Citrus Sinensis ID: 023605

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280
Protein Sequence
MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Secondary Structure (PSIPRED)
ccccccHHHHHHHHcccccccccHHHHHHHHcccccccHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHccccHHccccccccHHHHHHHHHcccccccEEEEccccccccccHHHHHcccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHcccccccccccccccEEEcccccccccHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccccEEEc
Secondary Structure Prediction (SSPRO)
cccEcccccEEEEEcccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHccccHHccccccccHHHHHHHHHHccccccEEEEccEEEEccHHHHHHHccccccccEccccccHHHHHHHHHccccccccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccHHccHEccHHHHHHccHHHHHHHHHHHHHHHHHHccccccccHHHHHEHHHHHHcccccEEc
Coil and Loop (DISEMBL)
mlcfcsneevkrlrsensdLSVTLGLRKHIGktykelppeqkARYKkrdermgnsgnsnshsgdneivetkcvpERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKimgvkdggmaikingasdHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCpigsyistlflhpimdvssikslnwaTFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Flexible Loop (DISEMBL)
mlcfcsneevkrlrsensdlsvtlglrkhigktykelppeqkarykkrdermgnsgnsnshsgdneivETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQlklsicll
Low Complexity Region (SEG)
MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMgnsgnsnshsgdnEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Disordered region (IsUnstruct)
******************************************************************IVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICL*
Disordered Region (DISOPRED)
*LCF*S****************************************************************KCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Disordered Region (DISEMBL)
***************ENSDLSVTLGLRKHIGKTYKELPPEQKA*********************NEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Disordered Region (DISPRO)
MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARY***********************ETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

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	280
147783848	708	hypothetical protein VITISV_032233 [Viti	0.939	0.371	0.329	3e-36
225453104	617	PREDICTED: uncharacterized protein LOC10	0.939	0.426	0.329	3e-36
296087190	766	unnamed protein product [Vitis vinifera]	0.939	0.343	0.322	1e-34
255583781	421	conserved hypothetical protein [Ricinus	0.932	0.619	0.313	2e-32
224077245	628	predicted protein [Populus trichocarpa]	0.85	0.378	0.327	6e-30
147795729	849	hypothetical protein VITISV_004916 [Viti	0.932	0.307	0.297	3e-29
147772140	637	hypothetical protein VITISV_026046 [Viti	0.853	0.375	0.296	9e-28
356533899	590	PREDICTED: uncharacterized protein LOC10	0.8	0.379	0.285	1e-23
147798273	326	hypothetical protein VITISV_001668 [Viti	0.775	0.665	0.302	3e-21
242077368	482	hypothetical protein SORBIDRAFT_06g03027	0.689	0.400	0.308	8e-20

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

 Score =  157 bits (398), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 141/270 (52%), Gaps = 7/270 (2%)

Query: 4   FCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR-----DERMGNSGNS 58
           FCS E ++   + + + S      K     +K +  E+KA+Y KR     D  +  +   
Sbjct: 85  FCSREFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPAR 144

Query: 59  NSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVN 118
                    + T+C P R   +++ L+ ++K A+R +GF SLL LRC  L+R LC WL+ 
Sbjct: 145 APKPRKQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLE 204

Query: 119 QFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIR 178
           +F   R  +E+ G+++ L PK    +MG+   G  +  +G  D I E+R  +  T  GI 
Sbjct: 205 RFNTARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGIS 264

Query: 179 IRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWAT 237
           +R LEE +    EA + FK +F L+A+ T+LCP     +S  FLH + ++ +I   NW  
Sbjct: 265 VRLLEERLAA-PEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGK 323

Query: 238 FCYDWLVKSICRFQNQQAAYIGGCLHFLQV 267
           F  D LV+ + RF   +   +GGCL FLQ+
Sbjct: 324 FLLDRLVREVSRFHQGKQRAVGGCLLFLQL 353

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 =  157 bits (398), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 141/270 (52%), Gaps = 7/270 (2%)

