Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200512
• Name: oriT_Tn6224
• Organism: Lactobacillus salivarius strain JCM 1046
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): CP007650 (1659..1791 [+], 133 nt)
• oriT length: 133 nt
• IRs (inverted repeats): 65..70, 83..88 (AAATCC..GGATTT) 6..12, 23..29 (ACCCCCC..GGGGGGT)
• Location of nic site: 75..76
• Conserved sequence flanking the nic site: TTTGGTTACA
• Note: Predicted by oriTfinder 2.0

oriT sequence

• Length: 133 nt

>oriT_Tn6224
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

oriT secondary structure

Predicted by RNAfold.

Relaxase

Rep_trans_LSJ_5002_Tn6224

• ID: 14566
• GenBank: AIR11891
• Name: Rep_trans_LSJ_5002_Tn6224
• UniProt ID: _
• Length: 401 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 401 a.a.
• Molecular weight: 47398.10 Da
• Isoelectric Point: 6.5091

>AIR11891.1 Replication initiation factor (plasmid) [Ligilactobacillus salivarius]
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKK

Protein domains

Predicted by InterproScan.

• Helix-turn-helix (HTH_3) (15-53)

• Replication initiation factor (Rep_trans) (169-373)

• Rolling Circle replication initiation protein N-terminal domain (Rol_Rep_N) (73-161)

Protein structure

No available structure.

Auxiliary protein

AIR11909_Tn6224

• ID: 7936
• GenBank: AIR11909
• Name: AIR11909_Tn6224
• UniProt ID: _
• Length: 405 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 405 a.a.
• Molecular weight: 47051.94 Da
• Isoelectric Point: 9.7978

>AIR11909.1 Tn916 integrase (plasmid) [Ligilactobacillus salivarius]
MSEKRRDNKGRILKTGESQRKDGRYLYKYIDSFGEPQFVYSWKLVATDRVPAGKRDCISLREKIAELQKD
IHDGIDVVGKKMTLCQLYAKQNAQRPKVRKNTETGRKYLMDILKKDKLGVRSIDSIKPSDAKEWAIRMSE
NGYAYQTINNYKRSLKASFYIAIQDDCVRKNPFDFQLKAVLDDDTVPKTVLTEEQEEKLLAFAKADKTYS
KNYDEILILLKTGLRISEFGGLTLPDLDFENRLVNIDHQLLRDTEIGYYIETPKTKSGERQVPMVEEAYQ
AFKRVLANRKNDKRVEIDGYSDFLFLNRKNYPKVASDYNGMMKGLVKKYNKYNEDKLPHITPHSLRHTFC
TNYANAGMNPKALQYIMGHANIAMTLNYYAHATFDSTMAEMKRLNKEKQQERLVA

Protein domains

Predicted by InterproScan.

• Phage integrase family (Phage_integrase) (190-383)

• DNA binding domain of tn916 integrase (Integrase_DNA) (1-71)

Protein structure

No available structure.

T4CP

tcpA_LSJ_5001_Tn6224

• ID: 17183
• GenBank: AIR11890
• Name: tcpA_LSJ_5001_Tn6224
• UniProt ID: _
• Length: 461 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 461 a.a.
• Molecular weight: 53370.27 Da
• Isoelectric Point: 9.0687

>AIR11890.1 Conjugative transposon-related FtsK/SpoIIIE family protein (plasmid) [Ligilactobacillus salivarius]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

Protein domains

Predicted by InterproScan.

• FtsK/SpoIIIE family (FtsK_SpoIIIE) (217-301)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 432..11097

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
LSJ_5000	194..313	+	120	AIR11889	Tn916-related conserved hypothetical protein	-
LSJ_5001	432..1817	+	1386	AIR11890	Conjugative transposon-related FtsK/SpoIIIE family protein	virb4
LSJ_5002	1995..3200	+	1206	AIR11891	Replication initiation factor	-
LSJ_5003	3243..3464	+	222	AIR11892	Hypothetical protein	orf19
LSJ_5004	3581..4078	+	498	AIR11893	Antirestriction (ArdA) protein/ Conjugative transposon protein	-
LSJ_5005	4053..4559	+	507	AIR11894	Conjugative transposon membrane protein, TcpE family	orf17a
LSJ_5006	4543..6990	+	2448	AIR11895	Conjugative transposon ATP/GTP-binding protein	virb4
LSJ_5007	6993..9170	+	2178	AIR11896	Conjugative transposon membrane protein	orf15
LSJ_5008	9167..10168	+	1002	AIR11897	TN916, NLP/P60 family protein	orf14
LSJ_5009	10165..11097	+	933	AIR11898	Tn916-related hypothetical protein	orf13
LSJ_5010	11372..11458	+	87	AIR11899	Tet (M) leader peptide	-
LSJ_5011	11474..13393	+	1920	AIR11900	Tetracycline resistance protein TetM	-
LSJ_5012	13491..13679	+	189	AIR11901	Tn916-related hypothetical protein	-
LSJ_5013c	13739..14092	-	354	AIR11902	Putative DNA binding protein	-
LSJ_5014	14297..14368	+	72	AIR11903	Conserved Tn916-related hypothetical protein	-
LSJ_5015	14597..15019	+	423	AIR11904	RNA polymerase sigma factor, sigma-70 family, region 4	-
LSJ_5016	15016..15246	+	231	AIR11905	Tn916 hypothetical protein containing a helix-turn-helix motif	-
LSJ_5017c	15310..15438	-	129	AIR11906	Hypothetical protein	-
LSJ_5018c	15472..15723	-	252	AIR11907	Tn916-related conserved hypothetical protein	-
LSJ_5019	15707..15910	+	204	AIR11908	Tn916 excisionase	-

Host bacterium

• ID: 455
• Element type: ICE (Integrative and conjugative element)
• Element name: Tn6224
• GenBank: CP007650
• Element size: 33315 bp
• Coordinate of oriT [Strand]: 1659..1791 [+]
• Host bacterium: Lactobacillus salivarius strain JCM 1046
• Coordinate of element: 194..17209

Cargo genes

• Drug resistance gene: tet(M)
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: -