Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200339
Name   oriT_ICE_SsuSC84_rplL in_silico
Organism   Streptococcus suis SC84
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NC_012924 (30692..30824 [-], 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_ICE_SsuSC84_rplL
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14361 GenBank   WP_011922430
Name   Relaxase_SSUSC84_RS04370_ICE_SsuSC84_rplL insolico UniProt ID   A8CUL8
Length   621 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 621 a.a.        Molecular weight: 73794.64 Da        Isoelectric Point: 7.0198

>WP_011922430.1 SAG1250 family conjugative relaxase [Streptococcus suis]
MVITKHYATHSRKYRKNLIRYILNPEKTAQLKLVSDFGMSNYLDFPSYEEMVKMYQANFLNNDGLYDSRN
DRQEKRQQKIHAHHLIQSFSPDDKLTPEEINRIGYETVKELTGGNFRFIVATHIDQSHIHNHILINSVDL
QSDKKLKWNYALERNLRMISDRISKEAGAKIITNRYSHQQYDVYRKTNHKFELKQRLYFLMEQSKDFEDF
LKKAEQLHLTIDFSSKHTTFLMTDRDQVKPIRGRQLNRREPYDESYFRQAFAKGAIEQRLHFLLPRVKTL
QELLEMAEELGLFIQLKQKNVTFTLTENDQKISLGHQQVSKKKLYDVSFFQDYFSERSDTDIELSDNIKE
DFEIFLAEQTEKLSTVESIVSDYETFSENRKAVHEFEVELAPHQVDKEVEGGIFIKVAFGVKKEGLIFIP
NYQLDEIEKEEEKRFKIFLREITSYFIYNKEGSDKNRYMKGRDLIRQLTQDNKSLPYRRRPNLKELQEKI
AEVNLLIELNVTNRAYTDIKDELVAEIATYDVSMSELNEKNATLNKMAEVLVNLKSHDIERRRLARYEFS
KLNLTESVTLEQIEREISNTQDQLSKLLDNYEESVRKLETFVAVLNRTAPRTRKDYDKELY

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(13-261)

Lantibiotic streptin immunity protein (Relaxase_C)

(517-608)


  Protein structure


Source ID Structure
AlphaFold DB A8CUL8

ID   14362 GenBank   WP_000398284
Name   mobT_SSUSC84_RS04460_ICE_SsuSC84_rplL insolico UniProt ID   A0A3P3PY43
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

>WP_000398284.1 MULTISPECIES: MobT family relaxase [Bacteria]
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


Source ID Structure
AlphaFold DB A0A3P3PY43


Auxiliary protein

ID   7880 GenBank   WP_001291561
Name   WP_001291561_ICE_SsuSC84_rplL insolico UniProt ID   A0A3P3Q021
Length   405 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


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

>WP_001291561.1 MULTISPECIES: tyrosine-type recombinase/integrase [Bacteria]
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


Source ID Structure
AlphaFold DB A0A3P3Q021


T4CP

ID   16852 GenBank   WP_000813488
Name   tcpA_SSUSC84_RS04465_ICE_SsuSC84_rplL insolico UniProt ID   _
Length   461 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 461 a.a.        Molecular weight: 53370.27 Da        Isoelectric Point: 9.0687

>WP_000813488.1 MULTISPECIES: FtsK/SpoIIIE domain-containing protein [Bacteria]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(217-301)

  Protein structure



No available structure.



ID   16853 GenBank   WP_011922464
Name   t4cp2_SSUSC84_RS04680_ICE_SsuSC84_rplL insolico UniProt ID   _
Length   605 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 605 a.a.        Molecular weight: 69397.18 Da        Isoelectric Point: 9.2929

>WP_011922464.1 MULTISPECIES: VirD4-like conjugal transfer protein, CD1115 family [Streptococcus]
MYSRRKAFVFGLLGLAFGYFCHRLTLLYDSLTNAPPMERFAYLLGEGLNQVFNPLWLFAFTQKSLLAFIL
GVLTMTLVYLYVSTGQKVYREGEEYGSARFGTSKEKRNFYSKNPFNDTILARDVRLTLLEKKKPLFDRNK
NLIVIGGSGAGKTFRFVKPNLIQLNCSNIVVDPKDHLAEKTGKLFLENGYQVKVLDLVNMTNSDGFNPFR
YVETENDLNRMLTVYFNNTRGSGSRSDPFWDEASMTLVRAIASYLVDFYNPPGSSKQEQEARRKRGRYPA
FSEIGKLIKLLSKGDNQDKSVLEVLFEDYAKKYGHENFTMRNWADFQNYKDKTLDSVIAVTTAKFALFNI
QSVIDLTQRDTMDLKTWGTQKTMVYLVIPDNDTTFRFLSALFFSTVFSTLTRQADVDFKGQLPIHVRSYL
DEFANVGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTILGNCDSLLYLGGNDEETFKFM
SGLLGKQTIDVRSTSRSFGQTGSSSTSHQKIARDLMTADEVGNMKRDECLVRIAGVPVFRTKKYFPLKHK
NWKWLADKETDERWWHYHINPLTAEEEVDLSGHKIRDLSTETTLH

  Protein domains


Predicted by InterproScan.

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

(135-555)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 894280..914416

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SSUSC84_RS04395 (SSUSC84_0824) 889468..889671 - 204 WP_000814511 excisionase -
SSUSC84_RS10980 889655..889906 + 252 WP_001845478 hypothetical protein -
SSUSC84_RS04400 (SSUSC84_0824a) 890132..890362 - 231 WP_000857133 helix-turn-helix domain-containing protein -
SSUSC84_RS04405 (SSUSC84_0825) 890359..890781 - 423 WP_000804885 sigma-70 family RNA polymerase sigma factor -
SSUSC84_RS04410 (SSUSC84_0826) 891285..891638 + 354 WP_001227347 helix-turn-helix transcriptional regulator -
SSUSC84_RS10485 891698..891865 - 168 WP_000336323 cysteine-rich KTR domain-containing protein -
SSUSC84_RS04420 (SSUSC84_0827) 891984..893903 - 1920 WP_001574275 tetracycline resistance ribosomal protection protein Tet(M) -
SSUSC84_RS10490 893919..894035 - 117 WP_001791010 tetracycline resistance determinant leader peptide -
SSUSC84_RS04425 (SSUSC84_0828) 894280..895212 - 933 WP_001224319 conjugal transfer protein orf13
SSUSC84_RS04430 (SSUSC84_0829) 895209..896210 - 1002 WP_000769868 bifunctional lysozyme/C40 family peptidase orf14
SSUSC84_RS04435 (SSUSC84_0830) 896207..898384 - 2178 WP_000804748 membrane protein orf15
SSUSC84_RS04440 (SSUSC84_0831) 898387..900834 - 2448 WP_000331160 ATP-binding protein virb4
SSUSC84_RS04445 (SSUSC84_0832) 900818..901210 - 393 WP_000723888 conjugal transfer protein orf17a
SSUSC84_RS04450 (SSUSC84_0833) 901299..901796 - 498 WP_000342539 antirestriction protein ArdA -
SSUSC84_RS04455 (SSUSC84_0834) 901913..902134 - 222 WP_001009056 hypothetical protein orf19
SSUSC84_RS04460 (SSUSC84_0835) 902177..903382 - 1206 WP_000398284 MobT family relaxase -
SSUSC84_RS10495 903405..903557 - 153 WP_000879507 hypothetical protein -
SSUSC84_RS04465 (SSUSC84_0836) 903560..904945 - 1386 WP_000813488 FtsK/SpoIIIE domain-containing protein virb4
SSUSC84_RS04470 (SSUSC84_0837) 904974..905360 - 387 WP_000985015 YdcP family protein orf23
SSUSC84_RS04475 (SSUSC84_0838) 905376..905690 - 315 WP_000420682 YdcP family protein orf23
SSUSC84_RS10750 906052..906351 + 300 WP_225938942 hypothetical protein -
SSUSC84_RS04480 (SSUSC84_0839) 906446..908263 - 1818 WP_012775114 ATP-dependent helicase -
SSUSC84_RS04485 (SSUSC84_0840) 908250..910337 - 2088 WP_011922436 AAA family ATPase -
SSUSC84_RS04490 (SSUSC84_0841) 910334..911110 - 777 WP_011922437 type II toxin-antitoxin system toxin PezT -
SSUSC84_RS04495 (SSUSC84_0842) 911110..911586 - 477 WP_012775115 type II toxin-antitoxin system antitoxin PezA -
SSUSC84_RS04500 (SSUSC84_0843) 911656..911946 - 291 WP_024379089 hypothetical protein -
SSUSC84_RS04505 (SSUSC84_0844) 911996..912385 - 390 WP_011922440 DUF5945 family protein gbs1346
SSUSC84_RS04510 (SSUSC84_0845) 912382..912609 - 228 WP_011922441 DUF5965 family protein gbs1347
SSUSC84_RS04515 (SSUSC84_0846) 912663..913739 - 1077 WP_011922442 toprim domain-containing protein -
SSUSC84_RS04520 (SSUSC84_0847) 913778..914416 - 639 WP_011922443 hypothetical protein prgL
SSUSC84_RS04525 (SSUSC84_0849) 915817..916416 - 600 WP_011922444 response regulator transcription factor -
SSUSC84_RS04530 (SSUSC84_0850) 916394..917377 - 984 WP_228480324 ATP-binding protein -
SSUSC84_RS04535 (SSUSC84_0852) 917906..918595 - 690 WP_012775116 ABC transporter permease -
SSUSC84_RS04540 (SSUSC84_0853) 918605..919324 - 720 WP_012028147 ABC transporter permease -

Region 2: 933350..958886

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SSUSC84_RS04595 (SSUSC84_0864) 929092..929619 + 528 WP_002294507 phosphoribosyltransferase family protein -
SSUSC84_RS04600 (SSUSC84_0865) 929847..931166 + 1320 WP_002338419 IS1380-like element ISSsu5 family transposase -
SSUSC84_RS04605 931355..932752 - 1398 WP_011922451 DUF4135 domain-containing protein -
SSUSC84_RS04610 (SSUSC84_0866) 932836..933009 - 174 WP_012775117 type A2 lanthipeptide -
SSUSC84_RS04615 (SSUSC84_0868) 933350..933646 - 297 WP_012775118 DUF5966 family protein gbs1350
SSUSC84_RS04620 (SSUSC84_0869) 933660..933959 - 300 WP_011922452 DUF5962 family protein -
SSUSC84_RS04625 (SSUSC84_0870) 934030..940854 - 6825 WP_012775119 SNF2-related protein -
SSUSC84_RS04630 (SSUSC84_0871) 940904..941455 - 552 WP_012775120 hypothetical protein gbs1354
SSUSC84_RS04635 (SSUSC84_0872) 941439..941630 - 192 WP_011922455 calcium-binding protein -
SSUSC84_RS04640 (SSUSC84_0873) 941631..946526 - 4896 WP_012775121 SspB-related isopeptide-forming adhesin prgB
SSUSC84_RS04645 (SSUSC84_0874) 946698..947288 + 591 WP_011922457 type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein -
SSUSC84_RS04650 (SSUSC84_0875) 947285..948130 + 846 WP_011922458 nucleotidyl transferase AbiEii/AbiGii toxin family protein -
SSUSC84_RS04655 (SSUSC84_0876) 948193..950994 - 2802 WP_011922459 phage tail tip lysozyme prgK
SSUSC84_RS04660 (SSUSC84_0877) 950996..953347 - 2352 WP_011922460 VirB4-like conjugal transfer ATPase, CD1110 family virb4
SSUSC84_RS04665 (SSUSC84_0878) 953304..953657 - 354 WP_012775123 PrgI family protein prgIc
SSUSC84_RS04670 (SSUSC84_0879) 953719..954573 - 855 WP_011922462 conjugal transfer protein TrbL prgHb
SSUSC84_RS04675 (SSUSC84_0880) 954592..954834 - 243 WP_001072182 hypothetical protein prgF
SSUSC84_RS04680 (SSUSC84_0881) 954852..956669 - 1818 WP_011922464 VirD4-like conjugal transfer protein, CD1115 family virb4
SSUSC84_RS04685 (SSUSC84_0882) 956669..957157 - 489 WP_012775124 hypothetical protein gbs1365
SSUSC84_RS04690 (SSUSC84_0883) 957235..957819 - 585 WP_012775125 CPBP family intramembrane glutamic endopeptidase -
SSUSC84_RS04695 (SSUSC84_0884) 957822..958055 - 234 WP_001005708 hypothetical protein -
SSUSC84_RS04700 (SSUSC84_0885) 958064..958447 - 384 WP_012775126 hypothetical protein -
SSUSC84_RS04705 (SSUSC84_0886) 958458..958886 - 429 WP_011922469 hypothetical protein gbs1369
SSUSC84_RS04710 (SSUSC84_0887) 958870..960225 - 1356 WP_011922470 DNA (cytosine-5-)-methyltransferase -
SSUSC84_RS04715 (SSUSC84_0889) 960374..961192 - 819 WP_011922472 replication initiator protein A -
SSUSC84_RS10855 (SSUSC84_0890) 961189..961362 - 174 WP_012775127 hypothetical protein -
SSUSC84_RS04725 (SSUSC84_0891) 961561..961926 - 366 WP_002936483 50S ribosomal protein L7/L12 -
SSUSC84_RS04730 (SSUSC84_0892) 961992..962486 - 495 WP_002936486 50S ribosomal protein L10 -

Host bacterium

ID   298 Element type   ICE (Integrative and conjugative element)
Element name   ICE_SsuSC84_rplL GenBank   NC_012924
Element size   2095898 bp Coordinate of oriT [Strand]   30692..30824 [-]
Host bacterium   Streptococcus suis SC84 Coordinate of element   872702..961575

Cargo genes

Drug resistance gene   tet(M), ant(6)-Ia
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA21, AcrIIA8