oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	114989
Name	oriT_pKM58_2
Organism	Enterobacter hormaechei strain 22KM1314
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP126809 (25388..25511 [+], 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_pKM58_2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_QPR76_RS23725_pKM58_2

ID	9598	GenBank	WP_306676110
Name	traI_QPR76_RS23725_pKM58_2	UniProt ID	_
Length	1756 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1756 a.a. Molecular weight: 191905.58 Da Isoelectric Point: 5.6449

          >WP_306676110.1 conjugative transfer relaxase/helicase TraI [Enterobacter hormaechei]

MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALVSTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA

LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT

LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW

QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL

ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA

QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI

LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM

VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT

LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF

EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG

IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWVDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTEQAVREIAGQERDRSAISEREAALPESVLRESQREQEAVREVARENLLQERLQQMERDMVRDLQKE

KTLGGD

Protein domains

Predicted by InterproScan.

AAA domain (AAA_30)

(968-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

Protein structure

No available structure.

ID	5643	GenBank	WP_000124981
Name	WP_000124981_pKM58_2	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

ID	5644	GenBank	WP_001254386
Name	WP_001254386_pKM58_2	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

T4CP

traC_QPR76_RS23640_pKM58_2
traD_QPR76_RS23720_pKM58_2

ID	11197	GenBank	WP_000069764
Name	traC_QPR76_RS23640_pKM58_2	UniProt ID	_
Length	876 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 876 a.a. Molecular weight: 99302.93 Da Isoelectric Point: 5.8486

                        >WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]

MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI

PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA

ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV

GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF

LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG

ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK

GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG

AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS

VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY

TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW

RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY

NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG

LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

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	11198	GenBank	WP_021573169
Name	traD_QPR76_RS23720_pKM58_2	UniProt ID	_
Length	735 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 735 a.a. Molecular weight: 83553.19 Da Isoelectric Point: 5.0504

                        >WP_021573169.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR

DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ

QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ

PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ

QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

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: 24816..51432

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
QPR76_RS23520 (QPR76_23505)	20612..21046	+	435	WP_306676112	conjugation system SOS inhibitor PsiB	-
QPR76_RS23525 (QPR76_23510)	21043..21762	+	720	WP_033803547	plasmid SOS inhibition protein A	-
QPR76_RS23530 (QPR76_23515)	21759..22073	+	315	WP_000870669	hypothetical protein	-
QPR76_RS23535 (QPR76_23520)	22263..22376	+	114	Protein_33	DUF5431 family protein	-
QPR76_RS23540 (QPR76_23525)	22321..22443	+	123	WP_223163518	Hok/Gef family protein	-
QPR76_RS23545 (QPR76_23530)	22744..22993	-	250	Protein_35	hypothetical protein	-
QPR76_RS23550 (QPR76_23535)	23293..23589	+	297	WP_001272251	hypothetical protein	-
QPR76_RS23555 (QPR76_23540)	23699..24520	+	822	WP_001234437	DUF932 domain-containing protein	-
QPR76_RS23560 (QPR76_23545)	24816..25463	-	648	WP_306676113	transglycosylase SLT domain-containing protein	virB1
QPR76_RS23565 (QPR76_23550)	25740..26123	+	384	WP_000124981	conjugal transfer relaxosome DNA-binding protein TraM	-
QPR76_RS23570 (QPR76_23555)	26314..27000	+	687	WP_000332484	PAS domain-containing protein	-
QPR76_RS23575 (QPR76_23560)	27094..27321	+	228	WP_001254386	conjugal transfer relaxosome protein TraY	-
QPR76_RS23580 (QPR76_23565)	27355..27714	+	360	WP_000340272	type IV conjugative transfer system pilin TraA	-
QPR76_RS23585 (QPR76_23570)	27729..28040	+	312	WP_000012103	type IV conjugative transfer system protein TraL	traL
QPR76_RS23590 (QPR76_23575)	28062..28628	+	567	WP_000399792	type IV conjugative transfer system protein TraE	traE
QPR76_RS23595 (QPR76_23580)	28615..29343	+	729	WP_001230798	type-F conjugative transfer system secretin TraK	traK
QPR76_RS23600 (QPR76_23585)	29343..30770	+	1428	WP_000146657	F-type conjugal transfer pilus assembly protein TraB	traB
QPR76_RS23605 (QPR76_23590)	30760..31350	+	591	WP_000002784	conjugal transfer pilus-stabilizing protein TraP	-
QPR76_RS23610 (QPR76_23595)	31337..31657	+	321	WP_001057307	conjugal transfer protein TrbD	-
QPR76_RS23615 (QPR76_23600)	31654..32169	+	516	WP_000809874	type IV conjugative transfer system lipoprotein TraV	traV
QPR76_RS23620 (QPR76_23605)	32304..32525	+	222	WP_001278695	conjugal transfer protein TraR	-
QPR76_RS23625 (QPR76_23610)	32518..32994	+	477	WP_000549579	hypothetical protein	-
QPR76_RS23630 (QPR76_23615)	33074..33291	+	218	Protein_52	hypothetical protein	-
QPR76_RS23635 (QPR76_23620)	33319..33666	+	348	WP_000802783	hypothetical protein	-
QPR76_RS23640 (QPR76_23625)	33793..36423	+	2631	WP_000069764	type IV secretion system protein TraC	virb4
QPR76_RS23645 (QPR76_23630)	36420..36806	+	387	WP_000214097	type-F conjugative transfer system protein TrbI	-
QPR76_RS23650 (QPR76_23635)	36803..37435	+	633	WP_001203720	type-F conjugative transfer system protein TraW	traW
QPR76_RS23655 (QPR76_23640)	37432..38424	+	993	WP_000830839	conjugal transfer pilus assembly protein TraU	traU
QPR76_RS23660 (QPR76_23645)	38433..39071	+	639	WP_000777692	type-F conjugative transfer system pilin assembly protein TrbC	trbC
QPR76_RS23665 (QPR76_23650)	39068..40918	+	1851	WP_306676107	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
QPR76_RS23670 (QPR76_23655)	40944..41201	+	258	WP_000864328	conjugal transfer protein TrbE	-
QPR76_RS23675 (QPR76_23660)	41194..41937	+	744	WP_001030390	type-F conjugative transfer system pilin assembly protein TraF	traF
QPR76_RS23680 (QPR76_23665)	41953..42300	+	348	WP_001287679	conjugal transfer protein TrbA	-
QPR76_RS23685 (QPR76_23670)	42419..42703	+	285	WP_000624110	type-F conjugative transfer system pilin chaperone TraQ	-
QPR76_RS23690 (QPR76_23675)	42690..43235	+	546	WP_000052618	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
QPR76_RS23695 (QPR76_23680)	43165..43527	+	363	WP_010379880	P-type conjugative transfer protein TrbJ	-
QPR76_RS23700 (QPR76_23685)	43527..44900	+	1374	WP_001137358	conjugal transfer pilus assembly protein TraH	traH
QPR76_RS23705 (QPR76_23690)	44897..47722	+	2826	WP_001007030	conjugal transfer mating-pair stabilization protein TraG	traG
QPR76_RS23710 (QPR76_23695)	47719..48228	+	510	WP_000628099	conjugal transfer entry exclusion protein TraS	-
QPR76_RS23715 (QPR76_23700)	48242..48973	+	732	WP_000850424	conjugal transfer complement resistance protein TraT	-
QPR76_RS23720 (QPR76_23705)	49225..51432	+	2208	WP_021573169	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

ID	15424	GenBank	NZ_CP126809
Plasmid name	pKM58_2	Incompatibility group	IncFII
Plasmid size	61092 bp	Coordinate of oriT [Strand]	25388..25511 [+]
Host baterium	Enterobacter hormaechei strain 22KM1314

Cargo genes

Drug resistance gene	tet(A)
Virulence gene	-
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-