Citrus Sinensis ID: 005942

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------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-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------67

MDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSSRDDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAGHGNRMNSENVHNREEENSGVHGPWGQNGAEAALLSAEKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLGPGGVPSQMNLPVVAPSMVNNNIGNNRPQVMSASSSQPSIPGYSANQPVHPHMQFRPQQMFPLGQRMPLTSLQASSSAPSNVMFNARGGPQPTLNHPMIRSASGTSSGLG

ccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHHHcccccEEEHHHHHcccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccEEEccccccccccHHHHHcccccccccccccEEccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

cHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccEEccccEEEEcccccHcccccHHHHHHHHcHHHHccccccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHcccEEEEEcccccccccccccccccccccEEEEcccccccccccccccccccccccccccHHHHccccccccHHHHHHHccccccccccccccEEEcccccccccccHHHHHccccccccccHHcEEccccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHcccHHHHccccccHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccc

MDIVAIEAAYLagdasgrsSAVALENisfgqlqalsvvpadsaaldpersdtscvitppqimegkgvvkrfgsrvhvlpmhsdwfspdtvhrlerqvvphffsgkspdhtpekYMECRNHIVAKymdnpekrlivsdcqglvdgvspeDLTRIFRFLNHWGIINYCaavqspepwnrgsylredsngevsvpsdaLKSIDSlikfdkpkcslkvadvyssscggadffdldNTIRERLSenhcnycsqpipavyyqsqkevdvllcpecfhegrfvtghssldyirvdpareygdidgetwsDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVrlpmedgilenvevpntsrtsnsssrddrgglhstvngdlpgaglqeadmenrlpfsnsgnPVMALVAFLASAVGPRVAAACAHASLAALSKQmegaghgnrmnsenvhnreeensgvhgpwgqngAEAALLSAEKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIvstrlgpggvpsqmnlpvvapsmvnnnignnrpqvmsasssqpsipgysanqpvhphmqfrpqqmfplgqrmpltslqasssapsnvmfnarggpqptlnhpmirsasgtssglg

MDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAaldpersdtscvitppqimegkgvVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHffsgkspdhtpeKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGrfvtghssldyiRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENvevpntsrtsnsssrddrgglhSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAGHGNRMNSENVHNREEENSGVHGPWGQNGAEAALLSAEKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKArqrfatertrivstrlgpggvpsqMNLPVVAPSMVNNNIGNNRPQVMSASSSQPSIPGYSANQPVHPHMQFRPQQMFPLGQRMPLTSLQASSSAPSNVMFNARGgpqptlnhpmirsasgtssglg

MDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPntsrtsnsssrddrGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVaaacahaslaalsKQMEGAGHGNRMNSENVHNREEENSGVHGPWGQNGaeaallsaekvkaaakaglaaaatkaklfaDHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLGPGGVPSQMNLPVVAPSMVNNNIGNNRPQVMSASSSQPSIPGYSANQPVHPHMQFRPQQMFPLGQRMPLTSLQASSSAPSNVMFNARGGPQPTLNHPMIRSASGTSSGLG

***VAIEAAYLAGD******AVALENISFGQLQALSVV***************CVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFS*********KYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPW**********************SIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILEN**************************************************PVMALVAFLASAVGPRVAAACAHASLA*****************************************************KAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKA**RFA*****I*******************************************************************************************************************

**************************************************************************VHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS**************************************CSLKVAD******************RERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEG**********************I*GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILEN*********************************************************************************************************************************************************RLSANIINHQLKRLELKLKQFAEVETLLMREC*********FATERTRI*******************************************************************************************************************

MDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPAD**********TSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVP***************GLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAGHGNRMNSENV**********HGPWGQNGAEAALLSAEK*************TKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLGPGGVPSQMNLPVVAPSMVNNNIGNNRP************PGYSANQPVHPHMQFRPQQMFPLGQRMPLTSLQASSSAPSNVMFNARGGPQPTLNHPMIRS*********

MD***IEAAYL******************************************************GVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKF***********************DLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDP********GETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILE******************************************RLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAG************************************EKVKAAAKAGLAAA***AKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLG**********************************************P*HPHMQFRPQQMFPLGQRMPLT*L**************************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSSRDDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAGHGNRMNSENVHNREEENSGVHGPWGQNGAEAALLSAEKVKAAAKAGLAAAATKAKLFxxxxxxxxxxxxxxxxxxxxxRLELKLKQFAEVETLLMRECEQVEKARQRFATERTRIVSTRLGPGGVPSQMNLPVVAPSMVNNNIGNNRPQVMSASSSQPSIPGYSANQPVHPHMQFRPQQMFPLGQRMPLTSLQASSSAPSNVMFNARGGPQPTLNHPMIRSASGTSSGLG

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		668	2.2.26 [Sep-21-2011]
Q9XI07		807	SWI/SNF complex subunit S	yes	no	0.967	0.800	0.587	0.0
O14470		503	SWI/SNF and RSC complexes	yes	no	0.568	0.755	0.266	2e-37
Q8VY05		985	SWI/SNF complex subunit S	no	no	0.440	0.298	0.358	4e-36
Q8W475		512	SWI/SNF complex subunit S	no	no	0.673	0.878	0.258	9e-32
O13788		527	SWI/SNF and RSC complexes	no	no	0.609	0.772	0.247	2e-30
Q84JG2		469	SWI/SNF complex subunit S	no	no	0.597	0.850	0.238	6e-29
P43609		557	Chromatin structure-remod	yes	no	0.420	0.504	0.286	9e-28
Q54J55		1620	Myb-like protein X OS=Dic	no	no	0.270	0.111	0.288	7e-18
Q6PDG5		1213	SWI/SNF complex subunit S	yes	no	0.136	0.075	0.404	4e-17
Q8TAQ2		1214	SWI/SNF complex subunit S	yes	no	0.136	0.074	0.404	5e-17

>sp\|Q9XI07\|SWI3C_ARATH SWI/SNF complex subunit SWI3C OS=Arabidopsis thaliana GN=SWI3C PE=1 SV=1	Back alignment and function desciption

 Score =  760 bits (1962), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 415/706 (58%), Positives = 498/706 (70%), Gaps = 60/706 (8%)

Query: 1   MDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSC---VIT 57
           M +VA E A L G+  G+ S  ALENISFGQLQALS VPADS  LD ERSD S    VI+
Sbjct: 100 MAVVAAERAGLIGETRGQGSLPALENISFGQLQALSTVPADS--LDLERSDGSSSAYVIS 157

Query: 58  PPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMEC 117
           PP IM+G+GVVKRFG  VHVLPMHSDWF+P+TV RLERQVVP FFSGKSP+HTPE YME 
Sbjct: 158 PPPIMDGEGVVKRFGDLVHVLPMHSDWFAPNTVDRLERQVVPQFFSGKSPNHTPESYMEF 217

Query: 118 RNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEPWN 176
           RN IV+KY++NPEK L +SDCQGLVDGV  ED  R+FRFL+HWGIINYCA  QS P P  
Sbjct: 218 RNAIVSKYVENPEKTLTISDCQGLVDGVDIEDFARVFRFLDHWGIINYCATAQSHPGPLR 277

Query: 177 RGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSS--SCGGADFFDLDNTI 234
             S +RED+NGEV+VPS AL SIDSLIKFDKP C  K  +VYSS  S  G D  DLD  I
Sbjct: 278 DVSDVREDTNGEVNVPSAALTSIDSLIKFDKPNCRHKGGEVYSSLPSLDG-DSPDLDIRI 336

Query: 235 RERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYG 294
           RE L ++HCN+CS+P+P VY+QSQK+ D+LLC +CFH GRFV GHS LD++RVDP + YG
Sbjct: 337 REHLCDSHCNHCSRPLPTVYFQSQKKGDILLCCDCFHHGRFVVGHSCLDFVRVDPMKFYG 396

Query: 295 DIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEV 354
           D DG+ W+DQET LLLE +E+YN+NW +IA+HV +KSKAQCILHF+RLP+EDG+L+NVEV
Sbjct: 397 DQDGDNWTDQETLLLLEAVELYNENWVQIADHVGSKSKAQCILHFLRLPVEDGLLDNVEV 456

Query: 355 PNTSRTSNSSSRDDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAV 414
              + T N ++  D  G  S  NGDLPG   Q +D E +LPF  S NPVMALVAFLASAV
Sbjct: 457 SGVTNTENPTNGYDHKGTDS--NGDLPGYSEQGSDTEIKLPFVKSPNPVMALVAFLASAV 514

Query: 415 GPRVAAACAHASLAALSKQMEGAGHGNRMNSENVHNRE--------EENSGVHGPWGQNG 466
           GPRVAA+CAH SL+ LS+        +RM SE +  +E        ++  G H    QNG
Sbjct: 515 GPRVAASCAHESLSVLSED-------DRMKSEGMQGKEASLLDGENQQQDGAHKTSSQNG 567

Query: 467 AEAAL-LSAEKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQF 525
           AEA   L  +KV AA +AGL+AAATKAKLFADHEEREIQRLSANI+NHQLKR+ELKLKQF
Sbjct: 568 AEAQTPLPQDKVMAAFRAGLSAAATKAKLFADHEEREIQRLSANIVNHQLKRMELKLKQF 627