Query: 4   FCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR-----DERMGNSGNS 58
           FCS E ++   + + + S      K     +K +  E+KA+Y KR     D  +  +   
Sbjct: 31  FCSREFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPAR 90

Query: 59  NSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVN 118
                    + T+C P R   +++ L+ ++K A+R +GF SLL LRC  L+R LC WL+ 
Sbjct: 91  APKPRKQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLE 150

Query: 119 QFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIR 178
           +F   R  +E+ G+++ L PK    +MG+   G  +  +G  D I E+R  +  T  GI 
Sbjct: 151 RFNTARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGIS 210

Query: 179 IRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWAT 237
           +R LEE +    EA + FK +F L+A+ T+LCP     +S  FLH + ++ +I   NW  
Sbjct: 211 VRLLEERLAA-PEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGK 269

Query: 238 FCYDWLVKSICRFQNQQAAYIGGCLHFLQV 267
           F  D LV+ + RF   +   +GGCL FLQ+
Sbjct: 270 FLLDRLVREVSRFHQGKQRAVGGCLLFLQL 299

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  153 bits (386), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 140/270 (51%), Gaps = 7/270 (2%)

Query: 4   FCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR-----DERMGNSGNS 58
           + S E ++   + + + S      K     +K +  E+KA+Y KR     D  +  +   
Sbjct: 169 YFSREFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPAR 228

Query: 59  NSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVN 118
                    + T+C P R   +++ L+ ++K A+R +GF SLL LRC  L+R LC WL+ 
Sbjct: 229 APKPRKQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLE 288

Query: 119 QFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIR 178
           +F   R  +E+ G+++ L PK    +MG+   G  +  +G  D I E+R  +  T  GI 
Sbjct: 289 RFNTARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGIS 348

Query: 179 IRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWAT 237
           +R LEE +    EA + FK +F L+A+ T+LCP     +S  FLH + ++ +I   NW  
Sbjct: 349 VRLLEERLAA-PEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGK 407

Query: 238 FCYDWLVKSICRFQNQQAAYIGGCLHFLQV 267
           F  D LV+ + RF   +   +GGCL FLQ+
Sbjct: 408 FLLDRLVREVSRFHQGKQRAVGGCLLFLQL 437

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 =  145 bits (365), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/268 (31%), Positives = 139/268 (51%), Gaps = 7/268 (2%)

Query: 6   SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR-----DERMGNSGNSNS 60
           S E +K   + + + S      K     +K +  E+KA+Y +R     D  +  +     
Sbjct: 45  SREFIKEYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTRRAREVWDNYLSTAPARTP 104

Query: 61  HSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQF 120
                  + T+C P R   +++ L+ E+K A++++GF SLL LRC  L+R LC WL+ +F
Sbjct: 105 KPRKQTKLVTRCSPGRLFNVLQRLTPEQKDAVKDLGFGSLLGLRCRTLRRSLCLWLLQRF 164

Query: 121 KPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIR 180
                 +E+ G ++ L PK    +MG+   G  +  +G  + I ++RR +  T +GI + 
Sbjct: 165 NTTGRSLEICGDRIPLSPKDVEFVMGLAASGKDVVNSGPDNLILDLRRNYNATNRGISVS 224

Query: 181 TLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWATFC 239
            LEE + +  EA + FK +F L+A+ TLL P     +S  FLH + +V  +   NW  F 
Sbjct: 225 LLEERL-KAPEAGEEFKRSFVLYALGTLLSPTARLDVSPSFLHFLTNVDVVHQYNWGKFL 283

Query: 240 YDWLVKSICRFQNQQAAYIGGCLHFLQV 267
            D LV+ + RF+  +   +GGCL FLQ+
Sbjct: 284 LDRLVREVARFRQGKQRAVGGCLLFLQL 311

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  137 bits (344), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 81/247 (32%), Positives = 131/247 (53%), Gaps = 9/247 (3%)

Query: 28  KHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHS------GDNEIVETKCVPERFCALV 81
           K     +K +  E+KA+Y K+   + +S  S + +         ++V T+C P R   ++
Sbjct: 73  KAASDAWKSMRVEEKAKYTKQARELWDSYLSTAPARIPKPRKQTKLV-TRCSPGRLFNVL 131

Query: 82  KSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMF 141
           + LS E+  A++ +GF SLL LRC  L+R LC WL+ +F      +E+ G  + L P+  
Sbjct: 132 QRLSPEQNAAVKSMGFGSLLGLRCRTLRRSLCLWLLERFNTAGCSLEICGMCIPLSPRDV 191

Query: 142 SKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFT 201
             ++G+   G  +  +G  D I ++RR +  T  GI +R LEE +    EA + FK +F 
Sbjct: 192 EIVLGLAASGKDVINSGPDDLIVDLRRSYNATNHGISVRLLEERL-TAPEAGEDFKRSFV 250

Query: 202 LFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGG 260
           L+A+ TLL P     +S  FLH + ++  +   NW  F  D LV+ + RF   +   +GG
Sbjct: 251 LYALGTLLSPTARLDVSPSFLHFLTNMDVVHQYNWGKFLLDRLVREVSRFHQGKQRAVGG 310

Query: 261 CLHFLQV 267
           CL FLQ+
Sbjct: 311 CLLFLQL 317

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  135 bits (339), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 78/262 (29%), Positives = 135/262 (51%), Gaps = 1/262 (0%)

Query: 7   NEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNE 66
           N+++  ++ ++  + +   LRK +GK +  L   +K  +  + +      +         
Sbjct: 197 NDQLAMMKEKDKGVKINDDLRKKLGKKWNALSKVEKENFMAKSKESSKQYSLQKGVVPKL 256

Query: 67  IVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNI 126
            ++T+C PER   +++ L  ++K AI EIGF SLL+LRC K+   LC  L+N F P   +
Sbjct: 257 YLQTRCSPERVIRVIEKLEPKQKAAIXEIGFGSLLQLRCRKIDHGLCLXLINSFNPNTYM 316

Query: 127 IELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVI 186
           ++L+   ++L P     IMG++  G  I +N    H  ++ + +      + +  LE  I
Sbjct: 317 LQLYNTCIKLSPIDVEFIMGLRARGFKIGMNKDVXHKNDLCKKYCDKKGRLPLVMLENQI 376

Query: 187 EQLDEANKIFKVAFTLFAIATLLCP-IGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVK 245
            +  E    FKV F LF +  LLCP +  +++  FLH + D+ SIK +NW  F   +LV 
Sbjct: 377 REDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKMNWXEFVLSYLVH 436

Query: 246 SICRFQNQQAAYIGGCLHFLQV 267
            I  F+ +Q + + GCL FL +
Sbjct: 437 GIEEFKKKQQSGVCGCLLFLML 458

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 =  130 bits (326), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 75/253 (29%), Positives = 128/253 (50%), Gaps = 14/253 (5%)

Query: 7   NEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNE 66
           N+++  ++ ++  + +   LRK +GK +  L   +K  +  + +      +         
Sbjct: 59  NDQLAMMKEKDKGVKINDDLRKKLGKKWNALSKVEKENFMAKXKESSKQYSLQKGVVPKL 118

Query: 67  IVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNI 126
            ++T+C PER   ++++L  ++K AI EIGF SLL+LRC K+   LC WL+N F P   +
Sbjct: 119 YLQTRCSPERVIRVIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCLWLINSFNPNTYM 178

Query: 127 IELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVI 186
           ++L+   ++L P     IMG++  G  I +N    H  +             +  LE  I
Sbjct: 179 LQLYNTCIKLSPIDVEFIMGLRARGFKIGMNKDVGHKND-------------LLMLENQI 225

Query: 187 EQLDEANKIFKVAFTLFAIATLLCP-IGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVK 245
            +  E    FKV F LF +  LLCP +  +++  FLH + D+ SIK +NWA F   +LV 
Sbjct: 226 REDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKMNWAEFVLSYLVH 285

Query: 246 SICRFQNQQAAYI 258
            I  F+ +Q + +
Sbjct: 286 GIEEFKKKQQSGV 298

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  115 bits (289), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 114/231 (49%), Gaps = 7/231 (3%)

Query: 28  KHIGKTYKELPPEQKARYKKR-----DERMGNSGNSNSHSGDNEIVETKCVPERFCALVK 82
           K     +K +  E+K +Y +      D  + +    N        + T+C P R   +++
Sbjct: 61  KAASNAWKSMSLEEKEKYARHAREVWDGYLSSGAAPNPKPRKQTKLVTRCSPGRLFKVLQ 120

Query: 83  SLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFS 142
            L+ E+K+A++ +GF SLL LRC  L+R LC WL+ +F      +E+    + L P    
Sbjct: 121 RLTPEQKEAVKSMGFGSLLGLRCRTLRRSLCLWLLERFDTTNCSLEICNVDVPLTPNDVE 180

Query: 143 KIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTL 202
            ++G+   G  +  +G  D I+++R  +     GI +R LEE +    E+   FK +F L
Sbjct: 181 MVLGLSASGKEVVNSGPEDMISDLRNSYNAINHGISVRLLEEQLATA-ESGDDFKRSFVL 239

Query: 203 FAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQN 252
           + + TLLCP     +S  FLH + ++  +   NW  F  D LV+ +  ++N
Sbjct: 240 YVLGTLLCPTARLDVSPSFLHFLTNMDLVHQYNWGKFLLDRLVRELFYYEN 290

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 111/218 (50%), Gaps = 1/218 (0%)

Query: 20  LSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCA 79
           +S  + LRK +G  +  L   +K  +  + +      +          ++T+C  ER   
Sbjct: 106 ISPDVQLRKKLGIKWNALSKVEKENFMAKSKESSKQYSLQKGVVPKLYLQTRCSXERVIR 165

Query: 80  LVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPK 139
           ++++L  ++K AI EIGF SLL+LRC K+   LC WL+N F     +++L+   ++L P 
Sbjct: 166 VIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCLWLINSFNXNTYMLQLYNTCIKLSPI 225

Query: 140 MFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVA 199
               IMG++  G  I +N    H  ++ + +      + +  LE  I +  E    FKV 
Sbjct: 226 DVEFIMGLRARGXKIGMNKDVGHKNDLCKKYCDKKGRLPLVMLENQIREDKEGGNDFKVR 285

Query: 200 FTLFAIATLLCP-IGSYISTLFLHPIMDVSSIKSLNWA 236
           F LF +  LLCP +  +++  FLH + D+ SIK +NWA
Sbjct: 286 FVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKINWA 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242077368|ref|XP_002448620.1| hypothetical protein SORBIDRAFT_06g030272 [Sorghum bicolor] gi|241939803|gb|EES12948.1| hypothetical protein SORBIDRAFT_06g030272 [Sorghum bicolor]

 Score =  103 bits (257), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 63/204 (30%), Positives = 110/204 (53%), Gaps = 11/204 (5%)

Query: 75  ERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFK-PERNIIELHGQK 133
           E F  +V +LS+++K+ ++++GF  LLEL C +L   L  WL++ F    R ++  +G  
Sbjct: 35  EMFVDVVSNLSQQQKEVVQDLGFSGLLELCCPRLPTNLLLWLIDHFNAATRTLMLPNGFN 94

Query: 134 LELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQL--DE 191
            EL PK   KI+G+ +GG+ I   G  +    ++   Q   +G+   T+ E+  Q+  D 
Sbjct: 95  FELNPKCVHKILGIPNGGLHILRFGTLESYKIIKD--QIYSRGVT-PTVSELCNQITPDL 151

Query: 192 ANKIFKVAFTLFAIATLLCP-IGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRF 250
           ++  F   F L A+++ LCP      ST + H ++++SS+   +W +F  DWLV  + +F
Sbjct: 152 SDFEFGRLFMLLALSSFLCPNTRGACSTRYYHAVLNISSVPKYDWCSFVLDWLVSYLVKF 211

Query: 251 QNQQ----AAYIGGCLHFLQVRPL 270
           +  +    +  IGGC H L +  L
Sbjct: 212 KVHKRTTGSNVIGGCCHILVISYL 235

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

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	280
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	6e-04
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	0.004

>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 6  SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 52
          S E+  +L++EN  L     + K +G+ +K L  E+K  Y+++ E+ 
Sbjct: 12 SQEQRAKLKAENPGLKNA-EISKILGEKWKNLSEEEKKPYEEKAEKE 57

Length = 69

>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 17/43 (39%), Positives = 29/43 (67%), Gaps = 1/43 (2%)

Query: 6  SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR 48
          S E+  +L+ EN D SVT  + K +G+ +KEL  E+K +Y+++
Sbjct: 12 SQEQRPKLKKENPDASVT-EVTKILGEKWKELSEEEKKKYEEK 53

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. Length = 66

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	280
PF10536	363	PMD: Plant mobile domain; InterPro: IPR019557 This	99.98
PTZ00199	94	high mobility group protein; Provisional	99.23
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.21
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.17
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.15
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.05
smart00398	70	HMG high mobility group.	99.03
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.02
PF09331	142	DUF1985: Domain of unknown function (DUF1985); Int	98.94
COG5648	211	NHP6B Chromatin-associated proteins containing the	98.9
KOG0381	96	consensus HMG box-containing protein [General func	98.88
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.82
KOG0527	331	consensus HMG-box transcription factor [Transcript	98.45
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	98.07
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	97.56
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	97.36
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	95.83
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	95.47
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	93.33
KOG2746	683	consensus HMG-box transcription factor Capicua and	90.59
COG5648	211	NHP6B Chromatin-associated proteins containing the	90.49
PF03078	458	ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 A	85.01

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

Probab=99.98  E-value=2.8e-33  Score=263.21  Aligned_cols=181  Identities=22%  Similarity=0.354  Sum_probs=157.0

Q ss_pred             CChhhhccc--ccccCHHHHHHHhcccCCCcceEEECCEEEEeCccccceeeeecCCCcccccCCCc---hHHHHHHHHh
Q 023605           96 GFESLLELR--CGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGAS---DHIAEVRRIF  170 (280)
Q Consensus        96 GFg~LL~i~--~~~l~~~l~~wL~~~~d~~t~~~~i~g~~i~it~~dV~~VlGLP~~G~~i~~~~~~---~~~~~l~~~~  170 (280)
                      |||+|+.|.  ..++++.|+.+|+++|+++|++|++++++++||++||..++|||+.|.+|......   +.++++.+..
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  89999999999999999999999999999999999999999999999999875433   2333333322


Q ss_pred             C----CCCCCcchhHHHHHHhhcccc-chhHHHHHHHhhhceeecccCCC--CCccccccccccCCCccccchHHHHHHH
Q 023605          171 Q----PTVKGIRIRTLEEVIEQLDEA-NKIFKVAFTLFAIATLLCPIGSY--ISTLFLHPIMDVSSIKSLNWATFCYDWL  243 (280)
Q Consensus       171 ~----~~~~~i~l~~L~~~l~~~~~~-~d~f~r~Fll~~~~~~L~Ptt~~--vs~~yl~~l~D~~~i~~ynW~~~Vl~~L  243 (280)
                      .    ..+..+.++++++.+.+.+++ .+.+.|||+++.+|++|||+++.  |+..|++++.|++.+++||||.+||++|
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            1    124556778898888544433 24899999999999999999877  9999999999999999999999999999


Q ss_pred             HHHHHHHhhcC--CcccchhHHHHHHHHhhCCCCc
Q 023605          244 VKSICRFQNQQ--AAYIGGCLHFLQVRPLLQLKLS  276 (280)
Q Consensus       244 ~~~i~k~~~~k--~~~i~GC~~lLqi~yld~l~~~  276 (280)
                      +++++++..+.  ..+++||..|||+|+|+|++++
T Consensus       161 y~~L~~~~~~~~~~~~~~g~~~llq~W~werf~~~  195 (363)
T PF10536_consen  161 YRDLCKASRKSASQSNIGGPLWLLQLWAWERFPVG  195 (363)
T ss_pred             HHHHHHHhhhcccccccccceeeeccchhheeecc
Confidence            99999988776  7899999999999999999865

>PTZ00199 high mobility group protein; Provisional

Probab=99.23  E-value=2e-12  Score=99.08  Aligned_cols=59  Identities=22%  Similarity=0.374  Sum_probs=55.6

Q ss_pred             cccchHHHHHHHHhhCCCCh-hhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLS-VTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~-~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+++.|+.++++||+.+ .+++|+|++|+.|++||++||++|.++|...+.+|..++
T Consensus        30 Y~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~   89 (94)
T PTZ00199         30 YMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEK   89 (94)
T ss_pred             HHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 489999999999999999999999999999999998654

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

Probab=99.21  E-value=4.5e-12  Score=90.04  Aligned_cols=57  Identities=28%  Similarity=0.464  Sum_probs=54.1

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      |++|++|+|+.++++||+.+ +.++++.+|+.|++||++||++|.+++++.+.+|..+
T Consensus         8 f~~f~~~~r~~~~~~~p~~~-~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e   64 (66)
T cd01390           8 YFLFSQEQRPKLKKENPDAS-VTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKE   64 (66)
T ss_pred             HHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHh
Confidence            89999999999999999975 9999999999999999999999999999999998754

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=99.17  E-value=7.7e-12  Score=91.01  Aligned_cols=59  Identities=15%  Similarity=0.218  Sum_probs=55.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|+++.|..++++||+.+ +..++|.+|+.|++||++||++|.+++.+.+.+|..+.+
T Consensus         9 f~~F~~~~r~~~~~~~p~~~-~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p   67 (72)
T cd01388           9 FMLFSKRHRRKVLQEYPLKE-NRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYP   67 (72)
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            89999999999999999985 999999999999999999999999999999999977653

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.

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

Probab=99.15  E-value=1.3e-11  Score=90.93  Aligned_cols=59  Identities=22%  Similarity=0.371  Sum_probs=56.1

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++++|+.++++||+.+ +..|++++|+.|+.||++||++|.++|++.+.+|..+.+
T Consensus         9 f~lf~~~~r~~~~~~~p~~~-~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p   67 (77)
T cd01389           9 FILYRQDKHAQLKTENPGLT-NNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYP   67 (77)
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            89999999999999999985 999999999999999999999999999999999988764

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.

>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=99.05  E-value=6.2e-11  Score=84.96  Aligned_cols=57  Identities=28%  Similarity=0.429  Sum_probs=53.9

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      |++|++++|..++++||+.+ ..+|++.+|+.|++||++||++|.+++.+.+.+|..+
T Consensus         8 f~lf~~~~~~~~k~~~p~~~-~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~   64 (69)
T PF00505_consen    8 FMLFCKEKRAKLKEENPDLS-NKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKE   64 (69)
T ss_dssp             HHHHHHHHHHHHHHHSTTST-HHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcccc-cccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999998 9999999999999999999999999999999888643

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=99.03  E-value=1.1e-10  Score=83.61  Aligned_cols=58  Identities=26%  Similarity=0.453  Sum_probs=54.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      |++|++++|+.++++||+.+ +.++++.+|..|++||++||++|.++++..+.+|....
T Consensus         9 y~~f~~~~r~~~~~~~~~~~-~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~   66 (70)
T smart00398        9 FMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEM   66 (70)
T ss_pred             HHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999987 89999999999999999999999999999999887643

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

Probab=99.02  E-value=1.1e-10  Score=82.60  Aligned_cols=57  Identities=25%  Similarity=0.405  Sum_probs=53.6

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|+.|+|+.++++||+.+ ..++.+.+|++|++||+++|++|.+++++.+.+|...
T Consensus         8 f~~f~~~~~~~~~~~~~~~~-~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~   64 (66)
T cd00084           8 YFLFSQEHRAEVKAENPGLS-VGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKE   64 (66)
T ss_pred             HHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHh
Confidence            89999999999999999976 8899999999999999999999999999999988654

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

>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=98.94  E-value=9.8e-10  Score=90.41  Aligned_cols=123  Identities=14%  Similarity=0.265  Sum_probs=89.8

Q ss_pred             ceEEECCEEEEeCccccceeeeecCCCcccccCCCch---HHHHHHHHhCCCCCCcchhHHHHHHhhc--cccchhHHHH
Q 023605          125 NIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASD---HIAEVRRIFQPTVKGIRIRTLEEVIEQL--DEANKIFKVA  199 (280)
Q Consensus       125 ~~~~i~g~~i~it~~dV~~VlGLP~~G~~i~~~~~~~---~~~~l~~~~~~~~~~i~l~~L~~~l~~~--~~~~d~f~r~  199 (280)
                      .-+.++|..|.++..+.+.|+|||++..|-.......   ....+.+.+-..+..+++..+.+++.+.  .+.++.+.-|
T Consensus        14 ~W~~~~g~piRfsl~Ef~lvTGL~C~~~p~~~~~~~~~~~~~~~fw~~Lf~~~~~vtv~dv~~~L~~~~~~~~~~Rlrla   93 (142)
T PF09331_consen   14 IWFVFNGVPIRFSLREFALVTGLNCGPYPKEKKVDKKGKKEKGSFWNKLFGREEDVTVEDVIAKLKKMKKWDSEDRLRLA   93 (142)
T ss_pred             EEEEECCEeeEecHHHHHhhcCCcCCCCCcccchhhccccchhhhhhhhccccccCcHHHHHHHHhhcccCChhhHHHHH
Confidence            4678899999999999999999999988776542111   1112322222345679999999999854  2233445555


Q ss_pred             HHHhhhceeecccCCC-CCccccccccccCCCccccchHHHHHHHHHHH
Q 023605          200 FTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWATFCYDWLVKSI  247 (280)
Q Consensus       200 Fll~~~~~~L~Ptt~~-vs~~yl~~l~D~~~i~~ynW~~~Vl~~L~~~i  247 (280)
                      +++++.|.+++++.+. |+..++..+.|++...+|-||.+.++.++++|
T Consensus        94 ~L~~v~gvl~~~~~~~~i~~~~~~~v~Dl~~f~~yPWGr~sF~~~~~sI  142 (142)
T PF09331_consen   94 LLLFVDGVLIATSKTTKIPKEHLKMVDDLEKFLNYPWGRYSFDMLMKSI  142 (142)
T ss_pred             HHHhhheeeeccCCCCCCCHHHHHHHhhHHHHhcCCcHHHHHHHHHhcC
Confidence            5555555555555556 99999999999999999999999999999874

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

Probab=98.90  E-value=3e-10  Score=97.11  Aligned_cols=58  Identities=24%  Similarity=0.303  Sum_probs=55.3

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+++.|++++++||+++ ++++||++|++||+|+|+||.||.+.+...+.+|.+.+
T Consensus        78 yf~y~~~~R~ei~~~~p~l~-~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek  135 (211)
T COG5648          78 YFLYSAENRDEIRKENPKLT-FGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREK  135 (211)
T ss_pred             HHHHHHHHHHHHHHhCCCCC-hHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHH
