Citrus Sinensis ID: 008612

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------56

MEMPQYDPNTKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVAGETGVKLPPLASYLDVFGDLVKLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLKEGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALCNESSCPREIFDGDEDYLANGLSSPTMVSDPERALQVDASKMEENQSETQDASSEKNDVPLNLRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSKWRS

cccccccccccccccEEEccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHcccccEEHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHcccccHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHHHcccccccccccccHHHcccccccccccccHHHHHHcccHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccc

cccccccccccccccEEEEcccccccccccHHHHHHHHcHHHHccccccccHHHHHHHHHHHHHHHccccHHEEEHHHHHHHHHHHHHHHHHHHHHHHHcccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccHHHcccccccccccccccccccccEEccccHccccccHHHHHcccccccccccccEEEccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHcccccccccccHHHcccHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccHHHHcccccHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHcc

mempqydpntkpefelytipshsswfrwddIHETERTALKeffdgssisrtpKIYKEYRDFMINKyreepsrrltFTQVRKSLVGDVSLLHKVFRLLDewglinfgavsrgddsdnrdsslgdtelknqvkieegapngvrvvalpnslkpisvpnsgadgsgngkvavagetgvklpplasyLDVFGDLVklkgfkcgscgeqcnsgcyeyskqgsfVICEkcfkngnygedkskddfrfsdlggnslthgatwTEAETLLLLESVMRHgdnwelvaqnvptkskLDCISKLielpfgefmmgsahemnssscptgslnslkegqsassenqndvkmEDQVHDQMneskqngdaateeppakrkriaplsdggsTLIKQVAHISTMVGPHVTAAAAEAAVAALCnesscpreifdgdedylanglssptmvsdperaLQVDASkmeenqsetqdassekndvplnLRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSKWRS

mempqydpntkpeFELYTIPSHSSWFRWDDIHETERTAlkeffdgssisrtpkiYKEYRDFMINKyreepsrrltftqVRKSLVGDVSLLHKVFRLLDEWGLINfgavsrgddsdnrdsslgdtelknqvkieegapngvRVVALPNSLKPisvpnsgadgsgNGKVAVAGETGVKLPPLASYLDVFGDLVKLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAqnvptksklDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLKEGQSASSENQNDVKMEDQVHDQMNESkqngdaateeppakrkriaplsdggSTLIKQVAHISTMVGPHVTAAAAEAAVAALCNESSCPREIFDGDEDYLANGlssptmvsdPERALQVDASKMEenqsetqdassekndvplNLRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERAlktgvskwrs

MEMPQYDPNTKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVsrgddsdnrdsslgdTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVAGETGVKLPPLASYLDVFGDLVKLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGatwteaetlllleSVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLKEGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTaaaaeaavaaLCNESSCPREIFDGDEDYLANGLSSPTMVSDPERALQVDASKMEENQSETQDASSEKNDVPLNLRIRtatatalgaaaanakllaDQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSKWRS

*************FELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAV**********************************************************VAVAGETGVKLPPLASYLDVFGDLVKLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGED***DDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMM************************************************************************TLIKQVAHISTMVGPHVTAAAAEAAVAALCNESSCPREIFDGDEDY********************************************NLRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKT*******

****************YTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR********************KIEEGAPNGVR**************************************************KLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFK*****************************TEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEF***************************************************************************************************************************************************************************************************HLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVL*************

*********TKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSRG**********GDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVAGETGVKLPPLASYLDVFGDLVKLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAH*****************************KMEDQV********************KRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALCNESSCPREIFDGDEDYLANGLSSPTMVSDPERALQVDA******************DVPLNLRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGVSKWRS

********NTKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSRG***DNR********LKNQVKIEEGAPN*V***************************************************KLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLG****THGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGS*****************KE*Q*************************************RKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALCNE*********************************************************LNLRIRTATATALGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVLERALKTGV*****

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		559	2.2.26 [Sep-21-2011]
Q8W475		512	SWI/SNF complex subunit S	yes	no	0.890	0.972	0.510	1e-127
Q84JG2		469	SWI/SNF complex subunit S	no	no	0.744	0.886	0.265	1e-45
Q9XI07		807	SWI/SNF complex subunit S	no	no	0.847	0.587	0.270	3e-44
O14470		503	SWI/SNF and RSC complexes	yes	no	0.545	0.606	0.297	1e-32
P43609		557	Chromatin structure-remod	yes	no	0.470	0.472	0.308	2e-31
O13788		527	SWI/SNF and RSC complexes	no	no	0.502	0.533	0.300	6e-31
Q8VY05		985	SWI/SNF complex subunit S	no	no	0.456	0.258	0.291	6e-24
Q8TAQ2		1214	SWI/SNF complex subunit S	yes	no	0.177	0.081	0.432	2e-21
Q6PDG5		1213	SWI/SNF complex subunit S	yes	no	0.177	0.081	0.432	2e-21
P32591		825	SWI/SNF complex subunit S	no	no	0.441	0.299	0.275	5e-21

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

 Score =  457 bits (1175), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 286/560 (51%), Positives = 368/560 (65%), Gaps = 62/560 (11%)

Query: 3   MPQYDPNTKPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFM 62
           M   DP+   E ELYTIP+ SSWF WDDIHE ER    EFF  SSI+RTPK+YKEYRDF+
Sbjct: 1   MEATDPSA--EIELYTIPAQSSWFLWDDIHEIERREFAEFFTESSITRTPKVYKEYRDFI 58

Query: 63  INKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSRGDDS----DNRD 118
           INK+RE+  RRLTFT VRK LVGDV+LL KVF  L++WGLINF +  + +D     DN  
Sbjct: 59  INKFREDTCRRLTFTSVRKFLVGDVNLLQKVFLFLEKWGLINFSSSLKKNDHLLSVDN-- 116

Query: 119 SSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVAGETGVKLP 178
                       KIE+G P G+RV A PNSL+PI+ P           V    ETG+K+P
Sbjct: 117 -----------AKIEQGTPAGIRVTATPNSLRPITAP---------PLVEERVETGIKVP 156

Query: 179 PLASYLDVFGDLVKLKG-FKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKD 237
           PL SY DVF DL K      C  CGE+C+S  Y+++K G   ICEKCFKNGNYGE+ + D
Sbjct: 157 PLTSYSDVFSDLKKPDHVLVCAHCGERCDSPFYQHNK-GIVNICEKCFKNGNYGENNTAD 215

Query: 238 DFRFSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELP 297
           DF+   L GNS    A WTE E LLLLESV++HGD+WEL++Q+V TKS+LDCISKLIELP
Sbjct: 216 DFK---LIGNS--AAAVWTEEEILLLLESVLKHGDDWELISQSVSTKSRLDCISKLIELP 270

Query: 298 FGEFMMGSAHEMNSSSCPTGSLNSLKEGQSASSENQNDVKMEDQVHDQMNESKQNGDAAT 357
           FGEF+MGSA         +G LN          EN   V+ + Q H++    ++  D   
Sbjct: 271 FGEFLMGSA---------SGRLNP---SILTEDENTEQVQTDGQEHEETETREEKEDRVN 318

Query: 358 E-EPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALCNESSCPREIFD 416
           E EPPAKRKR+A +S+G S+L+KQVA +++ VGP V  AAA+AA+AALC+E+SCP+EIFD
Sbjct: 319 EDEPPAKRKRVALISEGDSSLMKQVAAMASKVGPSVATAAAKAALAALCDEASCPKEIFD 378

Query: 417 GDEDYLANGLSSPTMVSDPERALQVDASKMEENQSETQDASSEKNDVPLNLRIRTATATA 476
            D DY     S+ T+    +RA     + MEE Q E          +P+ LRIR + ATA
Sbjct: 379 TD-DY-----SNFTV----DRANGEKDTDMEEQQEEKDGPQG----LPVALRIRASVATA 424

Query: 477 LGAAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKE 536
           LGAAAA AK+LADQE+RE+E L A +IE Q+KKL SK+ + DDLE IM++E   +  +KE
Sbjct: 425 LGAAAAQAKILADQEEREMEQLAATVIEQQLKKLQSKLKFLDDLESIMDEEEKVIEGVKE 484

Query: 537 CLVEERIDVLERALKTGVSK 556
            +++ER+ VL+ A ++G++K
Sbjct: 485 TIIQERVSVLQCAFRSGITK 504

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	Back alignment and function description

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

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

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

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

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

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

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

>sp\|P32591\|SWI3_YEAST SWI/SNF complex subunit SWI3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SWI3 PE=1 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		559
225456390		563	PREDICTED: SWI/SNF complex subunit SWI3A	0.960	0.953	0.607	1e-174
147858898		563	hypothetical protein VITISV_043833 [Viti	0.960	0.953	0.607	1e-174
224136238		570	chromatin remodeling complex subunit [Po	0.967	0.949	0.598	1e-174
255540147		547	DNA binding protein, putative [Ricinus c	0.953	0.974	0.582	1e-169
357465011		540	SWI/SNF complex subunit SMARCC2 [Medicag	0.944	0.977	0.561	1e-166
356509348		527	PREDICTED: SWI/SNF complex subunit SWI3A	0.919	0.975	0.553	1e-154
356518589		522	PREDICTED: SWI/SNF complex subunit SWI3A	0.912	0.977	0.557	1e-151
449523928		566	PREDICTED: SWI/SNF complex subunit SWI3A	0.951	0.939	0.528	1e-142
449440963		566	PREDICTED: SWI/SNF complex subunit SWI3A	0.951	0.939	0.530	1e-141
30690734		512	SWI/SNF complex subunit SWI3A [Arabidops	0.890	0.972	0.510	1e-126

>gi\|225456390\|ref\|XP_002280389.1\| PREDICTED: SWI/SNF complex subunit SWI3A [Vitis vinifera] gi\|297734457\|emb\|CBI15704.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

 Score =  619 bits (1597), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 340/560 (60%), Positives = 423/560 (75%), Gaps = 23/560 (4%)

Query: 7   DPNTK------PEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRD 60
           DP++K      PE +LYTIP HSSWF WD+IHE E+ +LKEFFDGSSISRTPKIYKEYRD
Sbjct: 6   DPSSKLTRHDEPELDLYTIPIHSSWFSWDEIHEKEKISLKEFFDGSSISRTPKIYKEYRD 65

Query: 61  FMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSRGDDSDNRDSS 120
           F+I+KYRE+PSRRLTF ++RKSLVGDVSLLHKVF  L+ WGLINFGA   G+DS    ++
Sbjct: 66  FIISKYREDPSRRLTFAEIRKSLVGDVSLLHKVFLFLERWGLINFGAPG-GEDS----AA 120

Query: 121 LGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVAGETGVKLPPL 180
           + +   +++V+ E+GAPNG+RVVA+PNSLKPI++P +      NG+V    E G +LPPL
Sbjct: 121 VAEGAERHRVRSEDGAPNGIRVVAMPNSLKPITMPLT---LDVNGEV---DENGFRLPPL 174

Query: 181 ASYLDVFGDLVKLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFR 240
           ASY DVF DL K KG  CG+CG+ C+SG Y   K GS VIC KCFKNGNYGE++S DDF+
Sbjct: 175 ASYSDVFSDLTKEKGLVCGNCGDNCDSGHYNCLK-GSPVICVKCFKNGNYGENRSVDDFK 233

Query: 241 FSDLGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGE 300
           F+D   N    GA WTEAETLLLLESV++HGD+WELV QNV TK+KLDCISKLIELPFGE
Sbjct: 234 FNDCNENRGNRGAVWTEAETLLLLESVLKHGDDWELVVQNVQTKTKLDCISKLIELPFGE 293

Query: 301 FMMGSAHEMNSSSCPTGSLNSLKEGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEP 360
            M+GS+  +  S     + +S+K  Q+ S E+Q ++K   Q  +Q+NES+QNGDA  + P
Sbjct: 294 LMLGSS--LGKSRASNDNTSSIKPVQT-SLESQENIKNGGQGDEQINESEQNGDAENQGP 350

Query: 361 PAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAALCNESSCPREIFDGDED 420
           P KRK I  LSD G +L++QVA ISTMVGPH++AAAA+AAVAALC+E+ C ++IFDG ED
Sbjct: 351 PLKRKCITSLSDAGISLMRQVAVISTMVGPHISAAAADAAVAALCDENPCVKDIFDGAED 410

Query: 421 YLANGLSSPTMVSDPERALQVDASKMEENQ--SETQDASSEKNDVPLNLRIRTATATALG 478
            +   L SP   +  ER+L V+ S++ E    SE Q  SSEKN +PL L++R A ATALG
Sbjct: 411 NVTEELGSPIRNNKLERSLMVEDSEINERPILSEIQKTSSEKNAIPLPLQMRAAIATALG 470

Query: 479 AAAANAKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECL 538
           AAAANAK LADQE REIEHLVA IIETQMKKLH KI +F+DLELIMEKEY  + +LKE +
Sbjct: 471 AAAANAKSLADQEHREIEHLVATIIETQMKKLHCKIQHFEDLELIMEKEYTHLKELKESI 530

Query: 539 VEERIDVLERALKTGVSKWR 558
           + ERID+L+R    G+S+WR
Sbjct: 531 IAERIDILQRVFNAGISRWR 550

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|147858898\|emb\|CAN80839.1\| hypothetical protein VITISV_043833 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|224136238\|ref\|XP_002322279.1\| chromatin remodeling complex subunit [Populus trichocarpa] gi\|222869275\|gb\|EEF06406.1\| chromatin remodeling complex subunit [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|255540147\|ref\|XP_002511138.1\| DNA binding protein, putative [Ricinus communis] gi\|223550253\|gb\|EEF51740.1\| DNA binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|357465011\|ref\|XP_003602787.1\| SWI/SNF complex subunit SMARCC2 [Medicago truncatula] gi\|355491835\|gb\|AES73038.1\| SWI/SNF complex subunit SMARCC2 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356509348\|ref\|XP_003523412.1\| PREDICTED: SWI/SNF complex subunit SWI3A-like [Glycine max]	Back alignment and taxonomy information

>gi\|356518589\|ref\|XP_003527961.1\| PREDICTED: SWI/SNF complex subunit SWI3A-like [Glycine max]	Back alignment and taxonomy information

>gi\|449523928\|ref\|XP_004168975.1\| PREDICTED: SWI/SNF complex subunit SWI3A-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449440963\|ref\|XP_004138253.1\| PREDICTED: SWI/SNF complex subunit SWI3A-like [Cucumis sativus]	Back alignment and taxonomy information

>gi|30690734|ref|NP_850476.1| SWI/SNF complex subunit SWI3A [Arabidopsis thaliana] gi|75331380|sp|Q8W475.1|SWI3A_ARATH RecName: Full=SWI/SNF complex subunit SWI3A; Short=AtSWI3A; AltName: Full=Transcription regulatory protein SWI3A gi|17065436|gb|AAL32872.1| putative SWI/SNF family transcription activator [Arabidopsis thaliana] gi|20148483|gb|AAM10132.1| putative SWI/SNF family transcription activator [Arabidopsis thaliana] gi|330255771|gb|AEC10865.1| SWI/SNF complex subunit SWI3A [Arabidopsis thaliana]

Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		559
TAIR\|locus:2043263		512	SWI3A "SWITCH/sucrose nonferme	0.475	0.519	0.462	5.2e-102
TAIR\|locus:2051028		469	SWI3B "switch subunit 3" [Arab	0.178	0.213	0.43	1.6e-34
DICTYBASE\|DDB_G0277033		1223	swi3 "SWIRM domain-containing	0.182	0.083	0.480	2.9e-33
MGI\|MGI:1203524		1104	Smarcc1 "SWI/SNF related, matr	0.155	0.078	0.494	2.9e-27
UNIPROTKB\|Q92922		1105	SMARCC1 "SWI/SNF complex subun	0.155	0.078	0.494	2.9e-27
ZFIN\|ZDB-GENE-080514-3		1089	smarcc1a "SWI/SNF related, mat	0.155	0.079	0.494	9.9e-27
ZFIN\|ZDB-GENE-060503-273		961	smarcc1b "SWI/SNF related, mat	0.155	0.090	0.494	1e-26
POMBASE\|SPAC23H3.10		503	ssr2 "SWI/SNF and RSC complex	0.155	0.172	0.517	1.9e-26
UNIPROTKB\|G5EF87		789	swsn-1 "SWI3-like protein" [Ca	0.186	0.131	0.361	2.5e-26
WB\|WBGene00004203		792	swsn-1 [Caenorhabditis elegans	0.186	0.131	0.361	2.5e-26

TAIR\|locus:2043263 SWI3A "SWITCH/sucrose nonfermenting 3A" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 609 (219.4 bits), Expect = 5.2e-102, Sum P(2) = 5.2e-102
 Identities = 137/296 (46%), Positives = 180/296 (60%)

Query:   128 NQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVAGETGVKLPPLASYLDVF 187
             +  KIE+G P G+RV A PNSL+PI+ P    +     +V    ETG+K+PPL SY DVF
Sbjct:   115 DNAKIEQGTPAGIRVTATPNSLRPITAPPLVEE-----RV----ETGIKVPPLTSYSDVF 165

Query:   188 GDLVKLKG-FKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLGG 246
              DL K      C  CGE+C+S  Y+++K G   ICEKCFKNGNYGE+ + DDF+   L G
Sbjct:   166 SDLKKPDHVLVCAHCGERCDSPFYQHNK-GIVNICEKCFKNGNYGENNTADDFK---LIG 221

Query:   247 NSLTHGXXXXXXXXXXXXXSVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSA 306
             NS                 SV++HGD+WEL++Q+V TKS+LDCISKLIELPFGEF+MGSA
Sbjct:   222 NSAA--AVWTEEEILLLLESVLKHGDDWELISQSVSTKSRLDCISKLIELPFGEFLMGSA 279

Query:   307 HEMNSSSCPTGSLNSLKEGQSASSENQNDVKMEDQVHDQMNESKQNGDAATE-EPPAKRK 365
                      +G LN          EN   V+ + Q H++    ++  D   E EPPAKRK
Sbjct:   280 ---------SGRLNP---SILTEDENTEQVQTDGQEHEETETREEKEDRVNEDEPPAKRK 327

Query:   366 RIAPLSDGGSTLIKQVAHISTMVGPHVTXXXXXXXXXXLCNESSCPREIFDGDEDY 421
             R+A +S+G S+L+KQVA +++ VGP V           LC+E+SCP+EIFD D DY
Sbjct:   328 RVALISEGDSSLMKQVAAMASKVGPSVATAAAKAALAALCDEASCPKEIFDTD-DY 382

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

GO:0005634 "nucleus" evidence=ISM

GO:0006338 "chromatin remodeling" evidence=ISS

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

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

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

TAIR\|locus:2051028 SWI3B "switch subunit 3" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0277033 swi3 "SWIRM domain-containing protein Swi3" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

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

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

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

ZFIN\|ZDB-GENE-060503-273 smarcc1b "SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1b" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

POMBASE\|SPAC23H3.10 ssr2 "SWI/SNF and RSC complex subunit Ssr2" [Schizosaccharomyces pombe (taxid:4896)]	Back alignment and assigned GO terms

UNIPROTKB\|G5EF87 swsn-1 "SWI3-like protein" [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

WB\|WBGene00004203 swsn-1 [Caenorhabditis elegans (taxid:6239)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8W475	SWI3A_ARATH	No assigned EC number	0.5107	0.8908	0.9726	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	CHB905	chromatin remodeling complex subunit (570 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	CHE901	condensin complex components subunit (244 aa)	•	•	0.544

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		559
COG5259		531	COG5259, RSC8, RSC chromatin remodeling complex su	1e-44
pfam04433		80	pfam04433, SWIRM, SWIRM domain	1e-28
cd00167		45	cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-	4e-07
smart00717		49	smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIII	6e-07
pfam00249		47	pfam00249, Myb_DNA-binding, Myb-like DNA-binding d	1e-05
COG5259		531	COG5259, RSC8, RSC chromatin remodeling complex su	3e-05
cd02336		45	cd02336, ZZ_RSC8, Zinc finger, ZZ type	4e-05

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

 Score =  165 bits (419), Expect = 1e-44
 Identities = 88/286 (30%), Positives = 137/286 (47%), Gaps = 22/286 (7%)

Query: 19  IPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQ 78
           IPS++ WF    IHE E+ +  EFF+G S S+TP++YK+YR+FMIN YR  P+  LT T 
Sbjct: 54  IPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTA 113

Query: 79  VRKSLVGDVSLLHKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPN 138
            R+++ GDV+ + +V R L++WGLIN+       D   R S++G   L +  +     P 
Sbjct: 114 CRRNVAGDVAAIVRVHRFLEKWGLINYQV-----DPGTRPSTIGPP-LTSHFQDLHDTPR 167

Query: 139 GVRVVALPNSLKPISVPNSGADGSGNGKVAVAGETGVKLPPLASYL-------DVFGDLV 191
           G+          PI+    GA            +     P L S         D   D  
Sbjct: 168 GLSPFLPWG---PINQRVLGAKEIEYETH----KEENYSPSLKSPKKESQGKVDELKDHS 220

Query: 192 KLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSDLGGNSLTH 251
           +     C  CG +  +  Y   +   +  C +C+  G +  + +  DF+   +       
Sbjct: 221 EKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVTISLLIRDK 280

Query: 252 GATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELP 297
              W+  E LLLLE +  +GD+W+ VA++V TK+K  CI   ++LP
Sbjct: 281 --NWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLP 324

Length = 531

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

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

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

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

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

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		559
COG5259		531	RSC8 RSC chromatin remodeling complex subunit RSC8	100.0
KOG1279		506	consensus Chromatin remodeling factor subunit and	100.0
PF04433		86	SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM	99.93
KOG0457		438	consensus Histone acetyltransferase complex SAGA/A	99.89
COG5114		432	Histone acetyltransferase complex SAGA/ADA, subuni	99.78
cd02336		45	ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present	99.1
PF00249		48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	99.04
PF13921		60	Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB:	98.82
PLN03000		881	amine oxidase	98.78
smart00717		49	SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-bindi	98.76
PLN02328		808	lysine-specific histone demethylase 1 homolog	98.69
cd00167		45	SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding do	98.67
cd02335		49	ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present	98.29
PLN02529		738	lysine-specific histone demethylase 1	98.19
PLN03212		249	Transcription repressor MYB5; Provisional	98.19
cd02249		46	ZZ Zinc finger, ZZ type. Zinc finger present in dy	98.15
TIGR01557		57	myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c	98.09
cd02341		48	ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present	97.98
PLN03091		459	hypothetical protein; Provisional	97.97
smart00291		44	ZnF_ZZ Zinc-binding domain, present in Dystrophin,	97.95
cd02345		49	ZZ_dah Zinc finger, ZZ type. Zinc finger present i	97.93
cd02340		43	ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger pre	97.93
cd02343		48	ZZ_EF Zinc finger, ZZ type. Zinc finger present in	97.92
cd02338		49	ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger pre	97.9
cd02334		49	ZZ_dystrophin Zinc finger, ZZ type. Zinc finger pr	97.83
KOG0048		238	consensus Transcription factor, Myb superfamily [T	97.8
PF00569		46	ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc	97.72
cd02344		45	ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present	97.55
PLN03212		249	Transcription repressor MYB5; Provisional	97.53
cd02339		45	ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger pre	97.45
PLN03091		459	hypothetical protein; Provisional	97.21
cd02337		41	ZZ_CBP Zinc finger, ZZ type. Zinc finger present i	97.19
cd02342		43	ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger pre	96.83
KOG0049		939	consensus Transcription factor, Myb superfamily [T	96.81
PLN02976		1713	amine oxidase	96.31
KOG0049		939	consensus Transcription factor, Myb superfamily [T	95.94
KOG0048		238	consensus Transcription factor, Myb superfamily [T	95.77
KOG4582		278	consensus Uncharacterized conserved protein, conta	95.54
KOG1280		381	consensus Uncharacterized conserved protein contai	95.21
PF13837		90	Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain;	94.99
KOG4286		966	consensus Dystrophin-like protein [Cell motility;	93.84
KOG0051		607	consensus RNA polymerase I termination factor, Myb	93.24
KOG0050		617	consensus mRNA splicing protein CDC5 (Myb superfam	92.1
KOG0051		607	consensus RNA polymerase I termination factor, Myb	91.74
KOG0050		617	consensus mRNA splicing protein CDC5 (Myb superfam	89.7
PF13873		78	Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain	89.16
KOG4167		907	consensus Predicted DNA-binding protein, contains	88.5
KOG4301		434	consensus Beta-dystrobrevin [Cytoskeleton]	88.02
KOG4329		445	consensus DNA-binding protein [General function pr	85.24
TIGR02894		161	DNA_bind_RsfA transcription factor, RsfA family. I	85.21
PF15324		1252	TALPID3: Hedgehog signalling target	84.95
COG5118		507	BDP1 Transcription initiation factor TFIIIB, Bdp1	84.69
KOG4468		782	consensus Polycomb-group transcriptional regulator	83.69
COG5147		512	REB1 Myb superfamily proteins, including transcrip	82.46
PRK00409		782	recombination and DNA strand exchange inhibitor pr	82.16
TIGR01069		771	mutS2 MutS2 family protein. Function of MutS2 is u	81.69
KOG4282		345	consensus Transcription factor GT-2 and related pr	80.59
COG5147		512	REB1 Myb superfamily proteins, including transcrip	80.06

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

Probab=100.00  E-value=4.3e-96  Score=761.79  Aligned_cols=415  Identities=27%  Similarity=0.484  Sum_probs=337.1

Q ss_pred             CCCcceeecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHH
Q 008612           11 KPEFELYTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLL   90 (559)
Q Consensus        11 ~~~~~~iiIPs~~~wF~~~~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i   90 (559)
                      -++.++||||||+.||++.+||+||+++.||||+|++++|||++|+.||||||++||+||.+|||+|+||||++||||+|
T Consensus        46 ~~Q~~piiiPs~a~WFd~SKiHeIE~~snPeFF~~rs~~KTP~vYk~YR~FminsyRL~p~eYLtvTa~RRNvagDV~ai  125 (531)
T COG5259          46 MEQTHPIIIPSYAEWFDGSKIHEIEKRSNPEFFNGRSPSKTPEVYKDYRNFMINSYRLNPNEYLTVTACRRNVAGDVAAI  125 (531)
T ss_pred             hccCCceeccchhhhccccccccccccCCchhhcCCCCCCCHHHHHHHHhhccceeecCCcceEEeeeehhccchhHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhhhcccccccCCCCCCCCCCCCCCCCccccccceeecCCCCccccccCCCCCCCCCCCCCCCCCCCCCccccc
Q 008612           91 HKVFRLLDEWGLINFGAVSRGDDSDNRDSSLGDTELKNQVKIEEGAPNGVRVVALPNSLKPISVPNSGADGSGNGKVAVA  170 (559)
Q Consensus        91 ~rvh~FLe~wGlIN~~~~~~~~~~~~~~~~~~~p~~tg~f~v~~dtP~gl~~~~~p~~~kp~~~~~~~~~~s~~~~~~~~  170 (559)
                      .|||+||++|||||||++|     .+||+.+|| |+||||++++|||+||+|+.+++...   ....+++.   .+....
T Consensus       126 vrvHrFLekWGLINYqvdp-----~trPs~IgP-plt~h~q~l~dtP~gl~p~l~~~~~~---~~~~~a~~---~e~~~~  193 (531)
T COG5259         126 VRVHRFLEKWGLINYQVDP-----GTRPSTIGP-PLTSHFQDLHDTPRGLSPFLPWGPIN---QRVLGAKE---IEYETH  193 (531)
T ss_pred             HHHHHHHHHhcceeeccCC-----CCCccccCC-CcchhhHHHhhCccccccccCCCCcc---ccccccch---hhhhhh
Confidence            9999999999999999999     578888887 58899999999999999986544331   11111110   110000


Q ss_pred             CCCCCCCCCcccch----hhhcccc---ccCCccCCCCCCCCCCceeEeccCCCcccchhhhhcCCCCCCCCCCCceecc
Q 008612          171 GETGVKLPPLASYL----DVFGDLV---KLKGFKCGSCGEQCNSGCYEYSKQGSFVICEKCFKNGNYGEDKSKDDFRFSD  243 (559)
Q Consensus       171 ~~~~~~~~~~~~~~----~~~~~~~---~~~~~~C~~Cg~~~~~~~y~~~k~~~~~lC~~Cf~~G~~~~~~ss~df~~~~  243 (559)
                      .+..+ .|++....    ..+.++.   ......|..||+.|..+||+..+...+++|..||.+|+||+..++.||..++
T Consensus       194 k~~~~-sps~~~~~k~s~~k~~el~~~~~~~~~~C~~cG~~~~~t~y~nlra~~~n~C~~C~~qg~f~s~~~ssDf~~v~  272 (531)
T COG5259         194 KEENY-SPSLKSPKKESQGKVDELKDHSEKHPSSCSCCGNKSFNTRYHNLRAEKYNSCSECYDQGRFPSEFTSSDFKPVT  272 (531)
T ss_pred             ccCCC-CchhhhhhhhcCCCccccccccccCCceeeccCccccchhhhhhhhhhcccchHHHhcCcCCCccccccchhhh
Confidence            11111 11111100    0111222   1234899999999999999999988999999999999999999999999998


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHcCCCCHHHHHHHHHcCCcCCCCCCCccccCCCCCCCCCCCccc
Q 008612          244 LGGNSLTHGATWTEAETLLLLESVMRHGDNWELVAQNVPTKSKLDCISKLIELPFGEFMMGSAHEMNSSSCPTGSLNSLK  323 (559)
Q Consensus       244 ~~~~~~~~~~~WT~~E~~~LLe~Ie~~g~nW~~Ia~~vg~kT~~eC~~~flqLPIeD~~l~~~~~~~~~~~~~~~~~~~~  323 (559)
                      ...+.  .+..||.+|+++|||||++||++|++||.|||+||++|||+|||||||+|.||...++..             
T Consensus       273 ~~~~~--~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~~~-------------  337 (531)
T COG5259         273 ISLLI--RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDGKG-------------  337 (531)
T ss_pred             hhccc--ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccCcC-------------
Confidence            87642  567999999999999999999999999999999999999999999999999998765310             


Q ss_pred             cccccccccccchhhhhhhhhhcccccccCCCCcCCCcccccCCCCCCCCCCcHHHHHHHHHhccChHHHHHHHHHHHHH
Q 008612          324 EGQSASSENQNDVKMEDQVHDQMNESKQNGDAATEEPPAKRKRIAPLSDGGSTLIKQVAHISTMVGPHVTAAAAEAAVAA  403 (559)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~p~lk~~~~~Pfs~a~NPVms~vAFLas~V~P~VAaaAA~aAl~~  403 (559)
                                                          +.  ..+..||..++||||++|+||+++|.|+|++-.+++.++.
T Consensus       338 ------------------------------------~~--~~G~~~f~~seNPVlstis~L~~iV~p~v~s~~q~~~~k~  379 (531)
T COG5259         338 ------------------------------------DN--SKGRLPFDGSENPVLSTISFLAGIVNPRVQSEKQRAIIKS  379 (531)
T ss_pred             ------------------------------------CC--CCCccccccCCCchhhHHHHHHHhcCHHHHHHHhhhhhhc
Confidence                                                00  0134799999999999999999999999988777665321


Q ss_pred             HhccCCCCccccCCCchhhccCCCCCCCCCChhhhhhhhhhhhccccccccccCCCCCCCchhhHHHHHHHHHHHHHHHH
Q 008612          404 LCNESSCPREIFDGDEDYLANGLSSPTMVSDPERALQVDASKMEENQSETQDASSEKNDVPLNLRIRTATATALGAAAAN  483 (559)
Q Consensus       404 l~~e~~~~~~~~~~~ed~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~Aaa~AL~aAA~k  483 (559)
                       .+. .                        .                          .+.-+...+...+-.||.+++.+
T Consensus       380 -g~~-~------------------------~--------------------------~n~e~~~~~~~~~~~al~s~~ek  407 (531)
T COG5259         380 -GKI-S------------------------H--------------------------INRESQEHIEEVIEYALDSGKEK  407 (531)
T ss_pred             -cce-e------------------------c--------------------------CccchhhHHHHHHHHHHHHHHHH
Confidence             000 0                        0                          00001123556677899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 008612          484 AKLLADQEDREIEHLVAIIIETQMKKLHSKINYFDDLELIMEKEYNEMMQLKECLVEERIDVL  546 (559)
Q Consensus       484 Ak~LA~~EEreI~~Lv~~lIe~QlkKLElKLk~feeLE~~~e~Er~~LE~~rq~L~~eR~~~~  546 (559)
                      ||+.|+.|||+|.+|+..+|+.||+||++||.||.+||+.+..||+.|+.   .|+..|+.+-
T Consensus       408 a~l~~~~Eerkm~rL~~~~iq~qleKlk~Kl~~~k~L~~~~~L~rqeLd~---nlll~rl~~~  467 (531)
T COG5259         408 AKLQATNEERKMERLRNVLIQAQLEKLKMKLGHLKELEKSTSLERQELDA---NLLLRRLNAE  467 (531)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhHH
Confidence            99999999999999999999999999999999999999999999999999   4555554443

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

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

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

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

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

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

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

>PLN03000 amine oxidase	Back alignment and domain information

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

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

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

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

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

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

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

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

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

>PLN03091 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

>PLN03091 hypothetical protein; Provisional	Back alignment and domain information

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

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

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

>PLN02976 amine oxidase	Back alignment and domain information

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG4329 consensus DNA-binding protein [General function prediction only]	Back alignment and domain information

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

>PF15324 TALPID3: Hedgehog signalling target	Back alignment and domain information

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

>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]	Back alignment and domain information

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

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

>TIGR01069 mutS2 MutS2 family protein	Back alignment and domain information

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

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		559
2fq3_A		104	Structure And Function Of The Swirm Domain, A Conse		3e-16
2dce_A		111	Solution Structure Of The Swirm Domain Of Human Kia		2e-05

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

Back alignment and structure

Iteration: 1

Score = 83.2 bits (204), Expect = 3e-16, Method: Composition-based stats. Identities = 34/85 (40%), Positives = 53/85 (62%) Query: 21 SHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVR 80 S+S WF + IH E +L EFF S+TP++Y YR+FM+N YR P+ + T R Sbjct: 15 SYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTAR 74 Query: 81 KSLVGDVSLLHKVFRLLDEWGLINF 105 +++ GD + L ++ + L +WGLIN+ Sbjct: 75 RNVSGDAAALFRLHKFLTKWGLINY 99

PyMOL of 2fq3

>pdb|2DCE|A Chain A, Solution Structure Of The Swirm Domain Of Human Kiaa1915 Protein Length = 111

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		559
2fq3_A		104	Transcription regulatory protein SWI3; four-helix	5e-44
2dce_A		111	KIAA1915 protein; swirm domain, structural genomic	1e-40
2yus_A		79	SWI/SNF-related matrix-associated actin- dependent	5e-13
1x41_A		60	Transcriptional adaptor 2-like, isoform B; transcr	5e-09
2elk_A		58	SPCC24B10.08C protein; hypothetical protein, struc	3e-07
2ltp_A		89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	5e-07
2cu7_A		72	KIAA1915 protein; nuclear protein, SANT domain, DN	7e-06
4a69_C		94	Nuclear receptor corepressor 2; transcription, hyd	3e-05
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
2eqr_A		61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	7e-05
2cqr_A		73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	2e-04
2dim_A		70	Cell division cycle 5-like protein; MYB_DNA-bindin	2e-04
2d9a_A		60	B-MYB, MYB-related protein B; DNA binding, structu	5e-04

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

 Score =  150 bits (381), Expect = 5e-44
 Identities = 35/94 (37%), Positives = 55/94 (58%)

Query: 17  YTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTF 76
               S+S WF  + IH  E  +L EFF     S+TP++Y  YR+FM+N YR  P+   + 
Sbjct: 11  GMASSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSV 70

Query: 77  TQVRKSLVGDVSLLHKVFRLLDEWGLINFGAVSR 110
           T  R+++ GD + L ++ + L +WGLIN+   S+
Sbjct: 71  TTARRNVSGDAAALFRLHKFLTKWGLINYQVDSK 104

PyMOL of 2fq3

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

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

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

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

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

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

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

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

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

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

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

>2d9a_A B-MYB, MYB-related protein B; DNA binding, structural genomics, unknown function, NPPSFA; NMR {Mus musculus} Length = 60	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		559
2fq3_A		104	Transcription regulatory protein SWI3; four-helix	100.0
2dce_A		111	KIAA1915 protein; swirm domain, structural genomic	100.0
2yus_A		79	SWI/SNF-related matrix-associated actin- dependent	99.63
2elk_A		58	SPCC24B10.08C protein; hypothetical protein, struc	99.33
1x41_A		60	Transcriptional adaptor 2-like, isoform B; transcr	99.22
2cqr_A		73	RSGI RUH-043, DNAJ homolog subfamily C member 1; m	99.1
1gvd_A		52	MYB proto-oncogene protein; transcription, transcr	98.98
1guu_A		52	C-MYB, MYB proto-oncogene protein; transcription,	98.98
1wgx_A		73	KIAA1903 protein; MYB DNA-binding domain, human cD	98.94
2d9a_A		60	B-MYB, MYB-related protein B; DNA binding, structu	98.94
1w0t_A		53	Telomeric repeat binding factor 1; telomere, DNA-b	98.93
2yum_A		75	ZZZ3 protein, zinc finger ZZ-type-containing prote	98.9
2dim_A		70	Cell division cycle 5-like protein; MYB_DNA-bindin	98.89
2cu7_A		72	KIAA1915 protein; nuclear protein, SANT domain, DN	98.89
3sjm_A		64	Telomeric repeat-binding factor 2; human telomeric	98.85
1ity_A		69	TRF1; helix-turn-helix, telomeres, DNA binding, MY	98.81
2eqr_A		61	N-COR1, N-COR, nuclear receptor corepressor 1; SAN	98.75
2din_A		66	Cell division cycle 5-like protein; MYB_DNA-bindin	98.73
2cjj_A		93	Radialis; plant development, DNA-binding protein,	98.67
2ltp_A		89	Nuclear receptor corepressor 2; SMRT, TRAC, SGC, s	98.07
2llk_A		73	Cyclin-D-binding MYB-like transcription factor 1;	98.61
2k9n_A		107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	98.6
1gv2_A		105	C-MYB, MYB proto-oncogene protein; transcription,	98.57
3osg_A		126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	98.55
2iw5_B		235	Protein corest, REST corepressor 1; oxidoreductase	98.49
1h8a_C		128	AMV V-MYB, MYB transforming protein; transcription	98.48
2k9n_A		107	MYB24; R2R3 domain, DNA-binding, nucleus, DNA bind	98.47
1gv2_A		105	C-MYB, MYB proto-oncogene protein; transcription,	98.47
3zqc_A		131	MYB3; transcription-DNA complex, DNA-binding prote	98.46
3osg_A		126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	98.46
2ckx_A		83	NGTRF1, telomere binding protein TBP1; nuclear pro	98.46
2z3y_A		662	Lysine-specific histone demethylase 1; chromatin,	98.45
4gut_A		776	Lysine-specific histone demethylase 1B; histone de	98.44
2yqk_A		63	Arginine-glutamic acid dipeptide repeats protein;	98.42
1h8a_C		128	AMV V-MYB, MYB transforming protein; transcription	98.39
3zqc_A		131	MYB3; transcription-DNA complex, DNA-binding prote	98.36
2xag_B		482	REST corepressor 1; amine oxidase, chromatin regul	98.24
2cqq_A		72	RSGI RUH-037, DNAJ homolog subfamily C member 1; m	98.21
2crg_A		70	Metastasis associated protein MTA3; transcription	98.2
1h89_C		159	C-MYB, MYB proto-oncogene protein; transcription/D	98.15
2roh_A		122	RTBP1, telomere binding protein-1; plant, nucleus,	98.15
1h89_C		159	C-MYB, MYB proto-oncogene protein; transcription/D	98.14
2aje_A		105	Telomere repeat-binding protein; DNA-binding, Trp,	98.13
4eef_G		74	F-HB80.4, designed hemagglutinin binding protein;	98.09
4a69_C		94	Nuclear receptor corepressor 2; transcription, hyd	98.09
2juh_A		121	Telomere binding protein TBP1; helix, nucleus, nuc	98.03
2e5r_A		63	Dystrobrevin alpha; ZZ domain, structural genomics	97.9
1x58_A		62	Hypothetical protein 4930532D21RIK; MUS musculus a	97.8
2dip_A		98	Zinc finger SWIM domain-containing protein 2; ZZ d	97.74
2xag_A		852	Lysine-specific histone demethylase 1; amine oxida	97.62
2fc7_A		82	ZZZ3 protein; structure genomics, ZZ domain, struc	97.53
1ign_A		246	Protein (RAP1); RAP1,yeast,telomeres,homoeodomain,	97.44
1tot_A		52	CREB-binding protein; zinc binding, CBP, TAZ2, tra	97.11
3hm5_A		93	DNA methyltransferase 1-associated protein 1; DNA	96.06
1fex_A		59	TRF2-interacting telomeric RAP1 protein; helix tur	95.99
2cuj_A		108	Transcriptional adaptor 2-like; transcriptional re	95.95
2aqe_A		90	Transcriptional adaptor 2, ADA2 alpha; helix-turn-	95.92
2ebi_A		86	DNA binding protein GT-1; DNA-binding domain, phos	95.83
1ug2_A		95	2610100B20RIK gene product; hypothetical protein,	95.8
2elj_A		88	Transcriptional adapter 2; YDR448W, structural gen	95.44
2xag_B		482	REST corepressor 1; amine oxidase, chromatin regul	95.18
1ofc_X		304	ISWI protein; nuclear protein, chromatin remodelin	95.02
2lr8_A		70	CAsp8-associated protein 2; structural genomics, n	93.25
4iej_A		93	DNA methyltransferase 1-associated protein 1; DNA	92.53
2xb0_X		270	Chromo domain-containing protein 1; hydrolase, DNA	91.44
4b4c_A		211	Chromodomain-helicase-DNA-binding protein 1; chrom	91.07
1irz_A		64	ARR10-B; helix-turn-helix, DNA binding protein; NM	87.56
4b4c_A		211	Chromodomain-helicase-DNA-binding protein 1; chrom	86.59
2y9y_A		374	Imitation switch protein 1 (DEL_ATPase); transcrip	82.46
1ofc_X		304	ISWI protein; nuclear protein, chromatin remodelin	80.52

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

Probab=100.00  E-value=7.3e-42  Score=297.77  Aligned_cols=93  Identities=38%  Similarity=0.746  Sum_probs=84.7

Q ss_pred             eecCCCCCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHh
Q 008612           17 YTIPSHSSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRL   96 (559)
Q Consensus        17 iiIPs~~~wF~~~~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~F   96 (559)
                      =.-|+|++||+|++||+||+++|||||+|++++|||++|++|||+||++||.||.+|||+|+||++|+|||++|+|||+|
T Consensus        11 ~~~p~~s~wF~~~~Ih~iEk~~lPEfF~g~~~~ktpe~Yl~iRN~iI~~yr~nP~~yLT~t~~r~~l~gDv~~i~RVh~F   90 (104)
T 2fq3_A           11 GMASSYSKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRNVSGDAAALFRLHKF   90 (104)
T ss_dssp             ------CTTCCTTCCCHHHHHHCGGGCCSSCTTSCHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHSCSCHHHHHHHHHH
T ss_pred             CCCCCcccccCcccCCHHHHHHChHHhcCCCCCCCHHHHHHHHHHHHHHHHhCCceeeeHHHHHHHccccHHHHHHHHHH
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcccccccCC
Q 008612           97 LDEWGLINFGAVS  109 (559)
Q Consensus        97 Le~wGlIN~~~~~  109 (559)
                      ||+|||||||++|
T Consensus        91 Le~wGLIN~~v~~  103 (104)
T 2fq3_A           91 LTKWGLINYQVDS  103 (104)
T ss_dssp             HHHTTSSSSCC--
T ss_pred             HHHcCeeccCCCC
Confidence            9999999999997

PyMOL of 2fq3

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>2y9y_A Imitation switch protein 1 (DEL_ATPase); transcription, nuclear protein complex, chromatin remodeling nucleosome remodeling; 3.25A {Saccharomyces cerevisiae} PDB: 2y9z_A	Back alignment and structure

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

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		559
d2fq3a1		85	a.4.1.18 (A:311-395) Transcription regulatory prot	8e-38
d2dw4a1		102	a.4.1.18 (A:172-273) Lysine-specific histone demet	6e-29
d1xc5a1		68	a.4.1.3 (A:413-480) Nuclear receptor corepressor 2	4e-06
d2iw5b1		65	a.4.1.3 (B:376-440) REST corepressor 1, CoREST {Hu	3e-05
d2crga1		57	a.4.1.3 (A:8-64) Metastasis associated protein MTA	3e-05
d2cu7a1		65	a.4.1.3 (A:8-72) MYSM1 (KIAA1915) {Human (Homo sap	8e-04
d1x41a1		47	a.4.1.1 (A:8-54) Transcriptional adaptor 2-like, T	0.001
d2cqra1		60	a.4.1.3 (A:7-66) DnaJ homolog subfamily C member 1	0.002
d1guua_		50	a.4.1.3 (A:) c-Myb, DNA-binding domain {Mouse (Mus	0.003

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


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

 Score =  132 bits (333), Expect = 8e-38
 Identities = 33/84 (39%), Positives = 51/84 (60%)

Query: 23  SSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKS 82
           S WF  + IH  E  +L EFF     S+TP++Y  YR+FM+N YR  P+   + T  R++
Sbjct: 1   SKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRN 60

Query: 83  LVGDVSLLHKVFRLLDEWGLINFG 106
           + GD + L ++ + L +WGLIN+ 
Sbjct: 61  VSGDAAALFRLHKFLTKWGLINYQ 84

PyMOL of d2fq3a1

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

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

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

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

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

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

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

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

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		559
d2fq3a1		85	Transcription regulatory protein swi3 {Baker's yea	100.0
d2dw4a1		102	Lysine-specific histone demethylase 1, LSD1 {Human	99.96
d1x41a1		47	Transcriptional adaptor 2-like, TADA2L, isoform b	99.4
d1gvda_		52	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	99.05
d1guua_		50	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	99.05
d2cjja1		63	Radialis {Garden snapdragon (Antirrhinum majus) [T	99.01
d2cqra1		60	DnaJ homolog subfamily C member 1 {Human (Homo sap	99.01
d2cu7a1		65	MYSM1 (KIAA1915) {Human (Homo sapiens) [TaxId: 960	99.01
d2iw5b1		65	REST corepressor 1, CoREST {Human (Homo sapiens) [	98.93
d1gv2a2		47	c-Myb, DNA-binding domain {Mouse (Mus musculus) [T	98.91
d1xc5a1		68	Nuclear receptor corepressor 2 {Human (Homo sapien	98.81
d1w0ua_		55	Telomeric repeat binding factor 2, TRF2 {Human (Ho	98.78
d1w0ta_		52	DNA-binding domain of human telomeric protein, hTR	98.77
d2crga1		57	Metastasis associated protein MTA3 {Mouse (Mus mus	98.59
d2ckxa1		83	Telomere binding protein TBP1 {Tobacco (Nicotiana	98.46
d1igna1		86	DNA-binding domain of rap1 {Baker's yeast (Sacchar	98.34
d1ug2a_		95	2610100b20rik gene product {Mouse (Mus musculus) [	98.05
d2cqqa1		59	DnaJ homolog subfamily C member 1 {Human (Homo sap	98.04
d2fc7a1		69	Zinc finger ZZ-type-containing protein 3, ZZZ3 {Hu	97.53
d1wgxa_		73	Hypothetical protein C14orf106 (KIAA1903) {Human (	97.53
d1tota1		52	CREB-binding protein, CBP {Mouse (Mus musculus) [T	97.05
d2dipa1		85	Zinc finger ZZ-type-containing protein 2 {Human (H	96.8
d1irza_		64	Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId	96.55
d2cuja1		101	Transcriptional adaptor 2-like, TADA2L {Mouse (Mus	96.43
d1ofcx1		52	SANT domain of the nucleosome remodeling ATPase IS	96.24
d1x58a1		49	Hypothetical protein 4930532d21rik {Mouse (Mus mus	93.94
d2cura1		31	Four and a half LIM domains protein 1, FHL-1 {Huma	80.69

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

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

Probab=100.00  E-value=6.6e-36  Score=250.76  Aligned_cols=85  Identities=39%  Similarity=0.838  Sum_probs=83.8

Q ss_pred             CCCCCCCCCCHHHHhhcccccCCCCCCCChhhHHHHHHHHHHHHHhCCCceeeHHHHhhhccchHHHHHHHHHhhhhhcc
Q 008612           23 SSWFRWDDIHETERTALKEFFDGSSISRTPKIYKEYRDFMINKYREEPSRRLTFTQVRKSLVGDVSLLHKVFRLLDEWGL  102 (559)
Q Consensus        23 ~~wF~~~~i~~iE~~~~peff~~~~~~ktp~~Y~~~RN~ii~~yr~np~~~lt~t~~r~~l~gD~~~i~rvh~FLe~wGl  102 (559)
                      |+||++++||+|||++|||||++++.+|||++|+.|||+||++||.||.+|||+|+||+++.||++++.|||+||++||+
T Consensus         1 s~WF~~~~i~~iE~~~lPeff~~~~~~kt~~~Yl~iRN~Il~~w~~np~~~Lt~~~~~~~~~~d~~~~~ri~~FL~~~G~   80 (85)
T d2fq3a1           1 SKWFNLEKIHSIEVQSLPEFFTNRIPSKTPEVYMRYRNFMVNSYRLNPNEYFSVTTARRNVSGDAAALFRLHKFLTKWGL   80 (85)
T ss_dssp             CTTCCTTCCCHHHHHHCGGGCCSSCTTSCHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHSCSCHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCcCCHHHHHHCHHHhcCCCCCCCHHHHHHHHHHHHHHHHhCCCeeeeHHHHHhhccCCHHHHHHHHHHHHHcCc
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q 008612          103 INFGA  107 (559)
Q Consensus       103 IN~~~  107 (559)
                      |||||
T Consensus        81 INf~v   85 (85)
T d2fq3a1          81 INYQV   85 (85)
T ss_dssp             SSSCC
T ss_pred             cCccC
Confidence            99997

PyMOL of d2fq3a1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure