oriTDB

Detailed information of oriT

oriT
Relaxase
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	104444
Name	oriT_pBY221-1
Organism	Klebsiella pneumoniae strain BY221
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP090219 (41625..41748 [+], 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_pBY221-1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Relaxase

traI_LVJ43_RS25855_pBY221-1

ID	3225	GenBank	WP_071177725
Name	traI_LVJ43_RS25855_pBY221-1	UniProt ID	A0A7G3L5Q3
Length	1711 a.a.	PDB ID
Note	Predicted by oriTfinder 2.0

Relaxase protein sequence

Download Length: 1711 a.a. Molecular weight: 186716.81 Da Isoelectric Point: 6.1728

          >WP_071177725.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]

MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ

DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV

MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA

LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT

LKETGFDIRAYRDAADQRAENRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE

NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS

DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR

RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW

QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT

MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS

SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL

ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI

KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA

QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI

LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT

QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA

ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA

QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM

VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT

LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI

TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL

EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG

IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE

GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP

DGKTEQAVREIAGQVRERAAITERETALLQS

Protein domains

Predicted by InterproScan.

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

(575-626)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

Protein structure

No available structure.

ID	1412	GenBank	WP_000124981
Name	WP_000124981_pBY221-1	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	1413	GenBank	WP_001254386
Name	WP_001254386_pBY221-1	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_LVJ43_RS25740_pBY221-1
traD_LVJ43_RS25850_pBY221-1

ID	3137	GenBank	WP_015059012
Name	traC_LVJ43_RS25740_pBY221-1	UniProt ID	_
Length	875 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 875 a.a. Molecular weight: 99393.22 Da Isoelectric Point: 6.3465

                        >WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]

MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP

INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA

TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG

EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL

WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE

LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG

LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA

GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV

MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT

ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR

LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN

QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL

SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

Protein structure

No available structure.

ID	3138	GenBank	WP_021573169
Name	traD_LVJ43_RS25850_pBY221-1	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: 41053..70289

