Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 104478
• Name: oriT_STIN_87|unnamed1
• Organism: Shigella flexneri strain STIN_87
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP054993 (48471..48822 [+], 352 nt)
• oriT length: 352 nt
• IRs (inverted repeats): 192..198, 206..212 (TATAAAA..TTTTATA) 104..110, 118..124 (TTTAAAT..ATTTAAA) 106..111, 113..118 (TAAATC..GATTTA) 93..98, 106..111 (GATTTA..TAAATC) 40..47, 50..57 (GCAAAAAC..GTTTTTGC) 4..11, 16..23 (TTGGTGGT..ACCACCAA)
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 352 nt

>oriT_STIN_87|unnamed1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTATTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCCAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_HUZ57_RS23725_STIN_87|unnamed1

• ID: 3245
• GenBank: WP_239612378
• Name: traI_HUZ57_RS23725_STIN_87|unnamed1
• UniProt ID: _
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 192146.85 Da
• Isoelectric Point: 5.8434

>WP_239612378.1 conjugative transfer relaxase/helicase TraI [Shigella flexneri]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGKGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQYNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DTVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMIFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMRDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVMEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGRSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRTATSERETALPESVLRESQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

• TrwC relaxase (TrwC) (10-283)

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

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

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

• AAA domain (AAA_30) (969-1156)

Protein structure

No available structure.

Auxiliary protein

WP_001151530_STIN_87|unnamed1

• ID: 1434
• GenBank: WP_001151530
• Name: WP_001151530_STIN_87|unnamed1
• UniProt ID: A0A385JKG6
• Length: 127 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 127 a.a.
• Molecular weight: 14525.54 Da
• Isoelectric Point: 4.8662

>WP_001151530.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacteriaceae]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVYEAQMERKESAFNQAEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSVEMERFFPKNDDE

Protein domains

Predicted by InterproScan.

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

Protein structure

• AlphaFold DB: A0A385JKG6

T4CP

traC_HUZ57_RS23620_STIN_87|unnamed1

• ID: 3166
• GenBank: WP_001064243
• Name: traC_HUZ57_RS23620_STIN_87|unnamed1
• UniProt ID: _
• Length: 875 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 875 a.a.
• Molecular weight: 99191.87 Da
• Isoelectric Point: 5.8486

>WP_001064243.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

• Family of unknown function (DUF5934) (DUF5934) (289-446)

• TraC protein (TraC_F_IV) (38-276)

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

Protein structure

No available structure.

traD_HUZ57_RS23720_STIN_87|unnamed1

• ID: 3167
• GenBank: WP_199266148
• Name: traD_HUZ57_RS23720_STIN_87|unnamed1
• UniProt ID: _
• Length: 750 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 750 a.a.
• Molecular weight: 85309.06 Da
• Isoelectric Point: 5.1657

>WP_199266148.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLILWVKISWQTFVNGCIYWWCTTLEGMR
DLIRSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGIS
ESGEVVDMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

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: 47900..75623

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
HUZ57_RS23515 (HUZ57_23315)	43973..44407	+	435	WP_042634413	conjugation system SOS inhibitor PsiB	-
HUZ57_RS23520 (HUZ57_23320)	44404..45190	+	787	Protein_54	plasmid SOS inhibition protein A	-
HUZ57_RS23525	45340..45492	+	153	Protein_55	DUF5431 family protein	-
HUZ57_RS23530 (HUZ57_23325)	45437..45559	+	123	WP_223163518	Hok/Gef family protein	-
HUZ57_RS23535 (HUZ57_23330)	45860..46156	-	297	Protein_57	hypothetical protein	-
HUZ57_RS25075	46226..46348	+	123	Protein_58	single-stranded DNA-binding protein	-
HUZ57_RS23540 (HUZ57_23335)	46380..46676	+	297	WP_001272240	hypothetical protein	-
HUZ57_RS23545 (HUZ57_23340)	46782..47603	+	822	WP_001234469	DUF932 domain-containing protein	-
HUZ57_RS23550 (HUZ57_23345)	47900..48547	-	648	WP_000601040	transglycosylase SLT domain-containing protein	virB1
HUZ57_RS23555 (HUZ57_23350)	48823..49206	+	384	WP_001151530	conjugal transfer relaxosome DNA-binding protein TraM	-
HUZ57_RS23560 (HUZ57_23355)	49398..50045	+	648	WP_000338012	transcriptional regulator TraJ family protein	-
HUZ57_RS23565 (HUZ57_23360)	50165..50392	+	228	WP_000589558	conjugal transfer relaxosome protein TraY	-
HUZ57_RS23570 (HUZ57_23365)	50426..50788	+	363	WP_033566647	type IV conjugative transfer system pilin TraA	-
HUZ57_RS23575 (HUZ57_23370)	50793..51104	+	312	WP_000012101	type IV conjugative transfer system protein TraL	traL
HUZ57_RS23580 (HUZ57_23375)	51126..51692	+	567	WP_000399793	type IV conjugative transfer system protein TraE	traE
HUZ57_RS23585 (HUZ57_23380)	51679..52407	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
HUZ57_RS23590 (HUZ57_23385)	52407..53834	+	1428	WP_000146685	F-type conjugal transfer pilus assembly protein TraB	traB
HUZ57_RS23595 (HUZ57_23390)	53824..54396	+	573	WP_063078161	conjugal transfer pilus-stabilizing protein TraP	-
HUZ57_RS23600 (HUZ57_23395)	54393..54590	+	198	WP_001324648	conjugal transfer protein TrbD	-
HUZ57_RS23605 (HUZ57_23400)	54602..54853	+	252	WP_001038341	conjugal transfer protein TrbG	-
HUZ57_RS23610 (HUZ57_23405)	54850..55365	+	516	WP_000809906	type IV conjugative transfer system lipoprotein TraV	traV
HUZ57_RS23615 (HUZ57_23410)	55500..55721	+	222	WP_001278689	conjugal transfer protein TraR	-
HUZ57_RS23620 (HUZ57_23415)	55881..58508	+	2628	WP_001064243	type IV secretion system protein TraC	virb4
HUZ57_RS23625 (HUZ57_23420)	58505..58891	+	387	WP_000214096	type-F conjugative transfer system protein TrbI	-
HUZ57_RS23630 (HUZ57_23425)	58888..59520	+	633	WP_001203720	type-F conjugative transfer system protein TraW	traW
HUZ57_RS23635 (HUZ57_23430)	59517..60509	+	993	WP_000830183	conjugal transfer pilus assembly protein TraU	traU
HUZ57_RS23640 (HUZ57_23435)	60535..60996	+	462	WP_000277845	hypothetical protein	-
HUZ57_RS23645 (HUZ57_23440)	61026..61478	+	453	WP_000069427	hypothetical protein	-
HUZ57_RS23650 (HUZ57_23445)	61506..62144	+	639	WP_001104248	type-F conjugative transfer system pilin assembly protein TrbC	trbC
HUZ57_RS23655 (HUZ57_23450)	62141..63949	+	1809	WP_063078212	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
HUZ57_RS23660 (HUZ57_23455)	63976..64236	+	261	WP_000864323	conjugal transfer protein TrbE	-
HUZ57_RS23665 (HUZ57_23460)	64229..64972	+	744	WP_001030376	type-F conjugative transfer system pilin assembly protein TraF	traF
HUZ57_RS23670 (HUZ57_23465)	64988..65335	+	348	WP_001287893	conjugal transfer protein TrbA	-
HUZ57_RS23675 (HUZ57_23470)	65454..65738	+	285	WP_000624108	type-F conjugative transfer system pilin chaperone TraQ	-
HUZ57_RS23680 (HUZ57_23475)	65725..66270	+	546	WP_000059818	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
HUZ57_RS23685 (HUZ57_23480)	66260..66574	+	315	WP_001384255	P-type conjugative transfer protein TrbJ	-
HUZ57_RS23690 (HUZ57_23485)	66528..66920	+	393	WP_062873756	F-type conjugal transfer protein TrbF	-
HUZ57_RS23695 (HUZ57_23490)	66907..68280	+	1374	WP_156841533	conjugal transfer pilus assembly protein TraH	traH
HUZ57_RS23700 (HUZ57_23495)	68277..71099	+	2823	WP_062873754	conjugal transfer mating-pair stabilization protein TraG	traG
HUZ57_RS23705 (HUZ57_23500)	71114..71617	+	504	WP_000605510	hypothetical protein	-
HUZ57_RS23710 (HUZ57_23505)	71649..72380	+	732	WP_000850424	conjugal transfer complement resistance protein TraT	-
HUZ57_RS23715 (HUZ57_23510)	72583..73320	+	738	WP_000199900	hypothetical protein	-
HUZ57_RS23720 (HUZ57_23515)	73371..75623	+	2253	WP_199266148	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 4917
• GenBank: NZ_CP054993
• Plasmid name: STIN_87|unnamed1
• Incompatibility group: -
• Plasmid size: 86160 bp
• Coordinate of oriT [Strand]: 48471..48822 [+]
• Host baterium: Shigella flexneri strain STIN_87

Cargo genes

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