254780837

254780837

putative restriction endonuclease S subunit

GeneID in NCBI database:8209848Locus tag:CLIBASIA_03660
Protein GI in NCBI database:254780837Protein Accession:YP_003065250.1
Gene range:+(807416, 808696)Protein Length:426aa
Gene description:putative restriction endonuclease S subunit
COG prediction:[V] Restriction endonuclease S subunits
KEGG prediction:putative restriction endonuclease S subunit; K01154 type I restriction enzyme, S subunit [EC:3.1.21.3]
SEED prediction:Type I restriction-modification system, specificity subunit S (EC 3.1.21.3)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Restriction-Modification System;
Type I Restriction-Modification
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420------
MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ
ccccccccccccccccHHcccccccEEEEcccEEEEcccccccccccccEEEEcccccccccEEccccccccccccccEEEccccEEEEEccccccEEEEEccccEEEccEEEEEcccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHccEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHccccccccEEEHHHHcccccccccccccccEEEEEEcccccccccccccccccccccccccccccEEEEEEcccccccccccccccccccccccEEEEccccccHHHHHHHHHcHHHHHHHHHHcccccccccHHHHcccEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEccccc
ccccccccccccccccEccccccccEEEEHHHEEEEEcccccccHHHEEEEccccccHHEEEEEcccccccccccccEEEEccccEEEEEcccccccEEEEccccEEcccEEEEccccccHHHHHHHHHcHHHHHHHHHHccccccccccHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccEccccccccEEEcHHHHHHHcccccccccccccccccccEEEEccccccccccccHccccEEEccccEEEEEcccccccEEEEEEEccccccEcccEEEEccccccHHHHHHHHccHHHHHHHHHHcccccccccHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEccccc
mkhykaypqykdsgvqwigaipkhwkvvpikrftklntgrtsesgkDIIYIGledvesgtgkylpkdgnsrqsdtstvsIFAKGQILYGKLGPYLRKAIIADFdgicstqflvlqpkdvlPELLQGWLLSIDVTQRIEAICEGatmshadwkgignipmpipplaEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTkglnpdvkmkdsgiewvglvpdhwevkpFFALVTELNRKNTKLIESNILSLSYGNIIQKLEtrnmglkpesyetyqivdpgeIVFRFIDlqndkrslRSAQVMERGIITSAYmavkphgidsTYLAWLMRSYDLCKVFYAMgsglrqslkfedvkrlpvlvppikeqfditnVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQidlrgesq
mkhykaypqykdsgvqWIGAIPKHWKVVPIKrftklntgrtsesgkdiiYIGLEDVESGTgkylpkdgnsrqsdtstvsiFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAetvridtliTERIRFIELLKEKKQALVSYIVtkglnpdvkmKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIesnilslsygnIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIItsaymavkphGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPvlvppikeqfditnviNVETARIDVLVEKIEQSIVLLkerrssfiaaavtgqidlrgesq
MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ
****KAY*QYKDSGVQWIGAIPKHWKVVPIKRFTKLNT**********IYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICE*ATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALV***********ESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR****
MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYL************TVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ
*KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR****
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MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ
MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ
MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRGESQ

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target426 putative restriction endonuclease S subunit [Candidatus
152973654438 putative restriction endonuclease S subunit [Klebsiella 1 1e-128
113477871415 restriction modification system DNA specificity subunit 1 5e-77
326201377 631 hypothetical protein Cpap_4212 [Clostridium papyrosolve 1 2e-70
326201377631 hypothetical protein Cpap_4212 [Clostridium papyrosolve 1 4e-09
145631519433 putative type I site-specific restriction-modification 1 3e-63
145629009433 putative type I site-specific restriction-modification 1 9e-63
120601537 438 restriction modification system DNA specificity subunit 1 4e-58
120601537438 restriction modification system DNA specificity subunit 1 2e-36
145642021411 putative type I site-specific restriction-modification 1 5e-57
154508213385 hypothetical protein ACTODO_00707 [Actinomyces odontoly 1 3e-52
>gi|152973654|ref|YP_001338694.1| putative restriction endonuclease S subunit [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] Length = 438 Back     alignment and organism information
 Score =  464 bits (1194), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 249/444 (56%), Positives = 300/444 (67%), Gaps = 27/444 (6%)

Query: 1   MKHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDI-IYIGLEDVESG 59
           M  YKAY  YKDSGV+WIG +P+HW+V  ++     + GR S SG D   Y   + VE  
Sbjct: 1   MSQYKAYTSYKDSGVEWIGQVPEHWEVKRLR-----HVGRYSNSGVDKKSYEDQQTVELC 55

Query: 60  T------GKYLPKDGNSRQSDTSTVSI----FAKGQILYGK-------LGPYLRKAIIAD 102
                   +++  D    Q+  S   I      KG ++  K       +G  +   +  D
Sbjct: 56  NYTDVYYNEFISDDMPFMQATASAHEIEQFTLKKGDVIITKDSEDPSDIG--IPAFVPHD 113

Query: 103 FDGI-CSTQFLVLQP-KDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP 160
             G+ C     +++   D     +   + S            G T    +   IGN P+ 
Sbjct: 114 MPGVVCGYHLTMIRALNDNYGSYIHRSIQSDHTRAHFFVESPGITRYGLNQNTIGNAPVA 173

Query: 161 IPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           +PP  EQ  I   +  ET RID L+ ++IRFIELLKEK+QAL+++ VTKGL+P+VKMKDS
Sbjct: 174 LPPPEEQATIAATLDRETARIDALVEKKIRFIELLKEKRQALITHAVTKGLDPNVKMKDS 233

Query: 221 GIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY 280
           G+EW+G VP+HWEVKPFFALV+ELNRKN  L E+NILSLSYGNIIQK ETRNMGL PESY
Sbjct: 234 GVEWIGQVPEHWEVKPFFALVSELNRKNVGLAETNILSLSYGNIIQKPETRNMGLTPESY 293

Query: 281 ETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY 340
           ETYQIV+ GE+VFRF DLQNDKRSLRSAQV +RGIITSAYMAVKPH I STY AWLMRSY
Sbjct: 294 ETYQIVESGEVVFRFTDLQNDKRSLRSAQVTQRGIITSAYMAVKPHSIGSTYFAWLMRSY 353

Query: 341 DLCKVFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSI 400
           DLCKVFYAMG GLRQSLKFEDV+RLPVL+PP+ EQ +ITN IN  TARID LVEK EQSI
Sbjct: 354 DLCKVFYAMGGGLRQSLKFEDVRRLPVLIPPVGEQSEITNTINAGTARIDALVEKTEQSI 413

Query: 401 VLLKERRSSFIAAAVTGQIDLRGE 424
            LLKERR++FI AAVTGQIDLRG+
Sbjct: 414 TLLKERRAAFITAAVTGQIDLRGK 437


Species: Klebsiella pneumoniae
Genus: Klebsiella
Family: Enterobacteriaceae
Order: Enterobacteriales
Class: Gammaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|113477871|ref|YP_723932.1| restriction modification system DNA specificity subunit [Trichodesmium erythraeum IMS101] Length = 415 Back     alignment and organism information
>gi|326201377|ref|ZP_08191249.1| hypothetical protein Cpap_4212 [Clostridium papyrosolvens DSM 2782] Length = 631 Back     alignment and organism information
>gi|326201377|ref|ZP_08191249.1| hypothetical protein Cpap_4212 [Clostridium papyrosolvens DSM 2782] Length = 631 Back     alignment and organism information
>gi|145631519|ref|ZP_01787287.1| putative type I site-specific restriction-modification system, S subunit [Haemophilus influenzae R3021] Length = 433 Back     alignment and organism information
>gi|145629009|ref|ZP_01784808.1| putative type I site-specific restriction-modification system, S subunit [Haemophilus influenzae 22.1-21] Length = 433 Back     alignment and organism information
>gi|120601537|ref|YP_965937.1| restriction modification system DNA specificity subunit [Desulfovibrio vulgaris DP4] Length = 438 Back     alignment and organism information
>gi|120601537|ref|YP_965937.1| restriction modification system DNA specificity subunit [Desulfovibrio vulgaris DP4] Length = 438 Back     alignment and organism information
>gi|145642021|ref|ZP_01797593.1| putative type I site-specific restriction-modification system, S subunit [Haemophilus influenzae R3021] Length = 411 Back     alignment and organism information
>gi|154508213|ref|ZP_02043855.1| hypothetical protein ACTODO_00707 [Actinomyces odontolyticus ATCC 17982] Length = 385 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target426 putative restriction endonuclease S subunit [Candidatus
pfam01420167 pfam01420, Methylase_S, Type I restriction modification 9e-08
COG0732391 COG0732, HsdS, Restriction endonuclease S subunits [Def 3e-04
PRK09737461 PRK09737, PRK09737, EcoKI restriction-modification syst 2e-06
COG0732391 COG0732, HsdS, Restriction endonuclease S subunits [Def 9e-13
>gnl|CDD|144860 pfam01420, Methylase_S, Type I restriction modification DNA specificity domain Back     alignment and domain information
>gnl|CDD|31076 COG0732, HsdS, Restriction endonuclease S subunits [Defense mechanisms] Back     alignment and domain information
>gnl|CDD|170075 PRK09737, PRK09737, EcoKI restriction-modification system protein HsdS; Provisional Back     alignment and domain information
>gnl|CDD|31076 COG0732, HsdS, Restriction endonuclease S subunits [Defense mechanisms] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 426 putative restriction endonuclease S subunit [Candidatus
PRK09737459 EcoKI restriction-modification system protein HsdS; Pro 100.0
COG0732391 HsdS Restriction endonuclease S subunits [Defense mecha 100.0
PRK09737459 EcoKI restriction-modification system protein HsdS; Pro 100.0
pfam01420167 Methylase_S Type I restriction modification DNA specifi 99.95
COG0732391 HsdS Restriction endonuclease S subunits [Defense mecha 99.7
pfam01420167 Methylase_S Type I restriction modification DNA specifi 99.86
>PRK09737 EcoKI restriction-modification system protein HsdS; Provisional Back     alignment and domain information
>COG0732 HsdS Restriction endonuclease S subunits [Defense mechanisms] Back     alignment and domain information
>PRK09737 EcoKI restriction-modification system protein HsdS; Provisional Back     alignment and domain information
>pfam01420 Methylase_S Type I restriction modification DNA specificity domain Back     alignment and domain information
>COG0732 HsdS Restriction endonuclease S subunits [Defense mechanisms] Back     alignment and domain information
>pfam01420 Methylase_S Type I restriction modification DNA specificity domain Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target426 putative restriction endonuclease S subunit [Candidatus
1yf2_A425 Three-Dimensional Structure Of Dna Sequence Specifi 2e-34
2y7c_A464 Atomic Model Of The Ocr-Bound Methylase Complex Fro 2e-31
1ydx_A406 Crystal Structure Of Type-I Restriction-Modificatio 0.002
1ydx_A 406 Crystal Structure Of Type-I Restriction-Modificatio 8e-05
gi|61680619|pdb|1YF2|A Chain A, Three-Dimensional Structure Of Dna Sequence Specificity (S) Subunit Of A Type I Restriction-Modification Enzyme And Its Functional Implications Length = 425 Back     alignment and structure
 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 72/438 (16%), Positives = 151/438 (34%), Gaps = 42/438 (9%)

Query: 8   PQYKDSGVQWIGAIPKHWKVVPIKRFTK-LNTGRTSE-------SGKDIIYIGLEDVESG 59
             +K +    IG IP+ W++V +K   K +  G T +           I ++ +ED+ + 
Sbjct: 6   ENFKKTE---IGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNS 62

Query: 60  TGKYLPKDGNSRQS--DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK 117
                       +   + S   I  K  +L+   G     A I   +   +   L + PK
Sbjct: 63  NKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETA-INKIEVATNQAILGIIPK 121

Query: 118 DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAE 177
           D + E    + +          +    T  + + + + +  +P+PPL EQ  I + +   
Sbjct: 122 DNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKIL--- 178

Query: 178 TVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPF 237
             +ID  I    + I  L+  K+ L+  ++TKG+      K      +G +P+ WEV   
Sbjct: 179 -TKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKS----EIGEIPEDWEVFEI 233

Query: 238 FALVTELNRKNTKLIESNILSLSYGNIIQ-------------KLETRNMGLKPESYETYQ 284
             +            +S        N I                  R +           
Sbjct: 234 KDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLN 293

Query: 285 IVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSYDLCK 344
           ++  G I+            L       +G             +++ + A+ ++      
Sbjct: 294 LIPKGSIIISTRAPVGYVAVLTVESTFNQGC--KGLFQKNNDSVNTEFYAYYLKFKKNLL 351

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
              + G    + L    ++   + +PP++EQ  I  +++      D  +E  +Q    L+
Sbjct: 352 ENLS-GGSTFKELSKSMLENFKIPLPPLEEQKQIAKILSSV----DKSIELKKQKKEKLQ 406

Query: 405 ERRSSFIAAAVTGQIDLR 422
             +   +   +TG++ ++
Sbjct: 407 RMKKKIMELLLTGKVRVK 424


gi|322812244|pdb|2Y7C|A Chain A, Atomic Model Of The Ocr-Bound Methylase Complex From The Type I Restriction-Modification Enzyme Ecoki (M2s1). Based On Fitting Into Em Map 1534. Length = 464 Back     alignment and structure
>gi|75765536|pdb|1YDX|A Chain A, Crystal Structure Of Type-I Restriction-Modification System S Subunit From M. Genitalium Length = 406 Back     alignment and structure
>gi|75765536|pdb|1YDX|A Chain A, Crystal Structure Of Type-I Restriction-Modification System S Subunit From M. Genitalium Length = 406 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target426 putative restriction endonuclease S subunit [Candidatus
1yf2_A425 Type I restriction-modification enzyme, S subunit; stru 2e-22
1ydx_A406 Type I restriction enzyme specificity protein Mg438; ty 5e-12
1yf2_A425 Type I restriction-modification enzyme, S subunit; stru 4e-11
1ydx_A406 Type I restriction enzyme specificity protein Mg438; ty 8e-07
>1yf2_A Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} SCOP: d.287.1.2 d.287.1.2 Length = 425 Back     alignment and structure
 Score =  102 bits (254), Expect = 2e-22
 Identities = 70/438 (15%), Positives = 157/438 (35%), Gaps = 40/438 (9%)

Query: 7   YPQYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGK-------DIIYIGLEDVES 58
              +K +    IG IP+ W++V +K    K+  G T ++          I ++ +ED+ +
Sbjct: 5   EENFKKT---EIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITN 61

Query: 59  GTGKYLPKDG---NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115
              KYL            + S   I  K  +L+   G     AI             ++ 
Sbjct: 62  S-NKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIP 120

Query: 116 PKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175
             ++L      + +          +    T  + + + + +  +P+PPL EQ  I + + 
Sbjct: 121 KDNILESEFL-YYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILT 179

Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235
                I+ +     +    L+  K+ L+  ++TKG+      K      +G +P+ WEV 
Sbjct: 180 KIDEGIEIIEKSINK----LERIKKGLMHKLLTKGIGHSRFKKSE----IGEIPEDWEVF 231

Query: 236 PFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295
               +            +S        N I  L+   +  K     + + V    +    
Sbjct: 232 EIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCN 291

Query: 296 IDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-----------IDSTYLAWLMRSYDLCK 344
           ++L      + S +     +      +    G           +++ + A+ ++      
Sbjct: 292 LNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLL 351

Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404
              + GS   + L    ++   + +PP++EQ  I  +++     +D  +E  +Q    L+
Sbjct: 352 ENLSGGST-FKELSKSMLENFKIPLPPLEEQKQIAKILS----SVDKSIELKKQKKEKLQ 406

Query: 405 ERRSSFIAAAVTGQIDLR 422
             +   +   +TG++ ++
Sbjct: 407 RMKKKIMELLLTGKVRVK 424


>1ydx_A Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium} SCOP: d.287.1.2 d.287.1.2 Length = 406 Back     alignment and structure
>1yf2_A Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} SCOP: d.287.1.2 d.287.1.2 Length = 425 Back     alignment and structure
>1ydx_A Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium} SCOP: d.287.1.2 d.287.1.2 Length = 406 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target426 putative restriction endonuclease S subunit [Candidatus
1yf2_A425 Type I restriction-modification enzyme, S subunit; stru 100.0
1ydx_A406 Type I restriction enzyme specificity protein Mg438; ty 100.0
1yf2_A425 Type I restriction-modification enzyme, S subunit; stru 99.94
1ydx_A406 Type I restriction enzyme specificity protein Mg438; ty 99.91
2ih2_A421 Modification methylase TAQI; DNA, DNA methyltransferase 92.89
>1yf2_A Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} SCOP: d.287.1.2 d.287.1.2 Back     alignment and structure
Probab=100.00  E-value=0  Score=418.06  Aligned_cols=395  Identities=17%  Similarity=0.264  Sum_probs=290.2

Q ss_pred             CCCCHHHCCCCCCCCCCCCCCCEEEECCCEEEEEE-CCCCCC-------CCCEEEEEEEEEEECCCEEEECCCCC--CCC
Q ss_conf             77880232589962370689886988412399850-667888-------77536887000020641233112222--346
Q gi|254780837|r    4 YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNT-GRTSES-------GKDIIYIGLEDVESGTGKYLPKDGNS--RQS   73 (426)
Q Consensus         4 ~~~~~~~k~s~~~w~g~iP~~We~~kL~~i~~i~~-g~~~~~-------~~~~~~~~~~~i~~~~~~~~~~~~~~--~~~   73 (426)
                      |-+|++||+|+   +|+||+||+++|||+||++.+ |.+|..       +.++++++..++.++...........  ...
T Consensus         2 ~~~~~~~~~~~---~~elP~~W~~~kLgdi~~~i~~g~~p~~~~~~~~~~g~ip~i~~~~i~~~~~~~~~~~~~i~~~~~   78 (425)
T 1yf2_A            2 FYKEENFKKTE---IGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGL   78 (425)
T ss_dssp             EECCCCCBCCS---SSSCBSSCCCEEHHHHEEEEEECCCCCTTCGGGTTTCCEEEECHHHHHTSSSEECCCSEEECHHHH
T ss_pred             CCCCCCCCCCC---CCCCCCCCEEEEHHHHHEEECCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEECCCEEEECHHHH
T ss_conf             88756757798---984798675999479425525787778752101178975899850013687064476089768785


Q ss_pred             CCCCEEEECCCCEEEEEECCCCCEEEEECCCEEEECCEEEECCC--CCCCHHHHHHHCHHHHHHHHHHCCCCCCEEEECH
Q ss_conf             65533784289789994228752379834648990743871466--6787022222111778898883156871666526
Q gi|254780837|r   74 DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPK--DVLPELLQGWLLSIDVTQRIEAICEGATMSHADW  151 (426)
Q Consensus        74 ~~~~~~~~~~gDil~s~~g~~~g~~~i~~~~~~~~~~~~vl~~~--~~~~~fl~y~l~s~~~~~~~~~~~~Gs~~~~i~~  151 (426)
                      .....+.+++||||++++|++ |.+++.+.+++++.+++.++++  ...+.|++|++.+.  ..++...++|+++++|+.
T Consensus        79 ~~~~~~~~~~gdili~~~g~~-G~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~l~s~--~~~~~~~~~g~~~~~i~~  155 (425)
T 1yf2_A           79 NNSNAWIVPKNSVLFAMYGSI-GETAINKIEVATNQAILGIIPKDNILESEFLYYILAKN--KNYYSKLGMQTTQKNLNA  155 (425)
T ss_dssp             HTSSCCCBCTTCEEEECSSST-TCEEEESSCBEECSSEEEEEECTTTCCHHHHHHHHHHT--HHHHHCCSSSSSCCCCCH
T ss_pred             HHCCCEEECCCCEEEEEECCC-CCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHH--HHHHHHHCCCCCCCCCCH
T ss_conf             120317606994899964588-83001134440025159999562115689999998767--888875245775440728


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHCCCCCCCC
Q ss_conf             66344555443323457799999999998887765433322223688999999998607881000235750006868665
Q gi|254780837|r  152 KGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDH  231 (426)
Q Consensus       152 ~~l~~~~iplPpl~eQ~kIv~~Ld~~~~~Id~~I~~~~~~i~~l~e~kqali~~~~tk~L~p~~~~k~s~~e~lG~IP~~  231 (426)
                      ++|.++.||+||++||++||++|+.    +|++|+.++++++.++++++++++++|+++.++....++    .+|++|++
T Consensus       156 ~~l~~~~iplP~l~eQ~~I~~~l~~----~~~~i~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~----~~~~~p~~  227 (425)
T 1yf2_A          156 QIVKSFKIPLPPLEEQKQIAKILTK----IDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKS----EIGEIPED  227 (425)
T ss_dssp             HHHHTCEECCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCCEECC----TTSSEETT
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC----CCCCCCCC
T ss_conf             8882510578887999999998766----767777789899999999999999766423575322322----02579876


