oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	114383
Name	oriT_pEF02
Organism	Escherichia fergusonii strain EFCF056
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP040807 (67719..67842 [-], 124 nt)
oriT length	124 nt
IRs (inverted repeats)	101..106, 119..124 (TTTAAT..ATTAAA) 91..99, 113..121 (AATAATGTA..TACATTATT) 90..95, 107..112 (AAATAA..TTATTT) 39..46, 49..56 (GCAAAAAC..GTTTTTGC) 3..10, 15..22 (TTGGTGGT..ACCACCAA)
*Location of nic* site**	_
Conserved sequence flanking the nic site	_
Note	Predicted by oriTfinder 2.0

oriT sequence

Download Length: 124 nt

                        >oriT_pEF02
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_D8Z79_RS23720_pEF02

ID	9224	GenBank	WP_061093447
Name	traI_D8Z79_RS23720_pEF02	UniProt ID	A0A2Z4I1F4
Length	1756 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1756 a.a. Molecular weight: 192119.90 Da Isoelectric Point: 6.0788

          >WP_061093447.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]

MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA

LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT

LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW

QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL

ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA

QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI

LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM

VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT

LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL

EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG

IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE

KTLGGD

Protein domains

Predicted by InterproScan.

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)

AAA domain (AAA_30)

(969-1156)

Protein structure

No available structure.

ID	5407	GenBank	WP_001254386
Name	WP_001254386_pEF02	UniProt ID	A0A3Z6KJB5
Length	75 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 75 a.a. Molecular weight: 9005.11 Da Isoelectric Point: 10.1422

                        >WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]

MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES

TFKEL

Protein domains

Predicted by InterproScan.

TraY domain (TraY)

(14-61)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A3Z6KJB5

ID	5408	GenBank	WP_000124981
Name	WP_000124981_pEF02	UniProt ID	A0A630FTW9
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 127 a.a. Molecular weight: 14542.59 Da Isoelectric Point: 5.0278

                        >WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]

MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL

LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

Protein domains

Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A630FTW9

T4CP

traD_D8Z79_RS23725_pEF02
traC_D8Z79_RS23830_pEF02

ID	10687	GenBank	WP_072646483
Name	traD_D8Z79_RS23725_pEF02	UniProt ID	_
Length	747 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 747 a.a. Molecular weight: 84966.71 Da Isoelectric Point: 5.0504

                        >WP_072646483.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR

DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ

QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESG

EVVDMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

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	10688	GenBank	WP_015059012
Name	traC_D8Z79_RS23830_pEF02	UniProt ID	_
Length	875 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 875 a.a. Molecular weight: 99393.22 Da Isoelectric Point: 6.3465

                        >WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]

MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP

INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA

TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG

EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL

WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE

LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG

LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA

GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV

MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT

ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR

LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN

QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL

SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40209..68414

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
D8Z79_RS23725 (D8Z79_023725)	40209..42452	-	2244	WP_072646483	type IV conjugative transfer system coupling protein TraD	virb4
D8Z79_RS23730 (D8Z79_023730)	42503..43240	-	738	WP_015059020	hypothetical protein	-
D8Z79_RS23735 (D8Z79_023735)	43443..44174	-	732	WP_021559024	conjugal transfer complement resistance protein TraT	-
D8Z79_RS23740 (D8Z79_023740)	44199..44720	-	522	WP_000632668	conjugal transfer entry exclusion protein TraS	-
D8Z79_RS23745 (D8Z79_023745)	44753..47568	-	2816	Protein_51	conjugal transfer mating-pair stabilization protein TraG	-
D8Z79_RS23750 (D8Z79_023750)	47565..48938	-	1374	WP_000944325	conjugal transfer pilus assembly protein TraH	traH
D8Z79_RS23755 (D8Z79_023755)	48925..49317	-	393	WP_000126338	F-type conjugal transfer protein TrbF	-
D8Z79_RS23760 (D8Z79_023760)	49271..49585	-	315	WP_001384255	P-type conjugative transfer protein TrbJ	-
D8Z79_RS23765 (D8Z79_023765)	49575..50120	-	546	WP_000059817	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
D8Z79_RS23770 (D8Z79_023770)	50107..50343	-	237	WP_000270010	type-F conjugative transfer system pilin chaperone TraQ	-
D8Z79_RS23775 (D8Z79_023775)	50504..51247	-	744	WP_015059017	type-F conjugative transfer system pilin assembly protein TraF	traF
D8Z79_RS23780 (D8Z79_023780)	51240..51497	-	258	WP_053913405	conjugal transfer protein TrbE	-
D8Z79_RS23785 (D8Z79_023785)	51524..53374	-	1851	WP_015059015	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
D8Z79_RS23790 (D8Z79_023790)	53371..53793	-	423	WP_001229309	HNH endonuclease	-
D8Z79_RS23795 (D8Z79_023795)	53819..54190	-	372	WP_000056336	hypothetical protein	-
D8Z79_RS23800 (D8Z79_023800)	54187..54825	-	639	WP_000087532	type-F conjugative transfer system pilin assembly protein TrbC	trbC
D8Z79_RS23805 (D8Z79_023805)	54852..55373	-	522	WP_015059014	hypothetical protein	-
D8Z79_RS23810 (D8Z79_023810)	55436..55744	-	309	WP_000412447	hypothetical protein	-
D8Z79_RS23815 (D8Z79_023815)	55771..56763	-	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
D8Z79_RS23820 (D8Z79_023820)	56760..57392	-	633	WP_001203735	type-F conjugative transfer system protein TraW	traW
D8Z79_RS23825 (D8Z79_023825)	57389..57775	-	387	WP_015059013	type-F conjugative transfer system protein TrbI	-
D8Z79_RS23830 (D8Z79_023830)	57772..60399	-	2628	WP_015059012	type IV secretion system protein TraC	virb4
D8Z79_RS23835 (D8Z79_023835)	60559..60780	-	222	WP_001278692	conjugal transfer protein TraR	-
D8Z79_RS23840 (D8Z79_023840)	60915..61430	-	516	WP_000809902	type IV conjugative transfer system lipoprotein TraV	traV
D8Z79_RS23845 (D8Z79_023845)	61427..61678	-	252	WP_001038341	conjugal transfer protein TrbG	-
D8Z79_RS23850 (D8Z79_023850)	61690..61887	-	198	WP_001324648	conjugal transfer protein TrbD	-
D8Z79_RS23855 (D8Z79_023855)	61874..62464	-	591	WP_000002778	conjugal transfer pilus-stabilizing protein TraP	-
D8Z79_RS23860 (D8Z79_023860)	62454..63881	-	1428	WP_032297072	F-type conjugal transfer pilus assembly protein TraB	traB
D8Z79_RS23865 (D8Z79_023865)	63881..64609	-	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
D8Z79_RS23870 (D8Z79_023870)	64596..65162	-	567	WP_000399794	type IV conjugative transfer system protein TraE	traE
D8Z79_RS23875 (D8Z79_023875)	65184..65495	-	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
D8Z79_RS23880 (D8Z79_023880)	65510..65875	-	366	WP_021519752	type IV conjugative transfer system pilin TraA	-
D8Z79_RS23885 (D8Z79_023885)	65909..66136	-	228	WP_001254386	conjugal transfer relaxosome protein TraY	-
D8Z79_RS23890 (D8Z79_023890)	66230..66916	-	687	WP_015059009	PAS domain-containing protein	-
D8Z79_RS23895 (D8Z79_023895)	67107..67490	-	384	WP_000124981	conjugal transfer relaxosome DNA-binding protein TraM	-
D8Z79_RS23900 (D8Z79_023900)	67767..68414	+	648	WP_015059008	transglycosylase SLT domain-containing protein	virB1
D8Z79_RS23905 (D8Z79_023905)	68711..69532	-	822	WP_001234445	DUF932 domain-containing protein	-
D8Z79_RS23910 (D8Z79_023910)	69643..69939	-	297	WP_001272251	hypothetical protein	-
D8Z79_RS26170	70239..70535	+	297	Protein_85	hypothetical protein	-
D8Z79_RS23930 (D8Z79_023930)	70854..70979	-	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
D8Z79_RS26625	70921..71070	-	150	Protein_87	plasmid maintenance protein Mok	-
D8Z79_RS26175	71092..71271	+	180	WP_001309233	hypothetical protein	-
D8Z79_RS23935 (D8Z79_023935)	71249..72011	-	763	Protein_89	plasmid SOS inhibition protein A	-
D8Z79_RS23940 (D8Z79_023940)	72008..72442	-	435	WP_000845953	conjugation system SOS inhibitor PsiB	-

Host bacterium

ID	14818	GenBank	NZ_CP040807
Plasmid name	pEF02	Incompatibility group	IncFII
Plasmid size	90871 bp	Coordinate of oriT [Strand]	67719..67842 [-]
Host baterium	Escherichia fergusonii strain EFCF056

Cargo genes

Drug resistance gene	blaCTX-M-55, blaTEM-1B, fosA3, rmtB, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR
Virulence gene	-
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-