Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 118060
• Name: oriT_pC252072-2
• Organism: Klebsiella aerogenes strain C252072
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP139410 (56157..56280 [+], 124 nt)
• oriT length: 124 nt
• IRs (inverted repeats): 101..106, 119..124 (TTTAAT..ATTAAA) 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_pC252072-2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATATTGTATTTTAATTTATTTTACATTATTAAA

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_SM910_RS25915_pC252072-2

• ID: 11461
• GenBank: WP_061093447
• Name: traI_SM910_RS25915_pC252072-2
• UniProt ID: A0A2Z4I1F4
• Length: 1756 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1756 a.a.
• Molecular weight: 192119.90 Da
• Isoelectric Point: 6.0788

>WP_061093447.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDKATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALNTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

Protein domains

Predicted by InterproScan.

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

• TrwC relaxase (TrwC) (10-283)

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

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

• AAA domain (AAA_30) (969-1156)

Protein structure

No available structure.

Auxiliary protein

WP_000124981_pC252072-2

• ID: 6583
• GenBank: WP_000124981
• Name: WP_000124981_pC252072-2
• UniProt ID: A0A630FTW9
• Length: 127 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 127 a.a.
• Molecular weight: 14542.59 Da
• Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

Protein domains

Predicted by InterproScan.

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

Protein structure

• AlphaFold DB: A0A630FTW9

WP_001254386_pC252072-2

• ID: 6584
• GenBank: WP_001254386
• Name: WP_001254386_pC252072-2
• UniProt ID: A0A3Z6KJB5
• Length: 75 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 75 a.a.
• Molecular weight: 9005.11 Da
• Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

Protein domains

Predicted by InterproScan.

• TraY domain (TraY) (14-61)

Protein structure

• AlphaFold DB: A0A3Z6KJB5

T4CP

traC_SM910_RS25805_pC252072-2

• ID: 13393
• GenBank: WP_015059012
• Name: traC_SM910_RS25805_pC252072-2
• UniProt ID: _
• Length: 875 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 875 a.a.
• Molecular weight: 99393.22 Da
• Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

Protein domains

Predicted by InterproScan.

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

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

• TraC protein (TraC_F_IV) (38-276)

Protein structure

No available structure.

traD_SM910_RS25910_pC252072-2

• ID: 13394
• GenBank: WP_275721194
• Name: traD_SM910_RS25910_pC252072-2
• UniProt ID: _
• Length: 747 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 747 a.a.
• Molecular weight: 84994.76 Da
• Isoelectric Point: 5.1083

>WP_275721194.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Klebsiella]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYARLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESG
EVVDMAAYEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

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: 55585..83791

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
SM910_RS25700 (SM910_25700)	51557..51991	+	435	WP_000845953	conjugation system SOS inhibitor PsiB	-
SM910_RS25705 (SM910_25705)	51988..52707	+	720	WP_001276217	plasmid SOS inhibition protein A	-
SM910_RS25710 (SM910_25710)	52929..53078	+	150	Protein_64	plasmid maintenance protein Mok	-
SM910_RS25715 (SM910_25715)	53020..53145	+	126	WP_001372321	type I toxin-antitoxin system Hok family toxin	-
SM910_RS25720 (SM910_25720)	53464..53760	-	297	Protein_66	hypothetical protein	-
SM910_RS25725 (SM910_25725)	54060..54356	+	297	WP_001272251	hypothetical protein	-
SM910_RS25730 (SM910_25730)	54467..55288	+	822	WP_001234445	DUF932 domain-containing protein	-
SM910_RS25735 (SM910_25735)	55585..56232	-	648	WP_015059008	transglycosylase SLT domain-containing protein	virB1
SM910_RS25740 (SM910_25740)	56509..56892	+	384	WP_000124981	conjugal transfer relaxosome DNA-binding protein TraM	-
SM910_RS25745 (SM910_25745)	57083..57769	+	687	WP_015059009	PAS domain-containing protein	-
SM910_RS25750 (SM910_25750)	57863..58090	+	228	WP_001254386	conjugal transfer relaxosome protein TraY	-
SM910_RS25755 (SM910_25755)	58124..58489	+	366	WP_021519752	type IV conjugative transfer system pilin TraA	-
SM910_RS25760 (SM910_25760)	58504..58815	+	312	WP_000012106	type IV conjugative transfer system protein TraL	traL
SM910_RS25765 (SM910_25765)	58837..59403	+	567	WP_000399794	type IV conjugative transfer system protein TraE	traE
SM910_RS25770 (SM910_25770)	59390..60118	+	729	WP_001230787	type-F conjugative transfer system secretin TraK	traK
SM910_RS25775 (SM910_25775)	60118..61545	+	1428	WP_032297072	F-type conjugal transfer pilus assembly protein TraB	traB
SM910_RS25780 (SM910_25780)	61535..62125	+	591	WP_000002778	conjugal transfer pilus-stabilizing protein TraP	-
SM910_RS25785 (SM910_25785)	62112..62309	+	198	WP_001324648	conjugal transfer protein TrbD	-
SM910_RS25790 (SM910_25790)	62321..62572	+	252	WP_001038341	conjugal transfer protein TrbG	-
SM910_RS25795 (SM910_25795)	62569..63084	+	516	WP_000809902	type IV conjugative transfer system lipoprotein TraV	traV
SM910_RS25800 (SM910_25800)	63219..63440	+	222	WP_001278692	conjugal transfer protein TraR	-
SM910_RS25805 (SM910_25805)	63600..66227	+	2628	WP_015059012	type IV secretion system protein TraC	virb4
SM910_RS25810 (SM910_25810)	66224..66610	+	387	WP_015059013	type-F conjugative transfer system protein TrbI	-
SM910_RS25815 (SM910_25815)	66607..67239	+	633	WP_001203735	type-F conjugative transfer system protein TraW	traW
SM910_RS25820 (SM910_25820)	67236..68228	+	993	WP_000830838	conjugal transfer pilus assembly protein TraU	traU
SM910_RS25825 (SM910_25825)	68255..68563	+	309	WP_000412447	hypothetical protein	-
SM910_RS25830 (SM910_25830)	68626..69147	+	522	WP_015059014	hypothetical protein	-
SM910_RS25835 (SM910_25835)	69174..69812	+	639	WP_000087532	type-F conjugative transfer system pilin assembly protein TrbC	trbC
SM910_RS25840 (SM910_25840)	69809..70180	+	372	WP_000056336	hypothetical protein	-
SM910_RS25845 (SM910_25845)	70206..70628	+	423	WP_001229309	HNH endonuclease	-
SM910_RS25850 (SM910_25850)	70625..72475	+	1851	WP_015059015	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
SM910_RS25855 (SM910_25855)	72502..72759	+	258	WP_053913405	conjugal transfer protein TrbE	-
SM910_RS25860 (SM910_25860)	72746..73495	+	750	WP_072354014	type-F conjugative transfer system pilin assembly protein TraF	traF
SM910_RS25865 (SM910_25865)	73656..73892	+	237	WP_000270010	type-F conjugative transfer system pilin chaperone TraQ	-
SM910_RS25870 (SM910_25870)	73879..74424	+	546	WP_000059817	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
SM910_RS25875 (SM910_25875)	74414..74728	+	315	WP_001384255	P-type conjugative transfer protein TrbJ	-
SM910_RS25880 (SM910_25880)	74682..75074	+	393	WP_000126338	F-type conjugal transfer protein TrbF	-
SM910_RS25885 (SM910_25885)	75061..76434	+	1374	WP_000944325	conjugal transfer pilus assembly protein TraH	traH
SM910_RS25890 (SM910_25890)	76431..79247	+	2817	WP_015059018	conjugal transfer mating-pair stabilization protein TraG	traG
SM910_RS25895 (SM910_25895)	79280..79801	+	522	WP_000632668	conjugal transfer entry exclusion protein TraS	-
SM910_RS25900 (SM910_25900)	79826..80557	+	732	WP_021559024	conjugal transfer complement resistance protein TraT	-
SM910_RS25905 (SM910_25905)	80760..81497	+	738	WP_015059020	hypothetical protein	-
SM910_RS25910 (SM910_25910)	81548..83791	+	2244	WP_275721194	type IV conjugative transfer system coupling protein TraD	virb4

Host bacterium

• ID: 18493
• GenBank: NZ_CP139410
• Plasmid name: pC252072-2
• Incompatibility group: IncFII
• Plasmid size: 93450 bp
• Coordinate of oriT [Strand]: 56157..56280 [+]
• Host baterium: Klebsiella aerogenes strain C252072

Cargo genes

• Drug resistance gene: aph(3')-IIa, qnrS1, mph(A), fosA3, blaTEM-1B, blaCTX-M-55
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -