Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200503
Name   oriT_ICESpnDCC1738 in_silico
Organism   Streptococcus pneumoniae integrative and
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   HG799492 (43792..43924 [-], 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  


Download         Length: 133 nt

>oriT_ICESpnDCC1738
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14550 GenBank   CDL73806
Name   Rep_trans_-_ICESpnDCC1738 insolico UniProt ID   _
Length   401 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


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

>CDL73806.1 putative conjugative transposon replication initiation factor [Streptococcus pneumoniae]
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.



ID   14551 GenBank   CDL73829
Name   Relaxase_-_ICESpnDCC1738 insolico UniProt ID   _
Length   609 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 609 a.a.        Molecular weight: 73453.95 Da        Isoelectric Point: 9.2584

>CDL73829.1 Relaxase [Streptococcus pneumoniae]
MVITKHFAIHGKSYRRKIIKYILNPDKTKNLALVSDYGMRNFLDFPSYDEMVQMYHENFISNDTLYNFRH
ARLEEKQRKIHAHHIIQSFSPDDHLTPEQINRIGYETAKELTGGRFRFIVATHVDKDHIHNHIILNSIDK
NSDKKFLWDYKAERNLRMVSDRLSKIVGAKIIENRYSHHQYEVYRKTNYKYEIKQRVYFLIENSKNFEDF
KKKAKDLHLKIDFRHKHVTFFMTDSNMKQVVRDNKLNRKQPYNETYFKKKFVQREIINILEFLLPKMKNM
NELIQQAEFFGLKIILKAKHVLFEFDGIKFSEQELVKSNQYSVSYFQDYFNNKNDTFGLDNKNLVELYNE
EKLIKEKKLPTEDMVWKSYQDFKRNRDAVHEFEVELNLNQIEEVVDDGIYIKVQFGIRQEGLIFVPNIQI
NMEEEKVKVFLRETSSYYVYHKDLAEKNRFMKGKTLIRQFNLQYEQQYMYRRISLSKIKEKIEQLDFLMS
AENSPNDFEDITNDFIAQISYLENMIEQVQNKIDDLTNLEEVLLNNTTNSSSNLENSIQDKSSVDKIEKD
LYIYKGKIEKLKEQHREAINLFEMFNKTIKKYKKKQNMKSIEENEIHLE

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(12-264)


  Protein structure



No available structure.




Auxiliary protein

ID   7925 GenBank   CDL73794
Name   CDL73794_ICESpnDCC1738 insolico UniProt ID   _
Length   361 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


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

>CDL73794.1 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

ID   17167 GenBank   CDL73780
Name   t4cp2_-_ICESpnDCC1738 insolico UniProt ID   _
Length   625 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 625 a.a.        Molecular weight: 72374.70 Da        Isoelectric Point: 9.6194

>CDL73780.1 putative conjugal transfer protein TraG [Streptococcus pneumoniae]
MYSGKKFLLFSLLGILLGYLFHRLTLLYDSYTGNTLDKWTHLLMEGQDEVLQSPWNVSFTGKSSAFFLLG
FVMMLLVYLYLETGKKQYREGVEYGSARFGTLKEKKLFYGKEFSHDTILAQDVRLTLLDKKPPQYDRNKN
IAVIGGSGSGKTFRFVKPNLIQMNSSNIVVDPKDHLAEKTGKLFLERGYQVKVLDLVNMKNSDGFNPFRY
IETENDLNRMLTVYFNNTKGSGSRSDPFWDEASMTLVRALASYLVDFYNPPKTREQLIEESRLSQKEYQN
LLKRQKKEVEERKKRGRYPSFAEISKLIKHLSKGENQEKSVLEILFENYAKKYGTENFTMRNWADFQNYK
DKTLDSVIAVTTAKFALFNIQSVMDLTKRDTLDMKTWGKEKSMVYLVIPDNDSTFRFLSALFFSTVFQTL
TRQADIDFKGQLPLHVRVYLDEFANIGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTIL
GNCDSLVYLGGNDEDTFKFMSGLLGKQTIDVRNTSRSFGQTGSGSLSHQKIARDLMTPDEVGNMKRHECL
VRIANMPVFKSKKYNSTKHPNWKYLANQENDERWWNYQINPLNQSQENHLEGLRIRDLTFESSLK

  Protein domains


Predicted by InterproScan.

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

(131-574)

  Protein structure



No available structure.



ID   17168 GenBank   CDL73807
Name   tcpA_-_ICESpnDCC1738 insolico UniProt ID   _
Length   460 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 460 a.a.        Molecular weight: 53241.16 Da        Isoelectric Point: 9.1761

>CDL73807.1 conjugative transposon FtsK/SpoIIIE-family protein [Streptococcus pneumoniae]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKKITYFPKMYYRLKNG
LIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRLM
KNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLLS
CIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLGR
QAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSVI
SEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(216-300)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2391..17619

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_0 1..174 + 174 CDL73766 conserved hypothetical protein -
Locus_1 171..950 + 780 CDL73767 putative replication initiator protein -
Locus_2 1049..2407 + 1359 CDL73768 methyl transferase -
Locus_3 1080..1622 + 543 CDL73769 methyl transferase -
Locus_4 2391..2840 + 450 CDL73770 conserved hypothetical protein gbs1369
Locus_5 2833..3213 + 381 CDL73771 conserved hypothetical protein -
Locus_6 3226..3459 + 234 Protein_6 putative uncharacterized protein -
Locus_7 3534..4049 + 516 CDL73773 Putative membrane protein -
Locus_8 4341..4976 + 636 CDL73774 hypothetical protein -
Locus_9 5031..5273 + 243 CDL73775 caax amino protease family -
Locus_10 5401..5991 + 591 CDL73776 conserved hypothetical protein -
Locus_11 5991..6827 + 837 CDL73777 abortive infection protein AbiGII, putative -
Locus_12 7109..7408 + 300 CDL73778 conserved hypothetical protein -
Locus_13 7422..7886 + 465 CDL73779 conserved hypothetical protein gbs1365
Locus_14 7886..9763 + 1878 CDL73780 putative conjugal transfer protein TraG virb4
Locus_15 9784..10026 + 243 CDL73781 conserved hypothetical protein prgF
Locus_16 10043..10897 + 855 CDL73782 membrane protein, putative prgHb
Locus_17 10951..11310 + 360 CDL73783 conserved hypothetical protein prgIc
Locus_18 11261..13618 + 2358 CDL73784 putative conjugal transfer protein virb4
Locus_19 13630..16443 + 2814 CDL73785 putative conjugal transfer protein prgK
Locus_20 16745..16858 - 114 CDL73786 Conserved hypothetical protein -
Locus_21 17209..17619 + 411 CDL73787 Hypothetical protein cd424

Region 2: 34676..51527

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_29 29863..30066 - 204 CDL73795 excisionase -
Locus_30 30754..31176 - 423 CDL73796 putative conjugative transposon regulatory protein -
Locus_31 31681..32034 + 354 CDL73797 putative conjugative transposon regulatory protein -
Locus_32 32380..34314 - 1935 CDL73798 conjugative transposon tetracycline resistance protein -
Locus_33 34676..35611 - 936 CDL73799 putative conjugative transposon exported protein orf13
Locus_34 35608..36609 - 1002 CDL73800 putative cell wall hydrolase orf14
Locus_35 36606..38717 - 2112 CDL73801 conjugative transposon membrane protein orf15
Locus_36 38786..41110 - 2325 CDL73802 conjugative transposon ATP/GTP-binding protein virb4
Locus_37 41217..41447 - 231 CDL73803 putative conjugative transposon membrane protein orf17a
Locus_38 41698..42195 - 498 CDL73804 conjugative transposon protein -
Locus_39 42312..42479 - 168 CDL73805 conjugative transposon protein orf19
Locus_40 42576..43781 - 1206 CDL73806 putative conjugative transposon replication initiation factor -
Locus_41 43959..45341 - 1383 CDL73807 conjugative transposon FtsK/SpoIIIE-family protein virb4
Locus_42 45370..45756 - 387 CDL73808 conjugative transposon protein orf23
Locus_43 45772..46059 - 288 CDL73809 conjugative transposon protein orf23
Locus_44 46392..47105 + 714 CDL73810 hypothetical protein -
Locus_45 47068..47964 - 897 CDL73811 HTH-domain DNA binding protein -
Locus_46 49127..49768 + 642 CDL73812 Conserved hypothetical protein prgL
Locus_47 49778..50863 + 1086 CDL73813 conserved hypothetical protein traP
Locus_48 50914..51147 + 234 CDL73814 conserved hypothetical protein gbs1347
Locus_49 51144..51527 + 384 CDL73815 conserved hypothetical protein gbs1346
Locus_50 51640..51840 + 201 CDL73816 conserved hypothetical protein -
Locus_51 51922..52554 + 633 CDL73817 Conserved hypothetical protein -
Locus_52 52545..52772 + 228 CDL73818 Conserved hypothetical protein -
Locus_53 52893..53072 - 180 CDL73819 Conserved hypothetical protein -
Locus_54 53142..53513 + 372 CDL73820 Conserved hypothetical protein -
Locus_55 53890..54786 - 897 CDL73821 Integrase -
Locus_56 54880..55452 + 573 CDL73822 Conserved hypothetical protein -

Host bacterium

ID   447 Element type   ICE (Integrative and conjugative element)
Element name   ICESpnDCC1738 GenBank   HG799492
Element size   67809 bp Coordinate of oriT [Strand]   43792..43924 [-]
Host bacterium   Streptococcus pneumoniae integrative and Coordinate of element   1..67809

Cargo genes

Drug resistance gene   tet(M)
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA21