Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200502
• Name: oriT_ICESpnDCC1524
• Organism: Streptococcus pneumoniae integrative and
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): HG799493 (19175..19307 [+], 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_ICESpnDCC1524
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

oriT secondary structure

Predicted by RNAfold.

Relaxase

Rep_trans_-_ICESpnDCC1524

• ID: 14547
• GenBank: CDL73854
• Name: Rep_trans_-_ICESpnDCC1524
• UniProt ID: _
• Length: 420 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 420 a.a.
• Molecular weight: 49663.70 Da
• Isoelectric Point: 7.3929

>CDL73854.1 putative conjugative transposon replication initiation factor [Streptococcus pneumoniae]
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKKGYLSTIPVDRYPKKRYNGR

Protein domains

Predicted by InterproScan.

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

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

• Helix-turn-helix (HTH_3) (15-53)

Protein structure

No available structure.

Auxiliary protein

CDL73868_ICESpnDCC1524

• ID: 7923
• GenBank: CDL73868
• Name: CDL73868_ICESpnDCC1524
• UniProt ID: _
• Length: 361 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 361 a.a.
• Molecular weight: 41696.88 Da
• Isoelectric Point: 9.6071

>CDL73868.1 integrase [Streptococcus pneumoniae]
MATDRVPAGKRDCISLREKIAELQKDIHDGIDVVGKKMTLCQLYAKQNAQRPKVRKNTETGRKYLMDILK
KDKLGVRSIDSIKPSDAKEWAIRMSENGYAYQTINNYKRSLKASFYIAIQDDCVRKNPFDFQLKAVLDDD
TVPKTVLTEEQEEKLLAFAKADKTYSKNYDEILILLKTGLRISEFGGLTLPDLDFENRLVNIDHQLLRDT
EIGYYIETPKTKSGERQVPMVEEAYQAFKRVLANRKNDKRVEIDGYSDFLFLNRKNYPKVASDYNGMMKG
LVKKYNKYNEDKLPHITPHSLRHTFCTNYANAGMNPKALQYIMGHANIAMTLNYYAHATFDSAMAEMKRL
NKEKQQERLVA

Protein domains

Predicted by InterproScan.

• Phage integrase family (Phage_integrase) (146-339)

Protein structure

No available structure.

T4CP

t4cp2_-_ICESpnDCC1524

• ID: 17164
• GenBank: CDL73845
• Name: t4cp2_-_ICESpnDCC1524
• UniProt ID: _
• Length: 626 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 626 a.a.
• Molecular weight: 72505.90 Da
• Isoelectric Point: 9.6194

>CDL73845.1 putative conjugal transfer protein TraG [Streptococcus pneumoniae]
MMYSGKKFLLFSLLGILLGYLFHRLTLLYDSYTGNTLDKWTHLLMEGQDEVLQSPWNVSFTGKSSAFFLL
GFVMMLLVYLYLETGKKQYREGVEYGSARFGTLKEKKLFYGKEFSHDTILAQDVRLTLLDKKPPQYDRNK
NIAVIGGSGSGKTFRFVKPNLIQMNSSNIVVDPKDHLAEKTGKLFLERGYQVKVLDLVNMKNSDGFNPFR
YIETENDLNRMLTVYFNNTKGSGSRSDPFWDEASMTLVRALASYLVDFYNPPKTREQLIEESRLSQKEYQ
NLLKRQKKEVEERKKRGRYPSFAEISKLIKHLSKGENQEKSVLEILFENYAKKYGTENFTMRNWADFQNY
KDKTLDSVIAVTTAKFALFNIQSVMDLTKRDTLDMKTWGKEKSMVYLVIPDNDSTFRFLSALFFSTVFQT
LTRQADIDFKGQLPLHVRVYLDEFANIGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTI
LGNCDSLVYLGGNDEDTFKFMSGLLGKQTIDVRNTSRSFGQTGSGSLSHQKIARDLMTPDEVGNMKRHEC
LVRIANMPVFKSKKYNSTKHPNWKYLANQENDERWWNYQINPLNQSQENHLEGLRIRDLTFESSLK

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (132-575)

Protein structure

No available structure.

tcpA_-_ICESpnDCC1524

• ID: 17165
• GenBank: CDL73853
• Name: tcpA_-_ICESpnDCC1524
• 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

>CDL73853.1 conjugative transposon FtsK/SpoIIIE-family protein [Streptococcus pneumoniae]
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: 2391..42660

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
Locus_0	1..174	+	174	CDL73831	conserved hypothetical protein	-
Locus_1	171..950	+	780	CDL73832	putative replication initiator protein	-
Locus_2	1049..2407	+	1359	CDL73833	methyl transferase	-
Locus_3	1080..1622	+	543	CDL73834	methyl transferase	-
Locus_4	2391..2840	+	450	CDL73835	conserved hypothetical protein	gbs1369
Locus_5	2833..3213	+	381	CDL73836	conserved hypothetical protein	-
Locus_6	3226..3459	+	234	Protein_6	putative uncharacterized protein	-
Locus_7	3462..4049	+	588	CDL73838	Putative membrane protein	-
Locus_8	4341..4976	+	636	CDL73839	hypothetical protein	-
Locus_9	5031..5273	+	243	CDL73840	caax amino protease family	-
Locus_10	5401..5991	+	591	CDL73841	conserved hypothetical protein	-
Locus_11	5991..6827	+	837	CDL73842	putative abortive infection protein AbiGII	-
Locus_12	7109..7408	+	300	CDL73843	conserved hypothetical protein	-
Locus_13	7422..7886	+	465	CDL73844	conserved hypothetical protein	gbs1365
Locus_14	7883..9763	+	1881	CDL73845	putative conjugal transfer protein TraG	virb4
Locus_15	9784..10026	+	243	CDL73846	conserved hypothetical protein	prgF
Locus_16	10043..10897	+	855	CDL73847	membrane protein, putative	prgHb
Locus_17	10951..11310	+	360	CDL73848	conserved hypothetical protein	prgIc
Locus_18	11303..13618	+	2316	CDL73849	putative conjugal transfer protein	virb4
Locus_19	13630..16443	+	2814	CDL73850	putative conjugal transfer protein	prgK
Locus_20	17037..17324	+	288	CDL73851	conjugative transposon protein	orf23
Locus_21	17340..17726	+	387	CDL73852	conjugative transposon protein	orf23
Locus_22	17755..19140	+	1386	CDL73853	conjugative transposon FtsK/SpoIIIE-family protein	virb4
Locus_23	19318..20580	+	1263	CDL73854	putative conjugative transposon replication initiation factor	-
Locus_24	20994..21731	+	738	CDL73855	rRNA adenine N-6-methyltransferase	-
Locus_25	21988..23235	-	1248	CDL73856	transposase	-
Locus_26	23415..23636	+	222	CDL73857	conjugative transposon protein	orf19
Locus_27	23753..24250	+	498	CDL73858	conjugative transposon protein	-
Locus_28	24501..24731	+	231	CDL73859	putative conjugative transposon membrane protein	orf17a
Locus_29	24838..27162	+	2325	CDL73860	conjugative transposon ATP/GTP-binding protein	virb4
Locus_30	27231..29342	+	2112	CDL73861	conjugative transposon membrane protein	orf15
Locus_31	29339..30340	+	1002	CDL73862	putative cell wall hydrolase	orf14
Locus_32	30337..31269	+	933	CDL73863	putative conjugative transposon exported protein	orf13
Locus_33	31631..33565	+	1935	CDL73864	conjugative transposon tetracycline resistance protein	-
Locus_34	33911..34264	-	354	CDL73865	putative conjugative transposon regulatory protein	-
Locus_35	34769..35191	+	423	CDL73866	putative conjugative transposon regulatory protein	-
Locus_36	35879..36082	+	204	CDL73867	excisionase	-
Locus_37	36296..37381	+	1086	CDL73868	integrase	-
Locus_38	37558..38238	+	681	CDL73869	hypothetical protein	-
Locus_39	38201..39097	-	897	CDL73870	HTH-domain DNA binding protein	-
Locus_40	39376..39564	-	189	CDL73871	Hypothetical protein	-
Locus_41	40260..40901	+	642	CDL73872	Conserved hypothetical protein	prgL
Locus_42	40911..41996	+	1086	CDL73873	conserved hypothetical protein	traP
Locus_43	42047..42280	+	234	CDL73874	conserved hypothetical protein	gbs1347
Locus_44	42277..42660	+	384	CDL73875	conserved hypothetical protein	gbs1346
Locus_45	42773..42973	+	201	CDL73876	conserved hypothetical protein	-
Locus_46	43055..43687	+	633	CDL73877	Conserved hypothetical protein	-
Locus_47	43678..43905	+	228	CDL73878	Conserved hypothetical protein	-
Locus_48	44026..44205	-	180	CDL73879	Conserved hypothetical protein	-
Locus_49	44275..44646	+	372	CDL73880	Conserved hypothetical protein	-
Locus_50	45023..45919	-	897	CDL73881	Integrase	-
Locus_51	46013..46585	+	573	CDL73882	Conserved hypothetical protein	-

Host bacterium

• ID: 446
• Element type: ICE (Integrative and conjugative element)
• Element name: ICESpnDCC1524
• GenBank: HG799493
• Element size: 58942 bp
• Coordinate of oriT [Strand]: 19175..19307 [+]
• Host bacterium: Streptococcus pneumoniae integrative and
• Coordinate of element: 1..58942

Cargo genes

• Drug resistance gene: erm(B), tet(M)
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: AcrIIA21