Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200504
Name   oriT_ICESpnDCC1902 in_silico
Organism   Streptococcus pneumoniae integrative and
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   HG799491 (46641..46773 [-], 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_ICESpnDCC1902
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14552 GenBank   CDL73741
Name   Rep_trans_-_ICESpnDCC1902 insolico UniProt ID   _
Length   472 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


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

>CDL73741.1 putative conjugative transposon replication initiation factor [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.



ID   14553 GenBank   CDL73764
Name   Relaxase_-_ICESpnDCC1902 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

>CDL73764.1 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   7926 GenBank   CDL73726
Name   CDL73726_ICESpnDCC1902 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

>CDL73726.1 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   17169 GenBank   CDL73712
Name   t4cp2_-_ICESpnDCC1902 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: 72386.76 Da        Isoelectric Point: 9.6194

>CDL73712.1 putative conjugal transfer protein TraG [Streptococcus pneumoniae]
MYSGKKFLLFSLLGILLGYLFHRLTLLYDSYTGNTLDKWTHLLMEGQDEVLQSPWNVSFTGKSSAFFLLG
FVMMLLVYLYLETGKKQYREGVEYGSARFGTLKEKKLFYGKEFSHDTILAQDVRLTLLDKKPPQYDRNKN
IAVIGGSGSGKTFRFVKPNLIQMNSSNIVVDPKDHLAEKTGKLFLERGYQVKVLDLVNMKNSDGFNPFRY
IETENDLNRMLTVYFNNTKGSGSRSDPFWDEASMTLVRALASYLVDFYNPPKTREQLIEESRLSQKEYQN
LLKRQKKEVEERKKRGRYPSFAEISKLIKHLSKGENQEKSVLEILFENYAKKYGTENFTMRNWADFQNYK
DKTLDSVIAVTTAKFALFNIQSVMDLTKRDTLDMKTWGKEKSMVYLVIPDNDSTFRFLSALFFSTVFQTL
TRQADIDFKGQLPLHVRVYLDEFANIGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTIL
GNCDSLVYLGGNDEDTFKFMSGLLGKQTIDVRNTSRSFGQIGSGSLSHQKIARDLMTPDEVGNMKRHECL
VRIANMPVFKSKKYNSTKHPNWKYLANQENDERWWNYQINPLNQSQENHLEGLRIRDLTFESSLK

  Protein domains


Predicted by InterproScan.

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

(131-574)

  Protein structure



No available structure.



ID   17170 GenBank   CDL73742
Name   tcpA_-_ICESpnDCC1902 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

>CDL73742.1 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 CDL73698 conserved hypothetical protein -
Locus_1 171..950 + 780 CDL73699 putative replication initiator protein -
Locus_2 1049..2407 + 1359 CDL73700 methyl transferase -
Locus_3 1080..1622 + 543 CDL73701 methyl transferase -
Locus_4 2391..2840 + 450 CDL73702 conserved hypothetical protein gbs1369
Locus_5 2833..3213 + 381 CDL73703 conserved hypothetical protein -
Locus_6 3226..3459 + 234 Protein_6 putative uncharacterized protein -
Locus_7 3534..4049 + 516 CDL73705 Putative membrane protein -
Locus_8 4341..4976 + 636 CDL73706 hypothetical protein -
Locus_9 5031..5273 + 243 CDL73707 caax amino protease family -
Locus_10 5347..5991 + 645 CDL73708 conserved hypothetical protein -
Locus_11 5991..6827 + 837 CDL73709 abortive infection protein AbiGII, putative -
Locus_12 7109..7408 + 300 CDL73710 conserved hypothetical protein -
Locus_13 7422..7886 + 465 CDL73711 conserved hypothetical protein gbs1365
Locus_14 7886..9763 + 1878 CDL73712 putative conjugal transfer protein TraG virb4
Locus_15 9784..10026 + 243 CDL73713 conserved hypothetical protein prgF
Locus_16 10043..10897 + 855 CDL73714 membrane protein, putative prgHb
Locus_17 10951..11310 + 360 CDL73715 conserved hypothetical protein prgIc
Locus_18 11261..13618 + 2358 CDL73716 putative conjugal transfer protein virb4
Locus_19 13630..16443 + 2814 CDL73717 putative conjugal transfer protein prgK
Locus_20 16745..16858 - 114 CDL73718 Conserved hypothetical protein -
Locus_21 17209..17619 + 411 CDL73719 Hypothetical protein cd424

Region 2: 34677..54376

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_29 29700..29828 + 129 CDL73727 hypothetical protein -
Locus_30 29864..30067 - 204 CDL73728 excisionase -
Locus_31 30755..31177 - 423 CDL73729 putative conjugative transposon regulatory protein -
Locus_32 31682..32035 + 354 CDL73730 putative conjugative transposon regulatory protein -
Locus_33 32381..34315 - 1935 CDL73731 conjugative transposon tetracycline resistance protein -
Locus_34 34677..35612 - 936 CDL73732 putative conjugative transposon exported protein orf13
Locus_35 35609..36610 - 1002 CDL73733 putative cell wall hydrolase orf14
Locus_36 36607..38718 - 2112 CDL73734 conjugative transposon membrane protein orf15
Locus_37 38787..41111 - 2325 CDL73735 conjugative transposon ATP/GTP-binding protein virb4
Locus_38 41218..41448 - 231 CDL73736 putative conjugative transposon membrane protein orf17a
Locus_39 41699..42196 - 498 CDL73737 conjugative transposon protein -
Locus_40 42313..42534 - 222 CDL73738 conjugative transposon protein orf19
Locus_41 42714..43961 + 1248 CDL73739 transposase -
Locus_42 44218..44955 - 738 CDL73740 rRNA adenine N-6-methyltransferase -
Locus_43 45212..46630 - 1419 CDL73741 putative conjugative transposon replication initiation factor -
Locus_44 46808..48190 - 1383 CDL73742 conjugative transposon FtsK/SpoIIIE-family protein virb4
Locus_45 48219..48605 - 387 CDL73743 conjugative transposon protein orf23
Locus_46 48621..48908 - 288 CDL73744 conjugative transposon protein orf23
Locus_47 49241..49954 + 714 CDL73745 hypothetical protein -
Locus_48 49917..50813 - 897 CDL73746 HTH-domain DNA binding protein -
Locus_49 51976..52617 + 642 CDL73747 Conserved hypothetical protein prgL
Locus_50 52627..53712 + 1086 CDL73748 conserved hypothetical protein traP
Locus_51 53763..53996 + 234 CDL73749 conserved hypothetical protein gbs1347
Locus_52 53993..54376 + 384 CDL73750 conserved hypothetical protein gbs1346
Locus_53 54489..54689 + 201 CDL73751 Conserved hypothetical protein -
Locus_54 54771..55403 + 633 CDL73752 Conserved hypothetical protein -
Locus_55 55394..55621 + 228 CDL73753 Conserved hypothetical protein -
Locus_56 55742..55921 - 180 CDL73754 Conserved hypothetical protein -
Locus_57 55991..56362 + 372 CDL73755 Conserved hypothetical protein -
Locus_58 56739..57635 - 897 CDL73756 Integrase -
Locus_59 57729..58979 + 1251 CDL73757 Conserved hypothetical protein -

Host bacterium

ID   448 Element type   ICE (Integrative and conjugative element)
Element name   ICESpnDCC1902 GenBank   HG799491
Element size   70658 bp Coordinate of oriT [Strand]   46641..46773 [-]
Host bacterium   Streptococcus pneumoniae integrative and Coordinate of element   1..70658

Cargo genes

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