Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 113933
• Name: oriT_pGDD25-21
• Organism: Salmonella enterica subsp. enterica serovar Indiana strain GDD25-21
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_MH316136 (91095..91180 [-], 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

• Length: 86 nt

>oriT_pGDD25-21
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_HTS77_RS00725_pGDD25-21

• ID: 8947
• GenBank: WP_000948354
• Name: traI_HTS77_RS00725_pGDD25-21
• UniProt ID: A0AA36L3I8
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• 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.

Auxiliary protein

WP_001354030_pGDD25-21

• ID: 5235
• GenBank: WP_001354030
• Name: WP_001354030_pGDD25-21
• UniProt ID: A0A734M5H3
• Length: 127 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• 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

• AlphaFold DB: A0A734M5H3

WP_000089263_pGDD25-21

• ID: 5236
• GenBank: WP_000089263
• Name: WP_000089263_pGDD25-21
• UniProt ID: A0A3U3XJL9
• Length: 75 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• 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

• AlphaFold DB: A0A3U3XJL9

T4CP

traC_HTS77_RS00625_pGDD25-21

• ID: 10394
• GenBank: WP_000069777
• Name: traC_HTS77_RS00625_pGDD25-21
• UniProt ID: _
• Length: 876 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• 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.

traD_HTS77_RS00720_pGDD25-21

• ID: 10395
• GenBank: WP_000009332
• Name: traD_HTS77_RS00720_pGDD25-21
• UniProt ID: _
• Length: 732 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 732 a.a.
• Molecular weight: 83193.81 Da
• Isoelectric Point: 5.1644

>WP_000009332.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQEN
HPDIQQHMQRREEVNINVHRERGEDVEPGDDF

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: 90527..120346

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HTS77_RS00500	86372..86806	+	435	WP_000845953	conjugation system SOS inhibitor PsiB	-
HTS77_RS00505	86803..87522	+	720	WP_001276217	plasmid SOS inhibition protein A	-
HTS77_RS00805	87744..87893	+	150	Protein_100	plasmid maintenance protein Mok	-
HTS77_RS00510	87835..87960	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
HTS77_RS00775	88279..88575	-	297	Protein_102	hypothetical protein	-
HTS77_RS00810	88711..88851	+	141	WP_001445060	hypothetical protein	-
HTS77_RS00525	89002..89298	+	297	WP_001272251	hypothetical protein	-
HTS77_RS00530	89409..90230	+	822	WP_001234445	DUF932 domain-containing protein	-
HTS77_RS00535	90527..91117	-	591	WP_000252683	transglycosylase SLT domain-containing protein	virB1
HTS77_RS00540	91452..91835	+	384	WP_001354030	conjugal transfer relaxosome DNA-binding protein TraM	-
HTS77_RS00545	92029..92700	+	672	WP_000283561	conjugal transfer transcriptional regulator TraJ	-
HTS77_RS00550	92837..93064	+	228	WP_000089263	conjugal transfer relaxosome protein TraY	-
HTS77_RS00555	93097..93456	+	360	WP_001098992	type IV conjugative transfer system pilin TraA	-
HTS77_RS00560	93471..93782	+	312	WP_000012113	type IV conjugative transfer system protein TraL	traL
HTS77_RS00565	93804..94370	+	567	WP_000399780	type IV conjugative transfer system protein TraE	traE
HTS77_RS00570	94357..95085	+	729	WP_001230772	type-F conjugative transfer system secretin TraK	traK
HTS77_RS00575	95085..96536	+	1452	WP_000146675	F-type conjugal transfer pilus assembly protein TraB	traB
HTS77_RS00580	96526..97092	+	567	WP_000896599	conjugal transfer pilus-stabilizing protein TraP	-
HTS77_RS00585	97079..97399	+	321	WP_001057307	conjugal transfer protein TrbD	-
HTS77_RS00590	97396..97911	+	516	WP_000809881	type IV conjugative transfer system lipoprotein TraV	traV
HTS77_RS00595	98046..98267	+	222	WP_001278683	conjugal transfer protein TraR	-
HTS77_RS00600	98260..98673	+	414	WP_000549589	hypothetical protein	-
HTS77_RS00605	98666..99139	+	474	WP_000549568	hypothetical protein	-
HTS77_RS00615	100555..100773	+	219	WP_000556745	hypothetical protein	-
HTS77_RS00620	100801..101148	+	348	WP_000836682	hypothetical protein	-
HTS77_RS00625	101274..103904	+	2631	WP_000069777	type IV secretion system protein TraC	virb4
HTS77_RS00630	103901..104287	+	387	WP_000214084	type-F conjugative transfer system protein TrbI	-
HTS77_RS00635	104284..104916	+	633	WP_001203728	type-F conjugative transfer system protein TraW	traW
HTS77_RS00640	104913..105905	+	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
HTS77_RS00645	105935..106240	+	306	WP_000224416	hypothetical protein	-
HTS77_RS00650	106249..106887	+	639	WP_001080256	type-F conjugative transfer system pilin assembly protein TrbC	trbC
HTS77_RS00655	106884..108734	+	1851	WP_000821856	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
HTS77_RS00660	108761..109018	+	258	WP_000864353	conjugal transfer protein TrbE	-
HTS77_RS00665	109011..109754	+	744	WP_001030371	type-F conjugative transfer system pilin assembly protein TraF	traF
HTS77_RS00670	109768..110112	+	345	WP_000556796	conjugal transfer protein TrbA	-
HTS77_RS00675	110231..110515	+	285	WP_000624194	type-F conjugative transfer system pilin chaperone TraQ	-
HTS77_RS00680	110502..111047	+	546	WP_000059831	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
HTS77_RS00685	110977..111324	+	348	WP_001309242	P-type conjugative transfer protein TrbJ	-
HTS77_RS00690	111305..111697	+	393	WP_000660699	F-type conjugal transfer protein TrbF	-
HTS77_RS00695	111684..113057	+	1374	WP_000944331	conjugal transfer pilus assembly protein TraH	traH
HTS77_RS00700	113054..115876	+	2823	WP_001007039	conjugal transfer mating-pair stabilization protein TraG	traG
HTS77_RS00705	115892..116377	+	486	WP_000605870	hypothetical protein	-
HTS77_RS00710	116426..117157	+	732	WP_000782451	conjugal transfer complement resistance protein TraT	-
HTS77_RS00715	117360..118097	+	738	WP_000199905	hypothetical protein	-
HTS77_RS00720	118148..120346	+	2199	WP_000009332	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 14368
• GenBank: NZ_MH316136
• Plasmid name: pGDD25-21
• Incompatibility group: IncFIB
• Plasmid size: 130794 bp
• Coordinate of oriT [Strand]: 91095..91180 [-]
• Host baterium: Salmonella enterica subsp. enterica serovar Indiana strain GDD25-21

Cargo genes

• Drug resistance gene: qepA1, rmtB, blaTEM-1B, blaCTX-M-27
• Virulence gene: -
• Metal resistance gene: pcoE
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -