oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	101494
Name	oriT_p2560-6
Organism	Escherichia coli strain GN02560
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_JALJQO010000007 (69673..70024 [-], 352 nt)
oriT length	352 nt
IRs (inverted repeats)	192..198, 206..212 (TATAAAA..TTTTATA) 104..110, 118..124 (TTTAAAT..ATTTAAA) 106..111, 113..118 (TAAATC..GATTTA) 93..98, 106..111 (GATTTA..TAAATC) 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

Download Length: 352 nt

                        >oriT_p2560-6
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTATTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCTAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_MWG49_RS25605_p2560-6

ID	1333	GenBank	WP_058661299
Name	traI_MWG49_RS25605_p2560-6	UniProt ID	_
Length	1756 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1756 a.a. Molecular weight: 191862.48 Da Isoelectric Point: 5.6929

          >WP_058661299.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]

MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA

LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIRMAEWMQT

LKETGFDIRAYRDAADQRAETRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW

QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLWDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL

ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA

QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI

LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVAIMKEIVRQTPELREAVYNLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGQEQVM

VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT

LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVFGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL

EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG

IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE

KTLGGD

Protein domains

Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(968-1156)

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

(633-712)

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

(575-626)

Protein structure

No available structure.

Auxiliary protein

WP_001151529_p2560-6

ID	469	GenBank	WP_001151529
Name	WP_001151529_p2560-6	UniProt ID	A0A7I0L277
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 127 a.a. Molecular weight: 14497.49 Da Isoelectric Point: 4.8662

                        >WP_001151529.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]

MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQAEFNKLL

LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSAEMERFFPKNDDE

Protein domains

Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A7I0L277

ID	954	GenBank	WP_268656398
Name	traD_MWG49_RS25610_p2560-6	UniProt ID	_
Length	747 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 747 a.a. Molecular weight: 84906.65 Da Isoelectric Point: 5.1647

                        >WP_268656398.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR

DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGHQGKQ

QSENEVTGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESG

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	955	GenBank	WP_000069777
Name	traC_MWG49_RS25710_p2560-6	UniProt ID	_
Length	876 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 876 a.a. Molecular weight: 99195.86 Da Isoelectric Point: 6.1126

                        >WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]

MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI

PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA

ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV

GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF

LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG

ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK

GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG

AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS

VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY

TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW

RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY

NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG

LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 42091..70595

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
MWG49_RS25610 (MWG49_25620)	42091..44334	-	2244	WP_268656398	type IV conjugative transfer system coupling protein TraD	virb4
MWG49_RS25615 (MWG49_25625)	44385..45122	-	738	WP_000199905	hypothetical protein	-
MWG49_RS25620 (MWG49_25630)	45325..46056	-	732	WP_000850422	conjugal transfer complement resistance protein TraT	-
MWG49_RS25625 (MWG49_25635)	46086..46578	-	493	Protein_54	entry exclusion protein	-
MWG49_RS25630 (MWG49_25640)	46603..49424	-	2822	Protein_55	conjugal transfer mating-pair stabilization protein TraG	-
MWG49_RS25635 (MWG49_25645)	49421..50347	-	927	Protein_56	conjugal transfer protein TraH	-
MWG49_RS26040	50380..50805	-	426	WP_327049698	conjugal transfer protein TraH	traH
MWG49_RS25640 (MWG49_25650)	50792..51184	-	393	WP_014106973	F-type conjugal transfer protein TrbF	-
MWG49_RS25645 (MWG49_25655)	51165..51512	-	348	WP_071840683	P-type conjugative transfer protein TrbJ	-
MWG49_RS25650 (MWG49_25660)	51442..51987	-	546	WP_021549723	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
MWG49_RS25655 (MWG49_25665)	51974..52258	-	285	WP_000624194	type-F conjugative transfer system pilin chaperone TraQ	-
MWG49_RS25660 (MWG49_25670)	52339..52674	+	336	WP_001620807	hypothetical protein	-
MWG49_RS25665 (MWG49_25675)	52655..52996	-	342	WP_000556795	conjugal transfer protein TrbA	-
MWG49_RS25670 (MWG49_25680)	53010..53753	-	744	WP_032362904	type-F conjugative transfer system pilin assembly protein TraF	traF
MWG49_RS25675 (MWG49_25685)	53746..54003	-	258	WP_021563038	conjugal transfer protein TrbE	-
MWG49_RS25680 (MWG49_25690)	54030..55880	-	1851	WP_268656400	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
MWG49_RS25685 (MWG49_25695)	55877..56515	-	639	WP_001080251	type-F conjugative transfer system pilin assembly protein TrbC	trbC
MWG49_RS25690 (MWG49_25700)	56524..56829	-	306	WP_000224418	hypothetical protein	-
MWG49_RS25695 (MWG49_25705)	56859..57851	-	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
MWG49_RS25700 (MWG49_25710)	57848..58480	-	633	WP_001203728	type-F conjugative transfer system protein TraW	traW
MWG49_RS25705 (MWG49_25715)	58477..58863	-	387	WP_000214084	type-F conjugative transfer system protein TrbI	-
MWG49_RS25710 (MWG49_25720)	58860..61490	-	2631	WP_000069777	type IV secretion system protein TraC	virb4
MWG49_RS25715 (MWG49_25725)	61616..61963	-	348	WP_000836682	hypothetical protein	-
MWG49_RS25720 (MWG49_25730)	61991..62209	-	219	WP_001377841	hypothetical protein	-
MWG49_RS25725 (MWG49_25735)	62287..62763	-	477	WP_000549580	hypothetical protein	-
MWG49_RS25730 (MWG49_25740)	62756..62977	-	222	WP_001278695	conjugal transfer protein TraR	-
MWG49_RS25735 (MWG49_25745)	63112..63627	-	516	WP_000809889	type IV conjugative transfer system lipoprotein TraV	traV
MWG49_RS25740 (MWG49_25750)	63624..63875	-	252	WP_001038342	conjugal transfer protein TrbG	-
MWG49_RS25745 (MWG49_25755)	63887..64084	-	198	WP_033544369	conjugal transfer protein TrbD	-
MWG49_RS25750 (MWG49_25760)	64071..64661	-	591	WP_000002787	conjugal transfer pilus-stabilizing protein TraP	-
MWG49_RS25755 (MWG49_25765)	64651..66078	-	1428	WP_001530447	F-type conjugal transfer pilus assembly protein TraB	traB
MWG49_RS25760 (MWG49_25770)	66078..66806	-	729	WP_001230769	type-F conjugative transfer system secretin TraK	traK
MWG49_RS25765 (MWG49_25775)	66793..67359	-	567	WP_000399780	type IV conjugative transfer system protein TraE	traE
MWG49_RS25770 (MWG49_25780)	67381..67692	-	312	WP_000012100	type IV conjugative transfer system protein TraL	traL
MWG49_RS25775 (MWG49_25785)	67707..68069	-	363	WP_001098993	type IV conjugative transfer system pilin TraA	-
MWG49_RS25780 (MWG49_25790)	68103..68330	-	228	WP_000589556	conjugal transfer relaxosome protein TraY	-
MWG49_RS25785 (MWG49_25795)	68450..69097	-	648	WP_000332523	transcriptional regulator TraJ family protein	-
MWG49_RS25790 (MWG49_25800)	69289..69672	-	384	WP_001151529	conjugal transfer relaxosome DNA-binding protein TraM	-
MWG49_RS25795 (MWG49_25805)	69948..70595	+	648	WP_072204760	transglycosylase SLT domain-containing protein	virB1
MWG49_RS25800 (MWG49_25810)	70892..71713	-	822	WP_059326940	DUF932 domain-containing protein	-
MWG49_RS25805 (MWG49_25815)	71823..72119	-	297	WP_001272251	hypothetical protein	-
MWG49_RS25810 (MWG49_25820)	72590..72826	-	237	WP_071594222	hypothetical protein	-
MWG49_RS25815 (MWG49_25825)	73092..73334	-	243	WP_000540588	hypothetical protein	-
MWG49_RS25820 (MWG49_25830)	73393..73677	-	285	WP_059326992	hypothetical protein	-
MWG49_RS25825 (MWG49_25835)	73752..74429	+	678	WP_001339397	IS66-like element accessory protein TnpA	-
MWG49_RS25830 (MWG49_25840)	74429..74776	+	348	WP_000624622	IS66 family insertion sequence element accessory protein TnpB	-

Host bacterium

ID	1938	GenBank	NZ_JALJQO010000007
Plasmid name	p2560-6	Incompatibility group	IncFII
Plasmid size	80303 bp	Coordinate of oriT [Strand]	69673..70024 [-]
Host baterium	Escherichia coli strain GN02560

Cargo genes

Drug resistance gene	blaTEM-1B
Virulence gene	-
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-