Citrus Sinensis ID: 016331

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Local Sequence Feature Prediction

Residue Number Marker
--------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-
Protein Sequence
MPASPSFHSDTRKWKRRKREPRKQLNKLDEDDVVEDEDEEQDNNETDNHNNNSNADHRDNGDDFQHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLSSVYLPA
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHcccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHccccEEEHHHHHHccccccHHHHHHHHHHHHHcccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccEEEEcccccccccccccccccEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccHHHHHHccccccccccccccccHccccccccccccccccccccccccccccHHccccccccccccEEEEcccccccccccccEEEEcccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccEEccccEEEEEccccccccccHHHHHHHHcHHHHccccccccHHHHHHHHHHHHHHHcccccHEEEHHHHHHHHcccHHHHHHHHHHHHHHcccEEEEEcccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccHHHHHccccccccccccccccccEEEccccccccccccccccccEEEEEHHEEcccc
Coil and Loop (DISEMBL)
mpaspsfhsdtrkwkrrkreprkqlnkldeddvvededeeqdnnetdnhnnnsnadhrdngddfqhatapdpasnetevlidggtricefptavqrvvnrphvsvMDIVAIEAAYLagdasgrsSAVALENisfgqlqalsvvpadsaaldpersdtscvitppqimegkgvvkrfgsrvhvlpmhsdwfspdtvhrlerqvvphffsgkspdhtpekYMECRNHIVAKymdnpekrlivsdcqglvdgvspeDLTRIFRFLNHWGIINYCaavqspepwnrgsylredsngevsvpsdaLKSIDSlikfdkpkcslkvadvyssscggadffdldNTIRERLSenhcnycsqpipavyyqsqkevdgrfsplTFVYLFICLFLSSVYLPA
Flexible Loop (DISEMBL)
mpaspsfhsdtrkwkrrkreprkqlnkldeddvvededeeqdnnetdnhnnnsnADHRDNGDDFQHATAPDPASNETEVLIDGGTRICEFPtavqrvvnrphVSVMDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAaldpersdtscvitppqimegkgvVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHffsgkspdhtpeKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLSSVYLPA
Low Complexity Region (SEG)
MPASPSFHSDTrkwkrrkreprkQLnkldeddvvededeeqdnnetdnhnnnsnadhrdnGDDFQHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLSSVYLPA
Disordered region (IsUnstruct)
******************************************************************************VLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVP*************SCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFS*********KYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPW**********************SIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLSSVYL**
Disordered Region (DISOPRED)
**********************************************************************************************************************************************************************************RVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAA***************************************************************NTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLS***L**
Disordered Region (DISEMBL)
**********************KQLNKLDE****************DNHNNNSNADHRDNGDDFQHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPAD**********TSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLSSVYLPA
Disordered Region (DISPRO)
*************************************************************************SNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLA**********************************************PQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPE*******************************************************DLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLSSVYLPA
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHii
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPASPSFHSDTRKWKRRKREPRKQLNKLDEDDVVEDEDEEQDNNETDNHNNNSNADHRDNGDDFQHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFICLFLSSVYLPA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	391	2.2.26 [Sep-21-2011]
Q9XI07	807	SWI/SNF complex subunit S	yes	no	0.782	0.379	0.640	1e-107
Q8VY05	985	SWI/SNF complex subunit S	no	no	0.250	0.099	0.383	7e-14
P32591	825	SWI/SNF complex subunit S	yes	no	0.225	0.106	0.393	3e-13
Q8TAQ2	1214	SWI/SNF complex subunit S	yes	no	0.232	0.074	0.357	2e-12
Q6PDG5	1213	SWI/SNF complex subunit S	yes	no	0.232	0.075	0.357	2e-12
P97496	1104	SWI/SNF complex subunit S	no	no	0.281	0.099	0.308	1e-11
Q92922	1105	SWI/SNF complex subunit S	no	no	0.217	0.076	0.336	2e-11
O14470	503	SWI/SNF and RSC complexes	yes	no	0.222	0.172	0.366	8e-11
Q8W475	512	SWI/SNF complex subunit S	no	no	0.242	0.185	0.302	3e-10
Q84JG2	469	SWI/SNF complex subunit S	no	no	0.250	0.208	0.339	1e-09

>sp|Q9XI07|SWI3C_ARATH SWI/SNF complex subunit SWI3C OS=Arabidopsis thaliana GN=SWI3C PE=1 SV=1

 Score =  389 bits (1000), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 203/317 (64%), Positives = 235/317 (74%), Gaps = 11/317 (3%)

Query: 59  DNGDDFQH--ATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYL 116
           +N D+ Q      PDP     EV+ D G+RI +FP  V+RVV RPH SVM +VA E A L
Sbjct: 51  ENADELQQNGGATPDPGLGIGEVVEDSGSRISDFPAVVKRVVIRPHASVMAVVAAERAGL 110

Query: 117 AGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSC---VITPPQIMEGKGVV 173
            G+  G+ S  ALENISFGQLQALS VPADS  LD ERSD S    VI+PP IM+G+GVV
Sbjct: 111 IGETRGQGSLPALENISFGQLQALSTVPADS--LDLERSDGSSSAYVISPPPIMDGEGVV 168

Query: 174 KRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDN 233
           KRFG  VHVLPMHSDWF+P+TV RLERQVVP FFSGKSP+HTPE YME RN IV+KY++N
Sbjct: 169 KRFGDLVHVLPMHSDWFAPNTVDRLERQVVPQFFSGKSPNHTPESYMEFRNAIVSKYVEN 228

Query: 234 PEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEPWNRGSYLREDSNG 292
           PEK L +SDCQGLVDGV  ED  R+FRFL+HWGIINYCA  QS P P    S +RED+NG
Sbjct: 229 PEKTLTISDCQGLVDGVDIEDFARVFRFLDHWGIINYCATAQSHPGPLRDVSDVREDTNG 288

Query: 293 EVSVPSDALKSIDSLIKFDKPKCSLKVADVYSS--SCGGADFFDLDNTIRERLSENHCNY 350
           EV+VPS AL SIDSLIKFDKP C  K  +VYSS  S  G D  DLD  IRE L ++HCN+
Sbjct: 289 EVNVPSAALTSIDSLIKFDKPNCRHKGGEVYSSLPSLDG-DSPDLDIRIREHLCDSHCNH 347

Query: 351 CSQPIPAVYYQSQKEVD 367
           CS+P+P VY+QSQK+ D
Sbjct: 348 CSRPLPTVYFQSQKKGD 364

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|Q8VY05|SWI3D_ARATH SWI/SNF complex subunit SWI3D OS=Arabidopsis thaliana GN=SWI3D PE=1 SV=3

 Score = 78.6 bits (192), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 38/99 (38%), Positives = 56/99 (56%), Gaps = 1/99 (1%)

Query: 172 VVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYM 231
            ++   S VHV+P H  WFS + +H LE + +P FF+GK    T E Y E RN I+ K+ 
Sbjct: 136 AIRSRDSNVHVVPNHCGWFSWEKIHPLEERSLPSFFNGKLEGRTSEVYREIRNWIMGKFH 195

Query: 232 DNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270
            NP  ++ + D   L  G S E    +  FL++WG+IN+
Sbjct: 196 SNPNIQIELKDLTELEVGDS-EAKQEVMEFLDYWGLINF 233

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|P32591|SWI3_YEAST SWI/SNF complex subunit SWI3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SWI3 PE=1 SV=1

 Score = 76.6 bits (187), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 35/89 (39%), Positives = 52/89 (58%), Gaps = 1/89 (1%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
           V+P +S WF+ + +H +E Q +P FF+ + P  TPE YM  RN +V  Y  NP +   V+
Sbjct: 306 VIPSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVT 365

Query: 242 DCQGLVDGVSPEDLTRIFRFLNHWGIINY 270
             +  V G +   L R+ +FL  WG+INY
Sbjct: 366 TARRNVSGDAAA-LFRLHKFLTKWGLINY 393

Involved in transcriptional activation. Component 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.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q8TAQ2|SMRC2_HUMAN SWI/SNF complex subunit SMARCC2 OS=Homo sapiens GN=SMARCC2 PE=1 SV=1

 Score = 73.9 bits (180), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 57/98 (58%), Gaps = 7/98 (7%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
           ++P ++ WF  ++VH +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct: 425 IIPSYAAWFDYNSVHAIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 484

Query: 242 DCQGLVDGVSPEDLTRIFR---FLNHWGIINYCAAVQS 276
            C+  + G    D+  I R   FL  WG+INY    +S
Sbjct: 485 ACRRNLAG----DVCAIMRVHAFLEQWGLINYQVDAES 518

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Can stimulate the ATPase activity of the catalytic subunit of these complexes. May be required for CoREST dependent repression of neuronal specific gene promoters in non-neuronal cells. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Homo sapiens (taxid: 9606)

>sp|Q6PDG5|SMRC2_MOUSE SWI/SNF complex subunit SMARCC2 OS=Mus musculus GN=Smarcc2 PE=1 SV=2

 Score = 73.6 bits (179), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 35/98 (35%), Positives = 57/98 (58%), Gaps = 7/98 (7%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
           ++P ++ WF  ++VH +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct: 425 IIPSYAAWFDYNSVHAIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 484

Query: 242 DCQGLVDGVSPEDLTRIFR---FLNHWGIINYCAAVQS 276
            C+  + G    D+  I R   FL  WG+INY    +S
Sbjct: 485 ACRRNLAG----DVCAIMRVHAFLEQWGLINYQVDAES 518

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Can stimulate the ATPase activity of the catalytic subunit of these complexes. May be required for CoREST dependent repression of neuronal specific gene promoters in non-neuronal cells. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Mus musculus (taxid: 10090)

>sp|P97496|SMRC1_MOUSE SWI/SNF complex subunit SMARCC1 OS=Mus musculus GN=Smarcc1 PE=1 SV=2

 Score = 70.9 bits (172), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 38/123 (30%), Positives = 66/123 (53%), Gaps = 13/123 (10%)

Query: 151 DPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGK 210
           DP + D S  + P     G+  V    + + ++P ++ WF  + +H +ER+ +P FF+GK
Sbjct: 424 DPSKGDPSRSVDP-----GEDNVTEQTNHI-IIPSYASWFDYNCIHVIERRALPEFFNGK 477

Query: 211 SPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFR---FLNHWGI 267
           +   TPE Y+  RN ++  Y  NP++ L  + C+  + G    D+  + R   FL  WG+
Sbjct: 478 NKSKTPEIYLAYRNFMIDTYRLNPQEYLTSTACRRNLTG----DVCAVMRVHAFLEQWGL 533

Query: 268 INY 270
           +NY
Sbjct: 534 VNY 536

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). May stimulate the ATPase activity of the catalytic subunit of the complex. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene (By similarity). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Mus musculus (taxid: 10090)

>sp|Q92922|SMRC1_HUMAN SWI/SNF complex subunit SMARCC1 OS=Homo sapiens GN=SMARCC1 PE=1 SV=3

 Score = 70.5 bits (171), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 54/92 (58%), Gaps = 7/92 (7%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
           ++P ++ WF  + +H +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct: 450 IIPSYASWFDYNCIHVIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 509

Query: 242 DCQGLVDGVSPEDLTRIFR---FLNHWGIINY 270
            C+  + G    D+  + R   FL  WG++NY
Sbjct: 510 ACRRNLTG----DVCAVMRVHAFLEQWGLVNY 537

Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). May stimulate the ATPase activity of the catalytic subunit of the complex. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.

Homo sapiens (taxid: 9606)

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

 Score = 68.6 bits (166), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 51/90 (56%), Gaps = 3/90 (3%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
           ++P ++ WF    +H +ER+  P FF+GKSP  TP  Y + R+ ++  Y   P + L V+
Sbjct: 19  IVPSYAGWFDMSKIHDIERRSNPEFFNGKSPLKTPSIYKDYRDFMINSYRLEPNEYLTVT 78

Query: 242 DC-QGLVDGVSPEDLTRIFRFLNHWGIINY 270
            C + LV  V    + R+  FL  WG+INY
Sbjct: 79  ACRRNLVGDVCA--IIRVHAFLEQWGLINY 106

Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. Controls particularly membrane and organelle development genes. Part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, 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.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q8W475|SWI3A_ARATH SWI/SNF complex subunit SWI3A OS=Arabidopsis thaliana GN=SWI3A PE=1 SV=1

 Score = 66.6 bits (161), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 29/96 (30%), Positives = 54/96 (56%), Gaps = 1/96 (1%)

Query: 180 VHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLI 239
           ++ +P  S WF  D +H +ER+    FF+  S   TP+ Y E R+ I+ K+ ++  +RL 
Sbjct: 12  LYTIPAQSSWFLWDDIHEIERREFAEFFTESSITRTPKVYKEYRDFIINKFREDTCRRLT 71

Query: 240 VSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQ 275
            +  +  + G     L ++F FL  WG+IN+ ++++
Sbjct: 72  FTSVRKFLVG-DVNLLQKVFLFLEKWGLINFSSSLK 106

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|Q84JG2|SWI3B_ARATH SWI/SNF complex subunit SWI3B OS=Arabidopsis thaliana GN=SWI3B PE=1 SV=1

 Score = 64.7 bits (156), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 57/103 (55%), Gaps = 5/103 (4%)

Query: 180 VHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLI 239
           +HV P +S WFS   ++  E + +P FF  +S    P+ Y+  RN I+ +Y D+  +++ 
Sbjct: 48  IHV-PSYSSWFSWTDINDCEVRSLPEFFDSRSSSKNPKFYLYLRNSIIKQYRDDHPRKIS 106

Query: 240 VSDC-QGLVDGVSPEDLTRIFRFLNHWGIINY-CAAVQSPEPW 280
            +D  + LV  V    + R+F FL+ WG+INY  +A   P  W
Sbjct: 107 FTDVRRTLVSDVVS--IRRVFDFLDSWGLINYNSSASAKPLKW 147

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. May play an essential role in the transition from the vegetative to the reproductive phase of development. May be a positive regulator of ABA signaling.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	391
224082324	796	chromatin remodeling complex subunit [Po	0.943	0.463	0.635	1e-125
255558620	771	DNA binding protein, putative [Ricinus c	0.930	0.472	0.614	1e-116
359492375	771	PREDICTED: SWI/SNF complex subunit SWI3C	0.905	0.459	0.621	1e-115
449449761	815	PREDICTED: SWI/SNF complex subunit SWI3C	0.884	0.424	0.582	1e-113
449500660	779	PREDICTED: LOW QUALITY PROTEIN: SWI/SNF	0.813	0.408	0.640	1e-111
357463551	874	SWI/SNF complex subunit SMARCC2 [Medicag	0.915	0.409	0.580	1e-110
357520333	884	SWI/SNF complex subunit SMARCC2 [Medicag	0.915	0.404	0.580	1e-110
356507640	785	PREDICTED: SWI/SNF complex subunit SWI3C	0.900	0.448	0.582	1e-109
356518555	785	PREDICTED: SWI/SNF complex subunit SWI3C	0.910	0.453	0.576	1e-108
15219067	807	SWI/SNF complex subunit SWI3C [Arabidops	0.782	0.379	0.640	1e-105

>gi|224082324|ref|XP_002306648.1| chromatin remodeling complex subunit [Populus trichocarpa] gi|222856097|gb|EEE93644.1| chromatin remodeling complex subunit [Populus trichocarpa]

 Score =  455 bits (1171), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 249/392 (63%), Positives = 282/392 (71%), Gaps = 23/392 (5%)

Query: 1   MPASPSF-HSDTR-KWKRRKR-------EPRKQLNKLDEDDVVEDEDEEQDNNETDNHNN 51
           MPASPSF  SD R KWKRRKR       +P K  ++ + ++  E++D        D   N
Sbjct: 1   MPASPSFPSSDGRGKWKRRKRGDSQITRKPPKHHHQEETEEPEEEDDA------VDADEN 54

Query: 52  NSNADHRDNGDD---FQHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDI 108
           N+N   R++ DD    Q  + PDP   ETEVLIDGG R+C+FP   +  VNRPH SVM I
Sbjct: 55  NNNVIDREDSDDPNPNQQPSGPDPNPQETEVLIDGGVRLCDFPPVTRLAVNRPHASVMAI 114

Query: 109 VAIEAAYLAGDASGRSS-AVALENISFGQLQALSVVPADSAALDPERSD---TSCVITPP 164
           VA E A LAG++S R    V+LEN+S+GQLQA+S V AD    D ERSD   T  V+TPP
Sbjct: 115 VAAERACLAGESSNRGQLVVSLENVSYGQLQAVSAVIADCDGSDLERSDGGNTGYVVTPP 174

Query: 165 QIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRN 224
           QIM+GKGVVKRF SRVH++PMHSDWFSP  V+RLERQVVPHFFSGKSPDHTPEKY ECRN
Sbjct: 175 QIMDGKGVVKRFWSRVHLVPMHSDWFSPALVNRLERQVVPHFFSGKSPDHTPEKYRECRN 234

Query: 225 HIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGS 284
            IVAKYM+NPEKRL V DCQGLV G+  ED TRIFRFL+HWGIINYCAA  S E WN GS
Sbjct: 235 RIVAKYMENPEKRLTVPDCQGLVVGIDNEDFTRIFRFLDHWGIINYCAAPPSCEYWNGGS 294

Query: 285 YLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSS-SCGGADFFDLDNTIRERL 343
           YLRED NGEV VPS ALKS DSLI+FDKPKC LK ADVYSS SC   D  DLDN IRE L
Sbjct: 295 YLREDPNGEVHVPSAALKSFDSLIQFDKPKCRLKAADVYSSLSCHDDDLSDLDNRIRECL 354

Query: 344 SENHCNYCSQPIPAVYYQSQKEVDGRFSPLTF 375
           SEN CN+CSQ +P+V YQSQKEVD    P  F
Sbjct: 355 SENRCNHCSQLLPSVCYQSQKEVDILLCPDCF 386

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558620|ref|XP_002520335.1| DNA binding protein, putative [Ricinus communis] gi|223540554|gb|EEF42121.1| DNA binding protein, putative [Ricinus communis]

 Score =  426 bits (1094), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 234/381 (61%), Positives = 284/381 (74%), Gaps = 17/381 (4%)

Query: 1   MPASPSF-HSDTR-KWKRRKREP---RKQLNKLDEDDVVEDEDEE------QDNNETDNH 49
           MPASPSF  SD R KWKRRKREP   RK   +  + +  +DEDE+       ++N  +N 
Sbjct: 1   MPASPSFPSSDGRGKWKRRKREPQNTRKHQQQPAKREEPDDEDEDAAVEDDNNHNNNNNE 60

Query: 50  NNNSNADHRDNGDDFQHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIV 109
           +++ + +   N +   + T PD   +ETEV+IDGG RIC+FP   + +VNRPH SV  IV
Sbjct: 61  DDSEDPNPNPNPNSNHNPTQPD---HETEVVIDGGVRICDFPCVTKLLVNRPHASVSAIV 117

Query: 110 AIEAAYLAGDASGRSSAVA--LENISFGQLQALSVVPADSAALDPERSDTSC-VITPPQI 166
           A+E A   G++S     V   LEN+S+GQLQA+S VP ++   D +  +++  V+TPP I
Sbjct: 118 ALERANSGGESSSSKGQVVPHLENMSYGQLQAVSAVPPEAFGCDQDDGNSAGYVVTPPVI 177

Query: 167 MEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHI 226
           +EGKGVVKRFGSR+HV+PMHSDWFSP TV+RLERQVVPHFFSGKSPDHTPEKYMECRN+I
Sbjct: 178 LEGKGVVKRFGSRIHVVPMHSDWFSPATVNRLERQVVPHFFSGKSPDHTPEKYMECRNYI 237

Query: 227 VAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYL 286
           VAKYM NPE+R+ VSDCQG V G+  EDLTRI RFL+ WGIINYCAA  S E W+ GSYL
Sbjct: 238 VAKYMGNPERRIAVSDCQGFVVGIENEDLTRIVRFLDQWGIINYCAAPSSRESWSGGSYL 297

Query: 287 REDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSEN 346
           RED NGEV VPS ALKSIDSLIKFDKP+CSLK A++YSS     DF DLD+ IRERLSEN
Sbjct: 298 REDPNGEVHVPSAALKSIDSLIKFDKPRCSLKAAEIYSSLSYHDDFSDLDSRIRERLSEN 357

Query: 347 HCNYCSQPIPAVYYQSQKEVD 367
           HC YCSQ +P+VYYQSQKE+D
Sbjct: 358 HCTYCSQSLPSVYYQSQKEID 378

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359492375|ref|XP_002284548.2| PREDICTED: SWI/SNF complex subunit SWI3C-like [Vitis vinifera]

 Score =  421 bits (1083), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 228/367 (62%), Positives = 265/367 (72%), Gaps = 13/367 (3%)

Query: 9   SDTR-KWKRRKREPRKQLNKLDEDDVVEDEDEEQDNNETDNHNNNSNADHRDNGDDFQHA 67
           SD R KW++RKR+P     +  E+D  +D+D + + +   + +N     H       Q  
Sbjct: 5   SDARTKWRKRKRDPHVSRRQKHEEDEEDDDDVDDELDADADDDNEQQPQHGP-----QSG 59

Query: 68  TAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGDASGRSSAV 127
             PDPA    EVL DG  RI +FP+ V+  VNRPH SV+ IV  E A   GD   + S +
Sbjct: 60  AVPDPAPLMREVLSDGAVRISDFPSVVKHTVNRPHSSVLAIVGTERAIQFGDTRNQQSPM 119

Query: 128 ALENISFGQLQALSVVPADSAAL---DPERSDTSC-VITPPQIMEGKGVVKRF-GSRVHV 182
            LENIS GQLQALS VPADS +L   D ERSD    V+ PPQIMEG+GV+KRF   RVH 
Sbjct: 120 FLENISHGQLQALSAVPADSPSLATSDQERSDGGGYVVAPPQIMEGRGVIKRFWNGRVHA 179

Query: 183 LPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSD 242
           +PMHSDWFSP+TVHRLERQVVPHFFSGKSPDHT E YMECRN IVAKYM++PEKRL VSD
Sbjct: 180 VPMHSDWFSPNTVHRLERQVVPHFFSGKSPDHTAELYMECRNLIVAKYMEDPEKRLSVSD 239

Query: 243 CQGLVDGVSPEDLTRIFRFLNHWGIINYCA-AVQSPEPWNRGSYLREDSNGEVSVPSDAL 301
           C+GLV G+  EDLTRI RFL+HWGIINYCA +V + EPW+  SYLREDSNGEV VPS AL
Sbjct: 240 CKGLVAGIQEEDLTRIVRFLDHWGIINYCASSVPNREPWSSTSYLREDSNGEVHVPSAAL 299

Query: 302 KSIDSLIKFDKPKCSLKVADVYSS-SCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYY 360
           KSIDSLIKFDKPKC LK A+VYSS SC G +  DLD  IRERLS+N CNYCS+P+P  YY
Sbjct: 300 KSIDSLIKFDKPKCRLKAAEVYSSLSCNGDEDSDLDCKIRERLSDNRCNYCSRPLPIGYY 359

Query: 361 QSQKEVD 367
           QSQKEVD
Sbjct: 360 QSQKEVD 366

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449449761|ref|XP_004142633.1| PREDICTED: SWI/SNF complex subunit SWI3C-like [Cucumis sativus]

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 220/378 (58%), Positives = 261/378 (69%), Gaps = 32/378 (8%)

Query: 13  KWKRRKREPRKQLNKLDEDDVVEDEDEEQDNNETDNH-------------NNNSNADHRD 59
           KW+++KR+   Q+ +        +      NN T+ H             N+    D+ D
Sbjct: 14  KWRKKKRD--SQIGR-------RNNYSNTFNNGTNRHDDDDEDEDLVAAENDEMERDNND 64

Query: 60  NGDDFQHATAPDPASN--ETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLA 117
           + +D Q    P P S   E E+L D   R+ EFP  V+R V RPH SV+ +VA+E     
Sbjct: 65  DSEDPQIGLHPTPNSTIQEPELLSDDKFRVSEFPQVVKRAVTRPHSSVLAVVAMERTNQY 124

Query: 118 GDASGR-SSAVALENISFGQLQALSVVPADS-AALDPER---SDTSCVITPPQIMEGKGV 172
           G++ G   +++ LEN+S+GQLQALS +PADS A LD ER    + + VITPP IMEG+GV
Sbjct: 125 GESKGVPGNSLILENVSYGQLQALSAMPADSPALLDQERVEAGNAAYVITPPPIMEGRGV 184

Query: 173 VKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMD 232
           VKRFGSRVHV+PMHSDWFSP TVHRLERQVVPHFFSGK PD TPEKYME RN +VAKYM+
Sbjct: 185 VKRFGSRVHVVPMHSDWFSPATVHRLERQVVPHFFSGKLPDRTPEKYMEIRNFVVAKYME 244

Query: 233 NPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNG 292
           NPEKR+ VSDCQGLVDGVS EDLTRI RFL+HWGIINYCA   S EPWN  SYLRED NG
Sbjct: 245 NPEKRVTVSDCQGLVDGVSNEDLTRIVRFLDHWGIINYCAPTPSCEPWNSNSYLREDMNG 304

Query: 293 EVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGAD---FFDLDNTIRERLSENHCN 349
           E+ VPS ALK IDSL+KFDKPKC LK ADVYS+     D     DLDN IRERL+ENHC+
Sbjct: 305 EIHVPSAALKPIDSLVKFDKPKCRLKAADVYSALPCRDDIDGLCDLDNRIRERLAENHCS 364

Query: 350 YCSQPIPAVYYQSQKEVD 367
            CS+ +P  YYQSQKEVD
Sbjct: 365 SCSRSVPIAYYQSQKEVD 382

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  409 bits (1051), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 210/328 (64%), Positives = 243/328 (74%), Gaps = 10/328 (3%)

Query: 50  NNNSNADHRDNGDDFQHATAPDPASN--ETEVLIDGGTRICEFPTAVQRVVNRPHVSVMD 107
           N+    D+ D+ +D Q    P P S   E E+L D   R+ EFP  V+R V RPH SV+ 
Sbjct: 41  NDEMERDNNDDSEDPQIGLHPTPNSTVQEPELLSDDKFRVSEFPQVVKRAVTRPHSSVLA 100

Query: 108 IVAIEAAYLAGDASGR-SSAVALENISFGQLQALSVVPADS-AALDPER---SDTSCVIT 162
           +VA+E     G++ G   +++ LEN+S+GQLQALS +PADS A LD ER    + + VIT
Sbjct: 101 VVAMERTNQYGESKGVPGNSLILENVSYGQLQALSAMPADSPALLDQERVEAGNAAYVIT 160

Query: 163 PPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMEC 222
           PP IMEG+GVVKRFGSRVHV+PMHSDWFSP TVHRLERQVVPH FSGK PD TPEKYME 
Sbjct: 161 PPPIMEGRGVVKRFGSRVHVVPMHSDWFSPATVHRLERQVVPHXFSGKLPDRTPEKYMEI 220

Query: 223 RNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNR 282
           RN +VAKYM+NPEKR+ VSDCQGLVDGVS EDLTRI RFL+HWGIINYCA   S EPWN 
Sbjct: 221 RNFVVAKYMENPEKRVTVSDCQGLVDGVSNEDLTRIVRFLDHWGIINYCAPTPSCEPWNS 280

Query: 283 GSYLREDSNGEVSVPSDALKSIDSLIKFDKPKCSLKVADVYSSSCGGAD---FFDLDNTI 339
            SYLRED NGE+ VPS ALK IDSL+KFDKPKC LK ADVYS+     D     DLDN I
Sbjct: 281 NSYLREDMNGEIHVPSAALKPIDSLVKFDKPKCRLKAADVYSALPCRDDIDGLCDLDNRI 340

Query: 340 RERLSENHCNYCSQPIPAVYYQSQKEVD 367
           RERL+ENHC+ CS+ +P  YYQSQKEVD
Sbjct: 341 RERLAENHCSSCSRSVPIAYYQSQKEVD 368

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357463551|ref|XP_003602057.1| SWI/SNF complex subunit SMARCC2 [Medicago truncatula] gi|355491105|gb|AES72308.1| SWI/SNF complex subunit SMARCC2 [Medicago truncatula]

 Score =  403 bits (1036), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 220/379 (58%), Positives = 258/379 (68%), Gaps = 21/379 (5%)

Query: 1   MPASPSFHSDTR-KWKRRKREPRKQLNKLDEDDVVEDEDEEQDNNETDNHNNNSNADHRD 59
           MPASPS   D R KW++RKRE R           +    ++    E D+   N NAD   
Sbjct: 1   MPASPS---DNRAKWRKRKRESR-----------INQRQQKLQEEEEDDDEENPNADEDH 46

Query: 60  NGDDF---QHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYL 116
           + D     QH     P   E EVL D   +I +FP  ++R VNRPH SV  IVA+E A  
Sbjct: 47  DRDYDSDDQHHPNSQP-QQEIEVLSDHAVQISQFPMVIKRAVNRPHSSVTAIVALERAME 105

Query: 117 AGDASGR-SSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKR 175
            GD+  +  +   LEN+S GQLQALS VP+DS ALD +R+++S VITPP I+EG+GVVKR
Sbjct: 106 LGDSKAQLQNTPFLENVSHGQLQALSAVPSDSLALDQDRAESSYVITPPPILEGRGVVKR 165

Query: 176 FGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPE 235
           FGSRV VLPMHSDWFSP TVHRLERQ VPHFFSGKS D TPEKYMECRN+IVA YM+ P 
Sbjct: 166 FGSRVLVLPMHSDWFSPGTVHRLERQAVPHFFSGKSQDLTPEKYMECRNYIVALYMEEPG 225

Query: 236 KRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVS 295
           KR+  SDCQGL  GV  EDLTRI RFL+HWGIINYCA   S EP N  S L+ED++GE+ 
Sbjct: 226 KRITASDCQGLQVGVGHEDLTRIVRFLDHWGIINYCARTPSHEPPNAVSCLKEDTSGEIR 285

Query: 296 VPSDALKSIDSLIKFDKPKCSLKVADVYSS-SCGGADFFDLDNTIRERLSENHCNYCSQP 354
           VPS+ALKSIDSLIKFDK  C LK  ++YS  +    D  DLD+ IRE LSENHCNYCS P
Sbjct: 286 VPSEALKSIDSLIKFDKTNCKLKAEEIYSPLTMHSGDVPDLDSRIREHLSENHCNYCSCP 345

Query: 355 IPAVYYQSQKEVDGRFSPL 373
           +PAVYYQSQKEV  +   L
Sbjct: 346 LPAVYYQSQKEVRAKVKSL 364

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357520333|ref|XP_003630455.1| SWI/SNF complex subunit SMARCC2 [Medicago truncatula] gi|355524477|gb|AET04931.1| SWI/SNF complex subunit SMARCC2 [Medicago truncatula]

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 220/379 (58%), Positives = 258/379 (68%), Gaps = 21/379 (5%)

Query: 1   MPASPSFHSDTR-KWKRRKREPRKQLNKLDEDDVVEDEDEEQDNNETDNHNNNSNADHRD 59
           MPASPS   D R KW++RKRE R           +    ++    E D+   N NAD   
Sbjct: 1   MPASPS---DNRAKWRKRKRESR-----------INQRQQKLQEEEEDDDEENPNADEDH 46

Query: 60  NGDDF---QHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYL 116
           + D     QH     P   E EVL D   +I +FP  ++R VNRPH SV  IVA+E A  
Sbjct: 47  DRDYDSDDQHHPNSQP-QQEIEVLSDHAVQISQFPMVIKRAVNRPHSSVTAIVALERAME 105

Query: 117 AGDASGR-SSAVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKR 175
            GD+  +  +   LEN+S GQLQALS VP+DS ALD +R+++S VITPP I+EG+GVVKR
Sbjct: 106 LGDSKAQLQNTPFLENVSHGQLQALSAVPSDSLALDQDRAESSYVITPPPILEGRGVVKR 165

Query: 176 FGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPE 235
           FGSRV VLPMHSDWFSP TVHRLERQ VPHFFSGKS D TPEKYMECRN+IVA YM+ P 
Sbjct: 166 FGSRVLVLPMHSDWFSPGTVHRLERQAVPHFFSGKSQDLTPEKYMECRNYIVALYMEEPG 225

Query: 236 KRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVS 295
           KR+  SDCQGL  GV  EDLTRI RFL+HWGIINYCA   S EP N  S L+ED++GE+ 
Sbjct: 226 KRITASDCQGLQVGVGHEDLTRIVRFLDHWGIINYCARTPSHEPPNAVSCLKEDTSGEIR 285

Query: 296 VPSDALKSIDSLIKFDKPKCSLKVADVYSS-SCGGADFFDLDNTIRERLSENHCNYCSQP 354
           VPS+ALKSIDSLIKFDK  C LK  ++YS  +    D  DLD+ IRE LSENHCNYCS P
Sbjct: 286 VPSEALKSIDSLIKFDKTNCKLKAEEIYSPLTMHSGDVPDLDSRIREHLSENHCNYCSCP 345

Query: 355 IPAVYYQSQKEVDGRFSPL 373
           +PAVYYQSQKEV  +   L
Sbjct: 346 LPAVYYQSQKEVRAKVKSL 364

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356507640|ref|XP_003522572.1| PREDICTED: SWI/SNF complex subunit SWI3C-like [Glycine max]

 Score =  400 bits (1027), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 218/374 (58%), Positives = 265/374 (70%), Gaps = 22/374 (5%)

Query: 1   MPASPSFHSDTRKWKRRKREP----RKQLNKLDEDDVVEDEDEEQDNNETDNHNNNSNAD 56
           MPASPS   +  +W++RKR+     R Q ++ D+DD  E+ + E+D  E D         
Sbjct: 1   MPASPS--ENRTRWRKRKRDSQISRRHQKHEEDDDDDDENPNAEEDLAERD--------- 49

Query: 57  HRDNGDDFQHATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYL 116
             D+ D   H         ETEVL D G +I +FP  ++R VNRPH SV  IVA+E A  
Sbjct: 50  -YDSEDQTHHNHPNSQPHVETEVLSDHGVQISQFPAVIKRSVNRPHSSVTAIVALERALE 108

Query: 117 AGDASGRSSAVA--LENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVK 174
           +G+    S+  A  LEN+S GQLQALS VP+DS A D    D+S VITPP I+EG+GVVK
Sbjct: 109 SGENKAPSALAAPVLENVSHGQLQALSSVPSDSFAFD---GDSSFVITPPPILEGRGVVK 165

Query: 175 RFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNP 234
           R+G++  V+PMHSDWFSP TVHRLERQVVPHFFSGKSPDHTPEKYMECRN IVA +M++P
Sbjct: 166 RYGTKALVVPMHSDWFSPATVHRLERQVVPHFFSGKSPDHTPEKYMECRNCIVALHMEDP 225

Query: 235 EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEV 294
            KR+ VSDC+GL+ GV+ EDLTRI RFL+HWGIINYC  + S E  N  S LRE+++GEV
Sbjct: 226 GKRITVSDCKGLLAGVNVEDLTRIVRFLDHWGIINYCVRMPSHESPNAVSCLREETSGEV 285

Query: 295 SVPSDALKSIDSLIKFDKPKCSLKVADVYSS-SCGGADFFDLDNTIRERLSENHCNYCSQ 353
            VPS+ALKSIDSLIKFDKP C LK  ++YSS S   AD  DL++ IRE LSENHCNYCS 
Sbjct: 286 RVPSEALKSIDSLIKFDKPNCKLKADEIYSSLSAHSADVLDLEDRIREHLSENHCNYCSC 345

Query: 354 PIPAVYYQSQKEVD 367
           P+P VYYQSQKEVD
Sbjct: 346 PLPVVYYQSQKEVD 359

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518555|ref|XP_003527944.1| PREDICTED: SWI/SNF complex subunit SWI3C-like [Glycine max]

 Score =  397 bits (1020), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 214/371 (57%), Positives = 270/371 (72%), Gaps = 15/371 (4%)

Query: 1   MPASPSFHSDTRKWKRRKREPRKQLNKLDEDDVVEDEDEEQDNNETDNHNNNSNADHRDN 60
           MPASPS   +  +W++RKR+   Q+++  +    E++D+E++ N  +      +A+   +
Sbjct: 1   MPASPS--ENRTRWRKRKRD--SQISRRHQKHEEEEDDDEENPNAAEE----DHAERDYD 52

Query: 61  GDDFQHATAPDPASN-ETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGD 119
            +D  H   P+   + E EVL D G +I +FP  ++R VNRPH SV  IVA+E A  +GD
Sbjct: 53  SEDQTHHNHPNSQPHVEAEVLSDHGVQISQFPAVIKRSVNRPHSSVTAIVALERALESGD 112

Query: 120 ASGRSS--AVALENISFGQLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFG 177
              +S+  A  LEN+S GQLQALS VP+D+ ALD    D+S VITPP I+EG+GVVKRFG
Sbjct: 113 NKAQSALDAPILENVSHGQLQALSSVPSDNFALD---CDSSFVITPPPILEGRGVVKRFG 169

Query: 178 SRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKR 237
           ++V V+PMHSDWFSP TVHRLERQVVPHFFSGKSPDHTPEKYMECRN IVA +M++P  R
Sbjct: 170 TKVLVVPMHSDWFSPATVHRLERQVVPHFFSGKSPDHTPEKYMECRNCIVALHMEDPGMR 229

Query: 238 LIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVP 297
           + VSDCQGL+ GV+ EDLTRI RFL+HWGIINYC  + S E  N  S LR++ +GEV VP
Sbjct: 230 ITVSDCQGLLAGVNVEDLTRIVRFLDHWGIINYCVRIPSHESPNAVSCLRDELSGEVRVP 289

Query: 298 SDALKSIDSLIKFDKPKCSLKVADVYSS-SCGGADFFDLDNTIRERLSENHCNYCSQPIP 356
           S+ALKSIDSLIKFDKP C LK  ++YSS +   AD  DL++ IRE LSENHCNYCS P+P
Sbjct: 290 SEALKSIDSLIKFDKPNCKLKADEIYSSLTAHSADVLDLEDRIREHLSENHCNYCSCPLP 349

Query: 357 AVYYQSQKEVD 367
            VYYQSQKEVD
Sbjct: 350 VVYYQSQKEVD 360

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>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]

 Score =  389 bits (1000), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 203/317 (64%), Positives = 235/317 (74%), Gaps = 11/317 (3%)

Query: 59  DNGDDFQH--ATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYL 116
           +N D+ Q      PDP     EV+ D G+RI +FP  V+RVV RPH SVM +VA E A L
Sbjct: 51  ENADELQQNGGATPDPGLGIGEVVEDSGSRISDFPAVVKRVVIRPHASVMAVVAAERAGL 110