Query: 526 AEVETLLMRECEQVEKARQRFATERTRIVSTRLG-PGGV-PSQMNLPVVAPSMVNNNIGN 583
           AE+ETLLM+ECEQVEK RQRF+ ER R++S R G PGG+ P   NL  ++ S   NNI +
Sbjct: 628 AEIETLLMKECEQVEKTRQRFSAERARMLSARFGSPGGISPQTNNLQGMSLSTGGNNINS 687

Query: 584 ----NRPQVMSASSSQPS-IPGYSANQPVHPHMQFRPQQM-------------FPLGQRM 625
                  Q  ++++SQPS IPG+S N  V   M F  +Q              F  G R+
Sbjct: 688 LMHQQHQQQQASATSQPSIIPGFSNNPQVQAQMHFMARQQQQQQQQQQQQQQAFSFGPRL 747

Query: 626 PLTSLQ--ASSSAPSNVMF--NARGGP---------QPTLNHPMIR 658
           PL ++Q  A S+A  NVMF  N    P         QP+ +HPM+R
Sbjct: 748 PLNAIQTNAGSTASPNVMFGNNQLNNPAAAGAASINQPSFSHPMVR 793

Component of a multiprotein complex equivalent of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors.
Arabidopsis thaliana (taxid: 3702)

>sp\|O14470\|SSR2_SCHPO SWI/SNF and RSC complexes subunit ssr2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ssr2 PE=1 SV=3	Back alignment and function description

>sp\|Q8VY05\|SWI3D_ARATH SWI/SNF complex subunit SWI3D OS=Arabidopsis thaliana GN=SWI3D PE=1 SV=3	Back alignment and function description

>sp\|Q8W475\|SWI3A_ARATH SWI/SNF complex subunit SWI3A OS=Arabidopsis thaliana GN=SWI3A PE=1 SV=1	Back alignment and function description

>sp\|O13788\|SSR1_SCHPO SWI/SNF and RSC complexes subunit ssr1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ssr1 PE=1 SV=1	Back alignment and function description

>sp\|Q84JG2\|SWI3B_ARATH SWI/SNF complex subunit SWI3B OS=Arabidopsis thaliana GN=SWI3B PE=1 SV=1	Back alignment and function description

>sp\|P43609\|RSC8_YEAST Chromatin structure-remodeling complex protein RSC8 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RSC8 PE=1 SV=1	Back alignment and function description

>sp\|Q54J55\|MYBX_DICDI Myb-like protein X OS=Dictyostelium discoideum GN=mybX PE=3 SV=1	Back alignment and function description

>sp\|Q6PDG5\|SMRC2_MOUSE SWI/SNF complex subunit SMARCC2 OS=Mus musculus GN=Smarcc2 PE=1 SV=2	Back alignment and function description

>sp\|Q8TAQ2\|SMRC2_HUMAN SWI/SNF complex subunit SMARCC2 OS=Homo sapiens GN=SMARCC2 PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		668
302141785		675	unnamed protein product [Vitis vinifera]	0.965	0.955	0.693	0.0
224082324		796	chromatin remodeling complex subunit [Po	0.980	0.822	0.696	0.0
359492375		771	PREDICTED: SWI/SNF complex subunit SWI3C	0.967	0.837	0.678	0.0
449449761		815	PREDICTED: SWI/SNF complex subunit SWI3C	1.0	0.819	0.630	0.0
356507640		785	PREDICTED: SWI/SNF complex subunit SWI3C	0.979	0.833	0.640	0.0
356518555		785	PREDICTED: SWI/SNF complex subunit SWI3C	0.989	0.842	0.642	0.0
449500660		779	PREDICTED: LOW QUALITY PROTEIN: SWI/SNF	0.977	0.838	0.630	0.0
255558620		771	DNA binding protein, putative [Ricinus c	0.941	0.815	0.632	0.0
356547495		761	PREDICTED: SWI/SNF complex subunit SWI3C	0.958	0.840	0.622	0.0
15219067		807	SWI/SNF complex subunit SWI3C [Arabidops	0.967	0.800	0.587	0.0

>gi\|302141785\|emb\|CBI18988.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  897 bits (2318), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 467/673 (69%), Positives = 535/673 (79%), Gaps = 28/673 (4%)

Query: 24  LENISFGQLQALSVVPADSAAL---DPERSDTS-CVITPPQIMEGKGVVKRF-GSRVHVL 78
           LENIS GQLQALS VPADS +L   D ERSD    V+ PPQIMEG+GV+KRF   RVH +
Sbjct: 3   LENISHGQLQALSAVPADSPSLATSDQERSDGGGYVVAPPQIMEGRGVIKRFWNGRVHAV 62

Query: 79  PMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDC 138
           PMHSDWFSP+TVHRLERQVVPHFFSGKSPDHT E YMECRN IVAKYM++PEKRL VSDC
Sbjct: 63  PMHSDWFSPNTVHRLERQVVPHFFSGKSPDHTAELYMECRNLIVAKYMEDPEKRLSVSDC 122

Query: 139 QGLVDGVSPEDLTRIFRFLNHWGIINYCAA-VQSPEPWNRGSYLREDSNGEVSVPSDALK 197
           +GLV G+  EDLTRI RFL+HWGIINYCA+ V + EPW+  SYLREDSNGEV VPS ALK
Sbjct: 123 KGLVAGIQEEDLTRIVRFLDHWGIINYCASSVPNREPWSSTSYLREDSNGEVHVPSAALK 182

Query: 198 SIDSLIKFDKPKCSLKVADVYSS-SCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQ 256
           SIDSLIKFDKPKC LK A+VYSS SC G +  DLD  IRERLS+N CNYCS+P+P  YYQ
Sbjct: 183 SIDSLIKFDKPKCRLKAAEVYSSLSCNGDEDSDLDCKIRERLSDNRCNYCSRPLPIGYYQ 242

Query: 257 SQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGETWSDQETFLLLEGIEMY 316
           SQKEVDV+LC +CF+EGRFVTGHSS+D+IR+D  ++YGDID E+WSDQET LLLE +E Y
Sbjct: 243 SQKEVDVMLCTDCFYEGRFVTGHSSIDFIRLDSTKDYGDIDSESWSDQETLLLLEAMESY 302

Query: 317 NDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSSRDDRGGLHSTV 376
           N+NWN+IAEHV TKSKAQCILHF+R+PMEDG+LEN+EVP+    SNS ++ D+   HS  
Sbjct: 303 NENWNDIAEHVGTKSKAQCILHFIRMPMEDGLLENIEVPSMPTLSNSLNKVDQERSHSNS 362

Query: 377 NGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQM-- 434
           NG+L G+ L   D ++RLPF+NSGNPVM++VAFLA+AVGPRVAAACAHASL ALS++   
Sbjct: 363 NGNLAGSCLPGLDSDSRLPFANSGNPVMSMVAFLATAVGPRVAAACAHASLIALSEENAL 422

Query: 435 ----------EGAGHGNRMNSENVH-------NREEENSGVHGPWGQNGAEAALLSAEKV 477
                     EG+GHGNRM     H         ++ N  + G WGQN AE A L  EKV
Sbjct: 423 AAASGFIIPPEGSGHGNRMKEGGPHGELTNSSQHQDGNIAIQGSWGQNDAEVASLPVEKV 482

Query: 478 KAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRECE 537
           +AAAKAGLAAAA KAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLM+ECE
Sbjct: 483 RAAAKAGLAAAAMKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMKECE 542

Query: 538 QVEKARQRFATERTRIVSTRLGPGGVPSQMNLPVVAPSMVNNNIGNNRPQVMSASSSQPS 597
           QVE+ARQRFA ER RI+STR GP GV S MNLP VAP++V+NN GNNR Q++SAS SQPS
Sbjct: 543 QVERARQRFAAERARIISTRFGPTGVTSPMNLPGVAPALVSNNTGNNRQQIISASPSQPS 602

Query: 598 IPGYSANQPVHPHMQFRPQQ-MFPLGQRMPLTSLQASSSAPS-NVMFNARGGPQPTLNHP 655
           I GY  NQ +HPHM F P+Q MF  G R+PL ++Q SSS PS N MFN  G  QPTLNHP
Sbjct: 603 ISGYGNNQQMHPHMSFMPRQPMFSFGPRLPLAAIQPSSSTPSPNAMFNNSGNSQPTLNHP 662

Query: 656 MIRSASGTSSGLG 668
           M+R  SGTSSGLG
Sbjct: 663 MMRPVSGTSSGLG 675

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224082324\|ref\|XP_002306648.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222856097\|gb\|EEE93644.1\| chromatin remodeling complex subunit [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|359492375\|ref\|XP_002284548.2\| PREDICTED: SWI/SNF complex subunit SWI3C-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449449761\|ref\|XP_004142633.1\| PREDICTED: SWI/SNF complex subunit SWI3C-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356507640\|ref\|XP_003522572.1\| PREDICTED: SWI/SNF complex subunit SWI3C-like [Glycine max]	Back alignment and taxonomy information

>gi\|356518555\|ref\|XP_003527944.1\| PREDICTED: SWI/SNF complex subunit SWI3C-like [Glycine max]	Back alignment and taxonomy information

>gi\|449500660\|ref\|XP_004161161.1\| PREDICTED: LOW QUALITY PROTEIN: SWI/SNF complex subunit SWI3C-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|255558620\|ref\|XP_002520335.1\| DNA binding protein, putative [Ricinus communis] gi\|223540554\|gb\|EEF42121.1\| DNA binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|356547495\|ref\|XP_003542147.1\| PREDICTED: SWI/SNF complex subunit SWI3C [Glycine max]	Back alignment and taxonomy information

