Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 109983
• Name: oriT_pHL21A
• Organism: Salmonella enterica subsp. enterica strain HL21
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP126326 (28704..28765 [-], 62 nt)
• oriT length: 62 nt
• IRs (inverted repeats): 18..25, 28..35 (GCAAAATT..AATTTTGC)
• Location of nic site: 44..45
• Conserved sequence flanking the nic site: GGTGTGGTGC
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 62 nt

>oriT_pHL21A
TTTATAAATAAAAATCAGCAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

oriT secondary structure

Predicted by RNAfold.

Relaxase

traI_QN088_RS23725_pHL21A

• ID: 6591
• GenBank: WP_079975180
• Name: traI_QN088_RS23725_pHL21A
• UniProt ID: _
• Length: 1755 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 1755 a.a.
• Molecular weight: 191781.65 Da
• Isoelectric Point: 5.7503

>WP_079975180.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSLEERWAGKGAEQLGLQGAVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTLHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQTIREAVGDDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYREAADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVYPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIAADRRSQTNLKQDERLSGELITGRR
QLQEGMSFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GGQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGVREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKIPVADGERLMVTGKIPGLRVSGGDRLQVSAVNDGMMTVIVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLHVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLHEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGEQQADI
PVLTTANIRDGELRRLSTWEAHQGALALVDRVYHRIAGISKEDGLITLEDKEGNIRLISPREASAEGVTL
YKPETIRVGTGDRMRFTKSDPERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAIT
AHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLE
PKSEREMMNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGI
WLNPLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGDG
RPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEILAQQQAEEAVRRETEQRAAEIVRKMAEDKTDLPE
EKTAQTVREVAGQEQDRMTPPERETPLPESVLREPVRERETIREVARENRVRERLQQMEQEMVRDLQKEK
TPGGD

Protein domains

Predicted by InterproScan.

• DNA relaxase TraI 2B/2B-like domain (TraI_2B) (632-711)

• TrwC relaxase (TrwC) (11-282)

• single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N) (574-626)

• AAA domain (AAA_30) (967-1158)

• DNA helicase TraI (TraI_C) (1433-1556)

Protein structure

No available structure.

Auxiliary protein

WP_001151568_pHL21A

• ID: 3542
• GenBank: WP_001151568
• Name: WP_001151568_pHL21A
• UniProt ID: Q8L369
• Length: 126 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 126 a.a.
• Molecular weight: 14293.25 Da
• Isoelectric Point: 4.8463

>WP_001151568.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Salmonella]
MAKVQAYVSDEVVEKINAIVEKRRSEGAKSTDVSFSSISTMLLELGLRVYEAQMERKESAFNQMEFNRVL
LENVLKTQSSVVKILGIGSISPHVAGNPKFEYANMVEDIKEKVSSEMERFFHENDE

Protein domains

Predicted by InterproScan.

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

Protein structure

• AlphaFold DB: Q8L369

WP_227005938_pHL21A

• ID: 3543
• GenBank: WP_227005938
• Name: WP_227005938_pHL21A
• UniProt ID: _
• Length: 133 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 133 a.a.
• Molecular weight: 15471.78 Da
• Isoelectric Point: 10.5644

>WP_227005938.1 conjugal transfer relaxosome DNA-bindin protein TraY [Salmonella enterica]
MSLKRFGTRSATGKMVKLKLPVDVEKLLREASDRSGRSRSFEAVIRLKDHLHRYPKFNRKGNVYGKSLVK
YLTMRLDDETNQLLITAKNRSGWCKTDEAADRVIDHLTKFPDFYNSDIFREANEGKKSTFKEL

Protein domains

Predicted by InterproScan.

• TraY domain (TraY) (72-119)

• TraY domain (TraY) (17-60)

Protein structure

No available structure.

T4CP

traC_QN088_RS23625_pHL21A

• ID: 7278
• GenBank: WP_284546342
• Name: traC_QN088_RS23625_pHL21A
• UniProt ID: _
• Length: 882 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 882 a.a.
• Molecular weight: 100531.27 Da
• Isoelectric Point: 6.6546

>WP_284546342.1 type IV secretion system protein TraC [Salmonella enterica]
MKNLLDTVTQAANSLLTALKLPDESAQANQILGEMSFPQFSRLLPYRDYNQESGLFMNDATMGFMLEATP
VNGANETIALSLDHLLRTKLPRGIPLCVHLMSSQLVGERIEYGLREFSWSGEQAERFNAITRAYYMKAAE
THFPLPEGMNLPLTLRHYRVFISYCAPSRKKSRADILEMENLVKIIRASLQGAYISTQTVDAQAFINIVG
EMINHNPESLHPTRRRLDPYSDLNYQCVDDSFDLKVRQDYLTLGLRDHGKNSTARIMNFHLARNPEIAFL
WNSADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGD
LRQRLASNQSSVVSYFFNITAFCRDNKETALETEQDILNSFRKNGFELISPRFNHMRNFLACLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERIRDQLSV
MASPNGNLDEVHEGLLLQAVRAAWLTKKNRARIDDVVDFLENARTSEQYAESPGIRSRLDEMIVLLNQYT
AAGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGDFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFPQLHREMIEKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLQEHETFRRTYEYRAETD

Protein domains

Predicted by InterproScan.

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

• TraG P-loop domain (P-loop_TraG) (467-763)

• TraC protein (TraC_F_IV) (38-276)

Protein structure

No available structure.

traD_QN088_RS23710_pHL21A

• ID: 7279
• GenBank: WP_284546308
• Name: traD_QN088_RS23710_pHL21A
• UniProt ID: _
• Length: 756 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 756 a.a.
• Molecular weight: 85739.61 Da
• Isoelectric Point: 5.2473

>WP_284546308.1 type IV conjugative transfer system coupling protein TraD [Salmonella enterica]
MSFNAKDMTQGGQIASMRIRMFSQIANIIFYCLFIFFWILVGLVLWVKLSWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIRYYGQTFRMNAAQVLQDKYTVWCGEQLWSAFVLAACVALVICLITFFMVTWILGRQGKQ
QSEDDVTGGRQLTDNPKDVARMLKKDGKASDILIGDLPIIKDSEIQNFLLHGTVGAGKSEIIRRLANYAR
QRGDMVVMYDRSGEFVKSYYDPSIDKILNPRDARCAAWDLWRECLTLPDFDNAANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDRDRSYSKLVDTLLSIKIEKLRTYLRDSSAANLVEEKIEKTAISIRAVLTNYVKA
VRYLQGIERNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEIVPEARKFGGCYVFGIQSSTQMEDIYGEKAAATLLDVMNTRAFFRSPSYKIA
DYVAHEIGEKEILKASEQYSYGADPVRDGVSTGKEMERVTLVSYSDIQSLPDLTCYVTLPGPYPAVKLTL
KYQERPKVAPEFIPREMNPEAEARLSAVLAAREAEGRQMSSLFEPDTEAVAPTAAEAQAEQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQPTVVSDKKSAAASTAVNTPAGGVGQELKMKPEDEEQPL
PPGINASGEVVDMAAYERWRQEQEVNTQQQMQRREEVNINVHRGHGKDEPEPGDDF

Protein domains

Predicted by InterproScan.

• Amelogenin (Amelogenin) (615-672)

• F sex factor protein N terminal (TraD_N) (32-128)

• Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind) (173-561)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 28160..55744

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
QN088_RS23525 (QN088_23525)	23315..25312	+	1998	WP_284546340	ParB/RepB/Spo0J family partition protein	-
QN088_RS23530 (QN088_23530)	25352..25786	+	435	WP_079975213	conjugation system SOS inhibitor PsiB	-
QN088_RS23535 (QN088_23535)	25783..26520	+	738	WP_284546341	plasmid SOS inhibition protein A	-
QN088_RS23540 (QN088_23540)	26769..26927	+	159	WP_176452916	hypothetical protein	-
QN088_RS23545 (QN088_23545)	27030..27849	+	820	Protein_38	DUF932 domain-containing protein	-
QN088_RS23550 (QN088_23550)	28160..28630	-	471	WP_042828200	transglycosylase SLT domain-containing protein	virB1
QN088_RS23555 (QN088_23555)	29054..29434	+	381	WP_001151568	conjugal transfer relaxosome DNA-binding protein TraM	-
QN088_RS23560 (QN088_23560)	29629..30318	+	690	WP_079841988	conjugal transfer transcriptional regulator TraJ	-
QN088_RS23565 (QN088_23565)	30417..30812	+	396	WP_001674566	conjugal transfer relaxosome DNA-bindin protein TraY	-
QN088_RS23570 (QN088_23570)	30854..31216	+	363	WP_001274202	type IV conjugative transfer system pilin TraA	-
QN088_RS23575 (QN088_23575)	31231..31542	+	312	WP_000012129	type IV conjugative transfer system protein TraL	traL
QN088_RS23580 (QN088_23580)	31564..32130	+	567	WP_079975214	type IV conjugative transfer system protein TraE	traE
QN088_RS23585 (QN088_23585)	32117..32857	+	741	WP_079955193	type-F conjugative transfer system secretin TraK	traK
QN088_RS23590 (QN088_23590)	32857..34278	+	1422	WP_079975215	F-type conjugal transfer pilus assembly protein TraB	traB
QN088_RS23595 (QN088_23595)	34268..34864	+	597	WP_058108410	conjugal transfer pilus-stabilizing protein TraP	-
QN088_RS23600 (QN088_23600)	34842..35087	+	246	WP_077950176	DUF2689 domain-containing protein	virb4
QN088_RS23605 (QN088_23605)	35084..35599	+	516	WP_079975216	type IV conjugative transfer system lipoprotein TraV	traV
QN088_RS23610 (QN088_23610)	35734..35955	+	222	WP_001278699	conjugal transfer protein TraR	-
QN088_RS23615 (QN088_23615)	35948..36415	+	468	WP_079955208	hypothetical protein	-
QN088_RS23620 (QN088_23620)	36412..36795	+	384	WP_079955209	hypothetical protein	-
QN088_RS23625 (QN088_23625)	36811..39459	+	2649	WP_284546342	type IV secretion system protein TraC	virb4
QN088_RS23630 (QN088_23630)	39434..39820	+	387	WP_053253594	type-F conjugative transfer system protein TrbI	-
QN088_RS23635 (QN088_23635)	39817..40449	+	633	WP_079975218	type-F conjugative transfer system protein TraW	traW
QN088_RS23640 (QN088_23640)	40446..41438	+	993	WP_079975219	conjugal transfer pilus assembly protein TraU	traU
QN088_RS23645 (QN088_23645)	41457..41765	+	309	WP_079975220	hypothetical protein	-
QN088_RS23650 (QN088_23650)	41750..42388	+	639	WP_079975221	type-F conjugative transfer system pilin assembly protein TrbC	trbC
QN088_RS23655 (QN088_23655)	42425..42844	+	420	WP_021003392	HNH endonuclease signature motif containing protein	-
QN088_RS23660 (QN088_23660)	42841..44667	+	1827	WP_079975222	type-F conjugative transfer system mating-pair stabilization protein TraN	traN
QN088_RS23665 (QN088_23665)	44678..44893	+	216	WP_000700023	conjugal transfer protein TrbE	-
QN088_RS23670 (QN088_23670)	44905..45654	+	750	WP_079975223	type-F conjugative transfer system pilin assembly protein TraF	traF
QN088_RS23675 (QN088_23675)	45868..46161	+	294	WP_001233881	type-F conjugative transfer system pilin chaperone TraQ	-
QN088_RS23680 (QN088_23680)	46148..46696	+	549	WP_079955199	type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB	traF
QN088_RS23685 (QN088_23685)	46686..48068	+	1383	WP_001161720	conjugal transfer pilus assembly protein TraH	traH
QN088_RS23690 (QN088_23690)	48065..50887	+	2823	WP_079975225	conjugal transfer mating-pair stabilization protein TraG	traG
QN088_RS23695 (QN088_23695)	50909..51388	+	480	WP_284546307	surface exclusion protein	-
QN088_RS23700 (QN088_23700)	51734..52465	+	732	WP_079975227	conjugal transfer complement resistance protein TraT	-
QN088_RS23705 (QN088_23705)	52717..53196	+	480	WP_079975228	hypothetical protein	-
QN088_RS23710 (QN088_23710)	53474..55744	+	2271	WP_284546308	type IV conjugative transfer system coupling protein TraD	virb4
QN088_RS23715 (QN088_23715)	55753..56151	-	399	WP_000911322	type II toxin-antitoxin system VapC family toxin	-
QN088_RS23720 (QN088_23720)	56151..56378	-	228	WP_000450263	toxin-antitoxin system antitoxin VapB	-

Host bacterium

• ID: 10418
• GenBank: NZ_CP126326
• Plasmid name: pHL21A
• Incompatibility group: -
• Plasmid size: 90249 bp
• Coordinate of oriT [Strand]: 28704..28765 [-]
• Host baterium: Salmonella enterica subsp. enterica strain HL21

Cargo genes

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