Citrus Sinensis ID: 039418

---

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-------
Protein Sequence
MKVRGSHKRKAGDFESSCEMLVDAHRSRGSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYKDEKLAHVGGCLLYL
Secondary Structure (PSIPRED)
ccccccccccccccccHHHcHHHHHcccccccccccccccHHHHHHHHHHHHcccccHHcHHHHHHHHHHHccccHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHcccccccEEEEccEEEccccccccEEEEcccccccccccccHHHHHHHHHHHccccccccHHHHHHHHccccccccHHHHHHHHHHHcEEEcccccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHccccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHHHEEEccccccccccccccccEEEEcHHHHHHHHHcccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHccccHcccccccccHHHHHHHHHHccccccEEEEccEEEEccHHHHHHHcccccccccEccccccHHHHHHHHHcccccccHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccHHHHHHHccHHHHHHccHHHHHHHHHHHHHHHHHHcccccccEEEEEc
Coil and Loop (DISEMBL)
mkvrgshkrkagdfeSSCEMLVDAHrsrgskdrennhgFISFFAESVRQLKAKDGRACITNEVRKEIRNAFknlpveekCQYKfqsrrggkanvEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIglgsiidlkcGRLKRKLCAWLVERIDTARCVLQLnghelelspnsfgyimgvtdggmpmelqgDSAEVAAYLDKFnatsrginiktMEDILLTSKDADNDFKVAFMLFTLCTllcppggvhisYSFLFTLKDVHSIRNRNWATFCFERLMRGItrykdeklahvggcllyl
Flexible Loop (DISEMBL)
mkvrgshkrkagdfesscEMLVDAHrsrgskdrennHGFISFFAESVRQLKAKDGRACITNEVRKEIrnafknlpveekcqykfqsrrggkanvekVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGlgsiidlkcgrLKRKLCAWLVERIDTARCVLQLNghelelspnSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITrykdeklahvggcllyl
Low Complexity Region (SEG)
MKVRGSHKRKAGDFESSCEMLVDAHRSRGSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYKDEKLAHVGGCLLYL
Disordered region (IsUnstruct)
*************************************GFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYKDEKLAHVGGCLLY*
Disordered Region (DISOPRED)
****************************************************************************************************TRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYKDEKLAHVGGCLLYL
Disordered Region (DISEMBL)
***************SSCEMLVD*********RENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQY*********ANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYKDEKLAHVGGCLLYL
Disordered Region (DISPRO)
***********************************NHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNL************************FLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYKDEKLAHVGGCLLYL
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MKVRGSHKRKAGDFESSCEMLVDAHRSRGSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGITRYKDEKLAHVGGCLLYL
Positional Conservation
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

No hits with e-value below 0.001 by BLAST

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	297
224077245	628	predicted protein [Populus trichocarpa]	0.868	0.410	0.333	1e-36
296087190	766	unnamed protein product [Vitis vinifera]	0.865	0.335	0.324	1e-36
225453104	617	PREDICTED: uncharacterized protein LOC10	0.845	0.406	0.328	9e-36
147783848	708	hypothetical protein VITISV_032233 [Viti	0.872	0.365	0.326	1e-35
255583781	421	conserved hypothetical protein [Ricinus	0.865	0.610	0.317	4e-35
356533899	590	PREDICTED: uncharacterized protein LOC10	0.835	0.420	0.307	6e-33
147795729	849	hypothetical protein VITISV_004916 [Viti	0.875	0.306	0.293	8e-30
147772140	637	hypothetical protein VITISV_026046 [Viti	0.824	0.384	0.284	5e-27
147798273	326	hypothetical protein VITISV_001668 [Viti	0.868	0.791	0.272	2e-21
147856790	479	hypothetical protein VITISV_019328 [Viti	0.747	0.463	0.275	7e-21

>gi|224077245|ref|XP_002305192.1| predicted protein [Populus trichocarpa] gi|222848156|gb|EEE85703.1| predicted protein [Populus trichocarpa]

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 90/270 (33%), Positives = 146/270 (54%), Gaps = 12/270 (4%)

Query: 39  FISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR-------GGK 91
           ++ F  E +++  A    +C      K   +A+K++ VEEK +Y  Q+R           
Sbjct: 47  WVHFSREFIKEYSASHPESCGLKAATKAASDAWKSMRVEEKAKYTKQARELWDSYLSTAP 106

Query: 92  ANVEK----VKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWL 147
           A + K     K +TRC+P RL  ++  L  +Q  AV  +G GS++ L+C  L+R LC WL
Sbjct: 107 ARIPKPRKQTKLVTRCSPGRLFNVLQRLSPEQNAAVKSMGFGSLLGLRCRTLRRSLCLWL 166

Query: 148 VERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRG 207
           +ER +TA C L++ G  + LSP     ++G+   G  +   G    +      +NAT+ G
Sbjct: 167 LERFNTAGCSLEICGMCIPLSPRDVEIVLGLAASGKDVINSGPDDLIVDLRRSYNATNHG 226

Query: 208 INIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNW 267
           I+++ +E+  LT+ +A  DFK +F+L+ L TLL P   + +S SFL  L ++  +   NW
Sbjct: 227 ISVRLLEE-RLTAPEAGEDFKRSFVLYALGTLLSPTARLDVSPSFLHFLTNMDVVHQYNW 285

Query: 268 ATFCFERLMRGITRYKDEKLAHVGGCLLYL 297
             F  +RL+R ++R+   K   VGGCLL+L
Sbjct: 286 GKFLLDRLVREVSRFHQGKQRAVGGCLLFL 315

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087190|emb|CBI33564.3| unnamed protein product [Vitis vinifera]

 Score =  159 bits (402), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 88/271 (32%), Positives = 147/271 (54%), Gaps = 14/271 (5%)

Query: 39  FISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSR----------- 87
           ++ F  E +R+  A    +       K   +A+K++ +EEK +Y  +SR           
Sbjct: 167 WVYFSREFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAP 226

Query: 88  -RGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAW 146
            R  K   ++   +TRC+P RL  ++  L   Q+ AV  +G GS++ L+C  L+R LC W
Sbjct: 227 ARAPKPR-KQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLW 285

Query: 147 LVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSR 206
           L+ER +TAR  L++ G  + LSP     +MG+   G  +   G    +    + +NAT+ 
Sbjct: 286 LLERFNTARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNH 345

Query: 207 GINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRN 266
           GI+++ +E+  L + +A  +FK +F+L+ L T+LCP   + +S SFL  L ++ +I   N
Sbjct: 346 GISVRLLEE-RLAAPEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYN 404

Query: 267 WATFCFERLMRGITRYKDEKLAHVGGCLLYL 297
           W  F  +RL+R ++R+   K   VGGCLL+L
Sbjct: 405 WGKFLLDRLVREVSRFHQGKQRAVGGCLLFL 435

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453104|ref|XP_002270459.1| PREDICTED: uncharacterized protein LOC100263780 [Vitis vinifera]

 Score =  156 bits (395), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 144/265 (54%), Gaps = 14/265 (5%)

Query: 45  ESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSR------------RGGKA 92
           E +R+  A    +       K   +A+K++ +EEK +Y  +SR            R  K 
Sbjct: 35  EFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPARAPKP 94

Query: 93  NVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERID 152
             ++   +TRC+P RL  ++  L   Q+ AV  +G GS++ L+C  L+R LC WL+ER +
Sbjct: 95  R-KQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLERFN 153

Query: 153 TARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKT 212
           TAR  L++ G  + LSP     +MG+   G  +   G    +    + +NAT+ GI+++ 
Sbjct: 154 TARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGISVRL 213

Query: 213 MEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCF 272
           +E+  L + +A  +FK +F+L+ L T+LCP   + +S SFL  L ++ +I   NW  F  
Sbjct: 214 LEE-RLAAPEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGKFLL 272

Query: 273 ERLMRGITRYKDEKLAHVGGCLLYL 297
           +RL+R ++R+   K   VGGCLL+L
Sbjct: 273 DRLVREVSRFHQGKQRAVGGCLLFL 297

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147783848|emb|CAN72428.1| hypothetical protein VITISV_032233 [Vitis vinifera]

 Score =  156 bits (395), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 146/273 (53%), Gaps = 14/273 (5%)

Query: 37  HGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSR--------- 87
           HG      E +R+  A    +       K   +A+K++ +EEK +Y  +SR         
Sbjct: 81  HGVNFCSREFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTT 140

Query: 88  ---RGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLC 144
              R  K   ++   +TRC+P RL  ++  L   Q+ AV  +G GS++ L+C  L+R LC
Sbjct: 141 APARAPKPR-KQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLC 199

Query: 145 AWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNAT 204
            WL+ER +TAR  L++ G  + LSP     +MG+   G  +   G    +    + +NAT
Sbjct: 200 LWLLERFNTARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNAT 259

Query: 205 SRGINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRN 264
           + GI+++ +E+  L + +A  +FK +F+L+ L T+LCP   + +S SFL  L ++ +I  
Sbjct: 260 NHGISVRLLEE-RLAAPEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQ 318

Query: 265 RNWATFCFERLMRGITRYKDEKLAHVGGCLLYL 297
            NW  F  +RL+R ++R+   K   VGGCLL+L
Sbjct: 319 YNWGKFLLDRLVREVSRFHQGKQRAVGGCLLFL 351

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583781|ref|XP_002532643.1| conserved hypothetical protein [Ricinus communis] gi|223527634|gb|EEF29746.1| conserved hypothetical protein [Ricinus communis]

 Score =  154 bits (389), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 86/271 (31%), Positives = 146/271 (53%), Gaps = 14/271 (5%)

Query: 39  FISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSR----------- 87
           ++ F  E +++  A    +       K   +A+K++ +EEK +Y  ++R           
Sbjct: 41  WVHFSREFIKEYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTRRAREVWDNYLSTAP 100

Query: 88  -RGGKANVEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAW 146
            R  K   ++ K +TRC+P RL  ++  L  +Q+ AV D+G GS++ L+C  L+R LC W
Sbjct: 101 ARTPKPR-KQTKLVTRCSPGRLFNVLQRLTPEQKDAVKDLGFGSLLGLRCRTLRRSLCLW 159

Query: 147 LVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSR 206
           L++R +T    L++ G  + LSP    ++MG+   G  +   G    +      +NAT+R
Sbjct: 160 LLQRFNTTGRSLEICGDRIPLSPKDVEFVMGLAASGKDVVNSGPDNLILDLRRNYNATNR 219

Query: 207 GINIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRN 266
           GI++  +E+  L + +A  +FK +F+L+ L TLL P   + +S SFL  L +V  +   N
Sbjct: 220 GISVSLLEE-RLKAPEAGEEFKRSFVLYALGTLLSPTARLDVSPSFLHFLTNVDVVHQYN 278

Query: 267 WATFCFERLMRGITRYKDEKLAHVGGCLLYL 297
           W  F  +RL+R + R++  K   VGGCLL+L
Sbjct: 279 WGKFLLDRLVREVARFRQGKQRAVGGCLLFL 309

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356533899|ref|XP_003535495.1| PREDICTED: uncharacterized protein LOC100782920 [Glycine max]

 Score =  147 bits (371), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 80/260 (30%), Positives = 142/260 (54%), Gaps = 12/260 (4%)

Query: 39  FISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR--------GG 90
           ++ F  E +++  A    +       K   NA+K++ +EEK +Y   +R         G 
Sbjct: 35  WVYFSKEFIKEYIASHPESPGLKAATKAASNAWKSMSLEEKEKYARHAREVWDGYLSSGA 94

Query: 91  KANVE---KVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWL 147
             N +   + K +TRC+P RL  ++  L  +Q++AV  +G GS++ L+C  L+R LC WL
Sbjct: 95  APNPKPRKQTKLVTRCSPGRLFKVLQRLTPEQKEAVKSMGFGSLLGLRCRTLRRSLCLWL 154

Query: 148 VERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRG 207
           +ER DT  C L++   ++ L+PN    ++G++  G  +   G    ++   + +NA + G
Sbjct: 155 LERFDTTNCSLEICNVDVPLTPNDVEMVLGLSASGKEVVNSGPEDMISDLRNSYNAINHG 214

Query: 208 INIKTMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNW 267
           I+++ +E+ L T++  D DFK +F+L+ L TLLCP   + +S SFL  L ++  +   NW
Sbjct: 215 ISVRLLEEQLATAESGD-DFKRSFVLYVLGTLLCPTARLDVSPSFLHFLTNMDLVHQYNW 273

Query: 268 ATFCFERLMRGITRYKDEKL 287
             F  +RL+R +  Y++  L
Sbjct: 274 GKFLLDRLVRELFYYENISL 293

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147795729|emb|CAN74236.1| hypothetical protein VITISV_004916 [Vitis vinifera]

 Score =  137 bits (344), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 78/266 (29%), Positives = 137/266 (51%), Gaps = 6/266 (2%)

Query: 38  GFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKAN---- 93
            +I ++ + +  +K KD    I +++RK++   +  L   EK  +  +S+   K      
Sbjct: 191 AWIHYYNDQLAMMKEKDKGVKINDDLRKKLGKKWNALSKVEKENFMAKSKESSKQYSLQK 250

Query: 94  --VEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERI 151
             V K+   TRC+P+R+  ++  L  KQ+ A+ +IG GS++ L+C ++   LC  L+   
Sbjct: 251 GVVPKLYLQTRCSPERVIRVIEKLEPKQKAAIXEIGFGSLLQLRCRKIDHGLCLXLINSF 310

Query: 152 DTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIK 211
           +    +LQL    ++LSP    +IMG+   G  + +  D         K+      + + 
Sbjct: 311 NPNTYMLQLYNTCIKLSPIDVEFIMGLRARGFKIGMNKDVXHKNDLCKKYCDKKGRLPLV 370

Query: 212 TMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFC 271
            +E+ +   K+  NDFKV F+LF L  LLCP   + ++ SFL  ++D+ SI+  NW  F 
Sbjct: 371 MLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKMNWXEFV 430

Query: 272 FERLMRGITRYKDEKLAHVGGCLLYL 297
              L+ GI  +K ++ + V GCLL+L
Sbjct: 431 LSYLVHGIEEFKKKQQSGVCGCLLFL 456

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147772140|emb|CAN64547.1| hypothetical protein VITISV_026046 [Vitis vinifera]

 Score =  127 bits (320), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 75/264 (28%), Positives = 132/264 (50%), Gaps = 19/264 (7%)

Query: 38  GFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKAN---- 93
            +I ++ + +  +K KD    I +++RK++   +  L   EK  +  + +   K      
Sbjct: 53  AWIHYYNDQLAMMKEKDKGVKINDDLRKKLGKKWNALSKVEKENFMAKXKESSKQYSLQK 112

Query: 94  --VEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERI 151
             V K+   TRC+P+R+  ++ +L  KQ+ A+ +IG GS++ L+C ++   LC WL+   
Sbjct: 113 GVVPKLYLQTRCSPERVIRVIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCLWLINSF 172

Query: 152 DTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIK 211
           +    +LQL    ++LSP    +IMG+   G  + +  D       L             
Sbjct: 173 NPNTYMLQLYNTCIKLSPIDVEFIMGLRARGFKIGMNKDVGHKNDLL------------- 219

Query: 212 TMEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFC 271
            +E+ +   K+  NDFKV F+LF L  LLCP   + ++ SFL  ++D+ SI+  NWA F 
Sbjct: 220 MLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKMNWAEFV 279

Query: 272 FERLMRGITRYKDEKLAHVGGCLL 295
              L+ GI  +K ++ + V   L+
Sbjct: 280 LSYLVHGIEEFKKKQQSGVXRLLI 303

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147798273|emb|CAN76862.1| hypothetical protein VITISV_001668 [Vitis vinifera]

 Score =  109 bits (272), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/286 (27%), Positives = 133/286 (46%), Gaps = 28/286 (9%)

Query: 5   GSHKRKAGDFESSCEMLVDAHRSRGSKDRENNHGFISFFAESVRQLKAKDGRACITNEV- 63
           G H R+    ++S ++  D HR      RE      S   + ++++  KD    I  EV 
Sbjct: 44  GDHLRRQPGSKTSSQVGGDHHR------REPGQPPPSRRLDLIKEVSLKDRELRIVGEVG 97

Query: 64  ---------------RKEIRNAFKNLPVEEKCQYKFQSRRGGKAN------VEKVKFLTR 102
                          RK++   +  L   EK  +  +S+   K        V K+   TR
Sbjct: 98  AKIRVLDFISPDVQLRKKLGIKWNALSKVEKENFMAKSKESSKQYSLQKGVVPKLYLQTR 157

Query: 103 CAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNG 162
           C+ +R+  ++ +L  KQ+ A+ +IG GS++ L+C ++   LC WL+   +    +LQL  
Sbjct: 158 CSXERVIRVIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCLWLINSFNXNTYMLQLYN 217

Query: 163 HELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKTMEDILLTSKD 222
             ++LSP    +IMG+   G  + +  D         K+      + +  +E+ +   K+
Sbjct: 218 TCIKLSPIDVEFIMGLRARGXKIGMNKDVGHKNDLCKKYCDKKGRLPLVMLENQIREDKE 277

Query: 223 ADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWA 268
             NDFKV F+LF L  LLCP   + ++ SFL  ++D+ SI+  NWA
Sbjct: 278 GGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKINWA 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147856790|emb|CAN83476.1| hypothetical protein VITISV_019328 [Vitis vinifera]

 Score =  107 bits (266), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 73/265 (27%), Positives = 125/265 (47%), Gaps = 43/265 (16%)

Query: 39  FISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKAN----- 93
           +I ++ + +  +K KD    I +++RK++   +  L   EK  +  +S+   K       
Sbjct: 29  WIHYYNDQLXMIKEKDKGVKINDDLRKKLGKKWNELSKVEKXDFMAKSKESSKQYSLQKG 88

Query: 94  -VEKVKFLTRCAPDRLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERID 152
            V K+   TRC+P+R+  ++  L  KQR A+ +IG GS++ L+C             +ID
Sbjct: 89  VVPKLYLQTRCSPERVIRVIEELEPKQRAAIEEIGFGSLLQLRC------------RKID 136

Query: 153 TARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVAAYLDKFNATSRGINIKT 212
                L++                     GM  ++  ++     Y DK       + +  
Sbjct: 137 HGARGLKI---------------------GMNKDVSHNNDLCKKYCDKKGQ----LPLVM 171

Query: 213 MEDILLTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCF 272
           +E+ +   K+  NDFKV F+LF L  LLCP   + +  SFL  ++D+ SI+  NWA F  
Sbjct: 172 LENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVKRSFLHLVEDIDSIKKMNWAEFVL 231

Query: 273 ERLMRGITRYKDEKLAHVGGCLLYL 297
             L+ GI  +K ++ + V GCLL+L
Sbjct: 232 SYLVHGIEEFKMKQQSGVCGCLLFL 256

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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)

No hits with e-value below 0.001 by BLAST

---

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	297
pfam09331	142	pfam09331, DUF1985, Domain of unknown function (DU	8e-04

>gnl|CDD|220183 pfam09331, DUF1985, Domain of unknown function (DUF1985)

 Score = 38.6 bits (90), Expect = 8e-04
 Identities = 25/126 (19%), Positives = 51/126 (40%), Gaps = 7/126 (5%)

Query: 160 LNGHELELSPNSFGYIMGVTDGGMPMELQGD---SAEVAAYLDKFNATSRGINIKTMEDI 216
             G  +  S   F  + G+  G  P E +     + +   + +K     + + +  +E+ 
Sbjct: 18  FAGKPIRFSLREFALVTGLPCGKYPKEKKVKKKGTLKKGPFWNKLFGLKKDVTVDDVEEK 77

Query: 217 LL--TSKDADNDFKVAFMLFTLCTLLCPP-GGVHISYSFLFTLKDVHSIRNRNWATFCFE 273
           L     KD+++  ++A +LF +  +L        I    L  ++D+ +     W    FE
Sbjct: 78  LKKKKKKDSEDRLRLALLLF-VDGVLLGTSKKTKIPKFHLEMVEDLEAFLTFPWGRLAFE 136

Query: 274 RLMRGI 279
            LM+ I
Sbjct: 137 MLMKSI 142

Members of this family of functionally uncharacterized domains are found in a set of Arabidopsis thaliana hypothetical proteins. Length = 142

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	297
PF10536	363	PMD: Plant mobile domain; InterPro: IPR019557 This	99.96
PTZ00199	94	high mobility group protein; Provisional	99.49
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.49
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.45
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.42
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.4
smart00398	70	HMG high mobility group.	99.37
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.37
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.35
KOG0381	96	consensus HMG box-containing protein [General func	99.2
PF09331	142	DUF1985: Domain of unknown function (DUF1985); Int	99.03
KOG0527	331	consensus HMG-box transcription factor [Transcript	98.98
COG5648	211	NHP6B Chromatin-associated proteins containing the	98.97
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	98.21
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	97.49
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	97.44
KOG2746	683	consensus HMG-box transcription factor Capicua and	95.48
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	95.38
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	94.97
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	93.06
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	91.71
COG5648	211	NHP6B Chromatin-associated proteins containing the	90.09

>PF10536 PMD: Plant mobile domain; InterPro: IPR019557 This entry represents a domain found in a variety of transposases []

Probab=99.96  E-value=2e-29  Score=241.61  Aligned_cols=171  Identities=19%  Similarity=0.322  Sum_probs=146.2

Q ss_pred             Ccccccccc--cccccHHHHHHHHhccccCcceEEECCeEeecCccchhheeccccCCccccccCChh---HHHHHHhhh
Q 039418          127 GLGSIIDLK--CGRLKRKLCAWLVERIDTARCVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSA---EVAAYLDKF  201 (297)
Q Consensus       127 GFg~LL~i~--~~~l~~~L~~wL~~~~d~~t~~~~i~g~~i~iT~~dV~~VLGLP~gG~~v~~~~~~~---~~~~l~~~~  201 (297)
                      |||+|+.|.  ..++++.|+.+|+++|+++|++|++++++++||++||..|+|||+.|.+|....+.+   .++++....
T Consensus         1 ~~g~~~~i~~s~~~~~~~li~al~erW~~et~tF~~~~gEmtiTL~DV~~llGLpi~G~pv~~~~~~~~~~~~~~ll~~~   80 (363)
T PF10536_consen    1 GFGILDAIMASRITIDRSLISALVERWDPETNTFHFPWGEMTITLEDVAMLLGLPIDGRPVTGPLPPDWRDLCEELLGVS   80 (363)
T ss_pred             CchhHhhhhhhcCCCCHHHHHHHHHHhCcccCeeecccccccchhhhhhhccccccccccccCccccchhhHHHHHhccc
Confidence            899999999  899999999999999999999999999999999999999999999999998754332   333333222


Q ss_pred             cc----CCCccchHHHHHHHhcCCCC-CchhhhHHHhhhhcceeCCCCCC-ccCcchhhhhhccccCcccchhHHHHHHH
Q 039418          202 NA----TSRGINIKTMEDILLTSKDA-DNDFKVAFMLFTLCTLLCPPGGV-HISYSFLFTLKDVHSIRNRNWATFCFERL  275 (297)
Q Consensus       202 ~~----~~~~isl~~L~~~ll~~~~~-~d~f~r~Fll~~i~~~L~Ptt~~-~vs~~yl~~l~D~~~I~~ynW~~~Vld~L  275 (297)
                      ..    .+..+.+++|++.+...+++ ++.+.||||++.+|++|||+++. +|+..|++++.|++.+++||||++||++|
T Consensus        81 ~~~~~~~~~~~~~~wl~~~~~~~~~~d~~~~~rAFll~~lg~~lfp~~~~~~v~~~~l~~~~~l~~~~~~~wg~a~La~l  160 (363)
T PF10536_consen   81 PQIKSKKGSSIRLSWLEEFFSNRPEDDEEQYHRAFLLYWLGSFLFPDKSGDYVSPRYLPLAVDLARIKRYAWGSAVLAYL  160 (363)
T ss_pred             ccccccccccchhhheeccccccccchHHHHHHHHHHHhhhceeccCCCcceeeeeEEeeeeccccccccccHHHHHHHH
Confidence            11    23456778888886333333 24799999999999999999998 89999999999999999999999999999


Q ss_pred             HHHHHhhhccC--CceeecceecC
Q 039418          276 MRGITRYKDEK--LAHVGGCLLYL  297 (297)
Q Consensus       276 ~~~l~k~~~~k--~~~i~GCllfL  297 (297)
                      +++|++...+.  ..+++||+.||
T Consensus       161 y~~L~~~~~~~~~~~~~~g~~~ll  184 (363)
T PF10536_consen  161 YRDLCKASRKSASQSNIGGPLWLL  184 (363)
T ss_pred             HHHHHHHhhhcccccccccceeee
Confidence            99999988876  78999999986

>PTZ00199 high mobility group protein; Provisional

Probab=99.49  E-value=3.3e-14  Score=111.64  Aligned_cols=61  Identities=18%  Similarity=0.269  Sum_probs=56.9

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCc-chhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRAC-ITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~-~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|++++|.+++++||+.. .+.+|++++|+.|++||++||++|.++|.+..
T Consensus        21 ~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk   82 (94)
T PTZ00199         21 NAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDK   82 (94)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999875 58999999999999999999999999998743

>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=99.49  E-value=3.8e-14  Score=106.96  Aligned_cols=59  Identities=22%  Similarity=0.259  Sum_probs=55.7

Q ss_pred             CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +||||+||||+|++++|++++++||+ .++.+|++.+|..|+.||++||++|.+.|.+..
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k   59 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPG-LTNNEISRIIGRMWRSESPEVKAYYKELAEEEK   59 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Confidence            58999999999999999999999994 689999999999999999999999999998754

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.

>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

Probab=99.45  E-value=1.1e-13  Score=100.46  Aligned_cols=57  Identities=23%  Similarity=0.332  Sum_probs=54.4

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      ||||+|||++|+.|+|.++++.||+ .++.+|++.+|..|++||++||++|.++|++.
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~   57 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKD   57 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            8999999999999999999999995 68999999999999999999999999999874

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.

>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

Probab=99.42  E-value=2.5e-13  Score=101.25  Aligned_cols=58  Identities=17%  Similarity=0.178  Sum_probs=54.7

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +|||+||||+|+++.|+.++++||+ .++.+|+|.+|+.|+.||++||++|.+.|++..
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k   59 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQPYYEEAKKLK   59 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            6999999999999999999999995 699999999999999999999999999998744

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.

>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin

Probab=99.40  E-value=2.7e-13  Score=99.44  Aligned_cols=58  Identities=26%  Similarity=0.386  Sum_probs=52.5

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ||||+|||++|+++++.++++.||+. ...+|++.+|..|++||++||++|.+.|.+..
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~-~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~   58 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDL-SNKEISKILAQMWKNLSEEEKAPYKEEAEEEK   58 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTS-THHHHHHHHHHHHHCSHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhccc-ccccchhhHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            89999999999999999999999955 59999999999999999999999999998744

HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....

>smart00398 HMG high mobility group

Probab=99.37  E-value=9e-13  Score=96.36  Aligned_cols=59  Identities=24%  Similarity=0.377  Sum_probs=55.0

Q ss_pred             CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +||||+|||++|++++|+.++++||+ ....++++.+|..|+.||++||++|.++|++..
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~   59 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPD-LSNAEISKKLGERWKLLSEEEKAPYEEKAKKDK   59 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            58999999999999999999999995 578999999999999999999999999988743

>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins

Probab=99.37  E-value=6.3e-13  Score=99.32  Aligned_cols=59  Identities=25%  Similarity=0.343  Sum_probs=51.0

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHh-CCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAK-DGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~-~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      +|||||+|||++|+.|++..+++. .+ .....+|.+.+|..|++||++||++|.++|++.
T Consensus         2 ~kpK~~~say~lF~~~~~~~~k~~G~~-~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~   61 (73)
T PF09011_consen    2 KKPKRPPSAYNLFMKEMRKEVKEEGGQ-KQSFREVMKEISERWKSLSEEEKEPYEERAKED   61 (73)
T ss_dssp             SS--SSSSHHHHHHHHHHHHHHHHT-T--SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHhccc-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            689999999999999999999999 55 778899999999999999999999999999874

It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....