>gi|15219067|ref|NP_173589.1| SWI/SNF complex subunit SWI3C [Arabidopsis thaliana] gi|75315301|sp|Q9XI07.1|SWI3C_ARATH RecName: Full=SWI/SNF complex subunit SWI3C; Short=AtSWI3C; AltName: Full=Transcription regulatory protein SWI3C gi|5263321|gb|AAD41423.1|AC007727_12 Contains similarity to gb|AF033823 moira protein from Drosophila melanogaster and contains a PF|00249 Myb-like DNA-binding domain. EST gb|Z25609 comes from this gene [Arabidopsis thaliana] gi|20259454|gb|AAM13847.1| putative transcriptional regulatory protein [Arabidopsis thaliana] gi|21436147|gb|AAM51320.1| putative transcriptional regulatory protein [Arabidopsis thaliana] gi|332192023|gb|AEE30144.1| SWI/SNF complex subunit SWI3C [Arabidopsis thaliana]

Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		668
TAIR\|locus:2036942		807	SWI3C "SWITCH/sucrose nonferme	0.965	0.799	0.547	5.9e-187
ZFIN\|ZDB-GENE-080514-3		1089	smarcc1a "SWI/SNF related, mat	0.086	0.053	0.534	2.3e-40
UNIPROTKB\|E2REF0		1107	SMARCC1 "Uncharacterized prote	0.101	0.061	0.5	3.3e-40
UNIPROTKB\|F1P1A8		1035	F1P1A8 "Uncharacterized protei	0.101	0.065	0.5	4.8e-40
UNIPROTKB\|F1MYU1		952	SMARCC1 "Uncharacterized prote	0.101	0.071	0.5	1.6e-39
UNIPROTKB\|Q92922		1105	SMARCC1 "SWI/SNF complex subun	0.101	0.061	0.5	3.5e-39
UNIPROTKB\|G3N0H4		925	SMARCC1 "Uncharacterized prote	0.101	0.073	0.5	3.6e-39
MGI\|MGI:1203524		1104	Smarcc1 "SWI/SNF related, matr	0.101	0.061	0.5	5.7e-39
UNIPROTKB\|I3LRY4		1212	I3LRY4 "Uncharacterized protei	0.079	0.043	0.566	1.2e-38
MGI\|MGI:1915344		1213	Smarcc2 "SWI/SNF related, matr	0.079	0.043	0.566	1.2e-38

TAIR\|locus:2036942 SWI3C "SWITCH/sucrose nonfermenting 3C" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1720 (610.5 bits), Expect = 5.9e-187, Sum P(2) = 5.9e-187
 Identities = 368/672 (54%), Positives = 442/672 (65%)

Query:     1 MDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSC---VIT 57
             M +VA E A L G+  G+ S  ALENISFGQLQALS VPADS  LD ERSD S    VI+
Sbjct:   100 MAVVAAERAGLIGETRGQGSLPALENISFGQLQALSTVPADS--LDLERSDGSSSAYVIS 157

Query:    58 PPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMEC 117
             PP IM+G+GVVKRFG  VHVLPMHSDWF+P+TV RLERQVVP FFSGKSP+HTPE YME 
Sbjct:   158 PPPIMDGEGVVKRFGDLVHVLPMHSDWFAPNTVDRLERQVVPQFFSGKSPNHTPESYMEF 217

Query:   118 RNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEPWN 176
             RN IV+KY++NPEK L +SDCQGLVDGV  ED  R+FRFL+HWGIINYCA  QS P P  
Sbjct:   218 RNAIVSKYVENPEKTLTISDCQGLVDGVDIEDFARVFRFLDHWGIINYCATAQSHPGPLR 277

Query:   177 RGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSS--SCGGADFFDLDNTI 234
               S +RED+NGEV+VPS AL SIDSLIKFDKP C  K  +VYSS  S  G D  DLD  I
Sbjct:   278 DVSDVREDTNGEVNVPSAALTSIDSLIKFDKPNCRHKGGEVYSSLPSLDG-DSPDLDIRI 336

Query:   235 RERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYG 294
             RE L ++HCN+CS+P+P VY+QSQK+ D+LLC +CFH GRFV GHS LD++RVDP + YG
Sbjct:   337 REHLCDSHCNHCSRPLPTVYFQSQKKGDILLCCDCFHHGRFVVGHSCLDFVRVDPMKFYG 396

Query:   295 DIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEV 354
             D DG+ W+DQET LLLE +E+YN+NW +IA+HV +KSKAQCILHF+RLP+EDG+L+NVEV
Sbjct:   397 DQDGDNWTDQETLLLLEAVELYNENWVQIADHVGSKSKAQCILHFLRLPVEDGLLDNVEV 456

Query:   355 PXXXXXXXXXXXXXXGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAV 414
                             G  S  NGDLPG   Q +D E +LPF  S NPVMALVAFLASAV
Sbjct:   457 SGVTNTENPTNGYDHKGTDS--NGDLPGYSEQGSDTEIKLPFVKSPNPVMALVAFLASAV 514

Query:   415 GPRVXXXXXXXXXXXXXK--QMEGAG-HGNRMNSENVHNREEENSGVHGPWGQNGXXXXX 471
             GPRV             +  +M+  G  G   +  +  N++++  G H    QNG     
Sbjct:   515 GPRVAASCAHESLSVLSEDDRMKSEGMQGKEASLLDGENQQQD--GAHKTSSQNGAEAQT 572

Query:   472 XX-XXXXXXXXXXXXXXXXXXXXXXXDHEEREIQRLSANIINHQLKRLELKLKQFAEVET 530
                                       DHEEREIQRLSANI+NHQLKR+ELKLKQFAE+ET
Sbjct:   573 PLPQDKVMAAFRAGLSAAATKAKLFADHEEREIQRLSANIVNHQLKRMELKLKQFAEIET 632

Query:   531 LLMRECEQVEKARQRFATERTRIVSTRLG-PGGV-PSQMNLPVVAPSMVNNNIGN----N 584
             LLM+ECEQVEK RQRF+ ER R++S R G PGG+ P   NL  ++ S   NNI +     
Sbjct:   633 LLMKECEQVEKTRQRFSAERARMLSARFGSPGGISPQTNNLQGMSLSTGGNNINSLMHQQ 692

Query:   585 RPQVMSASSSQPSI-PGYSANQPVHPHMQF--RPQQMFPLGQRMPLTSLQASSSAPSN-V 640
               Q  ++++SQPSI PG+S N  V   M F  R QQ     Q+    +       P N +
Sbjct:   693 HQQQQASATSQPSIIPGFSNNPQVQAQMHFMARQQQQQQQQQQQQQQAFSFGPRLPLNAI 752

Query:   641 MFNARGGPQPTL 652
               NA     P +
Sbjct:   753 QTNAGSTASPNV 764

GO:0003677 "DNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0006338 "chromatin remodeling" evidence=ISS

GO:0016514 "SWI/SNF complex" evidence=ISS

GO:0007062 "sister chromatid cohesion" evidence=RCA

GO:0031048 "chromatin silencing by small RNA" evidence=RCA

GO:0040029 "regulation of gene expression, epigenetic" evidence=RCA

GO:0045132 "meiotic chromosome segregation" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

ZFIN\|ZDB-GENE-080514-3 smarcc1a "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1a" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|E2REF0 SMARCC1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1P1A8 F1P1A8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MYU1 SMARCC1 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q92922 SMARCC1 "SWI/SNF complex subunit SMARCC1" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|G3N0H4 SMARCC1 "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

MGI\|MGI:1203524 Smarcc1 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LRY4 I3LRY4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

MGI\|MGI:1915344 Smarcc2 "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9XI07	SWI3C_ARATH	No assigned EC number	0.5878	0.9670	0.8004	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00015425001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (726 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00026891001	SubName- Full=Chromosome chr15 scaffold_40, whole genome shotgun sequence; (2105 aa)	•	•		0.701
	GSVIVG00002934001	SubName- Full=Chromosome chr18 scaffold_137, whole genome shotgun sequence; (486 aa)	•	•	•	0.412

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		668
COG5259		531	COG5259, RSC8, RSC chromatin remodeling complex su	5e-59
pfam04433		80	pfam04433, SWIRM, SWIRM domain	9e-21
cd02336		45	cd02336, ZZ_RSC8, Zinc finger, ZZ type	8e-09
smart00717		49	smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIII	1e-08
cd00167		45	cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-	2e-08
pfam00249		47	pfam00249, Myb_DNA-binding, Myb-like DNA-binding d	2e-08
COG5114		432	COG5114, COG5114, Histone acetyltransferase comple	5e-07
pfam13921		59	pfam13921, Myb_DNA-bind_6, Myb-like DNA-binding do	6e-06
smart00291		44	smart00291, ZnF_ZZ, Zinc-binding domain, present i	4e-05
pfam02841		297	pfam02841, GBP_C, Guanylate-binding protein, C-ter	0.004

>gnl\|CDD\|227584 COG5259, RSC8, RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]	Back alignment and domain information

 Score =  207 bits (527), Expect = 5e-59
 Identities = 132/475 (27%), Positives = 202/475 (42%), Gaps = 92/475 (19%)

Query: 77  VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 136
           ++P +++WF    +H +E++  P FF+G+SP  TPE Y + RN ++  Y  NP + L V+
Sbjct: 53  IIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVT 112

Query: 137 DCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDAL 196
            C+  V G     + R+ RFL  WG+INY       +P  R S +            D  
Sbjct: 113 ACRRNVAGDVAA-IVRVHRFLEKWGLINY-----QVDPGTRPSTIGPPLTSHFQDLHDTP 166

Query: 197 ---------KSIDSLI-KFDKPKCSLKVADVYSSS------CGGADFFDLDNTIRERLSE 240
                      I+  +    + +      + YS S             +L +        
Sbjct: 167 RGLSPFLPWGPINQRVLGAKEIEYETHKEENYSPSLKSPKKESQGKVDELKDHS--EKHP 224

Query: 241 NHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPAREYGDIDGET 300
           + C+ C        Y + +      C EC+ +GRF +  +S D+  V        I  + 
Sbjct: 225 SSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVT---ISLLIRDKN 281

Query: 301 WSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRT 360
           WS QE  LLLEGIEMY D+W+++A HV TK+K QCILHF++LP+ED              
Sbjct: 282 WSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIED-------------- 327

Query: 361 SNSSSRDDRGGLHSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAA 420
            N  S+ D  G +S                  RLPF  S NPV++ ++FLA  V PRV +
Sbjct: 328 -NYLSKGDGKGDNSKG----------------RLPFDGSENPVLSTISFLAGIVNPRVQS 370

Query: 421 ACAHASLAALSKQMEGAGHGNRMNSENVHNREEENSGVHGPWGQNGAEAALLSAEKVKAA 480
               A +    K  +           +  NRE +                          
Sbjct: 371 EKQRAII----KSGK----------ISHINRESQEHIEEV-------------------- 396

Query: 481 AKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLLMRE 535
            +  L +   KAKL A +EER+++RL   +I  QL++L++KL    E+E     E
Sbjct: 397 IEYALDSGKEKAKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKELEKSTSLE 451

Length = 531

>gnl\|CDD\|203011 pfam04433, SWIRM, SWIRM domain	Back alignment and domain information

>gnl\|CDD\|239076 cd02336, ZZ_RSC8, Zinc finger, ZZ type	Back alignment and domain information

>gnl\|CDD\|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains	Back alignment and domain information

>gnl\|CDD\|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains	Back alignment and domain information

>gnl\|CDD\|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain	Back alignment and domain information

>gnl\|CDD\|227445 COG5114, COG5114, Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]	Back alignment and domain information

>gnl\|CDD\|206092 pfam13921, Myb_DNA-bind_6, Myb-like DNA-binding domain	Back alignment and domain information

>gnl\|CDD\|197633 smart00291, ZnF_ZZ, Zinc-binding domain, present in Dystrophin, CREB-binding protein	Back alignment and domain information

>gnl\|CDD\|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		668
COG5259		531	RSC8 RSC chromatin remodeling complex subunit RSC8	100.0
KOG1279		506	consensus Chromatin remodeling factor subunit and	100.0
PF04433		86	SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM	99.93
KOG0457		438	consensus Histone acetyltransferase complex SAGA/A	99.89
COG5114		432	Histone acetyltransferase complex SAGA/ADA, subuni	99.81
cd02336		45	ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present	99.07
PF00249		48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	99.01
PF13921		60	Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB:	98.76
smart00717		49	SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-bindi	98.73
cd00167		45	SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding do	98.64
PLN03000		881	amine oxidase	98.6
PLN02328		808	lysine-specific histone demethylase 1 homolog	98.48
cd02335		49	ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present	98.43
cd02345		49	ZZ_dah Zinc finger, ZZ type. Zinc finger present i	98.17
PLN03212		249	Transcription repressor MYB5; Provisional	98.1
cd02338		49	ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger pre	98.08
TIGR01557		57	myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c	98.07
cd02343		48	ZZ_EF Zinc finger, ZZ type. Zinc finger present in	98.06
cd02334		49	ZZ_dystrophin Zinc finger, ZZ type. Zinc finger pr	98.06
smart00291		44	ZnF_ZZ Zinc-binding domain, present in Dystrophin,	98.03
cd02249		46	ZZ Zinc finger, ZZ type. Zinc finger present in dy	98.02
cd02340		43	ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger pre	97.99
PLN02529		738	lysine-specific histone demethylase 1	97.98
cd02341		48	ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present	97.89
PLN03091		459	hypothetical protein; Provisional	97.87
PF00569		46	ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc	97.74
KOG0048		238	consensus Transcription factor, Myb superfamily [T	97.71
PLN03212		249	Transcription repressor MYB5; Provisional	97.64
cd02344		45	ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present	97.57
PLN03091		459	hypothetical protein; Provisional	97.34
cd02339		45	ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger pre	97.31
KOG0048		238	consensus Transcription factor, Myb superfamily [T	96.85
cd02337		41	ZZ_CBP Zinc finger, ZZ type. Zinc finger present i	96.62
KOG0049		939	consensus Transcription factor, Myb superfamily [T	96.34
cd02342		43	ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger pre	96.25
PLN02976		1713	amine oxidase	95.91
KOG0049		939	consensus Transcription factor, Myb superfamily [T	95.57
KOG4582		278	consensus Uncharacterized conserved protein, conta	95.29
PF13837		90	Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain;	95.23
KOG4286		966	consensus Dystrophin-like protein [Cell motility;	94.44
KOG1280		381	consensus Uncharacterized conserved protein contai	93.54
KOG0051		607	consensus RNA polymerase I termination factor, Myb	93.42
KOG0051		607	consensus RNA polymerase I termination factor, Myb	90.82
KOG4167		907	consensus Predicted DNA-binding protein, contains	90.05
KOG0050		617	consensus mRNA splicing protein CDC5 (Myb superfam	89.85
KOG4301		434	consensus Beta-dystrobrevin [Cytoskeleton]	89.18
COG5118		507	BDP1 Transcription initiation factor TFIIIB, Bdp1	88.44
PF13873		78	Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain	88.37
KOG1924		1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	88.01
KOG0050		617	consensus mRNA splicing protein CDC5 (Myb superfam	86.05
KOG1924		1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	85.35
TIGR02894		161	DNA_bind_RsfA transcription factor, RsfA family. I	85.33
KOG4282		345	consensus Transcription factor GT-2 and related pr	84.93
PRK00409		782	recombination and DNA strand exchange inhibitor pr	82.86
TIGR01069		771	mutS2 MutS2 family protein. Function of MutS2 is u	82.59
COG5147		512	REB1 Myb superfamily proteins, including transcrip	81.54

>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]	Back alignment and domain information

Probab=100.00  E-value=4.2e-92  Score=748.90  Aligned_cols=404  Identities=32%  Similarity=0.551  Sum_probs=332.8

Q ss_pred             CCcceeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHH
Q 005942           72 GSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLT  151 (668)
Q Consensus        72 ~~~~ivIPs~S~WF~~~~Ih~iEk~~lPefF~g~~~~ktpe~Y~~~RN~iI~~yr~np~eyLT~t~cr~~L~gddv~~i~  151 (668)
                      |+|+|+||+|+.|||+.+||+||+++.||||+|++++|||++|++||||||+.||+||.+|||||+|||||+| |||+|.
T Consensus        48 Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvag-DV~aiv  126 (531)
T COG5259          48 QTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAG-DVAAIV  126 (531)
T ss_pred             cCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccch-hHHHHH
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999999 599999


Q ss_pred             HHHHhhhhhcccccccCCCCCCCCCCCCccccCCCCccccCCcccccccccccccCCCcCCCcc-------------ccc
Q 005942          152 RIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVA-------------DVY  218 (668)
Q Consensus       152 RVH~FLE~WGLINYqvdp~~~p~~~~~~~i~~~~~G~~~~~~~~l~~~~~l~~fd~~~~~~~~~-------------~i~  218 (668)
                      |||+|||+||||||||||.++|     +.|+++.+||++..+++   ++++.+|..+....+..             +.+
T Consensus       127 rvHrFLekWGLINYqvdp~trP-----s~IgPplt~h~q~l~dt---P~gl~p~l~~~~~~~~~~~a~~~e~~~~k~~~~  198 (531)
T COG5259         127 RVHRFLEKWGLINYQVDPGTRP-----STIGPPLTSHFQDLHDT---PRGLSPFLPWGPINQRVLGAKEIEYETHKEENY  198 (531)
T ss_pred             HHHHHHHHhcceeeccCCCCCc-----cccCCCcchhhHHHhhC---ccccccccCCCCccccccccchhhhhhhccCCC
Confidence            9999999999999999999998     45778889999988765   57888887665432211             222


Q ss_pred             CCCC------CCCCccCchhHHHhhccCCCCCCCCCCCCcceeecccCcCcccChhhhhcCCCCCCCCCCCceecCCCCC
Q 005942          219 SSSC------GGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDVLLCPECFHEGRFVTGHSSLDYIRVDPARE  292 (668)
Q Consensus       219 s~~~------~~~d~~~l~~~~~~~~~~~~C~~C~~~~~~~~y~~~k~~d~~LC~~CF~~G~~~~~hss~df~~vd~~~~  292 (668)
                      ++..      ..+++.++.....  .....|..||+.+...+|+.++..++.+|..||..|+|+.+..+.||..++....
T Consensus       199 sps~~~~~k~s~~k~~el~~~~~--~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~~~~~  276 (531)
T COG5259         199 SPSLKSPKKESQGKVDELKDHSE--KHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVTISLL  276 (531)
T ss_pred             CchhhhhhhhcCCCccccccccc--cCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhhhhcc
Confidence            2210      0111222211110  1237899999999999999998889999999999999999999999999987542


