oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	107824
Name	oriT_pSCLE3
Organism	Escherichia sp. SCLE84
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP051433 (58961..59312 [+], 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_pSCLE3
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTATTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCCAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_HGD79_RS26280_pSCLE3

ID	5250	GenBank	WP_112907288
Name	traI_HGD79_RS26280_pSCLE3	UniProt ID	_
Length	1756 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1756 a.a. Molecular weight: 192089.61 Da Isoelectric Point: 5.7905

          >WP_112907288.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Escherichia]

MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVANVTQYNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA

LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT

LKETGFDIRAYRDAADQRAEIRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DTVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLQEGMIFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMRDAGVNTYRW

QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL

ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA

QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI

LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLLQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMQNGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM

VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT

LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDGVTLSDGQQTRVIRPGQERAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF

EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG

IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTEQAVREIAGQERDRTATSERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE

KTLGGD

Protein domains

Predicted by InterproScan.

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

(633-712)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(575-626)

Protein structure

No available structure.

Auxiliary protein

WP_168848554_pSCLE3

ID	2407	GenBank	WP_168848554
Name	WP_168848554_pSCLE3	UniProt ID	_
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 127 a.a. Molecular weight: 14569.55 Da Isoelectric Point: 4.7367

                        >WP_168848554.1 conjugal transfer relaxosome DNA-binding protein TraM [Escherichia sp. SCLE84]

MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQAEFNKLL

LECVVKTQSSVAKILGIESLSPHVSGNPKFEYDNMVEDIREKVSVEMERFFPKNDDE

Protein domains

Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)

Protein structure

No available structure.

ID	5496	GenBank	WP_001064243
Name	traC_HGD79_RS26175_pSCLE3	UniProt ID	_
Length	875 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 875 a.a. Molecular weight: 99191.87 Da Isoelectric Point: 5.8486

                        >WP_001064243.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]

MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP

INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA

TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG

EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL

WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE

LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG

LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA

GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV

MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT

ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR

LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN

QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL

SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(289-446)

TraC protein (TraC_F_IV)

(38-276)

TraG P-loop domain (P-loop_TraG)

(467-771)

Protein structure

No available structure.

ID	5497	GenBank	WP_063078211
Name	traD_HGD79_RS26275_pSCLE3	UniProt ID	_
Length	732 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 732 a.a. Molecular weight: 83188.79 Da Isoelectric Point: 5.1657

                        >WP_063078211.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Escherichia]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR

DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ

QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ

PQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN

HPDIQQQMQRREEVNINVHRERGEDVEPGDDF

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.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 61283..86059

