Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200500
Name   oriT_ICESpn22664 in_silico
Organism   Streptococcus pneumoniae integrative and
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   HG799489 (37412..37544 [-], 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_ICESpn22664
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14543 GenBank   CDL73624
Name   Rep_trans_-_ICESpn22664 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

>CDL73624.1 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   14544 GenBank   CDL73647
Name   Relaxase_-_ICESpn22664 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

>CDL73647.1 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.




T4CP

ID   17160 GenBank   CDL73602
Name   t4cp2_-_ICESpn22664 insolico UniProt ID   _
Length   626 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


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

>CDL73602.1 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.



ID   17161 GenBank   CDL73625
Name   tcpA_-_ICESpn22664 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

>CDL73625.1 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..16444

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_0 1..174 + 174 CDL73588 conserved hypothetical protein -
Locus_1 171..950 + 780 CDL73589 putative replication initiator protein -
Locus_2 1049..2407 + 1359 CDL73590 methyl transferase -
Locus_3 1080..1622 + 543 CDL73591 methyl transferase -
Locus_4 2391..2840 + 450 CDL73592 conserved hypothetical protein gbs1369
Locus_5 2833..3213 + 381 CDL73593 conserved hypothetical protein -
Locus_6 3226..3459 + 234 Protein_6 conserved hypothetical protein -
Locus_7 3534..4049 + 516 CDL73595 Putative membrane protein -
Locus_8 4341..4976 + 636 CDL73596 hypothetical protein -
Locus_9 5031..5273 + 243 CDL73597 caax amino protease family -
Locus_10 5401..5991 + 591 CDL73598 conserved hypothetical protein -
Locus_11 5991..6827 + 837 CDL73599 abortive infection protein AbiGII, putative -
Locus_12 7110..7409 + 300 CDL73600 conserved hypothetical protein -
Locus_13 7423..7887 + 465 CDL73601 conserved hypothetical protein gbs1365
Locus_14 7884..9764 + 1881 CDL73602 putative conjugal transfer protein TraG virb4
Locus_15 9785..10027 + 243 CDL73603 conserved hypothetical protein prgF
Locus_16 10044..10898 + 855 CDL73604 membrane protein, putative prgHb
Locus_17 10952..11311 + 360 CDL73605 conserved hypothetical protein prgIc
Locus_18 11262..13619 + 2358 CDL73606 putative conjugal transfer protein virb4
Locus_19 13631..16444 + 2814 CDL73607 putative conjugal transfer protein prgK
Locus_21 18049..18177 + 129 CDL73609 hypothetical protein -
Locus_22 18213..18416 - 204 CDL73610 excisionase -
Locus_23 19104..19526 - 423 CDL73611 putative conjugative transposon regulatory protein -

Region 2: 28296..45147

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
Locus_27 24157..24894 - 738 CDL73615 rRNA adenine N-6-methyltransferase -
Locus_29 28296..29231 - 936 CDL73617 putative conjugative transposon exported protein orf13
Locus_30 29228..30229 - 1002 CDL73618 putative cell wall hydrolase orf14
Locus_31 30226..32337 - 2112 CDL73619 conjugative transposon membrane protein orf15
Locus_32 32406..34730 - 2325 CDL73620 conjugative transposon ATP/GTP-binding protein virb4
Locus_33 34837..35274 - 438 CDL73621 putative conjugative transposon membrane protein orf17a
Locus_34 35318..35815 - 498 CDL73622 conjugative transposon protein -
Locus_35 35932..36153 - 222 CDL73623 conjugative transposon protein orf19
Locus_36 36196..37401 - 1206 CDL73624 putative conjugative transposon replication initiation factor -
Locus_37 37579..38961 - 1383 CDL73625 conjugative transposon FtsK/SpoIIIE-family protein virb4
Locus_38 38990..39376 - 387 CDL73626 conjugative transposon protein orf23
Locus_39 39392..39679 - 288 CDL73627 conjugative transposon protein orf23
Locus_40 40012..40725 + 714 CDL73628 hypothetical protein -
Locus_41 40688..41584 - 897 CDL73629 HTH-domain DNA binding protein -
Locus_42 42747..43388 + 642 CDL73630 Conserved hypothetical protein prgL
Locus_43 43398..44483 + 1086 CDL73631 conserved hypothetical protein traP
Locus_44 44534..44767 + 234 CDL73632 conserved hypothetical protein gbs1347
Locus_45 44764..45147 + 384 CDL73633 conserved hypothetical protein gbs1346
Locus_46 45260..45460 + 201 CDL73634 conserved hypothetical protein -
Locus_47 45542..46174 + 633 CDL73635 Conserved hypothetical protein -
Locus_48 46165..46392 + 228 CDL73636 Conserved hypothetical protein -
Locus_49 46513..46692 - 180 CDL73637 Conserved hypothetical protein -
Locus_50 46762..47133 + 372 CDL73638 Conserved hypothetical protein -
Locus_51 47510..48406 - 897 CDL73639 Integrase -
Locus_52 48500..49750 + 1251 CDL73640 Conserved hypothetical protein -

Host bacterium

ID   444 Element type   ICE (Integrative and conjugative element)
Element name   ICESpn22664 GenBank   HG799489
Element size   61429 bp Coordinate of oriT [Strand]   37412..37544 [-]
Host bacterium   Streptococcus pneumoniae integrative and Coordinate of element   1..61429

Cargo genes

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