Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 102817
• Name: oriT_pPA35
• Organism: Pandoraea apista strain DSM 16535
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): NZ_CP013482 (28929..29029 [+], 101 nt)
• oriT length: 101 nt
• IRs (inverted repeats): _
• Location of nic site: _
• Conserved sequence flanking the nic site: _
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 101 nt

>oriT_pPA35
GCCTCGCAGAGCAGGATCCCCGTTGAGCACTCCGTGCGAATAAGGGATGTGAAAGTAGCTAACCGGCCTGCCGGTTAGCTACTTTCACCTATCCTGCCCGG

oriT secondary structure

Predicted by RNAfold.

Relaxase

Relaxase_AT395_RS24980_pPA35

• ID: 2087
• GenBank: WP_072633023
• Name: Relaxase_AT395_RS24980_pPA35
• UniProt ID: _
• Length: 894 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 894 a.a.
• Molecular weight: 99533.75 Da
• Isoelectric Point: 10.9694

>WP_072633023.1 TraI/MobA(P) family conjugative relaxase [Pandoraea apista]
MIARNLPMQSVKKSSYGRLVKYLCDPQTKQERVGAVTVTNCEQREALDAIYEVQAVQGMNLRAEGDKTYH
LLISFPPGEHPSSDVLSVVEAELCEALGYGEHQRISAVHHDTDNLHIHVAINKIHPEHLTMHTPYRDYKT
LARKCDELEQRFDLERDNHTARKSRSENRADDMERHSGVESLLGWIKRECVSELREANNWQELHDIARAR
GLAVREQGNGLVFESRDGIKVKASSVDRSLSRSRLLKQWGDYEPPRGAKRLAGDDVPDAAGRRGQVGRRG
VDRVTIAVPSTSAVASWRRRAPPVRSATTRPESPRAIRSGGLPGRRDLHAHIPRQAPDPDLISSWRRGRR
TVEAVGTRPPPAPYRHRVRPSIGNRDLPAQGAETSIGSPAPASWRQGKHGTSPTQQRQEWYAKRPVYPSA
EADALYRRYREEKADVQRSKQLHMGAARQARIQTIEDAKRSAARLRALIKLLKGSGYNKRFLYGIVSKRL
HGAISKAHANFNSQRPPKASKAHKALAWADWLRDRAEEGDQSALAVLRYQASWDARAQARAVERSSDSEA
LRPRAIDSITKAGTVIYRVANAAIRDDGRRLSVTRNAPDEVLATALQLAADRHGGKVSLTGSTEFQQRVA
DLAASARIRVSFVDPNLESRRVEALKQKHQQESFDERTQRNRPDGAQRSAGFNEQRHHERRGSGRSGGDV
GRGQYAESIKRGGGRGSDRFVRGRSSPFAPKPNVGAVGRKAPPPQAYRMRNLPTLYMEPHAGSPGLLVPR
DVRGSLDDKQADRGSGVRRAAPADRLSTSAWSAADKYVQEREGKRANSFDIQKHERYNDRHAGVLNFTGL
RTVDGHQLALLRHDDTVLVLPVDAATANRLRRLAIGAAISTEVGGKIRTRGRSL

Protein domains

Predicted by InterproScan.

• Large polyvalent protein-associated domain 7 (LPD7) (567-653)

• Relaxase/Mobilisation nuclease domain (Relaxase) (12-250)

Protein structure

No available structure.

T4CP

t4cp2_AT395_RS24975_pPA35

• ID: 1746
• GenBank: WP_048627760
• Name: t4cp2_AT395_RS24975_pPA35
• UniProt ID: _
• Length: 643 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 643 a.a.
• Molecular weight: 71736.30 Da
• Isoelectric Point: 9.1270

>WP_048627760.1 type IV secretory system conjugative DNA transfer family protein [Pandoraea apista]
MRQTLNNPVGPQVRQKRRKGKAVPVMALTSFAAGMQAATQYFAHGFEYHPTLGVNYGHMYAPWSILSWYS
KWAELFPEQFHTAGSVGVLAAGGGLLVTAAAANAIANSSRPNEYLHGSARWANKKDVKRMGLLGDSGVYV
GQWIDKAGNTHWLRHNGPEHVLCYAPTRSGKGVGLVVPTLLSWKHSTVVTDLKGELWAMTAGWRREYAKN
ITLKFEPAAVYGSVAWNPLDEIRMGTEYEVGDVQNLATLIVDPDGKGLNTHWQKTAQALLVGVILHALYK
AQIEGTPATLPYCDKMLADPNRPVAELWMEMTQYGHVNGKNHPVIGSAAQDMLDRPEEEGGSVLSTAKSY
LSLYRDPVVERNVSRSDFRIKDLMCHEFPVSLYIVTQPTDKDRLRPLVRVLLNMIVRVLADKMEFERLQK
EMDPWTRFLAKLGLRDSETTYVQAKKKYKHRLLGMLDEFPSLGKLDIIQQSLAFLAGYGIKFYLICQDIN
QLKSREEGYGPDETITSNCHIQNAYPPNRIETAEHLSKLTGTTTVLKEQVTTSGKRFGSMHGQVSRTVQE
VARPLLTPDECLRMPGPKKSPDGRIEEAGDMVIYVAGFPALYGRQGLFFDDPIFSRRAAIPEPKDTDRIR
PAAKLAEAEGIRL

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (445-621)

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (120-419)

Protein structure

No available structure.

t4cp2_AT395_RS25085_pPA35

• ID: 1747
• GenBank: WP_231606007
• Name: t4cp2_AT395_RS25085_pPA35
• UniProt ID: _
• Length: 859 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 859 a.a.
• Molecular weight: 94891.52 Da
• Isoelectric Point: 6.4752

>WP_231606007.1 conjugal transfer protein TrbE [Pandoraea apista]
MNATAFTSLFALIAGGVLIALFMRLRAVGESHKLKLHRSKQAGLADLLKHASIVDDGVILGKDGSLMAAW
FYRGNDNASATEREREYNSAQINKAIIRLGNGWACHVDAVRVKAPQYSHPNDSHFPDPVSAAIDEERRRF
FETNGKVFEGAFVATVTWFPPVLAERKLVELMYSDEAEKPDAQGVADELLAEFKQAVAGIESRLSSALKL
ERLGAQKVLNEDGTTTVFDQFLQWIHFCVTGVNHPIALPANPMYIDSLIGGKELYTGVIPKIGRNFVQVV
SIDGFPSASHPGILTALGEIPAQYRWSSRFIFLDQHVANSHLEKFKKRWRQRVRGFVTALVNPNSPDVDE
DAVNMVADAAAAIAETNSKMVAQGYYTSVVVIMDENRDVVEAAALLVERSINELGFTARIETVNAMDAFI
GSVPGHVVENVRRPIINTMNLADMLPTSSIWTGDERAPCPLFPPNAPALMHALTAGNAPFRVNMHVGDLG
HAAMFGPTRAGKSTHVGMLALQYLRYEGARVYVFEKGMSFYIACKAVGGVHYNIGDEKQRTAYAPLKDLR
SRSRRAWAMQWMATIMELNNVQMTPELSNEIATAVMTMARSASGGGSLTTFRTLVQSAEVRAVLQQYTVD
GVMGHLLDGQEDGFSIDEVSTMCFELEQLMHMGDKYALPVLLYMFRRIEESLDGRPTFIILDEAWLMLGN
PAFRAKLREWLKAFAKKNCHILLATQSLSDAKESGILDVIVESTATKIFLANPAANDEEFSATYTQMGLN
RRQIEIIQAATKKKDYYLTSEKGRRLYQLALGPLALAFVGATDPESIAEVQRLEEKHGGRRFASDLSEGW
VNEWLAGRNINLNDYGVAA

Protein domains

Predicted by InterproScan.

• CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB) (223-432)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 41012..51398

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
AT395_RS25045 (AT395_24975)	36375..36644	-	270	WP_048627712	hypothetical protein	-
AT395_RS25050 (AT395_24980)	36954..37721	-	768	WP_048627713	hypothetical protein	-
AT395_RS25055 (AT395_24985)	38688..39785	-	1098	WP_167370779	replication initiator protein A	-
AT395_RS25060 (AT395_24990)	39867..40220	-	354	WP_048627714	single-stranded DNA-binding protein	-
AT395_RS25065 (AT395_24995)	40334..40699	+	366	WP_048627715	transcriptional regulator	-
AT395_RS25070 (AT395_25000)	41012..41911	+	900	WP_231606006	P-type conjugative transfer ATPase TrbB	virB11
AT395_RS25075 (AT395_25005)	41927..42346	+	420	WP_082164638	TrbC/VirB2 family protein	virB2
AT395_RS25080 (AT395_25010)	42349..42660	+	312	WP_048627717	conjugal transfer protein TrbD	virB3
AT395_RS25085 (AT395_25015)	42657..45236	+	2580	WP_231606007	conjugal transfer protein TrbE	virb4
AT395_RS25090 (AT395_25020)	45248..45988	+	741	WP_072633032	VirB8/TrbF family protein	virB8
AT395_RS25095 (AT395_25025)	46043..46921	+	879	WP_048627772	P-type conjugative transfer protein TrbG	virB9
AT395_RS25100 (AT395_25030)	46923..47366	+	444	WP_048627719	hypothetical protein	-
AT395_RS25105 (AT395_25035)	47370..48824	+	1455	WP_048627720	TrbI/VirB10 family protein	virB10
AT395_RS25110 (AT395_25040)	48841..49617	+	777	WP_048627721	P-type conjugative transfer protein TrbJ	virB5
AT395_RS25115 (AT395_25045)	49659..51398	+	1740	WP_058375335	P-type conjugative transfer protein TrbL	virB6
AT395_RS25120 (AT395_25050)	51412..51990	+	579	WP_053086312	TrbM/KikA/MpfK family conjugal transfer protein	-
AT395_RS25125 (AT395_25055)	51993..52652	+	660	WP_048627723	hypothetical protein	-
AT395_RS25130 (AT395_25060)	52657..53391	+	735	WP_072633028	TraX family protein	-

Host bacterium

• ID: 3260
• GenBank: NZ_CP013482
• Plasmid name: pPA35
• Incompatibility group: -
• Plasmid size: 77293 bp
• Coordinate of oriT [Strand]: 28929..29029 [+]
• Host baterium: Pandoraea apista strain DSM 16535

Cargo genes

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