>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

Probab=99.35  E-value=1.2e-12  Score=94.54  Aligned_cols=59  Identities=20%  Similarity=0.306  Sum_probs=55.1

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCC
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGK   91 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k   91 (297)
                      ||||+|||++|+.|+++.+++.+|+ ....+|.+.+|..|+.||++||++|.++|++...
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~   59 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKE   59 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999995 6799999999999999999999999999987543

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member

>KOG0381 consensus HMG box-containing protein [General function prediction only]

Probab=99.20  E-value=2.4e-11  Score=95.03  Aligned_cols=60  Identities=25%  Similarity=0.314  Sum_probs=55.9

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +.||||++|||+|+.+++..++..||+ ..+.+|+|++|..|++|+++||.+|..++.+-.
T Consensus        21 ~~pkrp~sa~~~f~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k   80 (96)
T KOG0381|consen   21 QAPKRPLSAFFLFSSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYEEKASKLK   80 (96)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            479999999999999999999999996 899999999999999999999999988887643

>PF09331 DUF1985: Domain of unknown function (DUF1985); InterPro: IPR015410 This domain is functionally uncharacterised; it is found in a set of Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins

Probab=99.03  E-value=4.7e-10  Score=94.48  Aligned_cols=123  Identities=20%  Similarity=0.390  Sum_probs=91.2

Q ss_pred             ceEEECCeEeecCccchhheeccccCCccccccCChhHHH---HHH-hhhccCCCccchHHHHHHHhcC--CCCCchhhh
Q 039418          156 CVLQLNGHELELSPNSFGYIMGVTDGGMPMELQGDSAEVA---AYL-DKFNATSRGINIKTMEDILLTS--KDADNDFKV  229 (297)
Q Consensus       156 ~~~~i~g~~i~iT~~dV~~VLGLP~gG~~v~~~~~~~~~~---~l~-~~~~~~~~~isl~~L~~~ll~~--~~~~d~f~r  229 (297)
                      ..+.++|..|.++..+.+.|+|||++..|-..........   .+- ..++ .+..+++..+.++|...  .+.++.+.-
T Consensus        14 ~W~~~~g~piRfsl~Ef~lvTGL~C~~~p~~~~~~~~~~~~~~~fw~~Lf~-~~~~vtv~dv~~~L~~~~~~~~~~Rlrl   92 (142)
T PF09331_consen   14 IWFVFNGVPIRFSLREFALVTGLNCGPYPKEKKVDKKGKKEKGSFWNKLFG-REEDVTVEDVIAKLKKMKKWDSEDRLRL   92 (142)
T ss_pred             EEEEECCEeeEecHHHHHhhcCCcCCCCCcccchhhccccchhhhhhhhcc-ccccCcHHHHHHHHhhcccCChhhHHHH
Confidence            7889999999999999999999999887766543221111   232 2333 34569999999998654  234444555


Q ss_pred             HHHhhhhcceeCCCCCCccCcchhhhhhccccCcccchhHHHHHHHHHHH
Q 039418          230 AFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMRGI  279 (297)
Q Consensus       230 ~Fll~~i~~~L~Ptt~~~vs~~yl~~l~D~~~I~~ynW~~~Vld~L~~~l  279 (297)
                      ++++++.|.+++++....|+..++..++|++.+.+|-||.+.++.++++|
T Consensus        93 a~L~~v~gvl~~~~~~~~i~~~~~~~v~Dl~~f~~yPWGr~sF~~~~~sI  142 (142)
T PF09331_consen   93 ALLLFVDGVLIATSKTTKIPKEHLKMVDDLEKFLNYPWGRYSFDMLMKSI  142 (142)
T ss_pred             HHHHhhheeeeccCCCCCCCHHHHHHHhhHHHHhcCCcHHHHHHHHHhcC
Confidence            55555555555555556899999999999999999999999999999874

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=98.98  E-value=3.4e-10  Score=107.09  Aligned_cols=60  Identities=18%  Similarity=0.248  Sum_probs=56.2

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      .++|||-|||||+.++.||.+.+.|| .-.+++|+|.+|..||.|+|+||.||++-|++-.
T Consensus        61 ~hIKRPMNAFMVWSq~~RRkma~qnP-~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR  120 (331)
T KOG0527|consen   61 DRIKRPMNAFMVWSQGQRRKLAKQNP-KMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLR  120 (331)
T ss_pred             cccCCCcchhhhhhHHHHHHHHHhCc-chhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHH
Confidence            45799999999999999999999999 5599999999999999999999999999998755

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=98.97  E-value=6.6e-10  Score=97.67  Aligned_cols=61  Identities=18%  Similarity=0.251  Sum_probs=57.4

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +|.||||-||||.|.++-|.++.+.+|.. .+++|+|.+|++||+|++.||+||...+..-+
T Consensus        68 pN~PKRp~sayf~y~~~~R~ei~~~~p~l-~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~  128 (211)
T COG5648          68 PNGPKRPLSAYFLYSAENRDEIRKENPKL-TFGEVGKLLSEKWKELTDEEKEPYYKEANSDR  128 (211)
T ss_pred             CCCCCCchhHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHhccHhhhhhHHHHHhhHH
Confidence            48899999999999999999999999965 99999999999999999999999999988744

>KOG0526 consensus Nucleosome-binding factor SPN, POB3 subunit [Transcription; Replication, recombination and repair; Chromatin structure and dynamics]

Probab=98.21  E-value=8e-07  Score=87.50  Aligned_cols=56  Identities=11%  Similarity=0.243  Sum_probs=51.1

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |.||||-||||+|++.-|..+|++   .-.+.+|+|.+|++||.||.  |++|.++|.+-+
T Consensus       534 napkra~sa~m~w~~~~r~~ik~d---gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk  589 (615)
T KOG0526|consen  534 NAPKRATSAYMLWLNASRESIKED---GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDK  589 (615)
T ss_pred             CCCccchhHHHHHHHhhhhhHhhc---CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHH
Confidence            788999999999999999999998   45899999999999999999  788988887643

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=97.49  E-value=7.5e-05  Score=70.13  Aligned_cols=57  Identities=14%  Similarity=0.224  Sum_probs=53.1

Q ss_pred             CCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           33 RENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        33 ~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |.|.+||++||.|.|+-+-++-- .|..+++-+++|.+|-.||-+|.|.|..-|++..
T Consensus       193 KKPLNAFmlyMKEmRa~vvaEct-lKeSAaiNqiLGrRWH~LSrEEQAKYyElArKer  249 (421)
T KOG3248|consen  193 KKPLNAFMLYMKEMRAKVVAECT-LKESAAINQILGRRWHALSREEQAKYYELARKER  249 (421)
T ss_pred             cccHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHH
Confidence            89999999999999999999988 8999999999999999999999998888887643

>KOG0528 consensus HMG-box transcription factor SOX5 [Transcription]

Probab=97.44  E-value=4.6e-05  Score=74.59  Aligned_cols=63  Identities=14%  Similarity=0.181  Sum_probs=53.9

Q ss_pred             CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccc
Q 039418           31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANV   94 (297)
Q Consensus        31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v   94 (297)
                      -+|||-+||||+-.|=|+-.-...| .=.+..++|.+|..||.||..||.||..--.+-+|.+.
T Consensus       325 HIKRPMNAFMVWAkDERRKILqA~P-DMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~Hl  387 (511)
T KOG0528|consen  325 HIKRPMNAFMVWAKDERRKILQAFP-DMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHL  387 (511)
T ss_pred             cccCCcchhhcccchhhhhhhhcCc-cccccchhHHhcccccccccccccchHHHHHHHHHhhh
Confidence            3599999999999999999999999 45889999999999999999999977665555455554

>KOG2746 consensus HMG-box transcription factor Capicua and related proteins [Transcription]

Probab=95.48  E-value=0.0041  Score=63.40  Aligned_cols=62  Identities=15%  Similarity=0.096  Sum_probs=56.8

Q ss_pred             CCCCCcchhhhHHHHH--HHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccc
Q 039418           32 DRENNHGFISFFAESV--RQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANV   94 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~--~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v   94 (297)
                      +.||-+||+.|.+-+|  ...++.|| |..+..|+|.+|+.|=+|.+.||.-|++-|.+++-++-
T Consensus       182 irrPMnaf~ifskrhr~~g~vhq~~p-n~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahf  245 (683)
T KOG2746|consen  182 IRRPMNAFHIFSKRHRGEGRVHQRHP-NQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHF  245 (683)
T ss_pred             hhhhhHHHHHHHhhcCCccchhccCc-cccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHh
Confidence            3899999999999999  99999999 88999999999999999999999999988888774443

>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]

Probab=95.38  E-value=0.017  Score=54.26  Aligned_cols=61  Identities=21%  Similarity=0.230  Sum_probs=49.5