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCCCCHHHHHHHHhhCCCCCCCccCCCCCCCCCCCCCCCCCCCCCc
Q 005942          293 YGDIDGETWSDQETFLLLEGIEMYNDNWNEIAEHVSTKSKAQCILHFVRLPMEDGILENVEVPNTSRTSNSSSRDDRGGL  372 (668)
Q Consensus       293 ~~~~~~~~WT~~Eel~LLeaIe~~g~nW~~IAe~VgtKT~~eCi~hFlqLPIeD~fL~~~~~~~~s~~~~~~~~~d~~~~  372 (668)
                         ..+..||.+|+++|||||++||++|++||.||||||++|||+|||+|||+|.||.+...                . 
T Consensus       277 ---~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~----------------~-  336 (531)
T COG5259         277 ---IRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDG----------------K-  336 (531)
T ss_pred             ---cccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccC----------------c-
Confidence               25679999999999999999999999999999999999999999999999999976421                0 


Q ss_pred             ccCCCCCCCCCCcccccccCCccCCCCCCchHHHHHHHHhhcChHHHHHHHHHHHHHHHhhcccCCCCCCCCcccccccc
Q 005942          373 HSTVNGDLPGAGLQEADMENRLPFSNSGNPVMALVAFLASAVGPRVAAACAHASLAALSKQMEGAGHGNRMNSENVHNRE  452 (668)
Q Consensus       373 ~~dsng~~~g~~~~~~~~~~~~PFs~a~NPVMS~VAFLas~V~P~VAaAAA~aAl~~l~~~~~~~~~d~~~~se~~~~~~  452 (668)
                               |..     ..+.+||+.++||||++++||+++|.|+|+...+.+.++ ..+.     .             
T Consensus       337 ---------~~~-----~~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k-~g~~-----~-------------  383 (531)
T COG5259         337 ---------GDN-----SKGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIK-SGKI-----S-------------  383 (531)
T ss_pred             ---------CCC-----CCCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhh-ccce-----e-------------
Confidence                     000     123479999999999999999999999998777766522 0000     0             


Q ss_pred             ccCCCCCCCCCCCCcccccccHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 005942          453 EENSGVHGPWGQNGAEAALLSAEKVKAAAKAGLAAAATKAKLFADHEEREIQRLSANIINHQLKRLELKLKQFAEVETLL  532 (668)
Q Consensus       453 ~~~d~~~~~~~~n~~~~~~~s~~~vk~Aa~~aL~aAA~kAk~lA~~EErEI~rLv~~iIe~QLkKLElKLk~feeLE~~l  532 (668)
                                ..     ..-+.+-+...+..||.+++.|||++|+.|||+|++|+..+|+.||+||++||.+|++||+.+
T Consensus       384 ----------~~-----n~e~~~~~~~~~~~al~s~~eka~l~~~~Eerkm~rL~~~~iq~qleKlk~Kl~~~k~L~~~~  448 (531)
T COG5259         384 ----------HI-----NRESQEHIEEVIEYALDSGKEKAKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKELEKST  448 (531)
T ss_pred             ----------cC-----ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence                      00     011234566777789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH---HHHHHHHHHHHHH
Q 005942          533 MRECEQVEK---ARQRFATERTRIV  554 (668)
Q Consensus       533 e~Er~~LE~---~Rq~L~~eR~~~~  554 (668)
                      .+||.+|+.   .|+-.+.+.+-.+
T Consensus       449 ~L~rqeLd~nlll~rl~~~e~l~~~  473 (531)
T COG5259         449 SLERQELDANLLLRRLNAEEKLFAI  473 (531)
T ss_pred             HHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            999999999   4444444444333

>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]	Back alignment and domain information

>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins	Back alignment and domain information

>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]	Back alignment and domain information

>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]	Back alignment and domain information

>cd02336 ZZ_RSC8 Zinc finger, ZZ type	Back alignment and domain information

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins	Back alignment and domain information

>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A	Back alignment and domain information

>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains	Back alignment and domain information

>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains	Back alignment and domain information

>PLN03000 amine oxidase	Back alignment and domain information

>PLN02328 lysine-specific histone demethylase 1 homolog	Back alignment and domain information

>cd02335 ZZ_ADA2 Zinc finger, ZZ type	Back alignment and domain information

>cd02345 ZZ_dah Zinc finger, ZZ type	Back alignment and domain information

>PLN03212 Transcription repressor MYB5; Provisional	Back alignment and domain information

>cd02338 ZZ_PCMF_like Zinc finger, ZZ type	Back alignment and domain information

>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class	Back alignment and domain information

>cd02343 ZZ_EF Zinc finger, ZZ type	Back alignment and domain information

>cd02334 ZZ_dystrophin Zinc finger, ZZ type	Back alignment and domain information

>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein	Back alignment and domain information

>cd02249 ZZ Zinc finger, ZZ type	Back alignment and domain information

>cd02340 ZZ_NBR1_like Zinc finger, ZZ type	Back alignment and domain information

>PLN02529 lysine-specific histone demethylase 1	Back alignment and domain information

>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type	Back alignment and domain information

>PLN03091 hypothetical protein; Provisional	Back alignment and domain information

>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]	Back alignment and domain information

>PLN03212 Transcription repressor MYB5; Provisional	Back alignment and domain information

>cd02344 ZZ_HERC2 Zinc finger, ZZ type	Back alignment and domain information

>PLN03091 hypothetical protein; Provisional	Back alignment and domain information

>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type	Back alignment and domain information

>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]	Back alignment and domain information

>cd02337 ZZ_CBP Zinc finger, ZZ type	Back alignment and domain information

>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]	Back alignment and domain information

>cd02342 ZZ_UBA_plant Zinc finger, ZZ type	Back alignment and domain information

>PLN02976 amine oxidase	Back alignment and domain information

>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]	Back alignment and domain information

>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]	Back alignment and domain information

>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A	Back alignment and domain information

>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]	Back alignment and domain information

>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]	Back alignment and domain information

>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]	Back alignment and domain information

>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]	Back alignment and domain information

>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]	Back alignment and domain information

>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]	Back alignment and domain information

>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]	Back alignment and domain information

>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain	Back alignment and domain information

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]	Back alignment and domain information

>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]	Back alignment and domain information

>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family	Back alignment and domain information

>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]	Back alignment and domain information

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed	Back alignment and domain information

>TIGR01069 mutS2 MutS2 family protein	Back alignment and domain information

>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		668
2fq3_A		104	Structure And Function Of The Swirm Domain, A Conse		4e-12
2yus_A		79	Solution Structure Of The Sant Domain Of Human SwiS		3e-09

>pdb|2FQ3|A Chain A, Structure And Function Of The Swirm Domain, A Conserved Protein Module Found In Chromatin Regulatory Complexes Length = 104

Back alignment and structure

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 33/85 (38%), Positives = 48/85 (56%), Gaps = 1/85 (1%)
Query: 81  HSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQG 140
           +S WF+ + +H +E Q +P FF+ + P  TPE YM  RN +V  Y  NP +   V+  + 
Sbjct: 16  YSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARR 75
Query: 141 LVDGVSPEDLTRIFRFLNHWGIINY 165
            V G     L R+ +FL  WG+INY
Sbjct: 76  NVSG-DAAALFRLHKFLTKWGLINY 99

PyMOL of 2fq3

>pdb|2YUS|A Chain A, Solution Structure Of The Sant Domain Of Human SwiSNF- Related Matrix-Associated Actin-Dependent Regulator Of Chromatin Subfamily C Member 1 Length = 79

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		668
2fq3_A		104	Transcription regulatory protein SWI3; four-helix	3e-38
2dce_A		111	KIAA1915 protein; swirm domain, structural genomic	2e-33
2yus_A		79	SWI/SNF-related matrix-associated actin- dependent	6e-23
2elk_A		58	SPCC24B10.08C protein; hypothetical protein, struc	9e-16
1x41_A		60	Transcriptional adaptor 2-like, isoform B; transcr	2e-14
2ltp_A		89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	3e-11
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-10
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04
2cu7_A		72	KIAA1915 protein; nuclear protein, SANT domain, DN	4e-09
4a69_C		94	Nuclear receptor corepressor 2; transcription, hyd	1e-08
2z3y_A		662	Lysine-specific histone demethylase 1; chromatin,	6e-08
2eqr_A		61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	2e-07
2cqr_A		73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	8e-07
2xag_A		852	Lysine-specific histone demethylase 1; amine oxida	2e-06
2iw5_B		235	Protein corest, REST corepressor 1; oxidoreductase	2e-06
2yum_A		75	ZZZ3 protein, zinc finger ZZ-type-containing prote	6e-06
2xag_B		482	REST corepressor 1; amine oxidase, chromatin regul	4e-05
2e5r_A		63	Dystrobrevin alpha; ZZ domain, structural genomics	5e-04
2dim_A		70	Cell division cycle 5-like protein; MYB_DNA-bindin	8e-04

>2fq3_A Transcription regulatory protein SWI3; four-helix bundle; 1.40A {Saccharomyces cerevisiae} SCOP: a.4.1.18 Length = 104	Back alignment and structure

 Score =  136 bits (343), Expect = 3e-38
 Identities = 33/94 (35%), Positives = 50/94 (53%), Gaps = 1/94 (1%)

