Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200467
• Name: oriT_ICESpnA213
• Organism: Streptococcus pneumoniae partial Tn5253-like
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): FM201786 (49333..49465 [-], 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_ICESpnA213
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

oriT secondary structure

Predicted by RNAfold.

Relaxase

Relaxase_-_ICESpnA213

• ID: 14492
• GenBank: CAV31133
• Name: Relaxase_-_ICESpnA213
• UniProt ID: _
• Length: 375 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 375 a.a.
• Molecular weight: 45421.13 Da
• Isoelectric Point: 9.9540

>CAV31133.1 hypothetical protein [Streptococcus pneumoniae]
MVITKHFAIHGKNYRSKLIKYILNPSKTKNLTLVSDFGMRNYLDFPSYKELVKMYNDNFLSNDTLYEFRH
DRQEVNQRKIHSHHIIQSFSPDDHLTPEQINRIGYETVKELTGGRFRFIVATHVDKDHIHNHIILNSIDQ
NSDKKFLWDYKAEHNLRMVSDRLSKIAGAKIIENRYSHRQYDVYRKTNYKYEIKQRVYFLIENSKNFEDF
KNKAKALHLKIDFRHKHVTFFMTDSNMKQVVRDSKLSRKQPYNETYFKKKFVQREIINILEFLLPKMKNM
NELIQRAEFFGLKIIPKEKHVQFKFDEIKISEQELVKTNRYSVSYFQDYFNNKNETVVLDNKNLVELYNE
EKIIKEKELPSEEMVMEILSRFQEK

Protein domains

Predicted by InterproScan.

• Relaxase/Mobilisation nuclease domain (Relaxase) (12-264)

Protein structure

No available structure.

Rep_trans_-_ICESpnA213

• ID: 14493
• GenBank: CAV31169
• Name: Rep_trans_-_ICESpnA213
• UniProt ID: _
• Length: 472 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 472 a.a.
• Molecular weight: 55639.89 Da
• Isoelectric Point: 8.3884

>CAV31169.1 hypothetical protein [Streptococcus pneumoniae]
MEGFLLNEQTWLQHLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLWEALERFNPDAP
LEMLFDYVRIRFPTTDVQQVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKRLDLAINDKTGILNIPVLTEKCQQEECISVFRSFKSYRS
GELVRKEEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKKGYLSTIPVDRYPKKDIMGD
KTVRVRADLHHIIKIETAKNGGNVKEVMEIRLRSKLKSVLIVHYLKILYNRN

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)

• Omega Transcriptional Repressor (Omega_Repress) (414-453)

Protein structure

No available structure.

Auxiliary protein

CAV31149_ICESpnA213

• ID: 7914
• GenBank: CAV31149
• Name: CAV31149_ICESpnA213
• UniProt ID: _
• Length: 405 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

Auxiliary protein sequence

• Length: 405 a.a.
• Molecular weight: 47021.92 Da
• Isoelectric Point: 9.7978

>CAV31149.1 integrase [Streptococcus pneumoniae]
MSEKRRDNKGRILKTGESQRKDGRYLYKYIDSFGEPQFVYSWKLVATDRVPAGKRDCISLREKIAELQKD
IHDGIDVVGKKMTLCQLYAKQNAQRPKVRKNTETGRKYLMDILKKDKLGVRSIDSIKPSDAKEWAIRMSE
NGYAYQTINNYKRSLKASFYIAIQDDCVRKNPFDFQLKAVLDDDTVPKTVLTEEQEEKLLAFAKADKTYS
KNYDEILILLKTGLRISEFGGLTLPDLDFENRLVNIDHQLLRDTEIGYYIETPKTKSGERQVPMVEEAYQ
AFKRVLANRKNDKRVEIDGYSDFLFLNRKNYPKVASDYNGMMKGLVKKYNKYNEDKLPHITPHSLRHTFC
TNYANAGMNPKALQYIMGHANIAMTLNYYAHATFDSAMAEMKRLNKEKQQERLVA

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_-_ICESpnA213

• ID: 17099
• GenBank: CAV31170
• Name: tcpA_-_ICESpnA213
• 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

>CAV31170.1 hypothetical 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.

t4cp2_-_ICESpnA213

• ID: 17100
• GenBank: CBJ23514
• Name: t4cp2_-_ICESpnA213
• UniProt ID: _
• Length: 626 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 626 a.a.
• Molecular weight: 72539.96 Da
• Isoelectric Point: 9.6226

>CBJ23514.1 putative conjugal transfer protein TraG [Streptococcus pneumoniae]
MMYSGKKFLLFSLLGILLGYLFHRLTLLYDSYTGNSLDKWTHLLMEGQDEVLQSPWNVSFTGKSSAFFLL
GFVMMLLVYLYLETGKKQYREGVEYGSARFGTLKEKKLFYGKEFSHDTILAQDVRLTLLDKKPPQYDRNK
NIAVIGGSGSGKTFRFVKPNLIQMNTSNIVVDPKDHLAEKTGKLFLEHGYQVKVLDLVNMKNSDGFNPFR
YIETENDLNRMLTVYFNNTKGSGSRSDPFWDEASMTLVRALASYLVDFYNPPKTREQLIEESRLSQKEYQ
NLLKRQKKEVEERKKRGRYPSFAEISKLIKHLSKGENQEKSVLEILFENYAKKYGTENFTMRNWADFQNY
KDKTLDSVIAVTTAKFALFNIQSVMDLTKRDTLDMKTWGQEKSMVYLVIPDNDSTFRFLSALFFSTVFQT
LTRQADIDFKGQLPLHVRVYLDEFANIGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTI
LGNCDSLVYLGGNDEDTFKFMSGLLGKQTIDVRNTSRSFGQTGSGSLSHQKIARDLMTPDEVGNMKRHEC
LVRIANMPVFKSKKYNSIKHPNWKYLANQETDERWWNYQINPLNQRQQNHLDGLRIRDLTFESSLK

Protein domains

Predicted by InterproScan.

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

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17642..65692

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
Locus_18	13456..14106	-	651	CAR31463	chloramphenicol acetyltransferase	-
Locus_19	14278..14526	-	249	CAR31464	hypothetical protein	-
Locus_20	14766..15554	-	789	CAR31465	hypothetical protein	-
Locus_21	16030..16788	-	759	CAR31466	hypothetical protein	-
Locus_22	16788..17264	-	477	CAR31467	hypothetical protein	-
Locus_23	17332..17604	-	273	CAR31468	hypothetical protein	-
Locus_24	17642..18025	-	384	CAR31469	hypothetical protein	gbs1346
Locus_25	18022..18255	-	234	CAR31470	hypothetical protein	gbs1347
Locus_26	18306..19391	-	1086	CAR31471	hypothetical protein	traP
Locus_27	19401..20042	-	642	CAR31472	hypothetical protein	prgL
Locus_28	20202..20399	+	198	CAV31138	hypothetical protein	-
Locus_29	20413..20709	-	297	CAV31139	hypothetical protein	gbs1350
Locus_30	20723..21007	-	285	CAV31140	hypothetical protein	-
Locus_31	21082..21891	-	810	CAV31141	hypothetical protein	-
Locus_32	21931..25878	-	3948	CAV31142	hypothetical protein	-
Locus_33	25895..27313	-	1419	CAV31143	hypothetical protein	-
Locus_34	27346..27756	-	411	CAV31144	hypothetical protein	cd424
Locus_35	28187..28594	-	408	CAV31145	hypothetical protein	-
Locus_36	28579..29502	-	924	CAV31146	hypothetical protein	-
Locus_37	29520..30278	-	759	CAV31147	hypothetical protein	-
Locus_38	30816..31010	+	195	CAV31148	hypothetical protein	-
Locus_39	31261..32478	-	1218	CAV31149	integrase	-
Locus_40	32560..32763	-	204	CAV31150	excisionase	-
Locus_41	32747..32998	+	252	CAV31151	hypothetical protein	-
Locus_42	33224..33454	-	231	CAV31152	hypothetical protein	-
Locus_43	33451..33873	-	423	CAV31153	hypothetical protein	-
Locus_44	34102..34173	-	72	CAV31154	hypothetical protein	-
Locus_45	34378..34731	+	354	CAV31155	hypothetical protein	-
Locus_46	34791..34979	-	189	CAV31156	hypothetical protein	-
Locus_47	35076..36995	-	1920	CAV31157	tetracycline resistance protein TetM	-
Locus_48	37011..37097	-	87	CAV31158	hypothetical protein	-
Locus_49	37372..38034	-	663	CAV31159	hypothetical protein	orf13
Locus_50	38517..39032	-	516	CAV31160	hypothetical protein	orf14
Locus_51	39299..41410	-	2112	CAV31161	hypothetical protein	orf15
Locus_52	41479..43926	-	2448	CAV31162	hypothetical protein	virb4
Locus_53	43910..44416	-	507	CAV31163	hypothetical protein	orf17a
Locus_54	44391..44888	-	498	CAV31164	hypothetical protein	-
Locus_55	45005..45226	-	222	CAV31165	hypothetical protein	orf19
Locus_56	45406..46653	+	1248	CAV31166	hypothetical protein	-
Locus_57	46774..46965	-	192	CAV31167	hypothetical protein	-
Locus_58	46910..47547	-	638	CAV31168	hypothetical protein	-
Locus_59	47904..49322	-	1419	CAV31169	hypothetical protein	-
Locus_60	49500..50885	-	1386	CAV31170	hypothetical protein	virb4
Locus_61	50914..51300	-	387	CAV31171	hypothetical protein	orf23
Locus_62	51316..51630	-	315	CAV35217	hypothetical protein	orf23
Locus_63	51653..51772	-	120	CAV31172	hypothetical protein	-
Locus_64	51946..52155	-	210	CBJ23505	hypothetical protein	-
Locus_65	52197..53435	-	1239	CBJ23506	hypothetical protein	prgK
Locus_66	53443..54369	-	927	CBJ23507	hypothetical protein	prgK
Locus_67	54417..55010	-	594	CBJ23508	hypothetical protein	prgK
Locus_68	55022..56380	-	1359	CBJ23509	putative conjugal transfer protein	virb4
Locus_69	56412..57380	-	969	CBJ23510	hypothetical protein	virb4
Locus_70	57331..57690	-	360	CBJ23511	hypothetical protein	prgIc
Locus_71	57744..58445	-	702	CBJ23512	hypothetical protein	prgHb
Locus_72	58612..58854	-	243	CBJ23513	hypothetical protein	prgF
Locus_73	58875..60755	-	1881	CBJ23514	putative conjugal transfer protein TraG	virb4
Locus_74	60752..61240	-	489	CBJ23515	hypothetical protein	gbs1365
Locus_75	61230..61529	-	300	CBJ23516	hypothetical protein	-
Locus_76	61812..62648	-	837	CBJ23517	hypothetical protein	-
Locus_77	62648..63292	-	645	CBJ23518	hypothetical protein	-
Locus_78	63366..63953	-	588	CBJ23519	hypothetical protein	-
Locus_79	63956..64111	-	156	CBJ23520	hypothetical protein	-
Locus_80	64201..64581	-	381	CBJ23521	hypothetical protein	-
Locus_81	64574..65692	-	1119	CBJ23522	putative methyltransferase	gbs1369
Locus_82	66228..66512	-	285	CBJ23523	hypothetical protein	-
Locus_83	66624..67007	-	384	CBJ23524	putative replication initiator protein A	-

Host bacterium

• ID: 412
• Element type: ICE (Integrative and conjugative element)
• Element name: ICESpnA213
• GenBank: FM201786
• Element size: 67819 bp
• Coordinate of oriT [Strand]: 49333..49465 [-]
• Host bacterium: Streptococcus pneumoniae partial Tn5253-like
• Coordinate of element: 1..67819

Cargo genes

• Drug resistance gene: cat(pC194), tet(M), erm(B)
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: AcrIIA21