oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	108124
Name	oriT_p_dmcr749c_NDM5
Organism	Citrobacter sedlakii strain dmcr749c
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP095669 (56867..56952 [-], 86 nt)
oriT length	86 nt
IRs (inverted repeats)	61..68, 73..80 (TTGGTGGT..ACCACCAA) 27..34, 37..44 (GCAAAAAC..GTTTTTGC) 8..14, 20..26 (TGATTTA..TAAATCA)
*Location of nic* site**	53..54
Conserved sequence flanking the nic site	TGTGTGGTGC
Note	Predicted by oriTfinder 2.0

oriT sequence

Download Length: 86 nt

                        >oriT_p_dmcr749c_NDM5
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_KDV83_RS00530_p_dmcr749c_NDM5

ID	5446	GenBank	WP_000948354
Name	traI_KDV83_RS00530_p_dmcr749c_NDM5	UniProt ID	A0AA36L3I8
Length	1756 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1756 a.a. Molecular weight: 191683.22 Da Isoelectric Point: 5.6912

          >WP_000948354.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]

MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA

LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT

LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW

QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL

ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA

QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI

LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM

VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT

LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL

EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG

IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE

KTLGGD

Protein domains

Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

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	2575	GenBank	WP_001354030
Name	WP_001354030_p_dmcr749c_NDM5	UniProt ID	A0A734M5H3
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 127 a.a. Molecular weight: 14508.47 Da Isoelectric Point: 4.7116

                        >WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]

MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL

LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE

Protein domains

Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A734M5H3

ID	2576	GenBank	WP_000089263
Name	WP_000089263_p_dmcr749c_NDM5	UniProt ID	A0A3U3XJL9
Length	75 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 75 a.a. Molecular weight: 8541.74 Da Isoelectric Point: 8.6796

                        >WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]

MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS

IIKDL

Protein domains

Predicted by InterproScan.

TraY domain (TraY)

(14-60)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A3U3XJL9

T4CP

traC_KDV83_RS00430_p_dmcr749c_NDM5
traD_KDV83_RS00525_p_dmcr749c_NDM5

ID	5791	GenBank	WP_000069777
Name	traC_KDV83_RS00430_p_dmcr749c_NDM5	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.

ID	5792	GenBank	WP_046072940
Name	traD_KDV83_RS00525_p_dmcr749c_NDM5	UniProt ID	_
Length	753 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 753 a.a. Molecular weight: 85667.46 Da Isoelectric Point: 5.1644