Query: 77  VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 136
           +   +S WF+ + +H +E Q +P FF+ + P  TPE YM  RN +V  Y  NP +   V+
Sbjct: 12  MASSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVT 71

Query: 137 DCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQ 170
             +  V G     L R+ +FL  WG+INY    +
Sbjct: 72  TARRNVSG-DAAALFRLHKFLTKWGLINYQVDSK 104

PyMOL of 2fq3

>2dce_A KIAA1915 protein; swirm domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 111	Back alignment and structure

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens} Length = 79	Back alignment and structure

>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe} Length = 58	Back alignment and structure

>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1 Length = 60	Back alignment and structure

>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens} Length = 89	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Length = 72	Back alignment and structure

>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A Length = 94	Back alignment and structure

>2z3y_A Lysine-specific histone demethylase 1; chromatin, nucleosome, transcription, LSD1, alternative splicing, chromatin regulator, coiled coil; HET: F2N; 2.25A {Homo sapiens} SCOP: a.4.1.18 c.3.1.2 d.16.1.5 PDB: 2ejr_A* 2z5u_A* 3abt_A* 3abu_A* 2y48_A* 2v1d_A* 2h94_A* 2iw5_A* 2uxn_A* 2uxx_A* 2hko_A* 2dw4_A* 2x0l_A* 2l3d_A Length = 662	Back alignment and structure

>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 61	Back alignment and structure

>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3 Length = 73	Back alignment and structure

>2xag_A Lysine-specific histone demethylase 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_A* 2xah_A* 2xaj_A* 2xaq_A* 2xas_A* 2com_A Length = 852	Back alignment and structure

>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B* Length = 235	Back alignment and structure

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 75	Back alignment and structure

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B* Length = 482	Back alignment and structure

>2e5r_A Dystrobrevin alpha; ZZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 63	Back alignment and structure

>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 70	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		668
2fq3_A		104	Transcription regulatory protein SWI3; four-helix	100.0
2dce_A		111	KIAA1915 protein; swirm domain, structural genomic	100.0
2yus_A		79	SWI/SNF-related matrix-associated actin- dependent	99.57
2elk_A		58	SPCC24B10.08C protein; hypothetical protein, struc	99.34
1x41_A		60	Transcriptional adaptor 2-like, isoform B; transcr	99.23
2cqr_A		73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	99.0
1gvd_A		52	MYB proto-oncogene protein; transcription, transcr	98.94
1guu_A		52	C-MYB, MYB proto-oncogene protein; transcription,	98.93
2d9a_A		60	B-MYB, MYB-related protein B; DNA binding, structu	98.92
2yum_A		75	ZZZ3 protein, zinc finger ZZ-type-containing prote	98.92
1wgx_A		73	KIAA1903 protein; MYB DNA-binding domain, human cD	98.91
2cu7_A		72	KIAA1915 protein; nuclear protein, SANT domain, DN	98.9
1w0t_A		53	Telomeric repeat binding factor 1; telomere, DNA-b	98.89
2dim_A		70	Cell division cycle 5-like protein; MYB_DNA-bindin	98.86
3sjm_A		64	Telomeric repeat-binding factor 2; human telomeric	98.79
1ity_A		69	TRF1; helix-turn-helix, telomeres, DNA binding, MY	98.76
2din_A		66	Cell division cycle 5-like protein; MYB_DNA-bindin	98.73
2eqr_A		61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	98.65
2cjj_A		93	Radialis; plant development, DNA-binding protein,	98.63
2llk_A		73	Cyclin-D-binding MYB-like transcription factor 1;	98.63
2ltp_A		89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	98.05
2k9n_A		107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	98.52
1gv2_A		105	C-MYB, MYB proto-oncogene protein; transcription,	98.52
2k9n_A		107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	98.49
2iw5_B		235	Protein corest, REST corepressor 1; oxidoreductase	98.48
3osg_A		126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	98.47
2ckx_A		83	NGTRF1, telomere binding protein TBP1; nuclear pro	98.45
1gv2_A		105	C-MYB, MYB proto-oncogene protein; transcription,	98.45
1h8a_C		128	AMV V-MYB, MYB transforming protein; transcription	98.43
3osg_A		126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	98.43
1h8a_C		128	AMV V-MYB, MYB transforming protein; transcription	98.36
3zqc_A		131	MYB3; transcription-DNA complex, DNA-binding prote	98.34
3zqc_A		131	MYB3; transcription-DNA complex, DNA-binding prote	98.32
2cqq_A		72	RSGI RUH-037, DNAJ homolog subfamily C member 1; m	98.31
2yqk_A		63	Arginine-glutamic acid dipeptide repeats protein;	98.28
2z3y_A		662	Lysine-specific histone demethylase 1; chromatin,	98.19
2xag_B		482	REST corepressor 1; amine oxidase, chromatin regul	98.18
2roh_A		122	RTBP1, telomere binding protein-1; plant, nucleus,	98.17
1h89_C		159	C-MYB, MYB proto-oncogene protein; transcription/D	98.13
4gut_A		776	Lysine-specific histone demethylase 1B; histone de	98.13
2aje_A		105	Telomere repeat-binding protein; DNA-binding, Trp,	98.12
1h89_C		159	C-MYB, MYB proto-oncogene protein; transcription/D	98.11
2e5r_A		63	Dystrobrevin alpha; ZZ domain, structural genomics	98.09
2juh_A		121	Telomere binding protein TBP1; helix, nucleus, nuc	98.06
2crg_A		70	Metastasis associated protein MTA3; transcription	98.04
4eef_G		74	F-HB80.4, designed hemagglutinin binding protein;	97.92
4a69_C		94	Nuclear receptor corepressor 2; transcription, hyd	97.91
2dip_A		98	Zinc finger SWIM domain-containing protein 2; ZZ d	97.84
1x58_A		62	Hypothetical protein 4930532D21RIK; MUS musculus a	97.83
2fc7_A		82	ZZZ3 protein; structure genomics, ZZ domain, struc	97.75
1ign_A		246	Protein (RAP1); RAP1,yeast,telomeres,homoeodomain,	97.43
2xag_A		852	Lysine-specific histone demethylase 1; amine oxida	97.24
1tot_A		52	CREB-binding protein; zinc binding, CBP, TAZ2, tra	97.03
3hm5_A		93	DNA methyltransferase 1-associated protein 1; DNA	96.36
2ebi_A		86	DNA binding protein GT-1; DNA-binding domain, phos	96.07
1ug2_A		95	2610100B20RIK gene product; hypothetical protein,	96.02
1fex_A		59	TRF2-interacting telomeric RAP1 protein; helix tur	95.57
1ofc_X		304	ISWI protein; nuclear protein, chromatin remodelin	94.72
2xag_B		482	REST corepressor 1; amine oxidase, chromatin regul	94.43
4iej_A		93	DNA methyltransferase 1-associated protein 1; DNA	94.15
2lr8_A		70	CAsp8-associated protein 2; structural genomics, n	93.11
2cuj_A		108	Transcriptional adaptor 2-like; transcriptional re	92.57
2aqe_A		90	Transcriptional adaptor 2, ADA2 alpha; helix-turn-	92.32
2xb0_X		270	Chromo domain-containing protein 1; hydrolase, DNA	91.66
4b4c_A		211	Chromodomain-helicase-DNA-binding protein 1; chrom	90.66
2elj_A		88	Transcriptional adapter 2; YDR448W, structural gen	90.57
1irz_A		64	ARR10-B; helix-turn-helix, DNA binding protein; NM	87.12
4b4c_A		211	Chromodomain-helicase-DNA-binding protein 1; chrom	86.84
1ofc_X		304	ISWI protein; nuclear protein, chromatin remodelin	84.24

>2fq3_A Transcription regulatory protein SWI3; four-helix bundle; 1.40A {Saccharomyces cerevisiae} SCOP: a.4.1.18	Back alignment and structure

Probab=100.00  E-value=4.6e-42  Score=306.96  Aligned_cols=96  Identities=34%  Similarity=0.685  Sum_probs=84.2

Q ss_pred             cceeCCCCCCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHH
Q 005942           74 RVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRI  153 (668)
Q Consensus        74 ~~ivIPs~S~WF~~~~Ih~iEk~~lPefF~g~~~~ktpe~Y~~~RN~iI~~yr~np~eyLT~t~cr~~L~gddv~~i~RV  153 (668)
                      |+=.-|+|+.||+|++||+|||++|||||+|++++|||++|++|||+||++||+||.+|||+|+||++|+| |+++|+||
T Consensus         9 ~~~~~p~~s~wF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Yl~iRN~iI~~yr~nP~~yLT~t~~r~~l~g-Dv~~i~RV   87 (104)
T 2fq3_A            9 HHGMASSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRNVSG-DAAALFRL   87 (104)
T ss_dssp             --------CTTCCTTCCCHHHHHHCGGGCCSSCTTSCHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHSCS-CHHHHHHH
T ss_pred             cCCCCCCcccccCcccCCHHHHHHChHHhcCCCCCCCHHHHHHHHHHHHHHHHhCCceeeeHHHHHHHccc-cHHHHHHH
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999 59999999


Q ss_pred             HHhhhhhcccccccCCC
Q 005942          154 FRFLNHWGIINYCAAVQ  170 (668)
Q Consensus       154 H~FLE~WGLINYqvdp~  170 (668)
                      |+|||+||||||||||+
T Consensus        88 h~FLe~wGLIN~~v~~~  104 (104)
T 2fq3_A           88 HKFLTKWGLINYQVDSK  104 (104)
T ss_dssp             HHHHHHTTSSSSCC---
T ss_pred             HHHHHHcCeeccCCCCC
Confidence            99999999999999974

PyMOL of 2fq3

>2dce_A KIAA1915 protein; swirm domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2yus_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; SWI/SNF complex 155 kDa subunit, BRG1-associated factor 155; NMR {Homo sapiens}	Back alignment and structure

>2elk_A SPCC24B10.08C protein; hypothetical protein, structural genomics, NPPSFA; NMR {Schizosaccharomyces pombe}	Back alignment and structure

>1x41_A Transcriptional adaptor 2-like, isoform B; transcriptional adaptor protein2, transcriptional activation, MYB domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1	Back alignment and structure

>2cqr_A RSGI RUH-043, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>1gvd_A MYB proto-oncogene protein; transcription, transcription regulation, C-MYB, DNA binding, ION binding, nuclear protein; 1.45A {Mus musculus} SCOP: a.4.1.3 PDB: 1gv5_A 1mbg_A 1mbh_A	Back alignment and structure

>1guu_A C-MYB, MYB proto-oncogene protein; transcription, transcription regulation, DNA binding, ION bindi proto-oncogene, nuclear protein, activator; 1.6A {Mus musculus} SCOP: a.4.1.3 PDB: 1mbe_A 1mbf_A	Back alignment and structure

>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>2yum_A ZZZ3 protein, zinc finger ZZ-type-containing protein 3; transcription, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1wgx_A KIAA1903 protein; MYB DNA-binding domain, human cDNA, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>2cu7_A KIAA1915 protein; nuclear protein, SANT domain, DNA binding, regulation of transcription, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>1w0t_A Telomeric repeat binding factor 1; telomere, DNA-binding protein, homeodomain, mitosis, cell cycle; 2.00A {Homo sapiens} SCOP: a.4.1.4 PDB: 1ba5_A	Back alignment and structure

>2dim_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>3sjm_A Telomeric repeat-binding factor 2; human telomeric repeat binding protein 2, telomere, telomeri homeodomain proteins amino acid sequence; HET: DNA; 1.35A {Homo sapiens} PDB: 1xg1_A 1vfc_A 1vf9_A 1w0u_A	Back alignment and structure

>1ity_A TRF1; helix-turn-helix, telomeres, DNA binding, MYB domain, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.4 PDB: 1iv6_A	Back alignment and structure

>2din_A Cell division cycle 5-like protein; MYB_DNA-binding domain, cell cycle, DNA binding, spliceosome, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2eqr_A N-COR1, N-COR, nuclear receptor corepressor 1; SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2cjj_A Radialis; plant development, DNA-binding protein, MYB transcription FA DNA-binding, nuclear protein, floral asymmetry; 1.9A {Antirrhinum majus} SCOP: a.4.1.3	Back alignment and structure

>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle, SGC, structural genomics consortium, NESG, NOR structural genomics consortium; NMR {Homo sapiens}	Back alignment and structure

>2ltp_A Nuclear receptor corepressor 2; SMRT, TRAC, SGC, structural genomics consortium, NESG, north structural genomics consortium; NMR {Homo sapiens}	Back alignment and structure

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A	Back alignment and structure

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A	Back alignment and structure

>2k9n_A MYB24; R2R3 domain, DNA-binding, nucleus, DNA binding protein; NMR {Trichomonas vaginalis} PDB: 2kdz_A	Back alignment and structure

>2iw5_B Protein corest, REST corepressor 1; oxidoreductase-transcription regulator complex, oxidoreductase/repressor complex, histone demethylase, FAD; HET: FAD; 2.57A {Homo sapiens} SCOP: a.4.1.3 PDB: 2uxn_B* 2uxx_B* 2y48_B* 2v1d_B* 2x0l_B*	Back alignment and structure

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A	Back alignment and structure

>2ckx_A NGTRF1, telomere binding protein TBP1; nuclear protein; 1.9A {Nicotiana tabacum} SCOP: a.4.1.3 PDB: 2qhb_A	Back alignment and structure

>1gv2_A C-MYB, MYB proto-oncogene protein; transcription, DNA binding, ION binding; 1.68A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 PDB: 1mse_C* 1msf_C* 1a5j_A 1idy_A 1idz_A 1mbj_A 1mbk_A	Back alignment and structure

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3	Back alignment and structure

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A	Back alignment and structure

>1h8a_C AMV V-MYB, MYB transforming protein; transcription/DNA; 2.23A {Avian myeloblastosis virus} SCOP: a.4.1.3 a.4.1.3	Back alignment and structure

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}	Back alignment and structure

>3zqc_A MYB3; transcription-DNA complex, DNA-binding protein, nucleus; 2.90A {Trichomonas vaginalis}	Back alignment and structure

>2cqq_A RSGI RUH-037, DNAJ homolog subfamily C member 1; membrane protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.3	Back alignment and structure

>2yqk_A Arginine-glutamic acid dipeptide repeats protein; structure genomics, SANT domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2z3y_A Lysine-specific histone demethylase 1; chromatin, nucleosome, transcription, LSD1, alternative splicing, chromatin regulator, coiled coil; HET: F2N; 2.25A {Homo sapiens} SCOP: a.4.1.18 c.3.1.2 d.16.1.5 PDB: 2ejr_A* 2z5u_A* 3abt_A* 3abu_A* 2y48_A* 2v1d_A* 2h94_A* 2iw5_A* 2uxn_A* 2uxx_A* 2hko_A* 2dw4_A* 2x0l_A* 2l3d_A	Back alignment and structure

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*	Back alignment and structure

>2roh_A RTBP1, telomere binding protein-1; plant, nucleus, DNA binding protein; NMR {Oryza sativa}	Back alignment and structure

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C	Back alignment and structure

>4gut_A Lysine-specific histone demethylase 1B; histone demethylase; HET: FAD PGE; 2.00A {Homo sapiens} PDB: 4gur_A* 4gus_A* 4guu_A* 4fwe_A* 4fwf_A* 4fwj_A* 4gu1_A*	Back alignment and structure

>2aje_A Telomere repeat-binding protein; DNA-binding, Trp, MYB motif, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.3	Back alignment and structure

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C	Back alignment and structure

>2e5r_A Dystrobrevin alpha; ZZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2juh_A Telomere binding protein TBP1; helix, nucleus, nuclear protein; NMR {Nicotiana glutinosa}	Back alignment and structure

>2crg_A Metastasis associated protein MTA3; transcription factor, helix turn helix, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.3	Back alignment and structure

>4eef_G F-HB80.4, designed hemagglutinin binding protein; immunoglobulin, fusion of virus membrane with membrane, membrane fusion, sialic acid, virion; HET: NAG BMA; 2.70A {Artificial gene}	Back alignment and structure

>4a69_C Nuclear receptor corepressor 2; transcription, hydrolase; HET: I0P; 2.06A {Homo sapiens} PDB: 1xc5_A	Back alignment and structure

>2dip_A Zinc finger SWIM domain-containing protein 2; ZZ domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.44.1.6	Back alignment and structure

>1x58_A Hypothetical protein 4930532D21RIK; MUS musculus adult MALE testis cDNA, riken FULL-length enriched library, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1	Back alignment and structure

>2fc7_A ZZZ3 protein; structure genomics, ZZ domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.6	Back alignment and structure

>1ign_A Protein (RAP1); RAP1,yeast,telomeres,homoeodomain, DNA binding protein/DNA complex; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.6 a.4.1.6 PDB: 3ukg_A	Back alignment and structure

>2xag_A Lysine-specific histone demethylase 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_A* 2xah_A* 2xaj_A* 2xaq_A* 2xas_A* 2com_A	Back alignment and structure

>1tot_A CREB-binding protein; zinc binding, CBP, TAZ2, transferase; NMR {Mus musculus} SCOP: g.44.1.6	Back alignment and structure

>3hm5_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin, structural genomics consortium, SGC, activator, chromatin regulator; HET: DNA; 1.80A {Homo sapiens}	Back alignment and structure

>2ebi_A DNA binding protein GT-1; DNA-binding domain, phosphorylation; HET: DNA; NMR {Arabidopsis thaliana} PDB: 2jmw_A*	Back alignment and structure

>1ug2_A 2610100B20RIK gene product; hypothetical protein, MYB-like DNA binding domain, structural genomics, riken structural genomics/proteomics initiative; NMR {Mus musculus} SCOP: a.4.1.3	Back alignment and structure

>1fex_A TRF2-interacting telomeric RAP1 protein; helix turn helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Synthetic} SCOP: a.4.1.3	Back alignment and structure

>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase, SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A {Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13 a.187.1.1 PDB: 2nog_A	Back alignment and structure

>2xag_B REST corepressor 1; amine oxidase, chromatin regulator, histone inhibitor binding, methylation, nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A {Homo sapiens} PDB: 2xaf_B* 2xah_B* 2xaj_B* 2xaq_B* 2xas_B*	Back alignment and structure

>4iej_A DNA methyltransferase 1-associated protein 1; DNA methylation, chromatin regulator, repressor, structural joint center for structural genomics; HET: DNA; 1.45A {Homo sapiens} PDB: 3hm5_A*	Back alignment and structure

>2lr8_A CAsp8-associated protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, apoptosis; NMR {Homo sapiens}	Back alignment and structure

>2cuj_A Transcriptional adaptor 2-like; transcriptional regulation, nuclear protein, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.18	Back alignment and structure

>2aqe_A Transcriptional adaptor 2, ADA2 alpha; helix-turn-helix; NMR {Mus musculus} SCOP: a.4.1.18 PDB: 2aqf_A	Back alignment and structure

>2xb0_X Chromo domain-containing protein 1; hydrolase, DNA-binding protein, transcription, chromatin REG; HET: GOL; 2.00A {Saccharomyces cerevisiae} PDB: 3ted_A	Back alignment and structure

>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens}	Back alignment and structure

>2elj_A Transcriptional adapter 2; YDR448W, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11	Back alignment and structure

>4b4c_A Chromodomain-helicase-DNA-binding protein 1; chromatin-remodeling, histone acetylation COMP chromatin regulation, transcription; 1.62A {Homo sapiens}	Back alignment and structure

>1ofc_X ISWI protein; nuclear protein, chromatin remodeling factor, ATPase, SANT domain, nucleosome recognition; HET: GLC G4D; 1.9A {Drosophila melanogaster} SCOP: a.4.1.3 a.4.1.13 a.187.1.1 PDB: 2nog_A	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		668
d2fq3a1		85	a.4.1.18 (A:311-395) Transcription regulatory prot	1e-31
d2dw4a1		102	a.4.1.18 (A:172-273) Lysine-specific histone demet	5e-24
d1xc5a1		68	a.4.1.3 (A:413-480) Nuclear receptor corepressor 2	8e-10
d2iw5b1		65	a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Hu	1e-08
d2crga1		57	a.4.1.3 (A:8-64) Metastasis associated protein MTA	9e-08
d2cu7a1		65	a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sap	2e-06
d2cqra1		60	a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1	2e-06
d2cjja1		63	a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Anti	4e-06
d1x41a1		47	a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, T	7e-05
d1gv2a2		47	a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mou	3e-04
d1guua_		50	a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus	0.002

>d2fq3a1 a.4.1.18 (A:311-395) Transcription regulatory protein swi3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 85	Back information, alignment and structure


class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SWIRM domain
domain: Transcription regulatory protein swi3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  115 bits (290), Expect = 1e-31
 Identities = 33/84 (39%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 82  SDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL 141
           S WF+ + +H +E Q +P FF+ + P  TPE YM  RN +V  Y  NP +   V+  +  
Sbjct: 1   SKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRN 60

Query: 142 VDGVSPEDLTRIFRFLNHWGIINY 165
           V G     L R+ +FL  WG+INY
Sbjct: 61  VSG-DAAALFRLHKFLTKWGLINY 83

PyMOL of d2fq3a1

>d2dw4a1 a.4.1.18 (A:172-273) Lysine-specific histone demethylase 1, LSD1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102	Back information, alignment and structure

>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]} Length = 68	Back information, alignment and structure

>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]} Length = 65	Back information, alignment and structure

>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 57	Back information, alignment and structure

>d2cu7a1 a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 9606]} Length = 65	Back information, alignment and structure

>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 60	Back information, alignment and structure

>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]} Length = 63	Back information, alignment and structure

>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]} Length = 47	Back information, alignment and structure

>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 47	Back information, alignment and structure

>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 50	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		668
d2fq3a1		85	Transcription regulatory protein swi3 {Baker's yea	100.0
d2dw4a1		102	Lysine-specific histone demethylase 1, LSD1 {Human	99.96
d1x41a1		47	Transcriptional adaptor 2-like, TADA2L, isoform b	99.39
d1gvda_		52	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	99.02
d1guua_		50	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	98.99
d2cu7a1		65	MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 960	98.99
d2cjja1		63	Radialis {Garden snapdragon (Antirrhinum majus) [T	98.97
d2cqra1		60	DnaJ homolog subfamily C member 1 {Human (Homo sap	98.91
d2iw5b1		65	REST corepressor 1, CoREST {Human (Homo sapiens) [	98.87
d1gv2a2		47	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	98.87
d1w0ua_		55	Telomeric repeat binding factor 2, TRF2 {Human (Ho	98.73
d1w0ta_		52	DNA-binding domain of human telomeric protein, hTR	98.73
d1xc5a1		68	Nuclear receptor corepressor 2 {Human (Homo sapien	98.71
d2crga1		57	Metastasis associated protein MTA3 {Mouse (Mus mus	98.46
d2ckxa1		83	Telomere binding protein TBP1 {Tobacco (Nicotiana	98.41
d1igna1		86	DNA-binding domain of rap1 {Baker's yeast (Sacchar	98.22
d1ug2a_		95	2610100b20rik gene product {Mouse (Mus musculus) [	97.99
d2cqqa1		59	DnaJ homolog subfamily C member 1 {Human (Homo sap	97.96
d1wgxa_		73	Hypothetical protein C14orf106 (KIAA1903) {Human (	97.66
d2fc7a1		69	Zinc finger ZZ-type-containing protein 3, ZZZ3 {Hu	97.55
d2dipa1		85	Zinc finger ZZ-type-containing protein 2 {Human (H	96.85
d1tota1		52	CREB-binding protein, CBP {Mouse (Mus musculus) [T	96.83
d1irza_		64	Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId	96.15
d1ofcx1		52	SANT domain of the nucleosome remodeling ATPase IS	95.31
d2cuja1		101	Transcriptional adaptor 2-like, TADA2L {Mouse (Mus	94.06
d1x58a1		49	Hypothetical protein 4930532d21rik {Mouse (Mus mus	93.76

>d2fq3a1 a.4.1.18 (A:311-395) Transcription regulatory protein swi3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SWIRM domain
domain: Transcription regulatory protein swi3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=5.8e-36  Score=257.63  Aligned_cols=85  Identities=39%  Similarity=0.794  Sum_probs=83.2

Q ss_pred             CCCCCCCCCCHHHHhhcCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhhccCCCChhHHHHHHHhhhhhc
Q 005942           82 SDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWG  161 (668)
Q Consensus        82 S~WF~~~~Ih~iEk~~lPefF~g~~~~ktpe~Y~~~RN~iI~~yr~np~eyLT~t~cr~~L~gddv~~i~RVH~FLE~WG  161 (668)
                      |+|||+++||+|||++|||||+|++++|||++|++|||+||++||+||.+|||+|+||+++.| |++++.|||+||++||
T Consensus         1 s~WF~~~~i~~iE~~~lPeff~~~~~~kt~~~Yl~iRN~Il~~w~~np~~~Lt~~~~~~~~~~-d~~~~~ri~~FL~~~G   79 (85)
T d2fq3a1           1 SKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRNVSG-DAAALFRLHKFLTKWG   79 (85)
T ss_dssp             CTTCCTTCCCHHHHHHCGGGCCSSCTTSCHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHSCS-CHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCcCCHHHHHHCHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCCCeeeeHHHHHhhccC-CHHHHHHHHHHHHHcC
Confidence            689999999999999999999999999999999999999999999999999999999999998 5999999999999999


Q ss_pred             cccccc
Q 005942          162 IINYCA  167 (668)
Q Consensus       162 LINYqv  167 (668)
                      +|||||
T Consensus        80 ~INf~v   85 (85)
T d2fq3a1          80 LINYQV   85 (85)
T ss_dssp             SSSSCC
T ss_pred             ccCccC
Confidence            999997

PyMOL of d2fq3a1

>d2dw4a1 a.4.1.18 (A:172-273) Lysine-specific histone demethylase 1, LSD1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x41a1 a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, TADA2L, isoform b {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1gvda_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1guua_ a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cu7a1 a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cjja1 a.4.1.3 (A:8-70) Radialis {Garden snapdragon (Antirrhinum majus) [TaxId: 4151]}	Back information, alignment and structure

>d2cqra1 a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2iw5b1 a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1gv2a2 a.4.1.3 (A:144-190) c-Myb, DNA-binding domain {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1w0ua_ a.4.1.4 (A:) Telomeric repeat binding factor 2, TRF2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1w0ta_ a.4.1.4 (A:) DNA-binding domain of human telomeric protein, hTRF1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1xc5a1 a.4.1.3 (A:413-480) Nuclear receptor corepressor 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2crga1 a.4.1.3 (A:8-64) Metastasis associated protein MTA3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2ckxa1 a.4.1.3 (A:578-660) Telomere binding protein TBP1 {Tobacco (Nicotiana tabacum) [TaxId: 4097]}	Back information, alignment and structure

>d1igna1 a.4.1.6 (A:360-445) DNA-binding domain of rap1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1ug2a_ a.4.1.3 (A:) 2610100b20rik gene product {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqqa1 a.4.1.3 (A:8-66) DnaJ homolog subfamily C member 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wgxa_ a.4.1.3 (A:) Hypothetical protein C14orf106 (KIAA1903) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2fc7a1 g.44.1.6 (A:8-76) Zinc finger ZZ-type-containing protein 3, ZZZ3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2dipa1 g.44.1.6 (A:8-92) Zinc finger ZZ-type-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1tota1 g.44.1.6 (A:1-52) CREB-binding protein, CBP {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1ofcx1 a.4.1.3 (X:799-850) SANT domain of the nucleosome remodeling ATPase ISWI {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d2cuja1 a.4.1.18 (A:8-108) Transcriptional adaptor 2-like, TADA2L {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x58a1 a.4.1.1 (A:8-56) Hypothetical protein 4930532d21rik {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure