Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 117978
• Name: oriT_FDAARGOS_1334|unnamed2
• Organism: Klebsiella oxytoca strain FDAARGOS_1334
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP069928 (4428..4551 [+], 124 nt)
• oriT length: 124 nt
• IRs (inverted repeats): 92..99, 113..120 (ATAATGTA..TACATTAT) 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

• Length: 124 nt

>oriT_FDAARGOS_1334|unnamed2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_I6K64_RS29125_FDAARGOS_1334|unnamed2

• ID: 11404
• GenBank: WP_204724570
• Name: traI_I6K64_RS29125_FDAARGOS_1334|unnamed2
• UniProt ID: _
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 191793.67 Da
• Isoelectric Point: 5.9591

>WP_204724570.1 conjugative transfer relaxase/helicase TraI [Klebsiella oxytoca]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEGASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRTEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTEMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRSAISERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

• DNA relaxase TraI 2B/2B-like domain (TraI_2B) (633-712)

• DNA helicase TraI (TraI_C) (1434-1557)

• AAA domain (AAA_30) (968-1156)

• single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N) (575-626)

• TrwC relaxase (TrwC) (10-283)

Protein structure

No available structure.

Auxiliary protein

WP_001151564_FDAARGOS_1334|unnamed2

• ID: 6555
• GenBank: WP_001151564
• Name: WP_001151564_FDAARGOS_1334|unnamed2
• UniProt ID: A0AA36PD43
• Length: 127 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 127 a.a.
• Molecular weight: 14446.39 Da
• Isoelectric Point: 4.7197

>WP_001151564.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]
MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQAEFNKVL
LECAVKTQSTVAKILGIESLSPHVSGNPKFEYANMVEDIRDKVSSEMERFFPENDEE

Protein domains

Predicted by InterproScan.

• TraM protein, DNA-binding (Tra_M) (1-126)

Protein structure

No available structure.

WP_001254388_FDAARGOS_1334|unnamed2

• ID: 6556
• GenBank: WP_001254388
• Name: WP_001254388_FDAARGOS_1334|unnamed2
• UniProt ID: W9A0Z2
• Length: 75 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 75 a.a.
• Molecular weight: 9072.20 Da
• Isoelectric Point: 10.2071

>WP_001254388.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Enterobacterales]
MRRRNARGGISRTVSVYLDEDTNNRLIRAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVIEENES
TFKEL

Protein domains

Predicted by InterproScan.

• TraY domain (TraY) (14-61)

Protein structure

• AlphaFold DB: W9A0Z2

T4CP

traC_I6K64_RS29030_FDAARGOS_1334|unnamed2

• ID: 13326
• GenBank: WP_001064239
• Name: traC_I6K64_RS29030_FDAARGOS_1334|unnamed2
• UniProt ID: _
• Length: 875 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 875 a.a.
• Molecular weight: 99485.47 Da
• Isoelectric Point: 6.6265

>WP_001064239.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREGM
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

• TraG P-loop domain (P-loop_TraG) (467-771)

• Family of unknown function (DUF5934) (DUF5934) (290-446)

• TraC protein (TraC_F_IV) (38-276)

Protein structure

No available structure.

traD_I6K64_RS29120_FDAARGOS_1334|unnamed2

• ID: 13327
• GenBank: WP_000009360
• Name: traD_I6K64_RS29120_FDAARGOS_1334|unnamed2
• UniProt ID: _
• Length: 732 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 732 a.a.
• Molecular weight: 83294.06 Da
• Isoelectric Point: 5.1048

>WP_000009360.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGISTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPVSPAINDKKSDSGVNIPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQQMQRREEVNINVHRERGEDVEPGDDF

Protein domains

Predicted by InterproScan.

• F sex factor protein N terminal (TraD_N) (32-128)

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (173-560)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 3856..26520

