oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	102413
Name	oriT_SMG004F1\|unnamed1
Organism	Escherichia coli strain SMG004F1
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_JAKVSW010000019 (40751..40874 [+], 124 nt)
oriT length	124 nt
IRs (inverted repeats)	92..99, 113..120 (ATAATGTA..TACATTAT) 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_SMG004F1|unnamed1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_ML378_RS18175_SMG004F1|unnamed1

ID	1807	GenBank	WP_000948348
Name	traI_ML378_RS18175_SMG004F1\|unnamed1	UniProt ID	A0A7I0KNL8
Length	1756 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1756 a.a. Molecular weight: 191759.33 Da Isoelectric Point: 5.7433

          >WP_000948348.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]

MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA

LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT

LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW

QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL

ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA

QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI

LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM

EPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT

LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL

EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG

IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE

KTLGGD

Protein domains

Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)

AAA domain (AAA_30)

(968-1156)

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

(575-626)

Protein structure

No available structure.

ID	724	GenBank	WP_001151562
Name	WP_001151562_SMG004F1\|unnamed1	UniProt ID	A0A7I0KNG1
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 127 a.a. Molecular weight: 14420.36 Da Isoelectric Point: 4.8624

                        >WP_001151562.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]

MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVHEAQMERKESAFNQAEFNKVL

LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

Protein domains

Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A7I0KNG1

ID	725	GenBank	WP_001254388
Name	WP_001254388_SMG004F1\|unnamed1	UniProt ID	W9A0Z2
Length	75 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 75 a.a. Molecular weight: 9072.20 Da Isoelectric Point: 10.2071

                        >WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]

MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES

TFKEL

Protein domains

Predicted by InterproScan.

TraY domain (TraY)

(14-61)

Protein structure

Source	ID	Structure
AlphaFold DB	W9A0Z2

T4CP

traC_ML378_RS18070_SMG004F1|unnamed1
traD_ML378_RS18170_SMG004F1|unnamed1

ID	1388	GenBank	WP_000069778
Name	traC_ML378_RS18070_SMG004F1\|unnamed1	UniProt ID	_
Length	876 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 876 a.a. Molecular weight: 99300.06 Da Isoelectric Point: 6.3461

                        >WP_000069778.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]

MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI

PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA

ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV

GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF

LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG

ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK

GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG

AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS

VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY

TANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW

RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY

NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG

MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

Protein structure

No available structure.

ID	1389	GenBank	WP_032164615
Name	traD_ML378_RS18170_SMG004F1\|unnamed1	UniProt ID	_
Length	753 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 753 a.a. Molecular weight: 85681.49 Da Isoelectric Point: 5.1644

                        >WP_032164615.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR

DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ

QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP

GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

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: 40179..68686

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
ML378_RS17955 (ML378_17960)	36156..36590	+	435	WP_000845910	conjugation system SOS inhibitor PsiB	-
ML378_RS17960 (ML378_17965)	36587..37350	+	764	Protein_43	plasmid SOS inhibition protein A	-
ML378_RS17965 (ML378_17970)	37524..37673	+	150	Protein_44	DUF5431 family protein	-
ML378_RS17970 (ML378_17975)	37615..37740	+	126	WP_096937776	type I toxin-antitoxin system Hok family toxin	-
ML378_RS17975 (ML378_17980)	38058..38355	-	298	Protein_46	hypothetical protein	-
ML378_RS17980 (ML378_17985)	38656..38943	+	288	WP_000107526	hypothetical protein	-
ML378_RS17985 (ML378_17990)	39062..39883	+	822	WP_001234489	DUF932 domain-containing protein	-
ML378_RS17990 (ML378_17995)	40179..40781	-	603	WP_001323326	transglycosylase SLT domain-containing protein	virB1
ML378_RS17995 (ML378_18000)	41112..41495	+	384	WP_001151562	conjugal transfer relaxosome DNA-binding protein TraM	-
ML378_RS18000 (ML378_18005)	41689..42375	+	687	WP_000332487	PAS domain-containing protein	-
ML378_RS18005 (ML378_18010)	42469..42696	+	228	WP_001254388	conjugal transfer relaxosome protein TraY	-
ML378_RS18010 (ML378_18015)	42730..43089	+	360	WP_001098988	type IV conjugative transfer system pilin TraA	-
ML378_RS18015 (ML378_18020)	43104..43415	+	312	WP_000012100	type IV conjugative transfer system protein TraL	traL
ML378_RS18020 (ML378_18025)	43437..44003	+	567	WP_000399776	type IV conjugative transfer system protein TraE	traE
ML378_RS18025 (ML378_18030)	43990..44718	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
ML378_RS18030 (ML378_18035)	44718..46145	+	1428	WP_000146665	F-type conjugal transfer pilus assembly protein TraB	traB
ML378_RS18035 (ML378_18040)	46135..46725	+	591	WP_000002787	conjugal transfer pilus-stabilizing protein TraP	-
ML378_RS18040 (ML378_18045)	46712..47032	+	321	WP_001057275	conjugal transfer protein TrbD	virb4
ML378_RS18045 (ML378_18050)	47025..47277	+	253	Protein_60	conjugal transfer protein TrbG	-
ML378_RS18050 (ML378_18055)	47274..47789	+	516	WP_000809888	type IV conjugative transfer system lipoprotein TraV	traV
ML378_RS18055 (ML378_18060)	47924..48145	+	222	WP_001278694	conjugal transfer protein TraR	-
ML378_RS18060 (ML378_18065)	48138..48611	+	474	WP_000549566	hypothetical protein	-
ML378_RS18065 (ML378_18070)	48691..48909	+	219	WP_000556746	hypothetical protein	-
ML378_RS26540	48937..49150	+	214	Protein_65	hypothetical protein	-
ML378_RS18070 (ML378_18075)	49276..51906	+	2631	WP_000069778	type IV secretion system protein TraC	virb4
ML378_RS18075 (ML378_18080)	51903..52289	+	387	WP_000214082	type-F conjugative transfer system protein TrbI	-
ML378_RS18080 (ML378_18085)	52286..52918	+	633	WP_001203736	type-F conjugative transfer system protein TraW	traW
ML378_RS18085 (ML378_18090)	52915..53907	+	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
ML378_RS18090 (ML378_18095)	53937..54242	+	306	WP_000224418	hypothetical protein	-
ML378_RS18095 (ML378_18100)	54251..54889	+	639	WP_001080251	type-F conjugative transfer system pilin assembly protein TrbC	trbC
ML378_RS18100 (ML378_18105)	54886..56736	+	1851	WP_000821859	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
ML378_RS18105 (ML378_18110)	56763..57020	+	258	WP_000864314	conjugal transfer protein TrbE	-
ML378_RS18110 (ML378_18115)	57013..57756	+	744	WP_001030385	type-F conjugative transfer system pilin assembly protein TraF	traF
ML378_RS18115 (ML378_18120)	57770..58111	+	342	WP_001298557	conjugal transfer protein TrbA	-
ML378_RS18120 (ML378_18125)	58092..58427	-	336	WP_000736414	hypothetical protein	-
ML378_RS18125 (ML378_18130)	58508..58792	+	285	WP_000624107	type-F conjugative transfer system pilin chaperone TraQ	-
ML378_RS18130 (ML378_18135)	58779..59324	+	546	WP_000059830	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
ML378_RS18135 (ML378_18140)	59254..59601	+	348	WP_001309242	P-type conjugative transfer protein TrbJ	-
ML378_RS18140 (ML378_18145)	59582..59974	+	393	WP_000660700	F-type conjugal transfer protein TrbF	-
ML378_RS18145 (ML378_18150)	59961..61334	+	1374	WP_000944331	conjugal transfer pilus assembly protein TraH	traH
ML378_RS18150 (ML378_18155)	61331..64153	+	2823	WP_001007080	conjugal transfer mating-pair stabilization protein TraG	traG
ML378_RS18155 (ML378_18160)	64169..64654	+	486	WP_000605869	hypothetical protein	-
ML378_RS18160 (ML378_18165)	64703..65434	+	732	WP_000782451	conjugal transfer complement resistance protein TraT	-
ML378_RS18165 (ML378_18170)	65637..66374	+	738	WP_000199901	hypothetical protein	-
ML378_RS18170 (ML378_18175)	66425..68686	+	2262	WP_032164615	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

ID	2857	GenBank	NZ_JAKVSW010000019
Plasmid name	SMG004F1\|unnamed1	Incompatibility group	IncFIB
Plasmid size	82486 bp	Coordinate of oriT [Strand]	40751..40874 [+]
Host baterium	Escherichia coli strain SMG004F1

Cargo genes

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