                        >WP_046072940.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR

DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ

QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPP

GISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF

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: 56299..84442

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
KDV83_RS00315 (KDV83_000315)	52271..52705	+	435	WP_000845953	conjugation system SOS inhibitor PsiB	-
KDV83_RS00320 (KDV83_000320)	52702..53421	+	720	WP_001276217	plasmid SOS inhibition protein A	-
KDV83_RS00325 (KDV83_000325)	53643..53792	+	150	Protein_64	plasmid maintenance protein Mok	-
KDV83_RS00330 (KDV83_000330)	53734..53859	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
KDV83_RS00335 (KDV83_000335)	54178..54474	-	297	Protein_66	hypothetical protein	-
KDV83_RS00340 (KDV83_000340)	54774..55070	+	297	WP_001272251	hypothetical protein	-
KDV83_RS00345 (KDV83_000345)	55181..56002	+	822	WP_001234445	DUF932 domain-containing protein	-
KDV83_RS00350 (KDV83_000350)	56299..56901	-	603	WP_000243713	transglycosylase SLT domain-containing protein	virB1
KDV83_RS00355 (KDV83_000355)	57224..57607	+	384	WP_001354030	conjugal transfer relaxosome DNA-binding protein TraM	-
KDV83_RS00360 (KDV83_000360)	57801..58472	+	672	WP_000283561	conjugal transfer transcriptional regulator TraJ	-
KDV83_RS00365 (KDV83_000365)	58609..58836	+	228	WP_000089263	conjugal transfer relaxosome protein TraY	-
KDV83_RS00370 (KDV83_000370)	58869..59228	+	360	WP_001098992	type IV conjugative transfer system pilin TraA	-
KDV83_RS00375 (KDV83_000375)	59243..59554	+	312	WP_000012113	type IV conjugative transfer system protein TraL	traL
KDV83_RS00380 (KDV83_000380)	59576..60142	+	567	WP_000399780	type IV conjugative transfer system protein TraE	traE
KDV83_RS00385 (KDV83_000385)	60129..60857	+	729	WP_001230772	type-F conjugative transfer system secretin TraK	traK
KDV83_RS00390 (KDV83_000390)	60857..62308	+	1452	WP_000146675	F-type conjugal transfer pilus assembly protein TraB	traB
KDV83_RS00395 (KDV83_000395)	62298..62864	+	567	WP_000896599	conjugal transfer pilus-stabilizing protein TraP	-
KDV83_RS00400 (KDV83_000400)	62851..63171	+	321	WP_001057307	conjugal transfer protein TrbD	-
KDV83_RS00405 (KDV83_000405)	63168..63683	+	516	WP_000809881	type IV conjugative transfer system lipoprotein TraV	traV
KDV83_RS00410 (KDV83_000410)	63818..64039	+	222	WP_001278683	conjugal transfer protein TraR	-
KDV83_RS00415 (KDV83_000415)	64032..64508	+	477	WP_000549587	hypothetical protein	-
KDV83_RS00420 (KDV83_000420)	64588..64806	+	219	WP_000556745	hypothetical protein	-
KDV83_RS00425 (KDV83_000425)	64834..65181	+	348	WP_000836682	hypothetical protein	-
KDV83_RS00430 (KDV83_000430)	65307..67937	+	2631	WP_000069777	type IV secretion system protein TraC	virb4
KDV83_RS00435 (KDV83_000435)	67934..68320	+	387	WP_000214084	type-F conjugative transfer system protein TrbI	-
KDV83_RS00440 (KDV83_000440)	68317..68949	+	633	WP_001203728	type-F conjugative transfer system protein TraW	traW
KDV83_RS00445 (KDV83_000445)	68946..69938	+	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
KDV83_RS00450 (KDV83_000450)	69968..70273	+	306	WP_000224416	hypothetical protein	-
KDV83_RS00455 (KDV83_000455)	70282..70920	+	639	WP_001080256	type-F conjugative transfer system pilin assembly protein TrbC	trbC
KDV83_RS00460 (KDV83_000460)	70917..72767	+	1851	WP_000821856	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
KDV83_RS00465 (KDV83_000465)	72794..73051	+	258	WP_000864353	conjugal transfer protein TrbE	-
KDV83_RS00470 (KDV83_000470)	73044..73787	+	744	WP_001030371	type-F conjugative transfer system pilin assembly protein TraF	traF
KDV83_RS00475 (KDV83_000475)	73801..74145	+	345	WP_000556796	conjugal transfer protein TrbA	-
KDV83_RS00480 (KDV83_000480)	74264..74548	+	285	WP_000624194	type-F conjugative transfer system pilin chaperone TraQ	-
KDV83_RS00485 (KDV83_000485)	74535..75080	+	546	WP_000059831	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
KDV83_RS00490 (KDV83_000490)	75010..75357	+	348	WP_001309242	P-type conjugative transfer protein TrbJ	-
KDV83_RS00495 (KDV83_000495)	75338..75730	+	393	WP_000660699	F-type conjugal transfer protein TrbF	-
KDV83_RS00500 (KDV83_000500)	75717..77090	+	1374	WP_000944331	conjugal transfer pilus assembly protein TraH	traH
KDV83_RS00505 (KDV83_000505)	77087..79909	+	2823	WP_001007039	conjugal transfer mating-pair stabilization protein TraG	traG
KDV83_RS00510 (KDV83_000510)	79925..80410	+	486	WP_000605870	hypothetical protein	-
KDV83_RS00515 (KDV83_000515)	80459..81190	+	732	WP_000782451	conjugal transfer complement resistance protein TraT	-
KDV83_RS00520 (KDV83_000520)	81393..82130	+	738	WP_000199905	hypothetical protein	-
KDV83_RS00525 (KDV83_000525)	82181..84442	+	2262	WP_046072940	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

ID	8559	GenBank	NZ_CP095669
Plasmid name	p_dmcr749c_NDM5	Incompatibility group	IncFII
Plasmid size	94788 bp	Coordinate of oriT [Strand]	56867..56952 [-]
Host baterium	Citrobacter sedlakii strain dmcr749c

Cargo genes

Drug resistance gene	erm(B), mph(A), blaTEM-1B, rmtB, blaNDM-5, sul1, qacE, aadA2, dfrA12
Virulence gene	-
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	AcrIF11