Detailed information of oriT

oriT

The information of the oriT region

• oriTDB ID: 200516
• Name: oriT_ICESpn11876
• Organism: Streptococcus pneumoniae integrative and
• Sequence Completeness: -
• NCBI accession of oriT (coordinates [strand]): FR671404 (37573..37705 [-], 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_ICESpn11876
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

oriT secondary structure

Predicted by RNAfold.

Relaxase

Relaxase_-_ICESpn11876

• ID: 14572
• GenBank: CBW38846
• Name: Relaxase_-_ICESpn11876
• UniProt ID: _
• Length: 607 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 607 a.a.
• Molecular weight: 73058.26 Da
• Isoelectric Point: 6.6667

>CBW38846.1 Tn5252 relaxase [Streptococcus pneumoniae]
MVITKHFAIHGKSYRRKLIKYILNPDKTKNLTLVSDYDMRNFLDFPSYEEIVQMYHENFINNDTLYNFRH
DRLEEKQRQIHAHHIIQSFSPEDNLTPEQINQIGYETMKELTSGKFRFIVATHVDKDHLHNHIIINSVDS
NSDKKLKWDYKVERNLRMISDRFSKIAGAKIIENRYSHQQYEVYRKTNHKYELKQRLYFLMEHSRDFEDF
KKNAPLLHVEMDFSHKHATFFMTDSSMKQVVRGNKLNRKQPYTEEFFKNYFAKREMEELMEFLLSKAENI
DDLIETAKLFDLTIIPKQKHVYFQLAGVEVKETELDQKNLYGVEFFQDYFESRKDWQNPEIEDLVQFYQE
EKFSKEKELPRDEKFWEFYQEFKSNRDAVHEFEVELSLNQIEKVVDDGIYIKVKFGIRQEGLIFVPNMQL
DIEEEKVKVFIRETSSYYVYHKDDPEKNRYMKGRTLIRQFSSENQTIPFRRKTTVDMIKEKIEEVYTLLE
LDMDKHSYITIKDDLIHELAASELRINALQERVTTLNQVAEYLLASVENKQKMKLNLSKLNITDKIGIDV
VEKELNELGIQIELESNRYENIVFKVNKFINRLSKKISKEEGICFQK

Protein domains

Predicted by InterproScan.

• Relaxase/Mobilisation nuclease domain (Relaxase) (12-261)

• Lantibiotic streptin immunity protein (Relaxase_C) (510-593)

Protein structure

No available structure.

orf20_-_ICESpn11876

• ID: 14573
• GenBank: CBW38880
• Name: orf20_-_ICESpn11876
• UniProt ID: _
• Length: 420 a.a.
• Note: Predicted by oriTfinder 2.0

Relaxase protein sequence

• Length: 420 a.a.
• Molecular weight: 49619.65 Da
• Isoelectric Point: 7.4229

>CBW38880.1 putative conjugative transposon replication initiation factor [Streptococcus pneumoniae]
MEGFLLNEQTWLQQLKEKRLAYGLSQNRLAVATGITRQYLSDIETGKVKPSEDLQQSLFEALERFNPDAP
LEMLFDYVRIRFPTTDVQHVVENILQLKLSYFLHEDYGFYSYSEHYALGDIFVLCSHELDKGVLVELKGR
GCRQFESYLLAQQRSWYEFFMDVLVAGGVMKHLDLAINDKTGILNIPVLTEKCRQEECISVFRSFKSYRS
GELVRKDEKECMGNTLYIGSLQSEVYFCIYEKDYEQYKKNDIPIEDAEVKNRFEIRLKNERAYYAVRDLL
VYDNPEHTAFKIINRYIRFVDKDDSKPRSDWKLNEEWAWFIGNNRERLKLTTKPEPYSFQRTLNWLSHQV
APTLKVAIKLDEINQTQVVKDILDHAKLTDRHKQILKQQSVKEQDVITTKKGYLSTIPVDRYPKKRYNGR

Protein domains

Predicted by InterproScan.

• Helix-turn-helix (HTH_3) (15-61)

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

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

Protein structure

No available structure.