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HGD79_RS26425	56350..56646	-	297	Protein_70	hypothetical protein	-
HGD79_RS27015	56716..56838	+	123	Protein_71	single-stranded DNA-binding protein	-
HGD79_RS26095 (HGD79_26115)	56870..57166	+	297	WP_001272240	hypothetical protein	-
HGD79_RS26100 (HGD79_26120)	57272..58093	+	822	WP_001234469	DUF932 domain-containing protein	-
HGD79_RS26105 (HGD79_26125)	58390..59037	-	648	WP_162716379	transglycosylase SLT domain-containing protein	-
HGD79_RS26110 (HGD79_26130)	59313..59696	+	384	WP_168848554	conjugal transfer relaxosome DNA-binding protein TraM	-
HGD79_RS26115 (HGD79_26135)	59888..60535	+	648	WP_000338012	transcriptional regulator TraJ family protein	-
HGD79_RS26120 (HGD79_26140)	60655..60882	+	228	WP_000589558	conjugal transfer relaxosome protein TraY	-
HGD79_RS26125 (HGD79_26145)	60916..61278	+	363	WP_112889070	type IV conjugative transfer system pilin TraA	-
HGD79_RS26130 (HGD79_26150)	61283..61594	+	312	WP_000012101	type IV conjugative transfer system protein TraL	traL
HGD79_RS26135 (HGD79_26155)	61616..62182	+	567	WP_000399793	type IV conjugative transfer system protein TraE	traE
HGD79_RS26140 (HGD79_26160)	62169..62897	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
HGD79_RS26145 (HGD79_26165)	62897..64324	+	1428	WP_000146685	F-type conjugal transfer pilus assembly protein TraB	traB
HGD79_RS26150 (HGD79_26170)	64314..64886	+	573	WP_024179131	conjugal transfer pilus-stabilizing protein TraP	-
HGD79_RS26155 (HGD79_26175)	64883..65080	+	198	WP_001324648	conjugal transfer protein TrbD	-
HGD79_RS26160 (HGD79_26180)	65092..65343	+	252	WP_001038341	conjugal transfer protein TrbG	-
HGD79_RS26165 (HGD79_26185)	65340..65855	+	516	WP_000809906	type IV conjugative transfer system lipoprotein TraV	traV
HGD79_RS26170 (HGD79_26190)	65990..66211	+	222	WP_001278689	conjugal transfer protein TraR	-
HGD79_RS26175 (HGD79_26195)	66371..68998	+	2628	WP_001064243	type IV secretion system protein TraC	virb4
HGD79_RS26180 (HGD79_26200)	68995..69381	+	387	WP_000214096	type-F conjugative transfer system protein TrbI	-
HGD79_RS26185 (HGD79_26205)	69378..70010	+	633	WP_001203720	type-F conjugative transfer system protein TraW	traW
HGD79_RS26190 (HGD79_26210)	70007..70999	+	993	WP_000830839	conjugal transfer pilus assembly protein TraU	traU
HGD79_RS26195 (HGD79_26215)	71025..71486	+	462	WP_000277845	hypothetical protein	-
HGD79_RS26200 (HGD79_26220)	71516..71968	+	453	WP_000069427	hypothetical protein	-
HGD79_RS26205 (HGD79_26225)	71996..72634	+	639	WP_001104248	type-F conjugative transfer system pilin assembly protein TrbC	trbC
HGD79_RS26210 (HGD79_26230)	72631..74439	+	1809	WP_063078212	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
HGD79_RS26215 (HGD79_26235)	74466..74726	+	261	WP_000864323	conjugal transfer protein TrbE	-
HGD79_RS26220 (HGD79_26240)	74719..75462	+	744	WP_168848555	type-F conjugative transfer system pilin assembly protein TraF	traF
HGD79_RS26225 (HGD79_26245)	75478..75825	+	348	WP_001287893	conjugal transfer protein TrbA	-
HGD79_RS26230 (HGD79_26250)	75944..76228	+	285	WP_000624108	type-F conjugative transfer system pilin chaperone TraQ	-
HGD79_RS26235 (HGD79_26255)	76215..76760	+	546	WP_000059818	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
HGD79_RS26240 (HGD79_26260)	76750..77064	+	315	WP_001384255	P-type conjugative transfer protein TrbJ	-
HGD79_RS26245 (HGD79_26265)	77018..77410	+	393	WP_000126338	F-type conjugal transfer protein TrbF	-
HGD79_RS26250 (HGD79_26270)	77397..78770	+	1374	WP_000944325	conjugal transfer pilus assembly protein TraH	traH
HGD79_RS26255 (HGD79_26275)	78767..81589	+	2823	WP_168848556	conjugal transfer mating-pair stabilization protein TraG	traG
HGD79_RS26260 (HGD79_26280)	81604..82107	+	504	WP_000605510	hypothetical protein	-
HGD79_RS26265 (HGD79_26285)	82139..82870	+	732	WP_000850424	conjugal transfer complement resistance protein TraT	-
HGD79_RS26270 (HGD79_26290)	83073..83810	+	738	WP_000199900	hypothetical protein	-
HGD79_RS26275 (HGD79_26295)	83861..86059	+	2199	WP_063078211	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

ID	8259	GenBank	NZ_CP051433
Plasmid name	pSCLE3	Incompatibility group	-
Plasmid size	96595 bp	Coordinate of oriT [Strand]	58961..59312 [+]
Host baterium	Escherichia sp. SCLE84

Cargo genes

Drug resistance gene	-
Virulence gene	vat, cseA
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-