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LVJ43_RS25635 (LVJ43_25605)	36256..36975	+	720	WP_001276217	plasmid SOS inhibition protein A	-
LVJ43_RS25640 (LVJ43_25610)	37197..37346	+	150	Protein_49	plasmid maintenance protein Mok	-
LVJ43_RS25645 (LVJ43_25615)	37288..37413	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
LVJ43_RS25650 (LVJ43_25620)	37732..38028	-	297	Protein_51	hypothetical protein	-
LVJ43_RS25655 (LVJ43_25625)	38328..38624	+	297	WP_001272251	hypothetical protein	-
LVJ43_RS25660 (LVJ43_25630)	38805..39785	+	981	WP_000019473	IS5-like element ISKpn26 family transposase	-
LVJ43_RS25665 (LVJ43_25635)	39935..40756	+	822	WP_001234445	DUF932 domain-containing protein	-
LVJ43_RS25670 (LVJ43_25640)	41053..41700	-	648	WP_015059008	transglycosylase SLT domain-containing protein	virB1
LVJ43_RS25675 (LVJ43_25645)	41977..42360	+	384	WP_000124981	conjugal transfer relaxosome DNA-binding protein TraM	-
LVJ43_RS25680 (LVJ43_25650)	42551..43237	+	687	WP_015059009	PAS domain-containing protein	-
LVJ43_RS25685 (LVJ43_25655)	43331..43558	+	228	WP_001254386	conjugal transfer relaxosome protein TraY	-
LVJ43_RS25690 (LVJ43_25660)	43592..43957	+	366	WP_021519752	type IV conjugative transfer system pilin TraA	-
LVJ43_RS25695 (LVJ43_25665)	43972..44283	+	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
LVJ43_RS25700 (LVJ43_25670)	44305..44871	+	567	WP_000399794	type IV conjugative transfer system protein TraE	traE
LVJ43_RS25705 (LVJ43_25675)	44858..45586	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
LVJ43_RS25710 (LVJ43_25680)	45586..47013	+	1428	WP_032297072	F-type conjugal transfer pilus assembly protein TraB	traB
LVJ43_RS25715 (LVJ43_25685)	47003..47593	+	591	WP_000002778	conjugal transfer pilus-stabilizing protein TraP	-
LVJ43_RS25720 (LVJ43_25690)	47580..47777	+	198	WP_001324648	conjugal transfer protein TrbD	-
LVJ43_RS25725 (LVJ43_25695)	47789..48040	+	252	WP_001038341	conjugal transfer protein TrbG	-
LVJ43_RS25730 (LVJ43_25700)	48037..48552	+	516	WP_062955122	type IV conjugative transfer system lipoprotein TraV	traV
LVJ43_RS25735 (LVJ43_25705)	48687..48908	+	222	WP_001278692	conjugal transfer protein TraR	-
LVJ43_RS25740 (LVJ43_25710)	49068..51695	+	2628	WP_015059012	type IV secretion system protein TraC	virb4
LVJ43_RS25745 (LVJ43_25715)	51692..52078	+	387	WP_015059013	type-F conjugative transfer system protein TrbI	-
LVJ43_RS25750 (LVJ43_25720)	52075..52707	+	633	WP_001203735	type-F conjugative transfer system protein TraW	traW
LVJ43_RS25755 (LVJ43_25725)	52704..53696	+	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
LVJ43_RS25760 (LVJ43_25730)	53723..54031	+	309	WP_000412447	hypothetical protein	-
LVJ43_RS25765 (LVJ43_25735)	54094..54615	+	522	WP_015059014	hypothetical protein	-
LVJ43_RS25770 (LVJ43_25740)	54642..55280	+	639	WP_000087532	type-F conjugative transfer system pilin assembly protein TrbC	trbC
LVJ43_RS25775 (LVJ43_25745)	55277..55648	+	372	WP_000056336	hypothetical protein	-
LVJ43_RS25780 (LVJ43_25750)	55674..56096	+	423	WP_001229309	HNH endonuclease signature motif containing protein	-
LVJ43_RS25785 (LVJ43_25755)	56093..57943	+	1851	WP_015059015	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
LVJ43_RS25790 (LVJ43_25760)	57970..58227	+	258	WP_053913405	conjugal transfer protein TrbE	-
LVJ43_RS25795 (LVJ43_25765)	58214..58963	+	750	WP_072354014	type-F conjugative transfer system pilin assembly protein TraF	traF
LVJ43_RS25800 (LVJ43_25770)	59124..59360	+	237	WP_000270010	type-F conjugative transfer system pilin chaperone TraQ	-
LVJ43_RS25805 (LVJ43_25775)	59347..59892	+	546	WP_000059817	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
LVJ43_RS25810 (LVJ43_25780)	59882..60196	+	315	WP_001384255	P-type conjugative transfer protein TrbJ	-
LVJ43_RS25815 (LVJ43_25785)	60150..60542	+	393	WP_000126338	F-type conjugal transfer protein TrbF	-
LVJ43_RS25820 (LVJ43_25790)	60529..61902	+	1374	WP_000944325	conjugal transfer pilus assembly protein TraH	traH
LVJ43_RS25825 (LVJ43_25795)	61899..64715	+	2817	WP_015059018	conjugal transfer mating-pair stabilization protein TraG	traG
LVJ43_RS25830 (LVJ43_25800)	64748..65077	+	330	WP_227650653	hypothetical protein	-
LVJ43_RS25835 (LVJ43_25805)	65095..66063	+	969	WP_013362812	IS5-like element IS903B family transposase	-
LVJ43_RS25840 (LVJ43_25810)	66360..67091	+	732	WP_021559024	conjugal transfer complement resistance protein TraT	-
LVJ43_RS25845 (LVJ43_25815)	67294..68031	+	738	WP_015059020	hypothetical protein	-
LVJ43_RS25850 (LVJ43_25820)	68082..70289	+	2208	WP_021573169	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

ID	4883	GenBank	NZ_CP090219
Plasmid name	pBY221-1	Incompatibility group	IncR
Plasmid size	172001 bp	Coordinate of oriT [Strand]	41625..41748 [+]
Host baterium	Klebsiella pneumoniae strain BY221

Cargo genes

Drug resistance gene	blaCTX-M-65, fosA3, blaTEM-1B, rmtB, blaKPC-2, catA2
Virulence gene	-
Metal resistance gene	merE, merD, merA, merP, merT, merR
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	AcrIE9