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
I6K64_RS28935 (I6K64_28930)	1..257	+	257	WP_149020673	conjugation system SOS inhibitor PsiB	-
I6K64_RS28940 (I6K64_28935)	254..1016	+	763	Protein_1	plasmid SOS inhibition protein A	-
I6K64_RS29685	1195..1344	+	150	Protein_2	plasmid maintenance protein Mok	-
I6K64_RS28945 (I6K64_28940)	1286..1411	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
I6K64_RS29690	1631..1861	+	231	WP_071587244	hypothetical protein	-
I6K64_RS29695	1859..2032	-	174	Protein_5	hypothetical protein	-
I6K64_RS28950 (I6K64_28945)	2330..2617	+	288	WP_000107537	hypothetical protein	-
I6K64_RS28955 (I6K64_28950)	2738..3559	+	822	WP_001234469	DUF932 domain-containing protein	-
I6K64_RS28960 (I6K64_28955)	3856..4503	-	648	WP_000614282	transglycosylase SLT domain-containing protein	virB1
I6K64_RS28965 (I6K64_28960)	4789..5172	+	384	WP_001151564	conjugal transfer relaxosome DNA-binding protein TraM	-
I6K64_RS28970 (I6K64_28965)	5366..6052	+	687	WP_000332487	PAS domain-containing protein	-
I6K64_RS28975 (I6K64_28970)	6146..6373	+	228	WP_001254388	conjugal transfer relaxosome protein TraY	-
I6K64_RS28980 (I6K64_28975)	6407..6769	+	363	WP_001098998	type IV conjugative transfer system pilin TraA	-
I6K64_RS28985 (I6K64_28980)	6774..7085	+	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
I6K64_RS28990 (I6K64_28985)	7107..7673	+	567	WP_000399804	type IV conjugative transfer system protein TraE	traE
I6K64_RS28995 (I6K64_28990)	7660..8388	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
I6K64_RS29000 (I6K64_28995)	8388..9815	+	1428	WP_000146638	F-type conjugal transfer pilus assembly protein TraB	traB
I6K64_RS29005 (I6K64_29000)	9805..10389	+	585	WP_000002795	conjugal transfer pilus-stabilizing protein TraP	-
I6K64_RS29010 (I6K64_29005)	10376..10696	+	321	WP_001057302	conjugal transfer protein TrbD	virb4
I6K64_RS29015 (I6K64_29010)	10689..10940	+	252	WP_001038341	conjugal transfer protein TrbG	-
I6K64_RS29020 (I6K64_29015)	10937..11452	+	516	WP_000809893	type IV conjugative transfer system lipoprotein TraV	traV
I6K64_RS29025 (I6K64_29020)	11587..11808	+	222	WP_001278978	conjugal transfer protein TraR	-
I6K64_RS29030 (I6K64_29025)	11968..14595	+	2628	WP_001064239	type IV secretion system protein TraC	virb4
I6K64_RS29035 (I6K64_29030)	14592..14978	+	387	WP_000214082	type-F conjugative transfer system protein TrbI	-
I6K64_RS29040 (I6K64_29035)	14975..15607	+	633	WP_001203717	type-F conjugative transfer system protein TraW	traW
I6K64_RS29045 (I6K64_29040)	15604..16596	+	993	WP_204724569	conjugal transfer pilus assembly protein TraU	traU
I6K64_RS29050 (I6K64_29045)	16626..16931	+	306	WP_000224411	hypothetical protein	-
I6K64_RS29055 (I6K64_29050)	16940..17578	+	639	WP_001080257	type-F conjugative transfer system pilin assembly protein TrbC	trbC
I6K64_RS29060 (I6K64_29055)	17575..19383	+	1809	WP_000821863	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
I6K64_RS29065 (I6K64_29060)	19410..19667	+	258	WP_000864320	conjugal transfer protein TrbE	-
I6K64_RS29070 (I6K64_29065)	19654..20403	+	750	WP_001336806	type-F conjugative transfer system pilin assembly protein TraF	traF
I6K64_RS29075 (I6K64_29070)	20419..20757	+	339	WP_001287905	conjugal transfer protein TrbA	-
I6K64_RS29080 (I6K64_29075)	20884..21168	+	285	WP_001448202	type-F conjugative transfer system pilin chaperone TraQ	-
I6K64_RS29085 (I6K64_29080)	21155..21700	+	546	WP_000059824	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
I6K64_RS29090 (I6K64_29085)	21630..21971	+	342	WP_001448115	P-type conjugative transfer protein TrbJ	-
I6K64_RS29095 (I6K64_29090)	21952..22344	+	393	WP_000660703	F-type conjugal transfer protein TrbF	-
I6K64_RS29100 (I6K64_29095)	22331..23704	+	1374	WP_001137364	conjugal transfer pilus assembly protein TraH	traH
I6K64_RS29105 (I6K64_29100)	23701..26520	+	2820	WP_001007057	conjugal transfer mating-pair stabilization protein TraG	traG
I6K64_RS29110 (I6K64_29105)	26539..27036	+	498	WP_000605861	hypothetical protein	-
I6K64_RS29115 (I6K64_29110)	27068..27799	+	732	WP_000850422	conjugal transfer complement resistance protein TraT	-
I6K64_RS29120 (I6K64_29115)	28052..30250	+	2199	WP_000009360	type IV conjugative transfer system coupling protein TraD	-

Host bacterium

• ID: 18411
• GenBank: NZ_CP069928
• Plasmid name: FDAARGOS_1334|unnamed2
• Incompatibility group: IncFII
• Plasmid size: 45379 bp
• Coordinate of oriT [Strand]: 4428..4551 [+]
• Host baterium: Klebsiella oxytoca strain FDAARGOS_1334

Cargo genes

• Drug resistance gene: -
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -