Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200453
Name   oriT_ICESsu(BM407)1 in_silico
Organism   Streptococcus suis BM407 complet
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   FM252032 (46148..46280 [-], 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_ICESsu(BM407)1
ACTTAACCCCCCGTATCTAACAGGGGGGTACAAATCGACAGGAAACAGTCAAAAAAACATTAGAAAATCCTTTGGTTACAAGGGATTTACAAAATTTCAGCGTATGTCAAATGGGCTTTAAAAGTTGACATAC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14456 GenBank   CAZ55325
Name   Rep_trans_SSUBM407_0491_ICESsu(BM407)1 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

>CAZ55325.1 replication initiation factor [Streptococcus suis BM407]
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   14457 GenBank   CAZ55342
Name   Relaxase_SSUBM407_0508_ICESsu(BM407)1 insolico UniProt ID   _
Length   621 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 621 a.a.        Molecular weight: 74177.04 Da        Isoelectric Point: 6.7525

>CAZ55342.1 puative relaxase protein [Streptococcus suis BM407]
MVVTKHFATHGKKYRRRLIKYILNPDKTDNLKLVSDFGMSNYLDFPSYEEMVEMYNVNFTNNDKLYESRN
DRQEKHQQNIHSHHLIQSFSPEDNLTPEEINRIGYDTMMELTGGRFKFIVATHTDKDHVHNHILINAIDS
NSDKKLIWNYALERNLRMISDRISKIAGAKIIEKRFSYRDYQKYRQSSHKFELKQRLYFLMQHSKSFDDF
LEKAVQLHVHIDFSQKHSRFMMRDRAMTKPIRGRQLSKRDLYDEEFFRTHFAKHEIESRLEFLLNRVNFL
EELLTKAKELNLTIDLKQKNVIFILEENGKQFSLSHKKISDKKLYDVNFFQDYFKNKEVGDSEGLENLQE
QYHAFQEERDKEKVATEEIEEAFEEFKKKRDAVHEFEVELAGHQIEKLVDEGVYIKVSFGVKQSGFIFIP
NYQLDIIEEDNQKKYKVYIRETTSYFVYNKEHSDKNQYIKGRTLIRQLTNDSRAIPYRRPTVERLQEKIT
EINLLIELTETDKRYQYVKDELVAEIAELDVKLNQTNEKIAILNKMAEVLINLKSDDPNSRKLARYDFSK
LNLTESITLEQVTEEIRVLQEDLGHYLDEYEGLARKLETFVKILNTNKQTEHEFHGDIALE

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(11-254)

Lantibiotic streptin immunity protein (Relaxase_C)

(516-608)


  Protein structure



No available structure.




Auxiliary protein

ID   7890 GenBank   CAZ55312
Name   CAZ55312_ICESsu(BM407)1 insolico UniProt ID   _
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

>CAZ55312.1 integrase [Streptococcus suis BM407]
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

ID   17064 GenBank   CAZ55296
Name   t4cp2_SSUBM407_0464_ICESsu(BM407)1 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: 69412.15 Da        Isoelectric Point: 9.2874

>CAZ55296.1 putative conjugal transfer protein TraG [Streptococcus suis BM407]
MYSRQKAFVFGLLGLAFGYFCHRLTLLYDSLTNAPPMERIAYLLGEGLNQVFNPLWLFSFTQKSFLAFIL
GVLTMTLVYLYVSTGQKVYREGEEYGSARFGTSKEKRNFYSKNPFNDTILARDVRLTLLEKKKPQFDRNK
NLIVIGGSGAGKTFRFVKPNLIQLNCSNIVVDPKDHLAEKTGKLFLENGYQVKVLDLVNMTNSDGFNPFR
YVETENDLNRMLTVYFNNTKGNGSRSDPFWDEASMTLVRAIASYLVDFYNPPGSSKQEQEARRKRGRYPA
FSEIGKLIKLLSKGDNQDKSVLEVLFEDYAKKYGHENFTMRNWADFQNYKDKTLDSVIAVTTAKFALFNI
QSVIDLTQRDTMDLKTWGTQKTMVYLVIPDNDTTFRFLSALFFSTVFSTLTRQADVDFKGQLPIHVRSYL
DEFANVGEIPDFAEQTSTVRSRNMSLVPILQNIAQLQGLYKEKEAWKTILGNCDSLLYLGGNDEETFKFM
SGLLGKQTIDVRSTSRSFGQTGSSSTSHQKIARDLMTADEVGNMKRDECLVRIAGVPVFRTKKYFPLKHK
NWKWLADKESDERWWHYHINPLTAEEEVDLSGHKIRDLSTEKTLH

  Protein domains


Predicted by InterproScan.

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

(129-555)

  Protein structure



No available structure.



ID   17065 GenBank   CAZ55326
Name   tcpA_SSUBM407_0492_ICESsu(BM407)1 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

>CAZ55326.1 FtsK/SpoIIIE family protein [Streptococcus suis BM407]
MKQRGKRIRPSGKDLVFHFTIASLLPVFLLVVGLFHVKTIQQINWQDFNLSQADKIDIPYLIISFSVAIL
ICLLVAFVFKRVRYDTVKQLYHRQKLAKMILENKWYESEQVKTEGFFKDSAGRTKEKITYFPKMYYRLKN
GLIQIRVEITLGKYQDQLLHLEKKLESGLYCELTDKELKDSYVEYTLLYDTIASRISIDEVEAKDGKLRL
MKNVWWEYDKLPHMLIAGGTGGGKTYFILTLIEALLHTDSKLYILDPKNADLADLGSVMANVYYRKEDLL
SCIETFYEEMMKRSEEMKQMKNYKTGKNYAYLGLPAHFLIFDEYVAFMEMLGTKENTAVMNKLKQIVMLG
RQAGFFLILACQRPDAKYLGDGIRDQFNFRVALGRMSEMGYGMMFGSDVQKDFFLKRIKGRGYVDVGTSV
ISEFYTPLVPKGYDFLEEIKKLSNSRQSTQATCEAEVAGVD

  Protein domains


Predicted by InterproScan.

FtsK/SpoIIIE family (FtsK_SpoIIIE)

(217-301)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1008469..1026559

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SSUBM407_0932 1004869..1005363 + 495 CAZ55782 50S ribosomal protein L10 -
SSUBM407_0933 1005429..1005794 + 366 CAZ55783 50S ribosomal protein L7/L12 -
SSUBM407_0933a 1005993..1006166 + 174 CAZ55784 hypothetical protein -
SSUBM407_0934 1006163..1006981 + 819 CAZ55785 replication initiator protein A protein -
SSUBM407_0935 1007130..1008485 + 1356 CAZ55786 C-5 cytosine-specific DNA methylase -
SSUBM407_0936 1008469..1008897 + 429 CAZ55787 hypothetical protein gbs1369
SSUBM407_0937 1008908..1009291 + 384 CAZ55788 hypothetical protein -
SSUBM407_0938 1009300..1009533 + 234 CAZ55789 hypothetical protein -
SSUBM407_0939 1009536..1010120 + 585 CAZ55790 CAAX amino terminal protease family protein -
SSUBM407_0940 1010198..1010686 + 489 CAZ55791 hypothetical protein gbs1365
SSUBM407_0941 1010686..1012503 + 1818 CAZ55792 putative conjugal transfer protein TraG virb4
SSUBM407_0942 1012521..1012763 + 243 CAZ55793 putative membrane protein prgF
SSUBM407_0943 1012782..1013636 + 855 CAZ55794 putative TrbL/VirB6 plasmid conjugal transfer protein prgHb
SSUBM407_0944 1013698..1014051 + 354 CAZ55795 putative membrane protein prgIc
SSUBM407_0945 1014029..1016359 + 2331 CAZ55796 hypothetical protein virb4
SSUBM407_0946 1016361..1019162 + 2802 CAZ55797 hypothetical protein prgK
SSUBM407_0947 1019224..1020069 - 846 CAZ55798 hypothetical protein -
SSUBM407_0948 1020066..1020656 - 591 CAZ55799 hypothetical protein -
SSUBM407_0949 1020937..1025832 + 4896 CAZ55800 putative glucan-binding surface-anchored protein prgB
SSUBM407_0949a 1025833..1026024 + 192 CAZ55801 hypothetical protein -
SSUBM407_0950 1026008..1026559 + 552 CAZ55802 hypothetical protein gbs1354
SSUBM407_0951 1026609..1030454 + 3846 Protein_952 hypothetical protein (fragment) -
SSUBM407_0951a 1030458..1030832 + 375 Protein_953 hypothetical protein (fragment) -

Region 2: 507125..557007

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SSUBM407_0454 502560..503807 + 1248 CAZ55286 putative permease -
SSUBM407_0456 504649..504822 + 174 CAZ55288 hypothetical protein -
SSUBM407_0457 504819..505637 + 819 CAZ55289 replication initiator protein A protein -
SSUBM407_0458 505786..507141 + 1356 CAZ55290 C-5 cytosine-specific DNA methylase -
SSUBM407_0459 507125..507553 + 429 CAZ55291 hypothetical protein gbs1369
SSUBM407_0460 507564..507947 + 384 CAZ55292 hypothetical protein -
SSUBM407_0461 507950..508189 + 240 CAZ55293 hypothetical protein -
SSUBM407_0462 508192..508776 + 585 CAZ55294 CAAX amino terminal protease family protein -
SSUBM407_0463 508854..509342 + 489 CAZ55295 hypothetical protein gbs1365
SSUBM407_0464 509342..511159 + 1818 CAZ55296 putative conjugal transfer protein TraG virb4
SSUBM407_0465 511177..511419 + 243 CAZ55297 putative membrane protein prgF
SSUBM407_0466 511438..512292 + 855 CAZ55298 putative TrbL/VirB6 plasmid conjugal transfer protein prgHb
SSUBM407_0467 512354..512707 + 354 CAZ55299 putative membrane protein prgIc
SSUBM407_0468 512685..515015 + 2331 CAZ55300 hypothetical protein virb4
SSUBM407_0469 515017..517818 + 2802 CAZ55301 hypothetical protein prgK
SSUBM407_0470 518157..518792 + 636 CAZ55302 hypothetical protein -
SSUBM407_0471 518952..523847 + 4896 CAZ55303 putative glucan-binding surface-anchored protein prgB
SSUBM407_0471a 523848..524039 + 192 CAZ55304 hypothetical protein -
SSUBM407_0472 524023..524574 + 552 CAZ55305 hypothetical protein gbs1354
SSUBM407_0473 524624..531469 + 6846 CAZ55306 hypothetical protein -
SSUBM407_0474 531540..531839 + 300 CAZ55307 hypothetical protein -
SSUBM407_0475 531853..532152 + 300 CAZ55308 putative membrane protein gbs1350
SSUBM407_0476 532197..533084 - 888 CAZ55309 integrase -
SSUBM407_0477 533176..534126 + 951 CAZ55310 putative D-alanine--D-alanine ligase -
SSUBM407_0478 534107..535402 - 1296 CAZ55311 hypothetical protein -
SSUBM407_0479 535571..536788 - 1218 CAZ55312 integrase -
SSUBM407_0479a 536870..537073 - 204 CAZ55313 excisionase -
SSUBM407_0480 537534..537764 - 231 CAZ55314 hypothetical protein -
SSUBM407_0481 537761..538183 - 423 CAZ55315 putative DNA-binding protein -
SSUBM407_0482 538688..539041 + 354 CAZ55316 DNA-binding protein -
SSUBM407_0483 539387..541306 - 1920 CAZ55317 tetracycline resistance protein TetM 1 -
SSUBM407_0484 541683..542615 - 933 CAZ55318 putative membrane protein orf13
SSUBM407_0485 542612..543613 - 1002 CAZ55319 putative exported protein orf14
SSUBM407_0486 543610..545787 - 2178 CAZ55320 putative membrane protein orf15
SSUBM407_0487 545790..548237 - 2448 CAZ55321 hypothetical protein virb4
SSUBM407_0488 548221..548727 - 507 CAZ55322 putative membrane protein orf17a
SSUBM407_0489 548702..549199 - 498 CAZ55323 antirestriction protein -
SSUBM407_0490 549316..549537 - 222 CAZ55324 putative membrane protein orf19
SSUBM407_0491 549580..550785 - 1206 CAZ55325 replication initiation factor -
SSUBM407_0492 550963..552348 - 1386 CAZ55326 FtsK/SpoIIIE family protein virb4
SSUBM407_0493 552377..552763 - 387 CAZ55327 hypothetical protein orf23
SSUBM407_0494 552779..553093 - 315 CAZ55328 hypothetical protein orf23
SSUBM407_0495 553409..554452 - 1044 CAZ55329 hypothetical protein -
SSUBM407_0496 554587..555225 + 639 CAZ55330 putative exported protein prgL
SSUBM407_0497 555264..556340 + 1077 CAZ55331 DNA primase -
SSUBM407_0498 556394..556621 + 228 CAZ55332 hypothetical protein gbs1347
SSUBM407_0499 556618..557007 + 390 CAZ55333 hypothetical protein gbs1346
SSUBM407_0500 556997..557353 + 357 CAZ55334 hypothetical protein -
SSUBM407_0501 557362..557670 - 309 CAZ55335 hypothetical protein -
SSUBM407_0502 557657..558007 - 351 CAZ55336 hypothetical protein -
SSUBM407_0503 558004..559419 - 1416 CAZ55337 UmuC-like DNA-repair protein -
SSUBM407_0504 559562..560254 - 693 CAZ55338 putative DNA-binding protein -
SSUBM407_0505 561071..561250 + 180 CAZ55339 bacteriocin -

Region 3: 1041609..1063814

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SSUBM407_0957 1037077..1037550 - 474 CAZ55811 dihydrofolate reductase -
SSUBM407_0958 1037653..1038678 - 1026 CAZ55812 putative transposase -
SSUBM407_0959 1038786..1039655 - 870 CAZ55813 hypothetical protein -
SSUBM407_0960 1039670..1039894 - 225 CAZ55814 putative DNA-binding protein -
SSUBM407_0960a 1040037..1040117 - 81 Protein_964 DNA recombinase (fragment) -
SSUBM407_0960b 1040118..1040168 + 51 Protein_965 putative membrane protein (fragment) -
SSUBM407_0960c 1040172..1040201 + 30 Protein_966 two-component sensor histidine kinase (fragment) -
SSUBM407_0961 1041609..1042247 + 639 CAZ55819 putative exported protein prgL
SSUBM407_0962 1042286..1043362 + 1077 CAZ55820 DNA primase -
SSUBM407_0963 1043416..1043643 + 228 CAZ55821 hypothetical protein gbs1347
SSUBM407_0964 1043640..1044029 + 390 CAZ55822 hypothetical protein gbs1346
SSUBM407_0965 1044016..1044369 + 354 CAZ55823 hypothetical protein -
SSUBM407_0966 1044439..1044915 + 477 CAZ55824 antidote epsilon protein -
SSUBM407_0967 1044915..1045691 + 777 CAZ55825 zeta-toxin -
SSUBM407_0968 1045688..1047775 + 2088 CAZ55826 hypothetical protein -
SSUBM407_0969 1047762..1049579 + 1818 CAZ55827 DNA helicase -
SSUBM407_0970 1050335..1050649 + 315 CAZ55829 hypothetical protein orf23
SSUBM407_0971 1050665..1051051 + 387 CAZ55830 hypothetical protein orf23
SSUBM407_0972 1051080..1052462 + 1383 CAZ55831 FtsK/SpoIIIE family protein virb4
SSUBM407_0973 1052641..1053846 + 1206 CAZ55832 replication initiation factor -
SSUBM407_0974 1053889..1054110 + 222 CAZ55833 putative membrane protein orf19
SSUBM407_0975 1054227..1054724 + 498 CAZ55834 antirestriction protein -
SSUBM407_0976 1054699..1055205 + 507 CAZ55835 putative membrane protein orf17a
SSUBM407_0977 1055189..1057636 + 2448 CAZ55836 hypothetical protein virb4
SSUBM407_0978 1057639..1061887 + 4249 Protein_986 putative membrane protein (pseudogene) -
SSUBM407_0979 1059554..1060600 + 1047 CAZ55838 putative transposase -
SSUBM407_0980 1060737..1061360 + 624 CAZ55839 chloramphenicol acetyltransferase -
SSUBM407_0981 1061884..1062885 + 1002 CAZ55840 putative exported protein orf14
SSUBM407_0982 1062882..1063814 + 933 CAZ55841 putative membrane protein orf13
SSUBM407_0983 1064191..1066110 + 1920 CAZ55842 tetracycline resistance protein TetM 2 -
SSUBM407_0984 1066304..1067680 + 1377 CAZ55843 tetracycline resistance protein TetL -

Host bacterium

ID   402 Element type   ICE (Integrative and conjugative element)
Element name   ICESsu(BM407)1 GenBank   FM252032
Element size   2146229 bp Coordinate of oriT [Strand]   46148..46280 [-]
Host bacterium   Streptococcus suis BM407 complet Coordinate of element   504649..580365

Cargo genes

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