Q ss_pred             CCCCCHHHHCCCCCCCCC-----CC-CCCEEEEECCCCCCCCCCC----CCCCEE---CCCCCCCEEECCCCEEEEEECC
Q ss_conf             643302431013456764-----44-4321577404553246532----212100---0443320242288489974216
Q gi|254780837|r  232 WEVKPFFALVTELNRKNT-----KL-IESNILSLSYGNIIQKLET----RNMGLK---PESYETYQIVDPGEIVFRFIDL  298 (426)
Q Consensus       232 W~~~~l~~~~~~~~~~~~-----~~-~~~~~~~~~~~~~~~~~~~----~~~~~~---~~~~~~~~~~~~gdil~~~~~~  298 (426)
                      |++++|++++....+...     ++ ..+.++.+...++......    ......   ......+..+..||++++..+.
T Consensus       228 w~~~~l~~i~~~~~g~~~~~~~~~~~~~g~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gdil~~~~~~  307 (425)
T 1yf2_A          228 WEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAP  307 (425)
T ss_dssp             CEEEEHHHHEEEEECCCCCTTCGGGTTTCCEEEECHHHHHTTTTCSEECCCSSEECHHHHHHTTCCCBCTTCEEEECSSS
T ss_pred             CEEEEHHHEEEEECCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCEECCCCCEEECHHHHCCCCCCCCCCCCEEEEEECC
T ss_conf             44778225699967998875665434678602573133345577504157633412444122332102589889985301


Q ss_pred             CCCEEEEEEECCCCCEEEECH-H-EEC-CCCCCCHHHHHHHHHCHHHHHHHHHH-CCCEEEEECHHHHHCCEECCCCHHH
Q ss_conf             640379995023566077411-1-430-57768868899997098999999862-5840410028898247214898899
Q gi|254780837|r  299 QNDKRSLRSAQVMERGIITSA-Y-MAV-KPHGIDSTYLAWLMRSYDLCKVFYAM-GSGLRQSLKFEDVKRLPVLVPPIKE  374 (426)
Q Consensus       299 ~~~~~~~~~~~~~~~~~~~~~-~-~~~-~~~~~~~~yl~~~l~s~~~~~~~~~~-~~g~~~~i~~~~l~~~~i~lP~lee  374 (426)
                      .+..+.+.     ..+..+.+ . +.. ..+.+++.|++|+|++.  +.++... .++++++|+.++|.+++||+||++|
T Consensus       308 ~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~yl~~~l~~~--~~~~~~~~~gs~~~~i~~~~l~~~~ipiP~~~e  380 (425)
T 1yf2_A          308 VGYVAVLT-----VESTFNQGCKGLFQKNNDSVNTEFYAYYLKFK--KNLLENLSGGSTFKELSKSMLENFKIPLPPLEE  380 (425)
T ss_dssp             TTCEEEES-----SCBEECTTEEEEEESCTTSCCHHHHHHHHHHT--HHHHHHHHCSSSSCCCCHHHHHHCEEEECCHHH
T ss_pred             CCCEEEEE-----CCCCCCEEEEEEEECCCCCCCHHHHHHHHHHH--HHHHHHHCCEECCCEECHHHHCCCEEECCCHHH
T ss_conf             35314531-----13321100134442046644789999999999--999998667013216988994673882879999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECCC
Q ss_conf             9999999999999999999999999999999999977886223361487
Q gi|254780837|r  375 QFDITNVINVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLRG  423 (426)
Q Consensus       375 Q~~I~~~l~~~~~~id~li~~~~~~i~~L~~lk~sLl~~a~tGki~V~~  423 (426)
                      |++|++.++.    ++++++..+++++.|+++|++||++|||||+|||-
T Consensus       381 Q~~I~~~l~~----~~~~i~~~~~~~~~l~~lk~~LL~~~~tGel~v~~  425 (425)
T 1yf2_A          381 QKQIAKILSS----VDKSIELKKQKKEKLQRMKKKIMELLLTGKVRVKT  425 (425)
T ss_dssp             HHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHTTTSCEECC
T ss_pred             HHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEECC
T ss_conf             9999999999----99999999999999999999999998484068509



>1ydx_A Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium} SCOP: d.287.1.2 d.287.1.2 Back     alignment and structure
>1yf2_A Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} SCOP: d.287.1.2 d.287.1.2 Back     alignment and structure
>1ydx_A Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium} SCOP: d.287.1.2 d.287.1.2 Back     alignment and structure
>2ih2_A Modification methylase TAQI; DNA, DNA methyltransferase, target base partner, 5- methylpyrimidin-2(1H)-ONE, base flipping; HET: 5PY 6MA NEA; 1.61A {Thermus aquaticus} SCOP: c.66.1.27 d.287.1.1 PDB: 2ibs_A* 2ibt_A* 2ih4_A* 2ih5_A* 2jg3_A* 2np6_A* 2np7_A* 1aqj_A* 1aqi_A* 2adm_A* 1g38_A* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 426 putative restriction endonuclease S subunit [Candidatus
d1yf2a1220 d.287.1.2 (A:1-220) Bipartite methylase S protein MJ013 2e-11
d1yf2a2205 d.287.1.2 (A:221-425) Bipartite methylase S protein MJ0 1e-09
d1ydxa1193 d.287.1.2 (A:1-193) Bipartite methylase S protein MG438 0.003
d1yf2a1220 d.287.1.2 (A:1-220) Bipartite methylase S protein MJ013 2e-09
d1yf2a2205 d.287.1.2 (A:221-425) Bipartite methylase S protein MJ0 1e-08
>d1yf2a1 d.287.1.2 (A:1-220) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Length = 220 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: DNA methylase specificity domain
superfamily: DNA methylase specificity domain
family: Type I restriction modification DNA specificity domain
domain: Bipartite methylase S protein MJ0130
species: Methanocaldococcus jannaschii [TaxId: 2190]
 Score = 64.4 bits (155), Expect = 2e-11
 Identities = 41/227 (18%), Positives = 85/227 (37%), Gaps = 19/227 (8%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK--------DIIYIGLED 55
           +     +K +    IG IP+ W++V +K   K      +             I ++ +ED
Sbjct: 2   FYKEENFKKT---EIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIED 58

Query: 56  VESGTGKYLPKDGNSRQS--DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLV 113
           + +             +   + S   I  K  +L+   G     AI             +
Sbjct: 59  ITNSNKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGI 118

Query: 114 LQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREK 173
           +   ++L      ++L+ +       +    T  + + + + +  +P+PPL EQ    ++
Sbjct: 119 IPKDNILESEFLYYILAKN-KNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQ----KQ 173

Query: 174 IIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS 220
           I     +ID  I    + I  L+  K+ L+  ++TKG+    + K S
Sbjct: 174 IAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIG-HSRFKKS 219


>d1yf2a2 d.287.1.2 (A:221-425) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Length = 205 Back     information, alignment and structure
>d1ydxa1 d.287.1.2 (A:1-193) Bipartite methylase S protein MG438 {Mycoplasma genitalium [TaxId: 2097]} Length = 193 Back     information, alignment and structure
>d1yf2a1 d.287.1.2 (A:1-220) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Length = 220 Back     information, alignment and structure
>d1yf2a2 d.287.1.2 (A:221-425) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Length = 205 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target426 putative restriction endonuclease S subunit [Candidatus
d1yf2a1220 Bipartite methylase S protein MJ0130 {Methanocaldococcu 100.0
d1yf2a2205 Bipartite methylase S protein MJ0130 {Methanocaldococcu 99.96
d1ydxa2181 Bipartite methylase S protein MG438 {Mycoplasma genital 99.92
d1ydxa1193 Bipartite methylase S protein MG438 {Mycoplasma genital 99.91
d1yf2a1220 Bipartite methylase S protein MJ0130 {Methanocaldococcu 99.95
d1yf2a2205 Bipartite methylase S protein MJ0130 {Methanocaldococcu 99.94
d1ydxa1193 Bipartite methylase S protein MG438 {Mycoplasma genital 99.82
d1ydxa2181 Bipartite methylase S protein MG438 {Mycoplasma genital 99.82
>d1yf2a1 d.287.1.2 (A:1-220) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: DNA methylase specificity domain
superfamily: DNA methylase specificity domain
family: Type I restriction modification DNA specificity domain
domain: Bipartite methylase S protein MJ0130
species: Methanocaldococcus jannaschii [TaxId: 2190]
Probab=100.00  E-value=3.2e-33  Score=222.45  Aligned_cols=207  Identities=22%  Similarity=0.361  Sum_probs=160.4

Q ss_pred             CCCCHHHCCCCCCCCCCCCCCCEEEECCCEEEEE-ECCCCCCC-------CCEEEEEEEEEEECCCEEEECCCCC--CCC
Q ss_conf             7788023258996237068988698841239985-06678887-------7536887000020641233112222--346
Q gi|254780837|r    4 YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLN-TGRTSESG-------KDIIYIGLEDVESGTGKYLPKDGNS--RQS   73 (426)
Q Consensus         4 ~~~~~~~k~s~~~w~g~iP~~We~~kL~~i~~i~-~g~~~~~~-------~~~~~~~~~~i~~~~~~~~~~~~~~--~~~   73 (426)
                      |.++.+||+|+   ||+||++|++++|+++|+.. .|.+|+..       .+++++++.++..+.+.........  ...
T Consensus         2 ~~~~~~~~~se---lg~iP~~W~~~~L~~i~~~i~~g~~p~~~~~~~~~~~~~p~i~~~~i~~~~~~~~~~~~~~~~~~~   78 (220)
T d1yf2a1           2 FYKEENFKKTE---IGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGL   78 (220)
T ss_dssp             EECCCCCBCCS---SSSCBSSCCCEEHHHHEEEEEECCCCCTTCGGGTTTCCEEEECHHHHHTSSSEECCCSEEECHHHH
T ss_pred             CCCCCCCCCCC---CCCCCCCCEEEEHHHHHEEECCCCCCCCCCHHHCCCCCEEEEEECCCCCCCCCCCCCCEEEHHHHH
T ss_conf             87767768897---886899888999489544005885899850431268988999812215532114775166514443


Q ss_pred             CCCCEEEECCCCEEEEEECCCCCEEEEECCCEEEECCEEEECCCC-CCCHHHHHHHCHHHHHHHHHHCCCCCCEEEECHH
Q ss_conf             655337842897899942287523798346489907438714666-7870222221117788988831568716665266
Q gi|254780837|r   74 DTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD-VLPELLQGWLLSIDVTQRIEAICEGATMSHADWK  152 (426)
Q Consensus        74 ~~~~~~~~~~gDil~s~~g~~~g~~~i~~~~~~~~~~~~vl~~~~-~~~~fl~y~l~s~~~~~~~~~~~~Gs~~~~i~~~  152 (426)
                      .....+.++.||||++++|+. |.+++.+.+++++.+++++++.+ ..+.|++||+.+. ...+....+.|+++++|+.+
T Consensus        79 ~~~~~~~~~~gdil~~~~~~~-g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~g~~~~~i~~~  156 (220)
T d1yf2a1          79 NNSNAWIVPKNSVLFAMYGSI-GETAINKIEVATNQAILGIIPKDNILESEFLYYILAK-NKNYYSKLGMQTTQKNLNAQ  156 (220)
T ss_dssp             HTSSCCCBCTTCEEEECSSST-TCEEEESSCBEECSSEEEEEECTTTCCHHHHHHHHHH-THHHHHCCSSSSSCCCCCHH
T ss_pred             HHHHEEEECCCCCCCHHHCCC-HHHHHHCCCCEECCCEEEEECCCCCCHHHHHHHHHHH-HHHHHHHHCCCCCCCCCCHH
T ss_conf             210005504433310110100-1222202331021313798326432125666666401-35788875245551214565


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             63445554433234577999999999988877654333222236889999999986078810002357
Q gi|254780837|r  153 GIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDS  220 (426)
Q Consensus       153 ~l~~~~iplPpl~eQ~kIv~~Ld~~~~~Id~~I~~~~~~i~~l~e~kqali~~~~tk~L~p~~~~k~s  220 (426)
                      +|+++.||+||++||++||++|+    .+|++++.+++.++.|+++|+++++++||++|+ ..+++++
T Consensus       157 ~l~~~~i~iPp~~eQ~~I~~~l~----~i~~~i~~~~~~i~~L~~~r~~ll~~l~tg~l~-~~r~~~~  219 (220)
T d1yf2a1         157 IVKSFKIPLPPLEEQKQIAKILT----KIDEGIEIIEKSINKLERIKKGLMHKLLTKGIG-HSRFKKS  219 (220)
T ss_dssp             HHHTCEECCCCHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSS-CCCEECC
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC-CCCCCCC
T ss_conf             54324652245899999999999----999999999999999999999999998579999-8108999



>d1yf2a2 d.287.1.2 (A:221-425) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1ydxa2 d.287.1.2 (A:194-374) Bipartite methylase S protein MG438 {Mycoplasma genitalium [TaxId: 2097]} Back     information, alignment and structure
>d1ydxa1 d.287.1.2 (A:1-193) Bipartite methylase S protein MG438 {Mycoplasma genitalium [TaxId: 2097]} Back     information, alignment and structure
>d1yf2a1 d.287.1.2 (A:1-220) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1yf2a2 d.287.1.2 (A:221-425) Bipartite methylase S protein MJ0130 {Methanocaldococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1ydxa1 d.287.1.2 (A:1-193) Bipartite methylase S protein MG438 {Mycoplasma genitalium [TaxId: 2097]} Back     information, alignment and structure
>d1ydxa2 d.287.1.2 (A:194-374) Bipartite methylase S protein MG438 {Mycoplasma genitalium [TaxId: 2097]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 426 putative restriction endonuclease S subunit [Candi
1ydx_A_1-164164 (A:1-164) Type I restriction enzyme specificity pr 5e-11
1ydx_A_1-164164 (A:1-164) Type I restriction enzyme specificity pr 2e-06
1yf2_A_1-6_168-211_378-42598 (A:1-6,A:168-211,A:378-425) Type I restriction-mod 2e-08
1yf2_A_1-6_168-211_378-42598 (A:1-6,A:168-211,A:378-425) Type I restriction-mod 1e-06
>1ydx_A (A:1-164) Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium}Length = 164 Back     alignment and structure
 Score = 63.6 bits (154), Expect = 5e-11
 Identities = 28/162 (17%), Positives = 45/162 (27%), Gaps = 16/162 (9%)

Query: 4   YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKY 63
                  K    +       +W    I     L  G   E              +  GKY
Sbjct: 15  GHIDDDDKHXTPKLKLNNNINWTKRTIDSLFDLKKGEXLEKEL----------ITPEGKY 64

Query: 64  LPKDGNSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKD---VL 120
              +G  + S  +      K  I     G       +AD +  C      L   D   + 
Sbjct: 65  EYFNGGVKNSGRTDKFNTFKNTISVIVGG-SCGYVRLADKNFFCGQSNCTLNLLDPLELD 123

Query: 121 PELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIP 162
            +     L S    +RIEA+  G T+ +     +  + +P  
Sbjct: 124 LKFAYYALKSQ--QERIEALAFGTTIQNIRISDLKELEIPFT 163


>1ydx_A (A:1-164) Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium}Length = 164 Back     alignment and structure
>1yf2_A (A:1-6,A:168-211,A:378-425) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661}Length = 98 Back     alignment and structure
>1yf2_A (A:1-6,A:168-211,A:378-425) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661}Length = 98 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target426 putative restriction endonuclease S subunit [Candidatus
1ydx_A_1-164164 Type I restriction enzyme specificity protein Mg43 99.84
1ydx_A_1-164164 Type I restriction enzyme specificity protein Mg43 99.7
1yf2_A_1-6_168-211_378-42598 Type I restriction-modification enzyme, S subunit; 99.59
1yf2_A_1-6_168-211_378-42598 Type I restriction-modification enzyme, S subunit; 99.53
1yf2_A_235-371137 Type I restriction-modification enzyme, S subunit; 99.35
1yf2_A_28-145118 Type I restriction-modification enzyme, S subunit; 98.94
1yf2_A_235-371137 Type I restriction-modification enzyme, S subunit; 98.63
1yf2_A_28-145118 Type I restriction-modification enzyme, S subunit; 98.07
1yf2_A_7-27_146-16743 Type I restriction-modification enzyme, S subunit; 93.49
1yf2_A_212-234_372-37729 Type I restriction-modification enzyme, S subunit; 91.98
>1ydx_A (A:1-164) Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium} Back     alignment and structure
Probab=99.84  E-value=4.8e-21  Score=149.14  Aligned_cols=147  Identities=18%  Similarity=0.129  Sum_probs=113.4

Q ss_pred             CCCCHHHCCCCCCCCCCCCCCCEEEECCCEEEEEECCCCCCCCCEEEEEEEEEEECCCEEEECCCCCCCCCCCCEEEECC
Q ss_conf             77880232589962370689886988412399850667888775368870000206412331122223466553378428
Q gi|254780837|r    4 YKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAK   83 (426)
Q Consensus         4 ~~~~~~~k~s~~~w~g~iP~~We~~kL~~i~~i~~g~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (426)
                      ++.+|.++.+..+|+|++|++|++++|++||++.+|.+++...-          ...+.+..............++.+++
T Consensus        15 ~~~~~~~~~~~~~~~~~~p~~We~~~L~~i~~~~~g~~~~~~~~----------~~~g~~~~~~~~~~~~~~~~~~~~~~   84 (164)
T 1ydx_A           15 GHIDDDDKHXTPKLKLNNNINWTKRTIDSLFDLKKGEXLEKELI----------TPEGKYEYFNGGVKNSGRTDKFNTFK   84 (164)
T ss_dssp             ---------CCCSSCSSSSCCCEEEEHHHHEEEEECCCCCGGGC----------CTTCSEEEESSSSSCSCEESCCCBCS
T ss_pred             CCCCCCCCCCCCCEECCCCCCCEEEECCEEEEEECCCCCCCCCC----------CCCCCEEEEECCCCCCEEEEEEECCC
T ss_conf             34475300168726579999988999100999977988870303----------46887799976773045986763259


Q ss_pred             CCEEEEEECCCCCEEEEECCCEEEECCE--EEECCC-CCCCHHHHHHHCHHHHHHHHHHCCCCCCEEEECHHHHHHHHHH
Q ss_conf             9789994228752379834648990743--871466-6787022222111778898883156871666526663445554
Q gi|254780837|r   84 GQILYGKLGPYLRKAIIADFDGICSTQF--LVLQPK-DVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMP  160 (426)
Q Consensus        84 gDil~s~~g~~~g~~~i~~~~~~~~~~~--~vl~~~-~~~~~fl~y~l~s~~~~~~~~~~~~Gs~~~~i~~~~l~~~~ip  160 (426)
                      ||+|++++|+.+.++.. +.++.+..+.  ++++++ .+++.||+|+|++  ++.++...++|+++++|+.++|++++||
T Consensus        85 gdil~~~~g~~g~~~~~-~~~~~~~~~~~~~~~~~~~~i~~~yl~~~l~s--~~~~i~~~~~G~~~~~i~~~~l~~~~i~  161 (164)
T 1ydx_A           85 NTISVIVGGSCGYVRLA-DKNFFCGQSNCTLNLLDPLELDLKFAYYALKS--QQERIEALAFGTTIQNIRISDLKELEIP  161 (164)
T ss_dssp             SCEEEECBSSTTCEEEC-SSCBEECTTEEEEEESCTTTSCHHHHHHHHHT--THHHHHTTCBCSSSCBCCHHHHHHCEEE
T ss_pred             CEEEEECCCCCEEEEEE-CCCCCCCCCEEEEEECCCHHCCHHHCCCCCCC--HHHHHHHHCCCCCCCCCCHHHHHHHHHH
T ss_conf             81999856664279995-67731125529999777122287240110013--5899875405888885257676543220


Q ss_pred             HHH
Q ss_conf             433
Q gi|254780837|r  161 IPP  163 (426)
Q Consensus       161 lPp  163 (426)
                      +|+
T Consensus       162 iPS  164 (164)
T 1ydx_A          162 FTS  164 (164)
T ss_dssp             ECC
T ss_pred             HCC
T ss_conf             112



>1ydx_A (A:1-164) Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium} Back     alignment and structure
>1yf2_A (A:1-6,A:168-211,A:378-425) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure
>1yf2_A (A:1-6,A:168-211,A:378-425) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure
>1yf2_A (A:235-371) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure
>1yf2_A (A:28-145) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure
>1yf2_A (A:235-371) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure
>1yf2_A (A:28-145) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure
>1yf2_A (A:7-27,A:146-167) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure
>1yf2_A (A:212-234,A:372-377) Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} Back     alignment and structure