Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 116014
• Name: oriT_NCDC 599-52|p1
• Organism: Shigella dysenteriae strain NCDC 599-52
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP119452 (14110..14233 [+], 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_NCDC 599-52|p1
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTATTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_PWE30_RS25665_NCDC 599-52|p1

• ID: 10237
• GenBank: WP_315700217
• Name: traI_PWE30_RS25665_NCDC 599-52|p1
• UniProt ID: _
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 191829.64 Da
• Isoelectric Point: 5.8498

>WP_315700217.1 conjugative transfer relaxase/helicase TraI [Shigella dysenteriae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRIMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQT
LKETGFDIRAYRDAADQRAETRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTIHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFGASVKAGEESVAQVSGVREQAMLTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKIPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVVDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMQKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWEKNPDALALVDSVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQEQAEQHIDLAYAI
TVHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINKTVQKGTAHDVL
EPGADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRAITGGRVWGDIPDNSLQPGAGNGEPVTAEVLAQRQAEEAIRCETERRADEIVRKMAENKPDLP
DGRTEQAVREIVGQERDRTVTSEGEAVLPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

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

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

• AAA domain (AAA_30) (968-1156)

• TrwC relaxase (TrwC) (10-283)

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

Protein structure

No available structure.

Auxiliary protein

WP_001151564_NCDC 599-52|p1

• ID: 6026
• GenBank: WP_001151564
• Name: WP_001151564_NCDC 599-52|p1
• 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_NCDC 599-52|p1

• ID: 6027
• GenBank: WP_001254388
• Name: WP_001254388_NCDC 599-52|p1
• 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_PWE30_RS25565_NCDC 599-52|p1

• ID: 11961
• GenBank: WP_032250496
• Name: traC_PWE30_RS25565_NCDC 599-52|p1
• UniProt ID: _
• Length: 876 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 876 a.a.
• Molecular weight: 99304.97 Da
• Isoelectric Point: 6.0793

>WP_032250496.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESVVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAVRFNAITRAYYMRAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVIQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
MSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

• TraC protein (TraC_F_IV) (39-277)

• Family of unknown function (DUF5934) (DUF5934) (290-447)

• TraG P-loop domain (P-loop_TraG) (468-772)

Protein structure

No available structure.

traD_PWE30_RS25660_NCDC 599-52|p1

• ID: 11962
• GenBank: WP_128610773
• Name: traD_PWE30_RS25660_NCDC 599-52|p1
• UniProt ID: _
• Length: 735 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 735 a.a.
• Molecular weight: 83653.31 Da
• Isoelectric Point: 5.0541

>WP_128610773.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Shigella]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDDKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
KRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDTQQQMQRREEVNINVHRERGEDVEPGDDF

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: 13538..41815

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
PWE30_RS25440 (PWE30_25385)	8900..9154	+	255	WP_032250339	hypothetical protein	-
PWE30_RS25445 (PWE30_25390)	9151..9393	+	243	WP_000151456	hypothetical protein	-
PWE30_RS25450 (PWE30_25395)	9964..10257	+	294	WP_000673428	hypothetical protein	-
PWE30_RS25455 (PWE30_25400)	10562..10849	+	288	WP_100037732	hypothetical protein	-
PWE30_RS25460 (PWE30_25405)	11277..11510	+	234	WP_000093744	hypothetical protein	-
PWE30_RS25465 (PWE30_25410)	11586..11888	+	303	WP_000379301	hypothetical protein	-
PWE30_RS25470 (PWE30_25415)	12160..12309	+	150	WP_000903193	hypothetical protein	-
PWE30_RS25475 (PWE30_25420)	12420..13241	+	822	WP_073975216	DUF932 domain-containing protein	-
PWE30_RS25480 (PWE30_25425)	13538..14185	-	648	WP_000614287	transglycosylase SLT domain-containing protein	virB1
PWE30_RS25485 (PWE30_25430)	14471..14854	+	384	WP_001151564	conjugal transfer relaxosome DNA-binding protein TraM	-
PWE30_RS25490 (PWE30_25435)	15048..15734	+	687	WP_000332487	PAS domain-containing protein	-
PWE30_RS25495 (PWE30_25440)	15828..16055	+	228	WP_001254388	conjugal transfer relaxosome protein TraY	-
PWE30_RS25500 (PWE30_25445)	16089..16448	+	360	WP_019842162	type IV conjugative transfer system pilin TraA	-
PWE30_RS25505 (PWE30_25450)	16463..16774	+	312	WP_032250594	type IV conjugative transfer system protein TraL	traL
PWE30_RS25510 (PWE30_25455)	16796..17362	+	567	WP_000399805	type IV conjugative transfer system protein TraE	traE
PWE30_RS25515 (PWE30_25460)	17349..18077	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
PWE30_RS25520 (PWE30_25465)	18077..19504	+	1428	WP_315700229	F-type conjugal transfer pilus assembly protein TraB	traB
PWE30_RS25525 (PWE30_25470)	19494..20084	+	591	WP_000002782	conjugal transfer pilus-stabilizing protein TraP	-
PWE30_RS25530 (PWE30_25475)	20071..20391	+	321	WP_001057306	conjugal transfer protein TrbD	virb4
PWE30_RS25535 (PWE30_25480)	20384..20635	+	252	WP_001061854	conjugal transfer protein TrbG	-
PWE30_RS25540 (PWE30_25485)	20632..21147	+	516	WP_032324751	type IV conjugative transfer system lipoprotein TraV	traV
PWE30_RS25545 (PWE30_25490)	21282..21503	+	222	WP_001278695	conjugal transfer protein TraR	-
PWE30_RS25550 (PWE30_25495)	21496..21972	+	477	WP_032250499	hypothetical protein	-
PWE30_RS25555 (PWE30_25500)	22052..22270	+	219	WP_032250498	hypothetical protein	-
PWE30_RS25560 (PWE30_25505)	22298..22645	+	348	WP_315700231	hypothetical protein	-
PWE30_RS25565 (PWE30_25510)	22771..25401	+	2631	WP_032250496	type IV secretion system protein TraC	virb4
PWE30_RS25570 (PWE30_25515)	25398..25784	+	387	WP_000214082	type-F conjugative transfer system protein TrbI	-
PWE30_RS25575 (PWE30_25520)	25781..26413	+	633	WP_032250504	type-F conjugative transfer system protein TraW	traW
PWE30_RS25580 (PWE30_25525)	26410..27402	+	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
PWE30_RS25585 (PWE30_25530)	27411..28049	+	639	WP_001744737	type-F conjugative transfer system pilin assembly protein TrbC	trbC
PWE30_RS25590 (PWE30_25535)	28046..29896	+	1851	WP_000821864	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
PWE30_RS25595 (PWE30_25540)	29923..30180	+	258	WP_000864329	conjugal transfer protein TrbE	-
PWE30_RS25600 (PWE30_25545)	30173..30916	+	744	WP_001030371	type-F conjugative transfer system pilin assembly protein TraF	traF
PWE30_RS25605 (PWE30_25550)	30930..31271	+	342	WP_000556795	conjugal transfer protein TrbA	-
PWE30_RS25610 (PWE30_25555)	31252..31587	-	336	WP_000736414	hypothetical protein	-
PWE30_RS25615 (PWE30_25560)	31668..31952	+	285	WP_021566306	type-F conjugative transfer system pilin chaperone TraQ	-
PWE30_RS25620 (PWE30_25565)	31939..32484	+	546	WP_000059830	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
PWE30_RS25625 (PWE30_25570)	32414..32761	+	348	WP_072006150	P-type conjugative transfer protein TrbJ	-
PWE30_RS25630 (PWE30_25575)	32742..33134	+	393	WP_032250489	F-type conjugal transfer protein TrbF	-
PWE30_RS25635 (PWE30_25580)	33121..34494	+	1374	WP_021501421	conjugal transfer pilus assembly protein TraH	traH
PWE30_RS25640 (PWE30_25585)	34491..37307	+	2817	WP_126739281	conjugal transfer mating-pair stabilization protein TraG	traG
PWE30_RS25645 (PWE30_25590)	37340..37861	+	522	WP_000632668	conjugal transfer entry exclusion protein TraS	-
PWE30_RS25650 (PWE30_25595)	37886..38617	+	732	WP_000850429	conjugal transfer complement resistance protein TraT	-
PWE30_RS25655 (PWE30_25600)	38820..39557	+	738	WP_062877098	hypothetical protein	-
PWE30_RS25660 (PWE30_25605)	39608..41815	+	2208	WP_128610773	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 16447
• GenBank: NZ_CP119452
• Plasmid name: NCDC 599-52|p1
• Incompatibility group: -
• Plasmid size: 51197 bp
• Coordinate of oriT [Strand]: 14110..14233 [+]
• Host baterium: Shigella dysenteriae strain NCDC 599-52

Cargo genes

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