64_RS20800_pUnk_2670
traC_GKM64_RS20890_pUnk_2670

ID	651	GenBank	WP_021518367
Name	traD_GKM64_RS20800_pUnk_2670	UniProt ID	_
Length	717 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 717 a.a. Molecular weight: 81500.98 Da Isoelectric Point: 5.0541

                        >WP_021518367.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR

DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ

QSENEVTGGRQLTDNPKDVARMLKKDDKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQIASLFEPDVPEVVSGEDVTQAEQPQQPVSPAI

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.

ID	652	GenBank	WP_021518375
Name	traC_GKM64_RS20890_pUnk_2670	UniProt ID	_
Length	875 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 875 a.a. Molecular weight: 99196.80 Da Isoelectric Point: 5.8486

                        >WP_021518375.1 type IV secretion system protein TraC [Escherichia coli]

MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP

INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA

TQFPLPEGMNLPLTLRHYRVFISYCSSSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG

EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL

WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE

LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG

LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA

GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV

MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT

ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR

LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN

QLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL

SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraG P-loop domain (P-loop_TraG)

(467-763)

TraC protein (TraC_F_IV)

(38-276)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 69415..95718

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
GKM64_RS20800 (GKM64_20780)	69415..71568	-	2154	WP_021518367	type IV conjugative transfer system coupling protein TraD	virb4
GKM64_RS20805 (GKM64_20785)	71820..72551	-	732	WP_000850424	conjugal transfer complement resistance protein TraT	-
GKM64_RS20810 (GKM64_20790)	72565..73074	-	510	WP_021518368	conjugal transfer entry exclusion protein TraS	-
GKM64_RS20815 (GKM64_20795)	73071..75896	-	2826	WP_021518369	conjugal transfer mating-pair stabilization protein TraG	traG
GKM64_RS20820 (GKM64_20800)	75893..77266	-	1374	WP_021518370	conjugal transfer pilus assembly protein TraH	traH
GKM64_RS20825 (GKM64_20805)	77253..77645	-	393	WP_021518371	F-type conjugal transfer protein TrbF	-
GKM64_RS20830 (GKM64_20810)	77599..77913	-	315	WP_021518372	P-type conjugative transfer protein TrbJ	-
GKM64_RS20835 (GKM64_20815)	77903..78457	-	555	WP_001553830	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
GKM64_RS20840 (GKM64_20820)	78444..78728	-	285	WP_000624105	type-F conjugative transfer system pilin chaperone TraQ	-
GKM64_RS20845 (GKM64_20825)	78809..79144	+	336	WP_000415571	hypothetical protein	-
GKM64_RS20850 (GKM64_20830)	79125..79466	-	342	WP_000556794	conjugal transfer protein TrbA	-
GKM64_RS20855 (GKM64_20835)	79480..80223	-	744	WP_001030378	type-F conjugative transfer system pilin assembly protein TraF	traF
GKM64_RS20860 (GKM64_20840)	80216..80473	-	258	WP_000864318	conjugal transfer protein TrbE	-
GKM64_RS20865 (GKM64_20845)	80500..82308	-	1809	WP_021518373	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
GKM64_RS20870 (GKM64_20850)	82305..82943	-	639	WP_021518374	type-F conjugative transfer system pilin assembly protein TrbC	trbC
GKM64_RS20875 (GKM64_20855)	82952..83944	-	993	WP_000830839	conjugal transfer pilus assembly protein TraU	traU
GKM64_RS20880 (GKM64_20860)	83941..84573	-	633	WP_001203720	type-F conjugative transfer system protein TraW	traW
GKM64_RS20885 (GKM64_20865)	84570..84956	-	387	WP_000214096	type-F conjugative transfer system protein TrbI	-
GKM64_RS20890 (GKM64_20870)	84953..87580	-	2628	WP_021518375	type IV secretion system protein TraC	virb4
GKM64_RS20895 (GKM64_20875)	87740..87962	-	223	Protein_85	conjugal transfer protein TraR	-
GKM64_RS20900 (GKM64_20880)	88097..88612	-	516	WP_000809838	type IV conjugative transfer system lipoprotein TraV	traV
GKM64_RS20905 (GKM64_20885)	88609..88860	-	252	WP_001038342	conjugal transfer protein TrbG	-
GKM64_RS25020	88853..89173	-	321	Protein_88	conjugal transfer protein TrbD	-
GKM64_RS20920 (GKM64_20900)	89160..89750	-	591	WP_000002787	conjugal transfer pilus-stabilizing protein TraP	-
GKM64_RS20925 (GKM64_20905)	89740..91167	-	1428	WP_015387387	F-type conjugal transfer pilus assembly protein TraB	traB
GKM64_RS20930 (GKM64_20910)	91167..91895	-	729	WP_001230813	type-F conjugative transfer system secretin TraK	traK
GKM64_RS20935 (GKM64_20915)	91882..92448	-	567	WP_000399790	type IV conjugative transfer system protein TraE	traE
GKM64_RS20940 (GKM64_20920)	92470..92781	-	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
GKM64_RS20945 (GKM64_20925)	92796..93161	-	366	WP_000340282	type IV conjugative transfer system pilin TraA	-
GKM64_RS20950 (GKM64_20930)	93204..93419	-	216	WP_001352842	conjugal transfer relaxosome protein TraY	-
GKM64_RS20955 (GKM64_20935)	93555..94202	-	648	WP_015387377	conjugal transfer transcriptional regulator TraJ	-
GKM64_RS20960 (GKM64_20940)	94393..94776	-	384	WP_001063020	conjugal transfer relaxosome DNA-binding protein TraM	-
GKM64_RS20965 (GKM64_20945)	95116..95718	+	603	WP_000243701	transglycosylase SLT domain-containing protein	-
GKM64_RS20970 (GKM64_20950)	96014..96835	-	822	WP_001513505	DUF932 domain-containing protein	-
GKM64_RS20975 (GKM64_20955)	96954..97241	-	288	WP_001513506	hypothetical protein	-
GKM64_RS24620	97266..97472	-	207	WP_000547955	hypothetical protein	-
GKM64_RS20980 (GKM64_20960)	97554..97973	+	420	WP_309143924	hypothetical protein	-
GKM64_RS20985 (GKM64_20965)	98059..98622	-	564	WP_001513507	class I SAM-dependent methyltransferase	-
GKM64_RS20990 (GKM64_20970)	98670..100031	-	1362	WP_001513508	DUF3560 domain-containing protein	-
GKM64_RS20995 (GKM64_20975)	100083..100313	-	231	WP_000218642	hypothetical protein	-

Host bacterium

ID	1501	GenBank	NZ_WLVN01000005
Plasmid name	pUnk_2670	Incompatibility group	IncFIB
Plasmid size	162864 bp	Coordinate of oriT [Strand]	95065..95150 [+]
Host baterium	Escherichia coli strain PH-2670-18

Cargo genes

Drug resistance gene	dfrA14, sul2, aph(3'')-Ib, aph(6)-Id, blaTEM-1B, sitABCD
Virulence gene	iroB, iroC, iroD, iroE, iroN, iutA, iucC, iucB, iucA
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-