Auxiliary protein

CBW38860_ICESpn11876

• ID: 7939
• GenBank: CBW38860
• Name: CBW38860_ICESpn11876
• 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

>CBW38860.1 putative 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

orf21_-_ICESpn11876

• ID: 17189
• GenBank: CBW38881
• Name: orf21_-_ICESpn11876
• 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

>CBW38881.1 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.

traG_-_ICESpn11876

• ID: 17190
• GenBank: CBW38896
• Name: traG_-_ICESpn11876
• UniProt ID: _
• Length: 625 a.a.
• PDB ID: _
• Note: Predicted by oriTfinder 2.0

T4CP protein sequence

• Length: 625 a.a.
• Molecular weight: 72435.96 Da
• Isoelectric Point: 9.7089

>CBW38896.1 putative conjugal transfer protein TraG [Streptococcus pneumoniae]
MYSGKKFLLFSLLGILLGYLFHRLTLLYDSYTGNTLDKWIHLLMEGQDEVLQSPWNVSFTGKSSAFFLLG
FVMMLLVYLYLETGKKQYREGVEYGSARFGTLKEKKLFYGKEFLHDTILAQDVRLTLLDKKPPQYDRNKN
IAVIGGSGSGKTFRFVKPNLIQMNSSNIVVDPKDHLAEKTGKLFLEHGYQVKVLDLVNMKNSDGFNPFRY
IETENDLNRMLTVYFNNTKGSGSRSDPFWDEASMTLVRALASYLVDFYNPPKTREQLIEESRLSQKEYKN
LLKRQKKEVEERKKRGRYPSFAEISKLIKHLSKGENQEKSVLEILFENYAKKYGTENFTMRNWADFQNYK
DKTLDSVIAVTTAKFALFNIQSVMDLTKRDTLDMKTWGKEKSMVYLVIPDNDSTFRFLSALFFSTVFQTL
TRQADIDFKGQLPLHVRVYLDEFANIGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTIL
GNCDSLVYLGGNDEDTFKFMSGLLGKQTIDVRNTSRSFGQTGSGSLSHQKIARDLMTPDEVGNMKRHECL
VRIANMPVFKSKKYNSTKHPNWKYLANQESDERWWNYQINPLNQRKENHLEGLRIRDLTFESSLK

Protein domains

Predicted by InterproScan.

• Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf) (134-574)

Protein structure

No available structure.

T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11950..68990

Locus tag	Coordinates	Strand	Size (bp)	Protein ID	Product	Description
Locus_9	8689..9054	-	366	CBW38847	Tn5252 orf9 protein	-
Locus_10	9059..9403	-	345	CBW38848	Tn5252 orf10 protein	-
Locus_11	9791..10285	-	495	CBW38849	Conserved hypothetical protein	-
Locus_12	10406..10546	+	141	Protein_12	Transposase fragment (pseudogene)	-
Locus_13	10705..10848	-	144	CBW38851	Conserved hypothetical protein	-
Locus_14	10923..11555	-	633	CBW38852	Conserved hypothetical protein	-
Locus_15	11637..11912	-	276	CBW38853	putative uncharacterized protein	-
Locus_16	11950..12333	-	384	CBW38854	putative uncharacterized protein	gbs1346
Locus_17	12330..12563	-	234	CBW38855	putative uncharacterized protein	gbs1347
Locus_18	12614..13699	-	1086	CBW38856	putative uncharacterized protein	traP
Locus_19	13709..14350	-	642	CBW38857	putative uncharacterized protein	prgL
Locus_20	15513..16421	+	909	CBW38858	Putative helix-turn-helix DNA binding protein	-
Locus_22	17228..18445	-	1218	CBW38860	putative integrase	-
Locus_23	18527..18730	-	204	CBW38861	excisionase	-
Locus_24	19418..19840	-	423	CBW38862	putative conjugative transposon regulatory protein	-
Locus_25	20069..20215	-	147	CBW38863	putative uncharacterized protein	-
Locus_26	20345..20698	+	354	CBW38864	putative conjugative transposon regulatory protein	-
Locus_27	21044..22978	-	1935	CBW38865	conjugative transposon tetracycline resistance protein	-
Locus_28	23215..24150	-	936	CBW38866	putative conjugative transposon exported protein	orf13
Locus_29	24147..25148	-	1002	CBW38867	putative cell wall hydrolase	orf14
Locus_30	25145..27256	-	2112	CBW38868	conjugative transposon membrane protein	orf15
Locus_31	27325..29649	-	2325	CBW38869	conjugative transposon ATP/GTP-binding protein	virb4
Locus_32	29756..29986	-	231	CBW38870	putative conjugative transposon membrane protein	orf17a
Locus_33	30237..30734	-	498	CBW38871	conjugative transposon protein	-
Locus_34	30851..31072	-	222	CBW38872	conjugative transposon protein	orf19
Locus_35	31252..32499	+	1248	CBW38873	Transposase	-
Locus_36	32756..33493	-	738	CBW38874	rRNA methylase	-
Locus_37	33722..33991	-	270	CBW38875	Omega transcriptional repressor	-
Locus_38	34147..34296	-	150	CBW38876	Conserved hypothetical protein	-
Locus_40	35169..35963	-	795	CBW38878	Aminoglycoside phosphotransferase	-
Locus_41	36056..36277	-	222	CBW38879	Omega transcriptional regulator	-
Locus_42	36300..37562	-	1263	CBW38880	putative conjugative transposon replication initiation factor	-
Locus_43	37740..39125	-	1386	CBW38881	conjugative transposon FtsK/SpoIIIE-family protein	virb4
Locus_44	39154..39540	-	387	CBW38882	conjugative transposon protein	orf23
Locus_45	39556..39843	-	288	CBW38883	conjugative transposon protein	orf23
Locus_46	40685..41806	-	1122	CBW38884	HesA/MoeB/ThiF domain protein	-
Locus_47	42258..43652	-	1395	CBW38885	ABC transporter, ATPase subunit	-
Locus_48	44045..44341	-	297	CBW38886	Membrane protein	gbs1350
Locus_49	44355..44639	-	285	CBW38887	putative uncharacterized protein	-
Locus_50	44714..50959	-	6246	CBW38888	putative conjugative transposon DNA recombination protein	-
Locus_51	50992..51402	-	411	Protein_51	putative uncharacterized protein (pseudogene)	-
Locus_52	51553..52137	-	585	CBW38890	putative uncharacterized protein	-
Locus_53	52375..55188	-	2814	CBW38891	putative conjugal transfer protein	prgK
Locus_54	55200..57557	-	2358	CBW38892	putative conjugal transfer protein	virb4
Locus_55	57508..57867	-	360	CBW38893	putative uncharacterized protein	prgIc
Locus_56	57921..58775	-	855	CBW38894	putative uncharacterized protein	prgHb
Locus_57	58792..59034	-	243	CBW38895	putative uncharacterized protein	prgF
Locus_58	59055..60932	-	1878	CBW38896	putative conjugal transfer protein TraG	virb4
Locus_59	60932..61396	-	465	CBW38897	putative uncharacterized protein	gbs1365
Locus_60	61410..61709	-	300	CBW38898	putative uncharacterized protein	-
Locus_61	62303..62935	-	633	CBW38899	ABC efflux transporter, ATPase subunit	-
Locus_62	62937..64946	-	2010	CBW38900	ABC efflux transporter permease subunit	-
Locus_63	65008..65304	-	297	CBW38901	Bacteriocin	-
Locus_64	65601..66053	-	453	CBW38902	conserved hypothetical protein	-
Locus_65	66407..67042	-	636	CBW38903	Conserved hypothetical protein	-
Locus_66	67332..67919	-	588	CBW38904	putative CAAX amino terminal protease	-
Locus_67	67922..68155	-	234	CBW38905	putative uncharacterized protein	-
Locus_68	68168..68548	-	381	CBW38906	putative uncharacterized protein	-
Locus_69	68541..68990	-	450	CBW38907	putative uncharacterized protein	gbs1369
Locus_70	68974..70332	-	1359	CBW38908	putative DNA methylase	-
Locus_71	70431..71210	-	780	CBW38909	putative replication initiator protein	-
Locus_72	71207..71419	-	213	CBW38910	putative uncharacterized protein	-

Host bacterium

• ID: 459
• Element type: ICE (Integrative and conjugative element)
• Element name: ICESpn11876
• GenBank: FR671404
• Element size: 71516 bp
• Coordinate of oriT [Strand]: 37573..37705 [-]
• Host bacterium: Streptococcus pneumoniae integrative and
• Coordinate of element: 1..71516

Cargo genes

• Drug resistance gene: tet(M), erm(B), aph(3')-III
• Virulence gene: -
• Metal resistance gene: -
• Degradation gene: -
• Symbiosis gene: -
• Anti-CRISPR: AcrIIA21