Q ss_pred             hcCCCC-CCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhc
Q 039418           27 SRGSKD-RENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR   88 (297)
Q Consensus        27 ~~~~~~-~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~   88 (297)
                      -+|-|| -||.-.||-|+.-.-.+.|++||+. -.=++||.||..|+-|+++||.-|..-=+.
T Consensus        59 pkpPkppekpl~pymrySrkvWd~VkA~nPe~-kLWeiGK~Ig~mW~dLpd~EK~ey~~EYea  120 (410)
T KOG4715|consen   59 PKPPKPPEKPLMPYMRYSRKVWDQVKASNPEL-KLWEIGKIIGGMWLDLPDEEKQEYLNEYEA  120 (410)
T ss_pred             CCCCCCCCcccchhhHHhhhhhhhhhccCcch-HHHHHHHHHHHHHhhCcchHHHHHHHHHHH
Confidence            335444 5778889999999999999999955 678999999999999999999977654433

>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta

Probab=94.97  E-value=0.026  Score=48.92  Aligned_cols=48  Identities=19%  Similarity=0.324  Sum_probs=38.2

Q ss_pred             CCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhh
Q 039418           35 NNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSR   87 (297)
Q Consensus        35 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~   87 (297)
                      -.+||+-|+.||++.    |. .-+..++-..+...|..||++||.+|...+.
T Consensus        82 TnnaYLNFLReFRrk----h~-~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~  129 (183)
T PF06382_consen   82 TNNAYLNFLREFRRK----HC-GLSPQDLIQRAARAWCRLSEAEKNRYRRMAP  129 (183)
T ss_pred             cchHHHHHHHHHHHH----cc-CCCHHHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence            357999999888874    44 3455677777889999999999999998654

The function of this family is unknown.

>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A

Probab=93.06  E-value=0.15  Score=38.43  Aligned_cols=55  Identities=9%  Similarity=0.048  Sum_probs=43.0

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhc
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR   88 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~   88 (297)
                      |--|-+|==.+.+.-+..|-+.+++... ++ .|+....|++|++.||=+|..+|.+
T Consensus         4 PE~PKt~qe~Wqq~vi~dYla~~~~dr~-K~-~kam~~~W~~me~Kekl~WIkKA~E   58 (85)
T PF14887_consen    4 PETPKTAQEIWQQSVIGDYLAKFRNDRK-KA-LKAMEAQWSQMEKKEKLKWIKKAAE   58 (85)
T ss_dssp             S----THHHHHHHHHHHHHHHHTTSTHH-HH-HHHHHHHHHTTGGGHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhhHhHH-HH-HHHHHHHHHHhhhhhhhHHHHHHHH
Confidence            3445566667888899999999996643 33 6699999999999999999999987

>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ]

Probab=91.71  E-value=0.26  Score=42.76  Aligned_cols=44  Identities=14%  Similarity=0.291  Sum_probs=38.4

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCCh
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPV   76 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~   76 (297)
                      ..|-||||-.|+.|=++.+|++|| .-.++++=+++.+-|+..+.
T Consensus       122 RqR~psaYn~f~k~ei~rik~~~p-~ishkeaFs~aAknW~h~ph  165 (170)
T PF04690_consen  122 RQRVPSAYNRFMKEEIQRIKAENP-DISHKEAFSAAAKNWAHFPH  165 (170)
T ss_pred             cCCCchhHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHhhhhCcc
Confidence            368999999999999999999999 55788888888899987653

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=90.09  E-value=0.16  Score=45.27  Aligned_cols=56  Identities=16%  Similarity=0.119  Sum_probs=47.8

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhc
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRR   88 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~   88 (297)
                      +++|+..|+-+-++-|......+| .++....+|++|+.|++|++.-|++|.+.++.
T Consensus       144 ~~~~~~~~~e~~~~~r~~~~~~~~-~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk  199 (211)
T COG5648         144 NKAPIGPFIENEPKIRPKVEGPSP-DKALVEETKIISKAWSELDESKKKKYIDKYKK  199 (211)
T ss_pred             CCCCCchhhhccHHhccccCCCCc-chhhhHHhhhhhhhhhhhChhhhhHHHHHHHH
Confidence            467777777777778888888888 66888899999999999999999999998875

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	297
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05

>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 = 45.2 bits (106), Expect = 2e-05
 Identities = 59/320 (18%), Positives = 96/320 (30%), Gaps = 100/320 (31%)

Query: 7   HKRKAGDFESSCEMLVDAHRSRGSKDRENNHGFISFFAES-VRQLKAKD----GRACITN 61
           H     DFE+  E           KD       +S F ++ V     KD     ++ ++ 
Sbjct: 2   HHHHHMDFETG-EH------QYQYKD------ILSVFEDAFVDNFDCKDVQDMPKSILSK 48

Query: 62  EVRKEIRNAFKNLPVEEKCQYKF-----QSRRGGKANVEKV-----KFL-----TRCAPD 106
           E    I     +          F     +     +  VE+V     KFL     T     
Sbjct: 49  EEIDHI---IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQ--- 102

Query: 107 RLAALVSHLIEKQRKAVCDIGLGSIIDLKCGRLKRKLCAWLVERIDTARCVLQLNGHELE 166
           R  ++++ +  +QR  + +               +    + V R+   +  L+L    LE
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDN-------------QVFAKYNVSRL---QPYLKLRQALLE 146

Query: 167 LSPNSFGYIMGVTDGGMPMELQGDS---AEVAAYLDKFNATSRGI------NIKTMEDIL 217
           L P     I GV   G      G +    +V             I      N  + E +L
Sbjct: 147 LRPAKNVLIDGV--LGS-----GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVL 199

Query: 218 LTSKDADNDFKVAFMLFTLCTLLCPPGGVHISYSFLFTLKDVHSIRNRNWATFCFERLMR 277
                         ML  L   + P       +S    L  +HSI+          RL++
Sbjct: 200 E-------------MLQKLLYQIDPNWTSRSDHSSNIKL-RIHSIQAE------LRRLLK 239

Query: 278 GITRYKDEKLAHVGGCLLYL 297
               Y++        CLL L
Sbjct: 240 S-KPYEN--------CLLVL 250

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	297
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.67
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.6
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.57
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.55
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.55
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.53
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.52
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.52
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.52
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.51
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.51
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.51
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.51
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.5
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.5
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.5
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.5
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.5
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.49
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.49
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.48
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.47
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.46
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.46
2cto_A	93	Novel protein; high mobility group box domain, hel	99.44
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.43
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.4
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.39
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.37
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.33
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.28
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.25
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.24
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.24
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.17
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.15
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.12
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.05
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.98

>1l8y_A Upstream binding factor 1; HUBF, HMG box 5, DNA binding domain, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1l8z_A 2hdz_A

Probab=99.67  E-value=4.4e-17  Score=125.67  Aligned_cols=60  Identities=10%  Similarity=0.056  Sum_probs=56.6

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +||||||+||||+|+++||.+|++.+|+  .+.+|+|.+|++|++||++||.||.++|.+-+
T Consensus         2 ~~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK   61 (91)
T 1l8y_A            2 GKLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQ   61 (91)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999996  78999999999999999999999999987644

>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=1.1e-15  Score=115.81  Aligned_cols=61  Identities=15%  Similarity=0.200  Sum_probs=57.3

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|++++|++++++||+...+.+|+|.+|++|++||++||.+|.++|++..
T Consensus         4 ~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A            4 GSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            7899999999999999999999999976449999999999999999999999999999864

>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT DNA, protein-drug-DNA compl regulation-DNA complex; HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1j3x_A

Probab=99.57  E-value=2.2e-15  Score=110.59  Aligned_cols=59  Identities=19%  Similarity=0.249  Sum_probs=55.0

Q ss_pred             CCCCCCcchhhhHHHHHHHHHHhCCCCc-chhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           31 KDRENNHGFISFFAESVRQLKAKDGRAC-ITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~-~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      |||||+||||+|++++|+++++.||+.. ++.+|+|.+|..|++||++||++|.++|++.
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   60 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD   60 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            6999999999999999999999999765 4699999999999999999999999998863

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} SCOP: a.21.1.0

Probab=99.55  E-value=2.8e-15  Score=109.87  Aligned_cols=60  Identities=17%  Similarity=0.255  Sum_probs=52.6

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++||||+||||+|++++|+++++.||+ ..+.+|+|.+|..|++||++||++|.++|++..
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   60 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLR   60 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            369999999999999999999999995 569999999999999999999999999998743

>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A*

Probab=99.55  E-value=4.5e-15  Score=110.43  Aligned_cols=60  Identities=17%  Similarity=0.279  Sum_probs=56.3

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++||||+||||+|++|+|++++++||+ ..+.+|+|.+|..|++||++||++|.++|++..
T Consensus         3 ~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   62 (76)
T 1hry_A            3 DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ   62 (76)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHCSC-CSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999995 589999999999999999999999999998743

>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein, DNA sequence specific, testis determining.; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.53  E-value=6.3e-15  Score=111.08  Aligned_cols=61  Identities=13%  Similarity=0.147  Sum_probs=56.2

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +++||||+||||+|++|+|++++++||+ ..+.+|+|.+|..|++||++||++|.+.|++..
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   62 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLS   62 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHH
Confidence            3789999999999999999999999995 579999999999999999999999999888744

>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain, endodermal, activator, DNA- nucleus, transcription regulation, transcrip complex; HET: DNA; 2.75A {Mus musculus} SCOP: a.21.1.1 PDB: 2yul_A

Probab=99.52  E-value=7.4e-15  Score=111.06  Aligned_cols=62  Identities=18%  Similarity=0.247  Sum_probs=54.8

Q ss_pred             cCCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           28 RGSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        28 ~~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      .+++||||+||||+|++++|+.++++||+ ..+.+|+|.+|..|++||++||++|.+.|++..
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   64 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPD-LHNAELSKMLGKSWKALTLAEKRPFVEEAERLR   64 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999995 579999999999999999999999999998744

>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A

Probab=99.52  E-value=1.1e-14  Score=110.76  Aligned_cols=60  Identities=17%  Similarity=0.279  Sum_probs=56.5

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|+.|+|+++++.||+ ..+.+|+|.+|..|++||++||++|.+.|++..
T Consensus         3 ~~pKRP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   62 (85)
T 1j46_A            3 DRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ   62 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
Confidence            789999999999999999999999994 589999999999999999999999999998743

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=1.2e-14  Score=110.85  Aligned_cols=60  Identities=15%  Similarity=0.204  Sum_probs=56.1

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCc-chhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRAC-ITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~-~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      ++||||+||||+|++++|.++++.||+.. .+.+|+|.+|+.|++||++||++|.+.|++.
T Consensus        14 ~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   74 (86)
T 2eqz_A           14 KKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKAD   74 (86)
T ss_dssp             SSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            78999999999999999999999999775 3799999999999999999999999999863

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus}

Probab=99.51  E-value=1.4e-14  Score=109.34  Aligned_cols=61  Identities=16%  Similarity=0.170  Sum_probs=57.1

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      .++||||+||||+|++++|++++++||+ ..+.+|+|.+|..|++||++||++|.++|++..
T Consensus         5 ~~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   65 (82)
T 1wz6_A            5 SSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQKYTDMAKEYK   65 (82)
T ss_dssp             CCCSCCCCCHHHHHHHHHHHHHHHHCSS-SCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999995 689999999999999999999999999998744

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B

Probab=99.51  E-value=1.5e-14  Score=108.60  Aligned_cols=60  Identities=15%  Similarity=0.251  Sum_probs=56.1

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++||||+||||+|++++|+++++.||+ ..+.+|+|.+|..|++||++||++|.+.|++..
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   60 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPK-MHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR   60 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTT-SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            479999999999999999999999995 689999999999999999999999999998744

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A

Probab=99.51  E-value=1.2e-14  Score=108.36  Aligned_cols=60  Identities=15%  Similarity=0.263  Sum_probs=56.4

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|+.++|+++++.||+ .++.+|++.+|..|++||++||++|.++|++..
T Consensus         5 ~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   64 (77)
T 1hme_A            5 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLK   64 (77)
T ss_dssp             SCCCCCCCTTHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            789999999999999999999999995 689999999999999999999999999998743

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=2e-14  Score=111.05  Aligned_cols=61  Identities=16%  Similarity=0.196  Sum_probs=57.4

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      .++||||+||||+|++++|++++++||+ ..+.+|+|.+|+.|++||++||++|.++|++.+
T Consensus         5 p~~pKrP~say~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   65 (92)
T 2cs1_A            5 SSGIKKPMSASALFVQDHRPQFLIENPK-TSLEDATLQIEELWKTLSEEEKLKYEEKATKDL   65 (92)
T ss_dssp             CSSSCCCCCHHHHHHHHHHHHHHHHCCS-SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            3789999999999999999999999995 579999999999999999999999999999865

>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription factor 1, high mobility group box transcription factor 1, structural genomics; NMR {Homo sapiens}

Probab=99.50  E-value=1.1e-14  Score=111.35  Aligned_cols=60  Identities=12%  Similarity=0.145  Sum_probs=56.4

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++||||+||||+|++|+|+++++.||+ ..+.+|+|.+|..|++||++||++|.++|++..
T Consensus        16 ~~pKrP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   75 (87)
T 2e6o_A           16 NKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMYTLEAKALA   75 (87)
T ss_dssp             SSCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHH
Confidence            789999999999999999999999995 689999999999999999999999999998743

>1wgf_A Upstream binding factor 1; transcription factor, DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.50  E-value=1.3e-14  Score=111.75  Aligned_cols=63  Identities=17%  Similarity=0.252  Sum_probs=58.9

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCcc
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKAN   93 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~   93 (297)
                      |+||||+||||+|++|+|+++++.||+ ..+.+|+|.+|+.|++||++||++|.++|++.+..+
T Consensus        19 ~~pKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y   81 (90)
T 1wgf_A           19 EKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQS   81 (90)
T ss_dssp             CCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999995 689999999999999999999999999999866554

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens}

Probab=99.50  E-value=9.1e-15  Score=106.28  Aligned_cols=55  Identities=22%  Similarity=0.342  Sum_probs=51.7

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      |+||||+|||++|++++|.++++.||     .+|+|.+|..|++||++||++|.++|++.
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~   55 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKED   55 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHH
Confidence            57999999999999999999999888     58999999999999999999999998863

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1

Probab=99.50  E-value=8.5e-15  Score=110.85  Aligned_cols=61  Identities=20%  Similarity=0.247  Sum_probs=56.5

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCc-chhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRAC-ITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~-~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|++++|.++++.||+.. .+.+|+|.+|..|++||++||++|.+.|++..
T Consensus         6 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   67 (83)
T 1aab_A            6 KKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK   67 (83)
T ss_dssp             TCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999765 47999999999999999999999999998743

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1

Probab=99.50  E-value=1.7e-14  Score=108.00  Aligned_cols=60  Identities=13%  Similarity=0.182  Sum_probs=55.8

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +++|||+||||+|++++|+.++++|| ...+.+|+|.+|..|++||++||++|.+.|++..
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p-~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   60 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSP-DMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLR   60 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTST-TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCc-CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            35999999999999999999999999 5689999999999999999999999999998744

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus}

Probab=99.49  E-value=2.2e-14  Score=110.80  Aligned_cols=60  Identities=18%  Similarity=0.304  Sum_probs=56.4

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|++++|++++++||+ ..+.+|+|.+|..|++||++||++|.++|++..
T Consensus         6 ~~pKrP~~af~lF~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k   65 (92)
T 2crj_A            6 SGPKAPVTGYVRFLNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEK   65 (92)
T ss_dssp             SSSCCCCCHHHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            789999999999999999999999995 579999999999999999999999999998743

>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG, TCR-A, transcription factor; HET: DNA; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.49  E-value=2.7e-14  Score=108.85  Aligned_cols=59  Identities=14%  Similarity=0.209  Sum_probs=55.5

Q ss_pred             CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +||||+||||+|++++|.++++.||+ ..+.+|++.+|..|++||++||++|.+.|++..
T Consensus         2 ~pKRP~naf~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   60 (86)
T 2lef_A            2 HIKKPLNAFMLYMKEMRANVVAESTL-KESAAINQILGRRWHALSREEQAKYYELARKER   60 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSC-CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            59999999999999999999999995 589999999999999999999999999998744

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=99.48  E-value=2e-14  Score=106.31  Aligned_cols=57  Identities=11%  Similarity=0.213  Sum_probs=53.5

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      |+||||+||||+|++|+|++++++||+ .++.+|+|.+|..|++||+  |++|.++|++.
T Consensus         2 ~~PKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~   58 (73)
T 3nm9_A            2 DKPKRPLSAYALWLNSARESIKRENPG-IKVTEVAKRGGELWRAMKD--KSEWEAKAAKA   58 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSS-CCHHHHHHHHHHHHHHCSC--CHHHHHHHHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCc--hHHHHHHHHHH
Confidence            789999999999999999999999994 5799999999999999998  99999999874

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1

Probab=99.47  E-value=2.5e-14  Score=112.11  Aligned_cols=60  Identities=17%  Similarity=0.257  Sum_probs=56.3

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++||||+||||+|++++|.++++.||+ .++.+|+|.+|..|++||++||++|.++|++..
T Consensus         9 ~~PKRP~saf~lF~~~~r~~ik~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k   68 (99)
T 1k99_A            9 DFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQREK   68 (99)
T ss_dssp             SSCCCSCCHHHHHHHHHHHHHHTTCTT-SCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            679999999999999999999999995 589999999999999999999999999998743

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens}

Probab=99.46  E-value=5.5e-14  Score=111.48  Aligned_cols=62  Identities=15%  Similarity=0.175  Sum_probs=56.5

Q ss_pred             cCCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           28 RGSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        28 ~~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ..++||||+||||+|++++|+++++++|+ ..+.+|+|.+|..|++||++||++|.+.|++.+
T Consensus        26 ~~~~pKRP~naf~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k   87 (106)
T 4euw_A           26 NKPHVKRPMNAFMVWAQAARRKLADQYPH-LHNAELSKTLGKLWRLLNESEKRPFVEEAERLR   87 (106)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             CCCcCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            34789999999999999999999999994 588999999999999999999999999998754

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.46  E-value=5.5e-14  Score=110.69  Aligned_cols=61  Identities=18%  Similarity=0.295  Sum_probs=56.7

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      .|+||||+||||+|++++|.++++.||+ ..+.+|+|.+|..|++||++||++|.++|++..
T Consensus        15 p~~pKrP~say~lF~~~~r~~i~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k   75 (102)
T 2co9_A           15 PNEPQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAK   75 (102)
T ss_dssp             CCSCCCCCCHHHHTHHHHHHHHHHHCTT-SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHH
Confidence            3789999999999999999999999995 579999999999999999999999999998743

>2cto_A Novel protein; high mobility group box domain, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.44  E-value=3.4e-14  Score=110.21  Aligned_cols=58  Identities=19%  Similarity=0.287  Sum_probs=53.9

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHH---HhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEI---RNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~---g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|++|+|++++++   ...+.+|+|.+   |++|++||++||++|.++|++-+
T Consensus         9 ~~PKRP~sAf~lF~~e~R~~ik~e---~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K   69 (93)
T 2cto_A            9 PNRKASRNAYYFFVQEKIPELRRR---GLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWR   69 (93)
T ss_dssp             CCCCSSCCHHHHHHHTTHHHHHHH---TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            889999999999999999999998   46789999999   99999999999999999998654

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster}

Probab=99.43  E-value=1e-13  Score=102.37  Aligned_cols=58  Identities=12%  Similarity=0.281  Sum_probs=54.0

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|+++.|.+++++||+ .++.+|+|.+|..|++|  +||++|.++|++.+
T Consensus         2 ~~pKrP~say~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k   59 (73)
T 1wxl_A            2 HMPKRATTAFMLWLNDTRESIKRENPG-IKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDK   59 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTT-CCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHH
Confidence            689999999999999999999999995 67999999999999999  88999999998743

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A

Probab=99.40  E-value=4.6e-14  Score=109.24  Aligned_cols=60  Identities=17%  Similarity=0.277  Sum_probs=56.2

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++||||+||||+|++|+|.++++.||+ .++.+|+|.+|..|++||++||++|.++|++..
T Consensus        19 ~~pKrP~saf~lF~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   78 (93)
T 1cg7_A           19 NAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADK   78 (93)
T ss_dssp             SCCCSCCCHHHHHHHHHTSTTTTTCTT-SCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            779999999999999999999999995 479999999999999999999999999998743

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis}

Probab=99.39  E-value=6.9e-14  Score=109.02  Aligned_cols=59  Identities=20%  Similarity=0.241  Sum_probs=55.5

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcc--hhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACI--TNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~--~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      ++||||+||||+|++++|.++++.||+. .  +.+|+|.+|..|++||++||++|.+.|++.
T Consensus        21 ~~pKrP~say~lF~~~~r~~~k~~~p~~-~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~   81 (97)
T 2lhj_A           21 NAPKRALSSYMFFAKEKRVEIIAENPEI-AKDVAAIGKMIGAAWNALSDEEKKPYERMSDED   81 (97)
T ss_dssp             CCCCCCCCSSTHHHHGGGGGHHHHCTTS-TTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            7899999999999999999999999964 5  899999999999999999999999999874

>2yuk_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=99.37  E-value=4.9e-14  Score=108.54  Aligned_cols=56  Identities=9%  Similarity=0.137  Sum_probs=50.7

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcc--hhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACI--TNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~--~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||++|||+|++|+|+.++++||+ ..  +++|+    ++|++||++||+||.++|++-+
T Consensus        21 naPKRp~sAf~lf~~e~R~kik~enP~-~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K   78 (90)
T 2yuk_A           21 ALGEMATVAPVLYTNINFPNLKEEFPD-WTTRVKQIA----KLWRKASSQERAPYVQKARDNR   78 (90)
T ss_dssp             HHGGGCSSSHHHHHHHHCTTHHHHCCS-HHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCccHHHHHHHHhHHHHHHHCcC-ccchHHHHH----HHHHcCCHHHHHHHHHHHHHHH
Confidence            779999999999999999999999994 45  77777    9999999999999999998743

>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI, DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.33  E-value=1.1e-12  Score=103.13  Aligned_cols=81  Identities=19%  Similarity=0.220  Sum_probs=61.3

Q ss_pred             cCCCCCCCCcchhhhHHHHHHHHHHhCCCC--cchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccccccceeeecCH
Q 039418           28 RGSKDRENNHGFISFFAESVRQLKAKDGRA--CITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAP  105 (297)
Q Consensus        28 ~~~~~~r~~~~f~~~~~~~~~~~~~~~~~~--~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v~k~~~~trcS~  105 (297)
                      -|++||||+||||+|++|++.     +|+.  ..+.+|+|.+|.+|++||++||++|.++|++-+..+           .
T Consensus         5 ~~~~PKrP~say~lF~~e~~~-----~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y-----------~   68 (101)
T 1v63_A            5 SSGPKKPPMNGYQKFSQELLS-----NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQY-----------K   68 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHH-----HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHH-----------H
T ss_pred             CCCCCCCCCCHHHHHHHHHHh-----CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH-----------H
Confidence            468899999999999999964     4543  357899999999999999999999999998743322           1


Q ss_pred             HHHHHHHhhcCHHHHHHHH
Q 039418          106 DRLAALVSHLIEKQRKAVC  124 (297)
Q Consensus       106 ~~~~~~i~~Ls~~qk~~I~  124 (297)
                      ..+..-...++++++..+.
T Consensus        69 ~e~~~Y~~~~~~~~~~~~~   87 (101)
T 1v63_A           69 VHLDLWVKSLSPQDRAAYK   87 (101)
T ss_dssp             HHHHHHHHHSCTTHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHH
Confidence            2333344567777666544

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1

Probab=99.28  E-value=2.3e-12  Score=108.65  Aligned_cols=59  Identities=15%  Similarity=0.273  Sum_probs=55.9

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      ++||||+||||+|++|+|..+++.||+ .++.+|+|.+|..|++||++||++|.++|.+.
T Consensus        87 ~~pKrp~say~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~  145 (159)
T 2gzk_A           87 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL  145 (159)
T ss_dssp             TCCCCCCCHHHHHHHHHHHHHHHHCSC-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             ccccccccccchhhHhhHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            789999999999999999999999995 68999999999999999999999999999863

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.25  E-value=4.6e-12  Score=108.39  Aligned_cols=61  Identities=18%  Similarity=0.232  Sum_probs=57.1

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCC-cchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRA-CITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~-~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      .|+||||+||||+|++++|.++++.||+. ..+.+|+|.+|+.|++||++||++|.+.|++-
T Consensus        13 p~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   74 (173)
T 2yrq_A           13 PKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD   74 (173)
T ss_dssp             SSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            37899999999999999999999999976 48999999999999999999999999998873

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1

Probab=99.24  E-value=2.8e-12  Score=101.96  Aligned_cols=78  Identities=18%  Similarity=0.217  Sum_probs=62.4

Q ss_pred             CCC-CCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccccccceeeecCHHHH
Q 039418           30 SKD-RENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRL  108 (297)
Q Consensus        30 ~~~-~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v~k~~~~trcS~~~~  108 (297)
                      |+| |||+||||+|++|+|++++     ...+.+|+|.+|..|++||++||++|.++|++-...+           -..+
T Consensus        15 ~~P~KrP~say~lF~~e~r~~~k-----~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y-----------~~e~   78 (108)
T 1v64_A           15 GRPTKPPPNSYSLYCAELMANMK-----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDY-----------EVEL   78 (108)
T ss_dssp             TSCCCCCSSHHHHHHHHHHHHCT-----TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHH-----------HHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHh-----CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH-----------HHHH
Confidence            678 9999999999999999987     4588999999999999999999999999998733222           1223


Q ss_pred             HHHHhhcCHHHHHHH
Q 039418          109 AALVSHLIEKQRKAV  123 (297)
Q Consensus       109 ~~~i~~Ls~~qk~~I  123 (297)
                      ..-...+++++++.+
T Consensus        79 ~~Y~~~~~~~~r~~~   93 (108)
T 1v64_A           79 LRFLESLPEEEQQRV   93 (108)
T ss_dssp             HHHHHHSCHHHHHHH
T ss_pred             HHHHhhCCHHHHHHH
Confidence            344456777777654

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.24  E-value=4.8e-12  Score=108.30  Aligned_cols=59  Identities=15%  Similarity=0.273  Sum_probs=55.9

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      ++||||+||||+|++++|.++++.||+ ..+.+|+|.+|..|++||++||++|.++|.+.
T Consensus       100 ~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~  158 (173)
T 2yrq_A          100 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL  158 (173)
T ss_dssp             SSCCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHH
T ss_pred             ccccCcccHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            789999999999999999999999995 68999999999999999999999999999863

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=99.17  E-value=1.4e-11  Score=109.13  Aligned_cols=61  Identities=23%  Similarity=0.300  Sum_probs=56.7

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      .++||||+|||++|+++.|..+++.||+. ++.+|+|.+|+.|++||++||.+|.+.|++..
T Consensus         7 p~~PKrP~say~lF~~~~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k   67 (214)
T 3tq6_A            7 ASCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKKKIYQDAYRAEW   67 (214)
T ss_dssp             HHSCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHccCHHhhhHHHHHHHHHH
Confidence            47899999999999999999999999955 69999999999999999999999999998743

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=99.15  E-value=2e-11  Score=109.81  Aligned_cols=60  Identities=23%  Similarity=0.302  Sum_probs=56.1

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++||||+|||++|+++.|+++++.||+. ++.+|+|.+|+.|++||++||.+|.+.|++.+
T Consensus        40 ~~PKrP~say~lF~~e~r~~~k~~~P~~-~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k   99 (238)
T 3tmm_A           40 SCPKKPVSSYLRFSKEQLPIFKAQNPDA-KTTELIRRIAQRWRELPDSKKKIYQDAYRAEW   99 (238)
T ss_dssp             HSCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999955 69999999999999999999999999998733

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1

Probab=99.12  E-value=4.5e-11  Score=100.74  Aligned_cols=60  Identities=17%  Similarity=0.279  Sum_probs=56.3

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      .++||||++|||+|..+.+..+++.||+ ..+.+|+|.+|+.|++||++||.+|.+.|++.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~   61 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKL   61 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSS-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHhhHHHhccHHHHHHHH
Confidence            3689999999999999999999999996 78999999999999999999999999998763

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens}

Probab=99.05  E-value=2.7e-11  Score=107.30  Aligned_cols=56  Identities=21%  Similarity=0.315  Sum_probs=52.1

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      .|+||||+||||+|++|+|+.++..+|.     +|+|.+|..|++||++||++|.++|.+-
T Consensus       112 p~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~  167 (214)
T 3tq6_A          112 LGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKED  167 (214)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSSCSSHH-----HHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             ccCcccccchhhhhHHHHHHhhccCCHH-----HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4789999999999999999999988884     8999999999999999999999999873

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens}

Probab=98.98  E-value=5.5e-11  Score=106.97  Aligned_cols=56  Identities=21%  Similarity=0.315  Sum_probs=52.1

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      -++||||+||||+|++|+|+.++..||.     +|+|.+|..|++||++||++|.++|.+-
T Consensus       144 p~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~  199 (238)
T 3tmm_A          144 LGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKED  199 (238)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSCCSSHH-----HHHHHHHHHHHTCCTTTTHHHHHHHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHhccCHH-----HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            3789999999999999999999988884     7999999999999999999999999873

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	297
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.53
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.53
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.52
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.45
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.45
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.44
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.4
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.38
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.27
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.07

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.61  E-value=3.1e-16  Score=116.67  Aligned_cols=60  Identities=15%  Similarity=0.233  Sum_probs=57.0

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ||||||+||||+|++++|++++++|| +.++.+|+|.+|..|++||++||++|.++|++..
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p-~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k   60 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENP-KMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR   60 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTST-TSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999 5689999999999999999999999999998755

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: SRY
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.2e-15  Score=114.58  Aligned_cols=60  Identities=15%  Similarity=0.249  Sum_probs=56.9

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |+||||+||||+|++|+|++++++|| ...+.+|+|.+|..|++||++||++|.++|++..
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p-~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k   62 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENP-RMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ   62 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHST-TSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999 4589999999999999999999999999998755

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.53  E-value=2.8e-15  Score=108.57  Aligned_cols=59  Identities=14%  Similarity=0.148  Sum_probs=55.7

Q ss_pred             CCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           31 KDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      ++|||+||||+|+++.|+.++++|| ...+.+|+|.+|..|++||++||++|.++|++..
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p-~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k   60 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFP-DMHNSNISKILGSRWKAMTNLEKQPYYEEQARLS   60 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCS-SCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999 6789999999999999999999999999998743

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.53  E-value=3.7e-15  Score=107.96  Aligned_cols=60  Identities=18%  Similarity=0.272  Sum_probs=55.0

Q ss_pred             CCCCCCcchhhhHHHHHHHHHHhCCCCcc-hhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           31 KDRENNHGFISFFAESVRQLKAKDGRACI-TNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        31 ~~~r~~~~f~~~~~~~~~~~~~~~~~~~~-~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |||||.||||+|+.+.|.+++++||+... ..+|+|.+|..|++||++||++|.++|++.+
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k   61 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK   61 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence            79999999999999999999999997543 5799999999999999999999999998743

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.52  E-value=3.2e-15  Score=110.53  Aligned_cols=60  Identities=15%  Similarity=0.263  Sum_probs=56.2

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      |.||||+||||+|+.|.|.+++++||+ .++.+|+|.+|..|++||++||++|..+|++..
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~-~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k   60 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLK   60 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTT-CCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999995 588999999999999999999999999998743

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=3.1e-14  Score=106.95  Aligned_cols=58  Identities=14%  Similarity=0.215  Sum_probs=54.9

Q ss_pred             CCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           32 DRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        32 ~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      +|||+||||+|+++.|++++++|| ...+.+|++.+|..|++||++||++|.+.|++..
T Consensus         3 ikRP~naf~lF~~~~r~~~~~~~P-~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k   60 (86)
T d2lefa_           3 IKKPLNAFMLYMKEMRANVVAEST-LKESAAINQILGRRWHALSREEQAKYYELARKER   60 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSS-CCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            799999999999999999999999 5689999999999999999999999999998754

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.45  E-value=2.4e-14  Score=108.25  Aligned_cols=67  Identities=18%  Similarity=0.246  Sum_probs=60.4

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccccc
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEK   96 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v~k   96 (297)
                      -++||||+||||+|+.|+|.++++.|| ...+.+|++.+|..|+.||++||++|..+|++.....-++
T Consensus        18 ~~~PKrP~say~lF~~e~r~~~~~~~p-~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          18 SEKPKRPVSAMFIFSEEKRRQLQEERP-ELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             CCCCCCCCCHHHHHHHHTHHHHHHHCT-TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999 4578999999999999999999999999999876655433

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.44  E-value=2.7e-14  Score=103.95  Aligned_cols=57  Identities=11%  Similarity=0.274  Sum_probs=52.6

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      |+||||+||||+|+.|.|.+++++|| +.++.+|+|.+|..|++|+  ||++|..+|++.
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p-~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~   58 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENP-GIKVTEVAKRGGELWRAMK--DKSEWEAKAAKA   58 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTST-TCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHH
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHhcChh--HHHHHHHHHHHH
Confidence            79999999999999999999999999 5789999999999999986  489999998763

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: NHP6a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.40  E-value=1.2e-13  Score=105.20  Aligned_cols=59  Identities=17%  Similarity=0.288  Sum_probs=55.6

Q ss_pred             CCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcC
Q 039418           30 SKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRG   89 (297)
Q Consensus        30 ~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~   89 (297)
                      ++||||+||||+|++|.|.++++.||+ .+..+|++.+|..|++||++||.+|.++|++.
T Consensus        19 ~~PKrP~saf~lF~~e~r~~ik~~~p~-~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~   77 (93)
T d1lwma_          19 NAPKRALSAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD   77 (93)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHhCCC-CcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence            579999999999999999999999995 58999999999999999999999999999874

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=1e-13  Score=104.98  Aligned_cols=61  Identities=16%  Similarity=0.242  Sum_probs=57.2

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCC
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGG   90 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~   90 (297)
                      .++||||+|||++|+.+.|..++++|| +.++.+|++.+|..|+.||++||++|.++|.+..
T Consensus         8 p~~PKrP~say~lf~~~~r~~~~~~~p-~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~   68 (91)
T d1k99a_           8 PDFPKKPLTPYFRFFMEKRAKYAKLHP-EMSNLDLTKILSKKYKELPEKKKMKYIQDFQREK   68 (91)
T ss_dssp             SSSCCCSCCHHHHHHHHHHHHHHTTCT-TSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHH
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999 5689999999999999999999999999998754

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.27  E-value=1.3e-12  Score=100.54  Aligned_cols=61  Identities=15%  Similarity=0.177  Sum_probs=54.4

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCc
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKA   92 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~   92 (297)
                      +..||||+||||+|+.|+|+.++..||   .+.+|+|.+|..|++||++||++|.++|++....
T Consensus         6 ~~p~KrP~~ay~~F~~e~r~~~~~~~~---~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~   66 (101)
T d1v63a_           6 SGPKKPPMNGYQKFSQELLSNGELNHL---PLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQ   66 (101)
T ss_dssp             CSSCCCCSSSHHHHHHHHHHHCTTTTS---CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHhcCC---CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHH
Confidence            345799999999999999999998887   5789999999999999999999999999985433

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.07  E-value=3.3e-11  Score=93.71  Aligned_cols=79  Identities=18%  Similarity=0.205  Sum_probs=60.1

Q ss_pred             CCCCCCCCcchhhhHHHHHHHHHHhCCCCcchhHHHHHHHhhhcCCChHhhhhhhhhhhcCCCccccccceeeecCHHHH
Q 039418           29 GSKDRENNHGFISFFAESVRQLKAKDGRACITNEVRKEIRNAFKNLPVEEKCQYKFQSRRGGKANVEKVKFLTRCAPDRL  108 (297)
Q Consensus        29 ~~~~~r~~~~f~~~~~~~~~~~~~~~~~~~~~~~v~k~~g~~wk~ls~~ek~~~~~~~~~~~k~~v~k~~~~trcS~~~~  108 (297)
                      |..||||+||||+|+.|+|+++    | ...+.++.+.+|..|++||++||++|.++|++....+.           ..+
T Consensus        15 ~~p~K~P~~ay~lF~~~~r~~~----~-~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~-----------~~~   78 (108)
T d1v64a_          15 GRPTKPPPNSYSLYCAELMANM----K-DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYE-----------VEL   78 (108)
T ss_dssp             TSCCCCCSSHHHHHHHHHHHHC----T-TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH-----------HHH
T ss_pred             CCCCCCCCcHHHHHHHHHHHHc----c-CCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHH-----------HHH
Confidence            4556888999999999999875    4 45678999999999999999999999999998443331           223


Q ss_pred             HHHHhhcCHHHHHHH
Q 039418          109 AALVSHLIEKQRKAV  123 (297)
Q Consensus       109 ~~~i~~Ls~~qk~~I  123 (297)
                      ......+++++++.+
T Consensus        79 ~~y~~~~~~~~k~~~   93 (108)
T d1v64a_          79 LRFLESLPEEEQQRV   93 (108)
T ss_dssp             HHHHHHSCHHHHHHH
T ss_pred             HHHHhhCCHHHHHHH
Confidence            334456777666544