Query: 117 AGDASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSC---VITPPQIMEGKGVV 173
            G+  G+ S  ALENISFGQLQALS VPADS  LD ERSD S    VI+PP IM+G+GVV
Sbjct: 111 IGETRGQGSLPALENISFGQLQALSTVPADS--LDLERSDGSSSAYVISPPPIMDGEGVV 168

Query: 174 KRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDN 233
           KRFG  VHVLPMHSDWF+P+TV RLERQVVP FFSGKSP+HTPE YME RN IV+KY++N
Sbjct: 169 KRFGDLVHVLPMHSDWFAPNTVDRLERQVVPQFFSGKSPNHTPESYMEFRNAIVSKYVEN 228

Query: 234 PEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEPWNRGSYLREDSNG 292
           PEK L +SDCQGLVDGV  ED  R+FRFL+HWGIINYCA  QS P P    S +RED+NG
Sbjct: 229 PEKTLTISDCQGLVDGVDIEDFARVFRFLDHWGIINYCATAQSHPGPLRDVSDVREDTNG 288

Query: 293 EVSVPSDALKSIDSLIKFDKPKCSLKVADVYSS--SCGGADFFDLDNTIRERLSENHCNY 350
           EV+VPS AL SIDSLIKFDKP C  K  +VYSS  S  G D  DLD  IRE L ++HCN+
Sbjct: 289 EVNVPSAALTSIDSLIKFDKPNCRHKGGEVYSSLPSLDG-DSPDLDIRIREHLCDSHCNH 347

Query: 351 CSQPIPAVYYQSQKEVD 367
           CS+P+P VY+QSQK+ D
Sbjct: 348 CSRPLPTVYFQSQKKGD 364

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	391
TAIR|locus:2036942	807	SWI3C "SWITCH/sucrose nonferme	0.774	0.375	0.643	1e-98
CGD|CAL0002007	971	orf19.4488 [Candida albicans (	0.317	0.127	0.343	5.9e-12
DICTYBASE|DDB_G0277033	1223	swi3 "SWIRM domain-containing	0.301	0.096	0.333	1.7e-11
UNIPROTKB|G5EF87	789	swsn-1 "SWI3-like protein" [Ca	0.378	0.187	0.274	7.8e-11
WB|WBGene00004203	792	swsn-1 [Caenorhabditis elegans	0.378	0.186	0.274	7.8e-11
UNIPROTKB|F1PVA9	1092	SMARCC2 "Uncharacterized prote	0.245	0.087	0.36	9.4e-11
UNIPROTKB|F1N4N6	1094	SMARCC2 "Uncharacterized prote	0.245	0.087	0.36	9.4e-11
UNIPROTKB|F1SM00	1167	LOC100621845 "Uncharacterized	0.245	0.082	0.36	1e-10
UNIPROTKB|I3LRY4	1212	I3LRY4 "Uncharacterized protei	0.245	0.079	0.36	1.1e-10
MGI|MGI:1915344	1213	Smarcc2 "SWI/SNF related, matr	0.245	0.079	0.36	1.1e-10

TAIR|locus:2036942 SWI3C "SWITCH/sucrose nonfermenting 3C" [Arabidopsis thaliana (taxid:3702)]

 Score = 980 (350.0 bits), Expect = 1.0e-98, P = 1.0e-98
 Identities = 202/314 (64%), Positives = 233/314 (74%)

Query:    62 DDFQH--ATAPDPASNETEVLIDGGTRICEFPTAVQRVVNRPHVSVMDIVAIEAAYLAGD 119
             D+ Q      PDP     EV+ D G+RI +FP  V+RVV RPH SVM +VA E A L G+
Sbjct:    54 DELQQNGGATPDPGLGIGEVVEDSGSRISDFPAVVKRVVIRPHASVMAVVAAERAGLIGE 113

Query:   120 ASGRSSAVALENISFGQLQALSVVPADSAALDPERSDTSC---VITPPQIMEGKGVVKRF 176
               G+ S  ALENISFGQLQALS VPADS  LD ERSD S    VI+PP IM+G+GVVKRF
Sbjct:   114 TRGQGSLPALENISFGQLQALSTVPADS--LDLERSDGSSSAYVISPPPIMDGEGVVKRF 171

Query:   177 GSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEK 236
             G  VHVLPMHSDWF+P+TV RLERQVVP FFSGKSP+HTPE YME RN IV+KY++NPEK
Sbjct:   172 GDLVHVLPMHSDWFAPNTVDRLERQVVPQFFSGKSPNHTPESYMEFRNAIVSKYVENPEK 231

Query:   237 RLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEPWNRGSYLREDSNGEVS 295
              L +SDCQGLVDGV  ED  R+FRFL+HWGIINYCA  QS P P    S +RED+NGEV+
Sbjct:   232 TLTISDCQGLVDGVDIEDFARVFRFLDHWGIINYCATAQSHPGPLRDVSDVREDTNGEVN 291

Query:   296 VPSDALKSIDSLIKFDKPKCSLKVADVYSS--SCGGADFFDLDNTIRERLSENHCNYCSQ 353
             VPS AL SIDSLIKFDKP C  K  +VYSS  S  G D  DLD  IRE L ++HCN+CS+
Sbjct:   292 VPSAALTSIDSLIKFDKPNCRHKGGEVYSSLPSLDG-DSPDLDIRIREHLCDSHCNHCSR 350

Query:   354 PIPAVYYQSQKEVD 367
             P+P VY+QSQK+ D
Sbjct:   351 PLPTVYFQSQKKGD 364

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

CGD|CAL0002007 orf19.4488 [Candida albicans (taxid:5476)]

 Score = 192 (72.6 bits), Expect = 5.9e-12, P = 5.9e-12
 Identities = 46/134 (34%), Positives = 74/134 (55%)

Query:   182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
             V+P ++ WF+   +H++E++ +P FF    P  +P+ Y+  RN ++  Y  NP + L ++
Sbjct:   421 VIPSYASWFNMKKIHKIEKESLPEFFDSIHPSKSPKLYVNYRNFMINSYRLNPNEFLTLT 480

Query:   242 DCQ-GLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNRGSYLREDSNGEVSVPSDA 300
              C+  LV  V    L R+ RFLN WG+INY    Q  +P   G  L +  NG+ S+  D 
Sbjct:   481 SCRRNLVGDVGT--LMRVHRFLNKWGLINYQVRPQF-KP---GYALEKMPNGQ-SM--DL 531

Query:   301 LKSIDSLIKFDKPK 314
               + D  +KFD P+
Sbjct:   532 PYTGDYHVKFDTPR 545

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

GO:0044109 "cellular alcohol catabolic process" evidence=IEA

GO:0031496 "positive regulation of mating type switching" evidence=IEA

GO:0043044 "ATP-dependent chromatin remodeling" evidence=IEA

GO:0005987 "sucrose catabolic process" evidence=IEA

GO:0000436 "carbon catabolite activation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0042393 "histone binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

DICTYBASE|DDB_G0277033 swi3 "SWIRM domain-containing protein Swi3" [Dictyostelium discoideum (taxid:44689)]

 Score = 189 (71.6 bits), Expect = 1.7e-11, P = 1.7e-11
 Identities = 41/123 (33%), Positives = 64/123 (52%)

Query:   149 ALDPERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFS 208
             +L  + + T+     PQ    K V  +  S   + P    WF  + +H +E+  +P FF+
Sbjct:   611 SLPQQPTTTTTTSVQPQPQPPKNVTLQ--SSFTIPPSQCTWFKMERIHEVEKNQLPEFFT 668

Query:   209 GKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQ-GLVDGVSPEDLTRIFRFLNHWGI 267
             GKSP  TPE Y E R+ ++  Y+ NP + L ++  +  LV  V    + R+  FL HWG+
Sbjct:   669 GKSPSKTPEVYKEYRDFMINTYLQNPYQYLTLTAIRRNLVGDVC--SILRVHSFLEHWGL 726

Query:   268 INY 270
             INY
Sbjct:   727 INY 729

GO:0003682 "chromatin binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0006338 "chromatin remodeling" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|G5EF87 swsn-1 "SWI3-like protein" [Caenorhabditis elegans (taxid:6239)]

 Score = 181 (68.8 bits), Expect = 7.8e-11, P = 7.8e-11
 Identities = 42/153 (27%), Positives = 74/153 (48%)

Query:   119 DASGRSSAVALENISFG-QLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFG 177
             D   RS A     +  G +  A    P      D +          PQ+ EG  V+++  
Sbjct:    23 DDDSRSGAAVKVEVPKGKEKDAEFSAPKGQKLTDLDEEGVQSTKEAPQLAEGN-VIEQ-- 79

Query:   178 SRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKR 237
             +   V+P ++ WF  + +H++E++ +P FF+GK+   TP+ Y+  RN +V  Y  NP + 
Sbjct:    80 THYIVVPSYAGWFDYNAIHQIEKRAMPEFFNGKNKSKTPDVYVAYRNFMVDTYRLNPFEY 139

Query:   238 LIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270
             +  + C+  + G     + R+  FL  WG++NY
Sbjct:   140 VSATACRRNLAG-DVCSIVRLHSFLEQWGLLNY 171

GO:0042802 "identical protein binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

WB|WBGene00004203 swsn-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 181 (68.8 bits), Expect = 7.8e-11, P = 7.8e-11
 Identities = 42/153 (27%), Positives = 74/153 (48%)

Query:   119 DASGRSSAVALENISFG-QLQALSVVPADSAALDPERSDTSCVITPPQIMEGKGVVKRFG 177
             D   RS A     +  G +  A    P      D +          PQ+ EG  V+++  
Sbjct:    23 DDDSRSGAAVKVEVPKGKEKDAEFSAPKGQKLTDLDEEGVQSTKEAPQLAEGN-VIEQ-- 79

Query:   178 SRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKR 237
             +   V+P ++ WF  + +H++E++ +P FF+GK+   TP+ Y+  RN +V  Y  NP + 
Sbjct:    80 THYIVVPSYAGWFDYNAIHQIEKRAMPEFFNGKNKSKTPDVYVAYRNFMVDTYRLNPFEY 139

Query:   238 LIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINY 270
             +  + C+  + G     + R+  FL  WG++NY
Sbjct:   140 VSATACRRNLAG-DVCSIVRLHSFLEQWGLLNY 171

GO:0003682 "chromatin binding" evidence=IEA

GO:0000003 "reproduction" evidence=IGI;IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IGI;IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IGI;IMP

GO:0040018 "positive regulation of multicellular organism growth" evidence=IGI;IMP

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0040027 "negative regulation of vulval development" evidence=IMP

GO:0046662 "regulation of oviposition" evidence=IMP

GO:0002009 "morphogenesis of an epithelium" evidence=IMP

GO:0035262 "gonad morphogenesis" evidence=IMP

UNIPROTKB|F1PVA9 SMARCC2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 182 (69.1 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 36/100 (36%), Positives = 58/100 (58%)

Query:   182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
             ++P ++ WF  ++VH +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct:   418 IIPSYAAWFDYNSVHAIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 477

Query:   242 DCQ-GLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEP 279
              C+  L   V    + R+  FL  WG+INY    +S P P
Sbjct:   478 ACRRNLAGDVCA--IMRVHAFLEQWGLINYQVDAESRPTP 515

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1N4N6 SMARCC2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 182 (69.1 bits), Expect = 9.4e-11, P = 9.4e-11
 Identities = 36/100 (36%), Positives = 58/100 (58%)

Query:   182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
             ++P ++ WF  ++VH +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct:   389 IIPSYAAWFDYNSVHAIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 448

Query:   242 DCQ-GLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEP 279
              C+  L   V    + R+  FL  WG+INY    +S P P
Sbjct:   449 ACRRNLAGDVCA--IMRVHAFLEQWGLINYQVDAESRPTP 486

GO:0071565 "nBAF complex" evidence=IEA

GO:0071564 "npBAF complex" evidence=IEA

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

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

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

GO:0006338 "chromatin remodeling" evidence=IEA

GO:0006337 "nucleosome disassembly" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1SM00 LOC100621845 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 182 (69.1 bits), Expect = 1.0e-10, P = 1.0e-10
 Identities = 36/100 (36%), Positives = 58/100 (58%)

Query:   182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
             ++P ++ WF  ++VH +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct:   437 IIPSYAAWFDYNSVHAIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 496

Query:   242 DCQ-GLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEP 279
              C+  L   V    + R+  FL  WG+INY    +S P P
Sbjct:   497 ACRRNLAGDVCA--IMRVHAFLEQWGLINYQVDAESRPTP 534

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|I3LRY4 I3LRY4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 182 (69.1 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 36/100 (36%), Positives = 58/100 (58%)

Query:   182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
             ++P ++ WF  ++VH +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct:   391 IIPSYAAWFDYNSVHAIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 450

Query:   242 DCQ-GLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEP 279
              C+  L   V    + R+  FL  WG+INY    +S P P
Sbjct:   451 ACRRNLAGDVCA--IMRVHAFLEQWGLINYQVDAESRPTP 488

GO:0005634 "nucleus" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

 Score = 182 (69.1 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 36/100 (36%), Positives = 58/100 (58%)

Query:   182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
             ++P ++ WF  ++VH +ER+ +P FF+GK+   TPE Y+  RN ++  Y  NP++ L  +
Sbjct:   425 IIPSYAAWFDYNSVHAIERRALPEFFNGKNKSKTPEIYLAYRNFMIDTYRLNPQEYLTST 484

Query:   242 DCQ-GLVDGVSPEDLTRIFRFLNHWGIINYCAAVQS-PEP 279
              C+  L   V    + R+  FL  WG+INY    +S P P
Sbjct:   485 ACRRNLAGDVCA--IMRVHAFLEQWGLINYQVDAESRPTP 522

GO:0003677 "DNA binding" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0006337 "nucleosome disassembly" evidence=ISO

GO:0006338 "chromatin remodeling" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007399 "nervous system development" evidence=IEA

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

GO:0016568 "chromatin modification" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISO

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

GO:0071564 "npBAF complex" evidence=IDA

GO:0071565 "nBAF complex" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: CHB904 SubName- Full=Putative uncharacterized protein; (796 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	391
pfam04433	80	pfam04433, SWIRM, SWIRM domain	4e-20
COG5259	531	COG5259, RSC8, RSC chromatin remodeling complex su	3e-11

>gnl|CDD|203011 pfam04433, SWIRM, SWIRM domain

 Score = 83.4 bits (207), Expect = 4e-20
 Identities = 30/86 (34%), Positives = 48/86 (55%), Gaps = 6/86 (6%)

Query: 185 MHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQ 244
             S WF  D +H +E+ ++P FF       TPE Y++ RN I+ ++  NP K L  +D +
Sbjct: 1   ALSSWFDLDLLHEIEKALLPEFF-----LKTPEVYLKIRNFIINEWRLNPGKYLTKTDAR 55

Query: 245 GLVDGVSPEDLTRIFRFLNHWGIINY 270
            L+ G     ++R+  FL  WG+IN+
Sbjct: 56  RLLKG-DVNKISRVHDFLERWGLINF 80

This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA. Length = 80

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

 Score = 64.5 bits (157), Expect = 3e-11
 Identities = 34/89 (38%), Positives = 54/89 (60%), Gaps = 1/89 (1%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
           ++P +++WF    +H +E++  P FF+G+SP  TPE Y + RN ++  Y  NP + L V+
Sbjct: 53  IIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVT 112

Query: 242 DCQGLVDGVSPEDLTRIFRFLNHWGIINY 270
            C+  V G     + R+ RFL  WG+INY
Sbjct: 113 ACRRNVAGDVAA-IVRVHRFLEKWGLINY 140

Length = 531

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	391
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	99.95
PLN03000	881	amine oxidase	98.98
PLN02328	808	lysine-specific histone demethylase 1 homolog	98.97
cd02336	45	ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present	98.94
PLN02529	738	lysine-specific histone demethylase 1	98.47
PLN02976	1713	amine oxidase	97.0
smart00291	44	ZnF_ZZ Zinc-binding domain, present in Dystrophin,	90.9
KOG1279	506	consensus Chromatin remodeling factor subunit and	82.07
PF00569	46	ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc	80.18

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

Probab=100.00  E-value=3.9e-45  Score=369.63  Aligned_cols=222  Identities=22%  Similarity=0.383  Sum_probs=171.4

Q ss_pred             CCCcceecCCCccCCCccceecCCceeeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCC
Q 016331          155 SDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNP  234 (391)
Q Consensus       155 ~~~~~v~t~p~~~eg~~~~k~~~~~~~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP  234 (391)
                      +.+.+..+.+.+.+.+..---.|+++++||+++.||++.+||+||++..||||+|+++.|||++|+.||||||+.||+||
T Consensus        26 ~ks~~e~~~~~l~~e~~~Fl~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p  105 (531)
T COG5259          26 SKSANEKKTTILRVEAETFLMEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNP  105 (531)
T ss_pred             hcccCccccchhhhhhhhhhhccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCC
Confidence            34555555555554443332348999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccCCCCCCC---CC---CCCccccCCCCccccCCCcccccc---
Q 016331          235 EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEP---WN---RGSYLREDSNGEVSVPSDALKSID---  305 (391)
Q Consensus       235 ~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~~~~~p~---~~---~~~~~~~~p~G~~~~~~~~l~~~~---  305 (391)
                      .+|||+|+|||||+| ||++|.|||+|||+|||||||+++.++|.   |+   +.+.+.++|.|.+.+.+..+....   
T Consensus       106 ~eYLtvTa~RRNvag-DV~aivrvHrFLekWGLINYqvdp~trPs~IgPplt~h~q~l~dtP~gl~p~l~~~~~~~~~~~  184 (531)
T COG5259         106 NEYLTVTACRRNVAG-DVAAIVRVHRFLEKWGLINYQVDPGTRPSTIGPPLTSHFQDLHDTPRGLSPFLPWGPINQRVLG  184 (531)
T ss_pred             cceEEeeeehhccch-hHHHHHHHHHHHHHhcceeeccCCCCCccccCCCcchhhHHHhhCccccccccCCCCccccccc
Confidence            999999999999999 99999999999999999999999999995   33   334567788888666554443332   


Q ss_pred             -ccccccCCCcccccccccCCC---CC---CCCCCCccHHHHhc--ccCcccCcCCCCCCCceeeeeec----------c
Q 016331          306 -SLIKFDKPKCSLKVADVYSSS---CG---GADFFDLDNTIRER--LSENHCNYCSQPIPAVYYQSQKE----------V  366 (391)
Q Consensus       306 -~Li~fd~~~~~~~~~~v~~pt---~~---~~~~~dl~~~i~e~--l~ey~C~~Cg~DCs~~rYhsqK~----------~  366 (391)
                       +.+.|     ....++.++|+   +.   ...+-+    +.++  ..-++|..||..|...|||+++.          .
T Consensus       185 a~~~e~-----~~~k~~~~sps~~~~~k~s~~k~~e----l~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~  255 (531)
T COG5259         185 AKEIEY-----ETHKEENYSPSLKSPKKESQGKVDE----LKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYD  255 (531)
T ss_pred             cchhhh-----hhhccCCCCchhhhhhhhcCCCccc----cccccccCCceeeccCccccchhhhhhhhhhcccchHHHh
Confidence             22222     12233444442   10   011111    1222  23499999999999999999972          8


Q ss_pred             CcccCCCcchhhhHHhhhcc
Q 016331          367 DGRFSPLTFVYLFICLFLSS  386 (391)
Q Consensus       367 dg~f~p~~~s~dFi~~~~~~  386 (391)
                      .|+|+..+-+.||+|++..-
T Consensus       256 qg~f~s~~~ssDf~~v~~~~  275 (531)
T COG5259         256 QGRFPSEFTSSDFKPVTISL  275 (531)
T ss_pred             cCcCCCccccccchhhhhhc
Confidence            99999999999999998653

>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]

Probab=100.00  E-value=1.3e-42  Score=357.47  Aligned_cols=207  Identities=25%  Similarity=0.417  Sum_probs=163.6

Q ss_pred             CCCcceecCCCccCCCccceecCCceeeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCC
Q 016331          155 SDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNP  234 (391)
Q Consensus       155 ~~~~~v~t~p~~~eg~~~~k~~~~~~~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP  234 (391)
                      +...+++  |..+.......+.|++.|+||+|++||+|++||.||++.+||||+|++++|||++||+||||||++||+||
T Consensus        23 ~~~~~~~--~~~~~~~~~~~~~q~~~i~iPs~a~WFd~~~ih~iE~rs~pEFF~gks~sktPe~Y~~yRnfii~tyrlnp  100 (506)
T KOG1279|consen   23 SQETLGG--PAAHDAAKTVVSEQTHFIIIPSYAAWFDKSDIHDIERRSLPEFFNGKSKSKTPEVYMKYRNFIINTYRLNP  100 (506)
T ss_pred             Ccccccc--cchhhhcccccccccceeecccHHhhcChhhhhhHHhccchhhhcCCCCCCCHHHHHHHHHhhhhhhccCc
Confidence            4444555  55667788888999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CceeeHHHHhcccCCCCHHHHHHHHHhhhhhceeccccCCCCCCCC---C---CCCccccCCCCccccCCCccccccccc
Q 016331          235 EKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPW---N---RGSYLREDSNGEVSVPSDALKSIDSLI  308 (391)
Q Consensus       235 ~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLINy~~~~~~~p~~---~---~~~~~~~~p~G~~~~~~~~l~~~~~Li  308 (391)
                      .+|||+|+||++|+| ||++|.|||+|||+||||||+++++.+|..   +   +...+.++|.|.+...+...     ..
T Consensus       101 ~~ylt~ta~rrnl~g-Dv~ai~Rvh~FlE~WGLINy~~d~e~rp~~~~p~~t~h~~~~~~tp~~~~~~~~~~~-----~~  174 (506)
T KOG1279|consen  101 QEYLTFTACRRNLAG-DVCAIARVHAFLEQWGLINYQVDAESRPHPIEPPETSHFQVLADTPRGLAPLTPEDP-----QS  174 (506)
T ss_pred             ccchhHHHHHhcccc-hHHHHHHHHhhHHhhcccccccChhhCCcccCCCcccccccccCCCcccccCCCCCc-----cc
Confidence            999999999999999 999999999999999999999999999853   2   22344555666554333222     22


Q ss_pred             cccCCCcccccccccCCCCCCCCCCCccHHHHhcccCcccCcCCCCCCCceeeeeec----------cCcccCCCcchhh
Q 016331          309 KFDKPKCSLKVADVYSSSCGGADFFDLDNTIRERLSENHCNYCSQPIPAVYYQSQKE----------VDGRFSPLTFVYL  378 (391)
Q Consensus       309 ~fd~~~~~~~~~~v~~pt~~~~~~~dl~~~i~e~l~ey~C~~Cg~DCs~~rYhsqK~----------~dg~f~p~~~s~d  378 (391)
                      .++.+++...      ....-...+.+...+.+.+...||+.|+..    +||.++.          ..|+|+..+-..|
T Consensus       175 ~~~~~~~~~~------~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~----~~~~~~~~~~~~c~~c~~~g~~~~~~~~~D  244 (506)
T KOG1279|consen  175 QPDLGNPRME------TLSLESKIKSLHINAGEHLCAIHCFIKEDP----YYYDLTNRDVNLCADCYDQGEFPSEFKKSD  244 (506)
T ss_pred             cccccccccc------cccccccccccccChHhhccccchhccccc----hhhhcchhhhhhhHHHHhcCCccCcccccc
Confidence            2333333221      112222334445566778889999999887    7777775          7899999999999


Q ss_pred             h
Q 016331          379 F  379 (391)
Q Consensus       379 F  379 (391)
                      |
T Consensus       245 f  245 (506)
T KOG1279|consen  245 F  245 (506)
T ss_pred             c
Confidence            9

>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

Probab=99.95  E-value=1e-28  Score=199.42  Aligned_cols=86  Identities=43%  Similarity=0.962  Sum_probs=78.7

Q ss_pred             eeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHH
Q 016331          181 HVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFR  260 (391)
Q Consensus       181 ~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~  260 (391)
                      +++|.+++||+++.+|++|++.+||||.|    ++|+.||.|||.||+.|+.||.+|||+++|++++.|.|++.+.|||+
T Consensus         1 ~~~~~~~~~~~~~~l~~~E~~~~~e~~~~----~~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~   76 (86)
T PF04433_consen    1 VVIPAHSSWFDPDKLSEIEKQLCPEFFIG----KTPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYD   76 (86)
T ss_dssp             -HCHCCHTTTTTTSS-HHHHHHCHHCTTS----CHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHH
T ss_pred             CCCccccCCCCcccCCHHHHHHhHHHhcc----CChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHH
Confidence            36899999999999999999999999988    89999999999999999999999999999999998779999999999


Q ss_pred             hhhhhceecc
Q 016331          261 FLNHWGIINY  270 (391)
Q Consensus       261 FLE~WGLINy  270 (391)
                      ||++||+|||
T Consensus        77 FL~~~G~INf   86 (86)
T PF04433_consen   77 FLERWGLINF   86 (86)
T ss_dssp             HHHHTTSSSS
T ss_pred             HHHHcCccCC
Confidence            9999999998

It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....

>PLN03000 amine oxidase

Probab=98.98  E-value=5.5e-10  Score=123.07  Aligned_cols=86  Identities=22%  Similarity=0.322  Sum_probs=72.9

Q ss_pred             CCCCCCCCCCHHHHhh--CCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhh
Q 016331          187 SDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH  264 (391)
Q Consensus       187 s~WFd~d~Ih~iEk~~--lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~  264 (391)
                      +.=|+.+.+++.|..+  || ...    ...+..||.|||.||.+|+.||..+||+++|...+..--...+.++|+||.+
T Consensus        88 ~~~~p~d~l~~~e~~~~~~~-~~~----~~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~L~r  162 (881)
T PLN03000         88 TAGFPADSLTEEEIEFGVVP-IVG----GIEQVNYILIRNHIISKWRENISSWVTKEMFLGSIPKHCSSLLDSAYNYLVT  162 (881)
T ss_pred             HcCCCcccCCHHHHhccccC-ccc----ccchhhHHHHHHHHHHHHHHCCceeecHHHHhhhcchhHHHHHHHHHHHHHH
Confidence            4557999999999777  78 333    3678999999999999999999999999999988754234789999999999


Q ss_pred             hceeccccCCCCC
Q 016331          265 WGIINYCAAVQSP  277 (391)
Q Consensus       265 WGLINy~~~~~~~  277 (391)
                      .|+|||++.....
T Consensus       163 ~G~in~g~~~~~~  175 (881)
T PLN03000        163 HGYINFGIAQAIK  175 (881)
T ss_pred             cCcccHHHHHHHH
Confidence            9999999985443

>PLN02328 lysine-specific histone demethylase 1 homolog

Probab=98.97  E-value=6.8e-10  Score=121.56  Aligned_cols=88  Identities=23%  Similarity=0.288  Sum_probs=77.8

Q ss_pred             CCCCCCCCCCCHHHHhh-CCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhh
Q 016331          186 HSDWFSPDTVHRLERQV-VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH  264 (391)
Q Consensus       186 ~s~WFd~d~Ih~iEk~~-lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~  264 (391)
                      .+.=|..+.+|+.|..+ |++...+    ..+..||.|||.||.+|+.||..+||+++|+..+-......+.++|.||.+
T Consensus       138 ~~~~~p~~~l~~~e~~~~~~~~~~~----~~~~~yl~iRN~il~lW~~np~~~~t~~~a~~~~~~~~~~l~~~~~~~l~~  213 (808)
T PLN02328        138 ISVGFPVDSLTEEEIEANVVSTIGG----TEQANYIVVRNHILARWRSNVSNWLTRDHALESIRAEHKNLVDSAYNFLLE  213 (808)
T ss_pred             HHcCCCCccCCHHHHhhcCcchhcc----cceeehhhHHHHHHHHHHhCCcceecHHHHHhhcchhhHHHHHHHHHHHhc
Confidence            34568999999999888 8887766    779999999999999999999999999999988754456799999999999


Q ss_pred             hceeccccCCCCC
Q 016331          265 WGIINYCAAVQSP  277 (391)
Q Consensus       265 WGLINy~~~~~~~  277 (391)
                      .|.|||++.+..+
T Consensus       214 ~g~in~gv~~~~~  226 (808)
T PLN02328        214 HGYINFGVAPVIK  226 (808)
T ss_pred             cCceeeecccccc
Confidence            9999999998765

>cd02336 ZZ_RSC8 Zinc finger, ZZ type

Probab=98.94  E-value=3.1e-10  Score=83.74  Aligned_cols=35  Identities=31%  Similarity=0.488  Sum_probs=33.3

Q ss_pred             cccCcCCCCCCCceeeeeec----------cCcccCCCcchhhhH
Q 016331          346 NHCNYCSQPIPAVYYQSQKE----------VDGRFSPLTFVYLFI  380 (391)
Q Consensus       346 y~C~~Cg~DCs~~rYhsqK~----------~dg~f~p~~~s~dFi  380 (391)
                      |||+.||+|||++|||++|.          .+|+|++++.++|||
T Consensus         1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G~f~~~~~s~Dfv   45 (45)
T cd02336           1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQEGRFPSNFQSSDFI   45 (45)
T ss_pred             CcccCCCCccCceEEEecCCCccccChHHHhCcCCCCCCcccccC
Confidence            79999999999999999998          689999999999996

Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.

>PLN02529 lysine-specific histone demethylase 1

Probab=98.47  E-value=1.8e-07  Score=101.92  Aligned_cols=86  Identities=22%  Similarity=0.255  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCHHHHhh--CCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhh
Q 016331          187 SDWFSPDTVHRLERQV--VPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNH  264 (391)
Q Consensus       187 s~WFd~d~Ih~iEk~~--lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~  264 (391)
                      +-=|..+.+++.|+++  +|..     .++.++.||.|||.||.+|+.||..+||+++++..+..--...|...|+||.+
T Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~yl~irn~il~~w~~np~~~~~~~~a~~~~~~~i~~ci~~c~~~l~~  138 (738)
T PLN02529         64 SVGFPIDALLEEEIRAGVVREL-----GGKEQNDYIVVRNHILARWRSNVGIWLSKGQIKETVSSEYEHLISAAYDFLLY  138 (738)
T ss_pred             HcCCCccccCHHHHhccccCcc-----ccccceeeehHHHHHHHHHHHCCceeecHHHHhhhchhhHHHHHHHHHHHHHh
Confidence            4558899999999855  3332     35889999999999999999999999999999987654223467789999999


Q ss_pred             hceeccccCCCCC
Q 016331          265 WGIINYCAAVQSP  277 (391)
Q Consensus       265 WGLINy~~~~~~~  277 (391)
                      .|.|||++.++..
T Consensus       139 ~~~inc~vnp~~~  151 (738)
T PLN02529        139 NGYINFGVSPSFA  151 (738)
T ss_pred             CCCcceeeccccc
Confidence            9999999998764

>PLN02976 amine oxidase

Probab=97.00  E-value=0.00058  Score=79.85  Aligned_cols=81  Identities=22%  Similarity=0.391  Sum_probs=66.7

Q ss_pred             CCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhc---ccCC--CCHHHHHHHHHhhhhhc
Q 016331          192 PDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQG---LVDG--VSPEDLTRIFRFLNHWG  266 (391)
Q Consensus       192 ~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr---~L~G--~Dv~~I~RVh~FLE~WG  266 (391)
                      -..+.++||-.|.|...-+   -.-..||++||.||-+|-+|=.+-|.+++|-=   -+..  .-..+|..|+.||++-|
T Consensus       457 a~~~~~~e~~~~k~~lkr~---~~~q~yl~cr~~~l~~w~k~~~~~l~~~~c~v~~~~~~~e~~~~~l~r~~~~fld~~g  533 (1713)
T PLN02976        457 ARAVGPIEKIKFKEVLKRK---GGLQEYLECRNMILGLWSKDVSRILPLADCGVTDTPSEDESPRASLIREVYLFLDQRG  533 (1713)
T ss_pred             ccccChHHHHHHHHHHHhc---cchHHHHHHHHHHHHHhhhhhhhcccHhhccccCCcccccCchhhHHHHHHHHhhccC
Confidence            4568899999999998765   45678999999999999999999999999932   1111  24578999999999999


Q ss_pred             eeccccCCC
Q 016331          267 IINYCAAVQ  275 (391)
Q Consensus       267 LINy~~~~~  275 (391)
                      .||-++...
T Consensus       534 yin~g~~s~  542 (1713)
T PLN02976        534 YINAGIASE  542 (1713)
T ss_pred             ceecccccc
Confidence            999998753

>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein

Probab=90.90  E-value=0.13  Score=37.43  Aligned_cols=34  Identities=24%  Similarity=0.405  Sum_probs=29.9

Q ss_pred             cCcccCcCCCCCCCceeeeeeccCcccCCCcchh
Q 016331          344 SENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVY  377 (391)
Q Consensus       344 ~ey~C~~Cg~DCs~~rYhsqK~~dg~f~p~~~s~  377 (391)
                      ..+.|+.|+.+++..||||+.-.|+-..+.+|+.
T Consensus         3 ~~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~   36 (44)
T smart00291        3 HSYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFAK   36 (44)
T ss_pred             CCcCCCCCCCCCcCCEEECCCCCCccchHHHHhC
Confidence            4588999999999999999998888888888764

Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].

>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]

Probab=82.07  E-value=1.7  Score=46.84  Aligned_cols=97  Identities=10%  Similarity=-0.036  Sum_probs=76.6

Q ss_pred             eCCCCCCCCCCCCCCHHHHhhCCcccCCCC-CCCChHHHHHHHHHHHHHHHhCCCceee-----HHHHhcccCC-CCHHH
Q 016331          182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKS-PDHTPEKYMECRNHIVAKYMDNPEKRLI-----VSDCQGLVDG-VSPED  254 (391)
Q Consensus       182 vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks-~~kTPe~Yl~iRN~II~~yr~NP~~yLT-----~T~cRr~L~G-~Dv~~  254 (391)
                      ..+..++=++...=+.-.....++|+.+++ ....+..|+.||+.+++.++---..+.+     -+..+++... ..+-+
T Consensus       185 ~~~~~~~~~~~~~~~~~~l~~~~c~~~~~~~~~~~~~~~~~~c~~c~~~g~~~~~~~~~Df~~~~~~~~~~WT~qE~lLL  264 (506)
T KOG1279|consen  185 TLSLESKIKSLHINAGEHLCAIHCFIKEDPYYYDLTNRDVNLCADCYDQGEFPSEFKKSDFKVIGESARPNWTEQETLLL  264 (506)
T ss_pred             cccccccccccccChHhhccccchhccccchhhhcchhhhhhhHHHHhcCCccCccccccchhccccCCCCccHHHHHHH
Confidence            455566777777778888899999998873 3678889999999999999765555554     4556666653 57889


Q ss_pred             HHHHHHhhhhhceeccccCCCCCC
Q 016331          255 LTRIFRFLNHWGIINYCAAVQSPE  278 (391)
Q Consensus       255 I~RVh~FLE~WGLINy~~~~~~~p  278 (391)
                      |-+|+.|.+.|+-|+.++-.+++.
T Consensus       265 LE~ie~y~ddW~kVa~hVg~ks~e  288 (506)
T KOG1279|consen  265 LEAIEMYGDDWNKVADHVGTKSQE  288 (506)
T ss_pred             HHHHHHhcccHHHHHhccCCCCHH
Confidence            999999999999999999976654

>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

Probab=80.18  E-value=0.53  Score=34.52  Aligned_cols=34  Identities=24%  Similarity=0.319  Sum_probs=26.6

Q ss_pred             cCcccCcCCC-CCCCceeeeeeccCcccCCCcchh
Q 016331          344 SENHCNYCSQ-PIPAVYYQSQKEVDGRFSPLTFVY  377 (391)
Q Consensus       344 ~ey~C~~Cg~-DCs~~rYhsqK~~dg~f~p~~~s~  377 (391)
                      ..+.|+.|+. .-...||+|+.-.|+.+...+|..
T Consensus         3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~   37 (46)
T PF00569_consen    3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK   37 (46)
T ss_dssp             SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred             CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence            4588999999 558999999999999988888875

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	391
2fq3_A	104	Structure And Function Of The Swirm Domain, A Conse		1e-12

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

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 33/85 (38%), Positives = 48/85 (56%), Gaps = 1/85 (1%)
Query: 186 HSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQG 245
           +S WF+ + +H +E Q +P FF+ + P  TPE YM  RN +V  Y  NP +   V+  + 
Sbjct: 16  YSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARR 75
Query: 246 LVDGVSPEDLTRIFRFLNHWGIINY 270
            V G     L R+ +FL  WG+INY
Sbjct: 76  NVSG-DAAALFRLHKFLTKWGLINY 99

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	391
2fq3_A	104	Transcription regulatory protein SWI3; four-helix	2e-38
2dce_A	111	KIAA1915 protein; swirm domain, structural genomic	6e-33
2xag_A	852	Lysine-specific histone demethylase 1; amine oxida	2e-08
2z3y_A	662	Lysine-specific histone demethylase 1; chromatin,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

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

 Score =  132 bits (335), Expect = 2e-38
 Identities = 33/94 (35%), Positives = 50/94 (53%), Gaps = 1/94 (1%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
           +   +S WF+ + +H +E Q +P FF+ + P  TPE YM  RN +V  Y  NP +   V+
Sbjct: 12  MASSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVT 71

Query: 242 DCQGLVDGVSPEDLTRIFRFLNHWGIINYCAAVQ 275
             +  V G     L R+ +FL  WG+INY    +
Sbjct: 72  TARRNVSG-DAAALFRLHKFLTKWGLINYQVDSK 104

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

 Score =  118 bits (297), Expect = 6e-33
 Identities = 26/102 (25%), Positives = 45/102 (44%), Gaps = 5/102 (4%)

Query: 182 VLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVS 241
             P        + +   E+Q +P FF G+    TPE+Y++ RN+I+ ++     K L  +
Sbjct: 14  KPPEQEIEIDRNIIQEEEKQAIPEFFEGR-QAKTPERYLKIRNYILDQWEICKPKYLNKT 72

Query: 242 DCQ-GLVDGVSPEDLTRIFRFLNHWGIINYCAAVQSPEPWNR 282
             + GL +      + RI  +L   G IN+         +NR
Sbjct: 73  SVRPGLKNCGDVNCIGRIHTYLELIGAINFGCE---QAVYNR 111

>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

 Score = 55.8 bits (133), Expect = 2e-08
 Identities = 38/252 (15%), Positives = 68/252 (26%), Gaps = 30/252 (11%)

Query: 32  DVVEDEDEEQDNNETDNHNNNSNADHRDNGDDFQHATAPDPASNETEVLIDGGTRICEFP 91
           +V      E+   + +    +      +          P         +  G     E  
Sbjct: 49  EVGPGAVGERTPRKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGR 108

Query: 92  TAVQRVVNRPHVSVMDIVAIEAAYLAGDASGRSSAVALENISFGQLQALSVVPADSAALD 151
              +R   R  V   +            A+        E     + +    +P       
Sbjct: 109 RTSRR--KRAKVEYRE-------MDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAP 159

Query: 152 PERSDTSCVITPPQIMEGKGVVKRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKS 211
           PE  + S    P  +         F SR             D +   E    P   SG  
Sbjct: 160 PEEENESEPEEPSGV-----EGAAFQSR----------LPHDRMTSQEAACFPDIISG-- 202

Query: 212 PDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLV---DGVSPEDLTRIFRFLNHWGII 268
           P  T + ++  RN  +  ++DNP+ +L        +          + R+  +L   G+I
Sbjct: 203 PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLI 262

Query: 269 NY-CAAVQSPEP 279
           N+       P P
Sbjct: 263 NFGIYKRIKPLP 274

>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

 Score = 54.9 bits (131), Expect = 2e-08
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 5/84 (5%)

Query: 190 FSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDG 249
              D +   E    P   SG  P  T + ++  RN  +  ++DNP+ +L        ++ 
Sbjct: 12  LPHDRMTSQEAACFPDIISG--PQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEA 69

Query: 250 ---VSPEDLTRIFRFLNHWGIINY 270
                   + R+  +L   G+IN+
Sbjct: 70  PYNSDTVLVHRVHSYLERHGLINF 93

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

 Score = 51.0 bits (121), Expect = 5e-07
 Identities = 69/496 (13%), Positives = 134/496 (27%), Gaps = 168/496 (33%)

Query: 20  EPRKQLNKLDEDDVVEDEDEEQDNNETDN-----HNNNSNADHRDNGDDFQ--------- 65
            P+  L+K + D ++  +D       T        +       +   +  +         
Sbjct: 41  MPKSILSKEEIDHIIMSKDAVS---GTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSP 97

Query: 66  -HATAPDPASNETEVLIDGGTRIC-EFPTAVQRVVNRPH-----------VSVMDIVAIE 112
                  P S  T + I+   R+  +     +  V+R             +     V I+
Sbjct: 98  IKTEQRQP-SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID 156

Query: 113 AAYLAGDASGRSS--AVALEN-------------ISFG----------QLQALSVVPADS 147
              + G  SG++        +             ++             LQ L       
Sbjct: 157 G--VLG--SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQ---- 208

Query: 148 AALDP---ERSDTSCVITPPQIMEGKGVVKR-FGSRVH-----VL-----PMHSDWFSP- 192
             +DP    RSD S  I   +I   +  ++R   S+ +     VL         + F+  
Sbjct: 209 --IDPNWTSRSDHSSNI-KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS 265

Query: 193 -------------DTVHRLERQVVP--HFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKR 237
                        D +       +   H     +PD            ++ KY+D   + 
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS--------LLLKYLDCRPQD 317

Query: 238 LIVSDCQGLVDGVSPEDLTRI---FR-FLNHWG------------IINYCAAVQSPEPWN 281
           L            +P  L+ I    R  L  W             II     V  P  + 
Sbjct: 318 LPREVLTT-----NPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEY- 371

Query: 282 RGSY-----LREDSNGEVSVPSDAL-------KSID-----------SLIKFDKPKCSLK 318
           R  +         ++    +P+  L          D           SL++    + ++ 
Sbjct: 372 RKMFDRLSVFPPSAH----IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS 427

Query: 319 VADVY-SSSCGGADFFDLDNTIRER--LSENHC-NYCSQPIPAVY-YQ------SQKEVD 367
           +  +Y        + + L  +I +   + +    +    P    Y Y          E  
Sbjct: 428 IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHP 487

Query: 368 GRFSPLTFVYL---FI 380
            R +    V+L   F+
Sbjct: 488 ERMTLFRMVFLDFRFL 503

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

 Score = 46.0 bits (108), Expect = 2e-05
 Identities = 31/246 (12%), Positives = 67/246 (27%), Gaps = 65/246 (26%)

Query: 174 KRFGSRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDN 233
           + +  +   L   +  F+   V R                   + Y++ R  +       
Sbjct: 110 RMYIEQRDRLYNDNQVFAKYNVSR------------------LQPYLKLRQAL---LELR 148

Query: 234 PEKRLIVSDCQG--------LV-DGVSPEDLTRIFRFLNHW-GIINYCAAVQSPEPWNRG 283
           P K +++    G        +  D      +     F   W  + N  +     E   + 
Sbjct: 149 PAKNVLI---DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL 205

Query: 284 SYL-------REDSNGEVSVPSDALKSIDSLIKFDK--PKCSLKVADVYSSSCGGADFFD 334
            Y        R D +  + +   ++++    +   K    C L + +V ++     + F+
Sbjct: 206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA--WNAFN 263

Query: 335 L---------DNTIRERLSENHCNYCSQPIPAVYYQSQKEVDGRFSPLTFVYLFI-CLFL 384
           L            + + LS               + S        +P     L +  L  
Sbjct: 264 LSCKILLTTRFKQVTDFLSAAT----------TTHISLDHHSMTLTPDEVKSLLLKYLDC 313

Query: 385 SSVYLP 390
               LP
Sbjct: 314 RPQDLP 319

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	391
2fq3_A	104	Transcription regulatory protein SWI3; four-helix	100.0
2dce_A	111	KIAA1915 protein; swirm domain, structural genomic	100.0
2z3y_A	662	Lysine-specific histone demethylase 1; chromatin,	98.78
4gut_A	776	Lysine-specific histone demethylase 1B; histone de	98.55
2xag_A	852	Lysine-specific histone demethylase 1; amine oxida	98.02
2aqe_A	90	Transcriptional adaptor 2, ADA2 alpha; helix-turn-	96.18
2cuj_A	108	Transcriptional adaptor 2-like; transcriptional re	95.97
2elj_A	88	Transcriptional adapter 2; YDR448W, structural gen	95.71

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

Probab=100.00  E-value=1.1e-41  Score=287.08  Aligned_cols=94  Identities=35%  Similarity=0.704  Sum_probs=84.5

Q ss_pred             eeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHH
Q 016331          181 HVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFR  260 (391)
Q Consensus       181 ~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~  260 (391)
                      -..|+++.||+|++||+|||++|||||+|++++|||++||+|||+||++||+||.+|||+|+||++|+| |+++|+|||+
T Consensus        11 ~~~p~~s~wF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Yl~iRN~iI~~yr~nP~~yLT~t~~r~~l~g-Dv~~i~RVh~   89 (104)
T 2fq3_A           11 GMASSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRNVSG-DAAALFRLHK   89 (104)
T ss_dssp             ------CTTCCTTCCCHHHHHHCGGGCCSSCTTSCHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHSCS-CHHHHHHHHH
T ss_pred             CCCCCcccccCcccCCHHHHHHChHHhcCCCCCCCHHHHHHHHHHHHHHHHhCCceeeeHHHHHHHccc-cHHHHHHHHH
Confidence            467999999999999999999999999999999999999999999999999999999999999999998 9999999999


Q ss_pred             hhhhhceeccccCCC
Q 016331          261 FLNHWGIINYCAAVQ  275 (391)
Q Consensus       261 FLE~WGLINy~~~~~  275 (391)
                      |||+|||||||++++
T Consensus        90 FLe~wGLIN~~v~~~  104 (104)
T 2fq3_A           90 FLTKWGLINYQVDSK  104 (104)
T ss_dssp             HHHHTTSSSSCC---
T ss_pred             HHHHcCeeccCCCCC
Confidence            999999999999873

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

Probab=100.00  E-value=2.5e-41  Score=287.71  Aligned_cols=97  Identities=24%  Similarity=0.367  Sum_probs=92.9

Q ss_pred             CceeeCCCCCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhccc--CCCCHHHH
Q 016331          178 SRVHVLPMHSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLV--DGVSPEDL  255 (391)
Q Consensus       178 ~~~~vIPs~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L--~G~Dv~~I  255 (391)
                      .++++||+|+.||++++||+|||++|||||+|+ ++|||++||+|||+||++||+||.+|||+|+||++|  +| |+++|
T Consensus        10 ~~~~~iP~~~~wf~~~~ih~iEk~~lPefF~g~-~~ktpe~Yl~iRN~iI~~yr~np~~yLT~t~~rr~L~~~g-Dv~~i   87 (111)
T 2dce_A           10 EEELKPPEQEIEIDRNIIQEEEKQAIPEFFEGR-QAKTPERYLKIRNYILDQWEICKPKYLNKTSVRPGLKNCG-DVNCI   87 (111)
T ss_dssp             CCSCCCCSSCCCCCSSCCCHHHHTTSGGGGSCC-SSCCHHHHHHHHHHHHHHHHHHTTSCCCGGGTTTTTSSSS-CHHHH
T ss_pred             CcCCcCCCcccccCcccCCHHHHHhChHHhcCC-cccCHHHHHHHHHHHHHHHHhCCcceeeHHHHHHhccccc-CHHHH
Confidence            357999999999999999999999999999998 799999999999999999999999999999999999  47 99999


Q ss_pred             HHHHHhhhhhceeccccCCCC
Q 016331          256 TRIFRFLNHWGIINYCAAVQS  276 (391)
Q Consensus       256 ~RVh~FLE~WGLINy~~~~~~  276 (391)
                      +|||+|||+|||||||+++..
T Consensus        88 ~RVh~FLe~wGLIN~~~~~~~  108 (111)
T 2dce_A           88 GRIHTYLELIGAINFGCEQAV  108 (111)
T ss_dssp             HHHHHHHHHHSSSSCSCTTSS
T ss_pred             HHHHHHHHHcCeeecCCChhh
Confidence            999999999999999999864

>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

Probab=98.78  E-value=5.6e-09  Score=108.62  Aligned_cols=85  Identities=20%  Similarity=0.378  Sum_probs=73.2

Q ss_pred             CCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhccc----CCCCHHHHHHHHHhhhhh
Q 016331          190 FSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLV----DGVSPEDLTRIFRFLNHW  265 (391)
Q Consensus       190 Fd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L----~G~Dv~~I~RVh~FLE~W  265 (391)
                      |+.+.+|+.|+.+|||+..+.  ..+...||.|||.|+.+|+.||..+||+.+|...+    .. |...|.+|+.||..+
T Consensus        12 l~~~~l~~~E~~~~~~~~~~~--~~~~~~yl~irn~~~~~w~~~~~~~~~~~~~~~~~~r~~~~-~~~~i~~~~~~~~~~   88 (662)
T 2z3y_A           12 LPHDRMTSQEAACFPDIISGP--QQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNS-DTVLVHRVHSYLERH   88 (662)
T ss_dssp             CCTTSCCHHHHHHCHHHHTSC--HHHHHHHHHHHHHHHHHHHTCTTBCCCHHHHHHHSCTTGGG-CHHHHHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHhHHHHcCc--hHHHHHHHHHHHHHHHHHHHCCCcccCHHHHHHhcCCCccC-ChHHHHHHHHHHHHH
Confidence            589999999999999999762  34567999999999999999999999999994433    33 778999999999999


Q ss_pred             ceeccccCCCCC
Q 016331          266 GIINYCAAVQSP  277 (391)
Q Consensus       266 GLINy~~~~~~~  277 (391)
                      |+||++......
T Consensus        89 ~~~~~~~~~~~~  100 (662)
T 2z3y_A           89 GLINFGIYKRIK  100 (662)
T ss_dssp             TSSSCSSCBCSS
T ss_pred             HHHhcCCccccC
Confidence            999998876533

>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*

Probab=98.55  E-value=1.4e-07  Score=101.09  Aligned_cols=88  Identities=24%  Similarity=0.320  Sum_probs=74.0

Q ss_pred             eeCCCCCCCCCC------------CCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccC
Q 016331          181 HVLPMHSDWFSP------------DTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVD  248 (391)
Q Consensus       181 ~vIPs~s~WFd~------------d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~  248 (391)
                      ..+..+-.||-.            +.|+..|+.+||||..+      +..||.|||.|+.+|+.||...||...|.+.+.
T Consensus       217 ~~~~~~~~~~~~~~~~~~a~~~~p~~~~~~e~~~fp~~~~~------~~~yl~irn~il~~w~~np~~~l~~~~~~~~~~  290 (776)
T 4gut_A          217 PGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRD------PTMYLALRNLILALWYTNCKEALTPQKCIPHII  290 (776)
T ss_dssp             -CCCTTCCCBCCTTCCCCSSCBCTTSCCHHHHHHCGGGSSC------CHHHHHHHHHHHHHHHHCTTSCCCHHHHGGGCC
T ss_pred             cccccccccccCCCccccchhcCCCcCChHHHHhChHHHhc------CceeeeehHHHHHHHHHCCceeeeHHHhhhhcc
Confidence            445567777755            99999999999999965      569999999999999999999999999987663


Q ss_pred             --C-C---CHHHHHHHHHhhhhhceeccccCC
Q 016331          249 --G-V---SPEDLTRIFRFLNHWGIINYCAAV  274 (391)
Q Consensus       249 --G-~---Dv~~I~RVh~FLE~WGLINy~~~~  274 (391)
                        + .   .+..+.+|+.||.++|+||++...
T Consensus       291 ~r~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  322 (776)
T 4gut_A          291 VRGLVRIRCVQEVERILYFMTRKGLINTGVLS  322 (776)
T ss_dssp             CSSTHHHHHHHHHHHHHHHHHHHTSSSCTTCC
T ss_pred             cccccccccHHHHHHHHHHHHHhhhhhccccc
Confidence              2 1   345689999999999999998754

>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

Probab=98.02  E-value=6.1e-06  Score=89.58  Aligned_cols=86  Identities=20%  Similarity=0.364  Sum_probs=71.6

Q ss_pred             CCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHh----cccCCCCHHHHHHHHHhhh
Q 016331          188 DWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQ----GLVDGVSPEDLTRIFRFLN  263 (391)
Q Consensus       188 ~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cR----r~L~G~Dv~~I~RVh~FLE  263 (391)
                      ..|..+.+|..|+.+|+++-..-  .....+|+.|||+|+.+|+.||...|+...|.    +.+.. |...|.+|++||.
T Consensus       181 ~r~p~~~~~~~e~~~f~~~~~~~--~~~~~~~~~~rn~i~~~w~~~P~~a~~~~~~~~~~~r~~~~-~p~~i~~~~~~~~  257 (852)
T 2xag_A          181 SRLPHDRMTSQEAACFPDIISGP--QQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNS-DTVLVHRVHSYLE  257 (852)
T ss_dssp             TTCCTTSCCHHHHHHCHHHHTSC--HHHHHHHHHHHHHHHHHHHTCTTBCCCHHHHHHHCCTTTTS-CHHHHHHHHHHHH
T ss_pred             hcCCCcccChHHHHHHHHHHHhh--hhhcCeeeEeecchhHHHhcCCHHHhhHHHHHHhCCCcccC-CcHHHHHHHHHHH
Confidence            44688899999999999988651  23567999999999999999999999987773    33334 7889999999999


Q ss_pred             hhceeccccCCCC
Q 016331          264 HWGIINYCAAVQS  276 (391)
Q Consensus       264 ~WGLINy~~~~~~  276 (391)
                      +|++||++.....
T Consensus       258 ~~~~~~~~~~~~~  270 (852)
T 2xag_A          258 RHGLINFGIYKRI  270 (852)
T ss_dssp             HTTSSSCSSCBCS
T ss_pred             HHHHHhcCccccc
Confidence            9999999887544

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

Probab=96.18  E-value=0.006  Score=49.73  Aligned_cols=70  Identities=16%  Similarity=0.378  Sum_probs=58.6

Q ss_pred             CCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceec
Q 016331          191 SPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIIN  269 (391)
Q Consensus       191 d~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLIN  269 (391)
                      +.+-+|+-|++.+-..      .=.|..||.+...||.-...+..  |+.++|+..+. +|++-..||++||.+.|+|+
T Consensus        19 ~~~lLs~~E~~LC~~l------rL~P~~YL~~K~~li~E~~~~g~--l~k~da~~~~k-iD~~K~~~iydf~~~~Gwi~   88 (90)
T 2aqe_A           19 GTEKLNEKEKELCQVV------RLVPGAYLEYKSALLNECHKQGG--LRLAQARALIK-IDVNKTRKIYDFLIREGYIT   88 (90)
T ss_dssp             STTTSCHHHHHHHHHT------TCCHHHHHHHHHHHHHHHHHHSC--CCHHHHHTTSS-SSSHHHHHHHHHHHHTTSSC
T ss_pred             CchhcCHHHHHHHHHh------CCCHHHHHHHHHHHHHHHHHcCC--CcHHHHHHHHc-ccHHHHHHHHHHHHHcCCCC
Confidence            4567889999886543      35699999999999999966433  89999999764 69999999999999999995

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

Probab=95.97  E-value=0.0088  Score=50.53  Aligned_cols=70  Identities=16%  Similarity=0.377  Sum_probs=59.2

Q ss_pred             CCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceec
Q 016331          191 SPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIIN  269 (391)
Q Consensus       191 d~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLIN  269 (391)
                      ..+-+|+-|++.+-..      .=.|..||.+.+.||.-+..+-  .|+.++||..+. +|++-..||++||.+.|+|+
T Consensus        37 g~~LLs~~E~~LCs~l------rL~P~~YL~iK~~Li~E~~k~g--~lkk~dA~~l~k-ID~~K~~rIydff~~~GWi~  106 (108)
T 2cuj_A           37 GTEKLNEKEKELCQVV------RLVPGAYLEYKSALLNECHKQG--GLRLAQARALIK-IDVNKTRKIYDFLIREGYIT  106 (108)
T ss_dssp             TTTTSCHHHHHHHHHT------TCCHHHHHHHHHHHHHHHHHSS--CCCHHHHHHHHT-SCHHHHHHHHHHHHTTTSSC
T ss_pred             CchhcCHHHHHHHHHh------CCCHHHHHHHHHHHHHHHHHcC--CCcHHHHHHHhc-ccHHHHHHHHHHHHHcCCCC
Confidence            5678899999986554      3569999999999999996543  399999999765 69999999999999999995

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

Probab=95.71  E-value=0.012  Score=47.68  Aligned_cols=70  Identities=17%  Similarity=0.361  Sum_probs=58.4

Q ss_pred             CCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhcee
Q 016331          191 SPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGII  268 (391)
Q Consensus       191 d~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLI  268 (391)
                      +.+-.|+-|++.+-..      .=.|..||.+.+.||.-+..+ ...++.++|+..+. +|++-..||++||.+.|+|
T Consensus        19 ~~~lLs~~E~~LC~~l------rL~P~~YL~~K~~Li~E~~k~-g~~lkk~da~~~~k-iD~~K~~~iydf~~~~Gwi   88 (88)
T 2elj_A           19 DYALLSNDEQQLCIQL------KILPKPYLVLKEVMFRELLKT-GGNLSKSACRELLN-IDPIKANRIYDFFQSQNWM   88 (88)
T ss_dssp             TCSSSCHHHHHHHHHT------TCCHHHHHHHHHHHHHHHHHH-SSCCCHHHHHHHTT-SCHHHHHHHHHHHHHTTCC
T ss_pred             CchhcCHHHHHHHHHh------CCCHHHHHHHHHHHHHHHHHh-CCCccHHHHHHHHc-ccHHHHHHHHHHHHHcCCC
Confidence            5567888898875543      356999999999999999654 45688999999764 6999999999999999987

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	391
d2fq3a1	85	a.4.1.18 (A:311-395) Transcription regulatory prot	2e-31
d2dw4a1	102	a.4.1.18 (A:172-273) Lysine-specific histone demet	2e-24

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

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 =  112 bits (281), Expect = 2e-31
 Identities = 33/84 (39%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 187 SDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL 246
           S WF+ + +H +E Q +P FF+ + P  TPE YM  RN +V  Y  NP +   V+  +  
Sbjct: 1   SKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRN 60

Query: 247 VDGVSPEDLTRIFRFLNHWGIINY 270
           V G     L R+ +FL  WG+INY
Sbjct: 61  VSG-DAAALFRLHKFLTKWGLINY 83

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

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SWIRM domain
domain: Lysine-specific histone demethylase 1, LSD1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 94.1 bits (234), Expect = 2e-24
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 187 SDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGL 246
                 D +   E    P   SG     T + ++  RN  +  ++DNP+ +L        
Sbjct: 9   QSRLPHDRMTSQEAACFPDIISGPQ--QTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQ 66

Query: 247 VDGVSPEDLT---RIFRFLNHWGIINY 270
           ++     D     R+  +L   G+IN+
Sbjct: 67  LEAPYNSDTVLVHRVHSYLERHGLINF 93

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	391
d2fq3a1	85	Transcription regulatory protein swi3 {Baker's yea	100.0
d2dw4a1	102	Lysine-specific histone demethylase 1, LSD1 {Human	99.97
d2cuja1	101	Transcriptional adaptor 2-like, TADA2L {Mouse (Mus	96.89

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

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=9.6e-37  Score=246.30  Aligned_cols=85  Identities=39%  Similarity=0.794  Sum_probs=83.4

Q ss_pred             CCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhc
Q 016331          187 SDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWG  266 (391)
Q Consensus       187 s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WG  266 (391)
                      |+||+|++||+|||++|||||+|++..|||++||+|||+||++|++||.+|||+|+|++++.| |++++.|||+||++||
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 9999999999999999


Q ss_pred             eecccc
Q 016331          267 IINYCA  272 (391)
Q Consensus       267 LINy~~  272 (391)
                      +||||+
T Consensus        80 ~INf~v   85 (85)
T d2fq3a1          80 LINYQV   85 (85)
T ss_dssp             SSSSCC
T ss_pred             ccCccC
Confidence            999996

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

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SWIRM domain
domain: Lysine-specific histone demethylase 1, LSD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.1e-31  Score=223.06  Aligned_cols=91  Identities=19%  Similarity=0.346  Sum_probs=85.4

Q ss_pred             CCCCCCCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCC---CCHHHHHHHHHhh
Q 016331          186 HSDWFSPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDG---VSPEDLTRIFRFL  262 (391)
Q Consensus       186 ~s~WFd~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G---~Dv~~I~RVh~FL  262 (391)
                      +++||++++||++|+++|||||+|.  ++||+.||.|||+||++|++||.+|||+|+|+++|..   .|+++++|||+||
T Consensus         8 ~~s~l~~d~l~~~E~~~fpe~~~~~--~~~~~~Yl~iRN~Il~~w~~np~~~Lt~~~~~~~l~~~~~~d~~li~ri~~FL   85 (102)
T d2dw4a1           8 FQSRLPHDRMTSQEAACFPDIISGP--QQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYL   85 (102)
T ss_dssp             HHTTCCTTSCCHHHHHHCHHHHTSC--HHHHHHHHHHHHHHHHHHHHCTTBCCCHHHHHHHSCTTGGGCHHHHHHHHHHH
T ss_pred             HHccCCCCcCCHHHHHHChHhhcCC--CCCHHHHHHHHHHHHHHHHhCCCeeeeHHHHHhhccccccccHHHHHHHHHHH
Confidence            3589999999999999999999884  7899999999999999999999999999999999872   3999999999999


Q ss_pred             hhhceeccccCCCCCC
Q 016331          263 NHWGIINYCAAVQSPE  278 (391)
Q Consensus       263 E~WGLINy~~~~~~~p  278 (391)
                      ++||+||||++++.+|
T Consensus        86 ~~~G~INfGv~~r~~P  101 (102)
T d2dw4a1          86 ERHGLINFGIYKRIKP  101 (102)
T ss_dssp             HHTTSSSCSSCBCCSC
T ss_pred             HHcCceeeCcCcCCCC
Confidence            9999999999998887

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

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: SWIRM domain
domain: Transcriptional adaptor 2-like, TADA2L
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.89  E-value=0.00082  Score=54.17  Aligned_cols=70  Identities=16%  Similarity=0.366  Sum_probs=60.4

Q ss_pred             CCCCCCHHHHhhCCcccCCCCCCCChHHHHHHHHHHHHHHHhCCCceeeHHHHhcccCCCCHHHHHHHHHhhhhhceec
Q 016331          191 SPDTVHRLERQVVPHFFSGKSPDHTPEKYMECRNHIVAKYMDNPEKRLIVSDCQGLVDGVSPEDLTRIFRFLNHWGIIN  269 (391)
Q Consensus       191 d~d~Ih~iEk~~lPEFF~gks~~kTPe~Yl~iRN~II~~yr~NP~~yLT~T~cRr~L~G~Dv~~I~RVh~FLE~WGLIN  269 (391)
                      ..+-+|+-|++.+-..=      =-|..||.+.+.||.-+..+  ..++.++||+.+. +|++-..||++||.+-|+||
T Consensus        30 ~~~lLs~~E~~LC~~lr------L~P~~YL~~K~~l~~E~~k~--g~l~k~da~~~~k-iD~~K~~rIydfl~~~GWi~   99 (101)
T d2cuja1          30 GTEKLNEKEKELCQVVR------LVPGAYLEYKSALLNECHKQ--GGLRLAQARALIK-IDVNKTRKIYDFLIREGYIT   99 (101)
T ss_dssp             TTTTSCHHHHHHHHHTT------CCHHHHHHHHHHHHHHHHHS--SCCCHHHHHHHHT-SCHHHHHHHHHHHHTTTSSC
T ss_pred             ChhhcCHHHHHHHHHhC------CChHHHHHHHHHHHHHHHHc--CCCcHHHHHHHhc-ccHHHHHHHHHHHHHccCcc
Confidence            56789999999865543      45999999999999988774  4699999999765 69999999999999999997