oriTDB

Detailed information of oriT

oriT
Auxiliary protein
T4CP
T4SS
Host bacterium
Cargo genes

oriT

The information of the oriT region

oriTDB ID	114032
Name	oriT_pA6817
Organism	Shigella flexneri 1b strain A-6817
Sequence Completeness	-
*NCBI accession of oriT* (coordinates [strand])**	NZ_CP130062 (132326..132449 [+], 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

Download Length: 124 nt

                        >oriT_pA6817
GGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTGCTACTTGAATCATTAACTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATAAAA                      

Visualization of oriT structure

oriT secondary structure

Predicted by RNAfold.

Download structure file

Auxiliary protein

ID	5253	GenBank	WP_001354030
Name	WP_001354030_pA6817	UniProt ID	A0A734M5H3
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download 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

Source	ID	Structure
AlphaFold DB	A0A734M5H3

ID	5254	GenBank	WP_000089263
Name	WP_000089263_pA6817	UniProt ID	A0A3U3XJL9
Length	75 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download 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

Source	ID	Structure
AlphaFold DB	A0A3U3XJL9

ID	5255	GenBank	WP_001151566
Name	WP_001151566_pA6817	UniProt ID	A0A142CMX1
Length	127 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

Auxiliary protein sequence

Download Length: 127 a.a. Molecular weight: 14476.46 Da Isoelectric Point: 4.8498

                        >WP_001151566.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Enterobacterales]

MAKVQAYVSDEIVYKINKIVERRRAEGAKSTDVSFSSISTMLLELGLRVYETQMERKESAFNQTEFNKLL

LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPENDEG

Protein domains

Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)

Protein structure

Source	ID	Structure
AlphaFold DB	A0A142CMX1

ID	10450	GenBank	WP_302085048
Name	traD_QS140_RS23420_pA6817	UniProt ID	_
Length	741 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 741 a.a. Molecular weight: 84213.92 Da Isoelectric Point: 5.1647

                        >WP_302085048.1 type IV conjugative transfer system coupling protein TraD [Shigella flexneri]

MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTTLEGMR

DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGHQGKQ

QSENEVTGGRQLTDNPKEVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR

QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG

SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA

IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV

WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA

EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL

KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEGVTQAEQPQQPQQPQQPQQ

PQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMA

AYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

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.

ID	10451	GenBank	WP_000069772
Name	traC_QS140_RS23785_pA6817	UniProt ID	_
Length	876 a.a.	PDB ID	_
Note	Predicted by oriTfinder 2.0

T4CP protein sequence

Download Length: 876 a.a. Molecular weight: 99344.15 Da Isoelectric Point: 6.4096

                        >WP_000069772.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]

MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI

PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA

ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV

GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF

LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG

ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK

GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG

AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS

VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY

TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW

RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY

NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG

LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(291-447)

TraG P-loop domain (P-loop_TraG)

(468-764)

TraC protein (TraC_F_IV)

(39-277)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 76240..97679

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
QS140_RS23645 (QS140_23645)	72206..72640	+	435	WP_000845940	conjugation system SOS inhibitor PsiB	-
QS140_RS23650 (QS140_23650)	72637..73356	+	720	WP_001276232	plasmid SOS inhibition protein A	-
QS140_RS23655 (QS140_23655)	73368..73556	-	189	WP_001299721	hypothetical protein	-
QS140_RS23660 (QS140_23660)	73578..73727	+	150	Protein_95	plasmid maintenance protein Mok	-
QS140_RS23665 (QS140_23665)	73669..73794	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
QS140_RS23670 (QS140_23670)	74014..74244	+	231	WP_001426396	hypothetical protein	-
QS140_RS23675 (QS140_23675)	74242..74415	-	174	Protein_98	hypothetical protein	-
QS140_RS23680 (QS140_23680)	74485..74691	+	207	WP_000275859	hypothetical protein	-
QS140_RS23685 (QS140_23685)	74716..75003	+	288	WP_000107535	hypothetical protein	-
QS140_RS23690 (QS140_23690)	75122..75943	+	822	WP_001234469	DUF932 domain-containing protein	-
QS140_RS23695 (QS140_23695)	76240..76830	-	591	WP_001376243	transglycosylase SLT domain-containing protein	virB1
QS140_RS23700 (QS140_23700)	77165..77548	+	384	WP_001354030	conjugal transfer relaxosome DNA-binding protein TraM	-
QS140_RS23705 (QS140_23705)	77742..78413	+	672	WP_000283561	conjugal transfer transcriptional regulator TraJ	-
QS140_RS23710 (QS140_23710)	78550..78777	+	228	WP_000089263	conjugal transfer relaxosome protein TraY	-
QS140_RS23715 (QS140_23715)	78810..79172	+	363	WP_001098993	type IV conjugative transfer system pilin TraA	-
QS140_RS23720 (QS140_23720)	79187..79498	+	312	WP_000012100	type IV conjugative transfer system protein TraL	traL
QS140_RS23725 (QS140_23725)	79520..80086	+	567	WP_000399780	type IV conjugative transfer system protein TraE	traE
QS140_RS23730 (QS140_23730)	80073..80801	+	729	WP_001230769	type-F conjugative transfer system secretin TraK	traK
QS140_RS23735 (QS140_23735)	80801..82252	+	1452	WP_052922044	F-type conjugal transfer pilus assembly protein TraB	traB
QS140_RS23740 (QS140_23740)	82242..82808	+	567	WP_000896598	conjugal transfer pilus-stabilizing protein TraP	-
QS140_RS23745 (QS140_23745)	82795..83115	+	321	WP_052922045	conjugal transfer protein TrbD	virb4
QS140_RS23750 (QS140_23750)	83108..83359	+	252	WP_001038333	conjugal transfer protein TrbG	-
QS140_RS23755 (QS140_23755)	83356..83871	+	516	WP_000809867	type IV conjugative transfer system lipoprotein TraV	traV
QS140_RS23760 (QS140_23760)	84006..84227	+	222	WP_001278695	conjugal transfer protein TraR	-
QS140_RS23765 (QS140_23765)	84220..84633	+	414	WP_000549581	hypothetical protein	-
QS140_RS23770 (QS140_23770)	84626..85099	+	474	WP_001620797	hypothetical protein	-
QS140_RS23775 (QS140_23775)	85177..85395	+	219	WP_001405917	hypothetical protein	-
QS140_RS23780 (QS140_23780)	85423..85770	+	348	WP_000836682	hypothetical protein	-
QS140_RS23785 (QS140_23785)	85896..88526	+	2631	WP_000069772	type IV secretion system protein TraC	virb4
QS140_RS23790 (QS140_23790)	88523..88909	+	387	WP_000214084	type-F conjugative transfer system protein TrbI	-
QS140_RS23795 (QS140_23795)	88906..89538	+	633	WP_001203720	type-F conjugative transfer system protein TraW	traW
QS140_RS23800 (QS140_23800)	89535..90527	+	993	WP_000830849	conjugal transfer pilus assembly protein TraU	traU
QS140_RS23805 (QS140_23805)	90557..90862	+	306	WP_000224418	hypothetical protein	-
QS140_RS23810 (QS140_23810)	90871..91509	+	639	WP_001080251	type-F conjugative transfer system pilin assembly protein TrbC	trbC
QS140_RS23815 (QS140_23815)	91506..93356	+	1851	WP_000821860	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
QS140_RS23820 (QS140_23820)	93383..93640	+	258	WP_000864353	conjugal transfer protein TrbE	-
QS140_RS23825 (QS140_23825)	93633..94376	+	744	WP_001030371	type-F conjugative transfer system pilin assembly protein TraF	traF
QS140_RS23830 (QS140_23830)	94390..94734	+	345	WP_000556796	conjugal transfer protein TrbA	-
QS140_RS23835 (QS140_23835)	94853..95137	+	285	WP_000624107	type-F conjugative transfer system pilin chaperone TraQ	-
QS140_RS23840 (QS140_23840)	95124..95669	+	546	WP_000059831	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
QS140_RS23845 (QS140_23845)	95599..95946	+	348	WP_001309242	P-type conjugative transfer protein TrbJ	-
QS140_RS23850 (QS140_23850)	95927..96319	+	393	WP_000660700	F-type conjugal transfer protein TrbF	-
QS140_RS23855 (QS140_23855)	96306..97679	+	1374	WP_001535740	conjugal transfer pilus assembly protein TraH	traH
QS140_RS23860 (QS140_23860)	97676..99493	+	1818	Protein_135	conjugal transfer mating-pair stabilization protein TraG	-
QS140_RS23865 (QS140_23865)	99546..100250	-	705	WP_001067855	IS6-like element IS26 family transposase	-
QS140_RS23870 (QS140_23870)	100502..100693	-	192	WP_001027516	hypothetical protein	-
QS140_RS23875 (QS140_23875)	100690..101112	-	423	WP_000271753	DUF1380 family protein	-
QS140_RS23880 (QS140_23880)	101159..101584	-	426	WP_001198928	antirestriction protein	-

Host bacterium

ID	14467	GenBank	NZ_CP130062
Plasmid name	pA6817	Incompatibility group	IncFIB
Plasmid size	150284 bp	Coordinate of oriT [Strand]	132326..132449 [+]
Host baterium	Shigella flexneri 1b strain A-6817

Cargo genes

Drug resistance gene	dfrA14, mph(A), blaTEM-1B, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene	-
Metal resistance gene	-
Degradation gene	-
Symbiosis gene	-
Anti-CRISPR	-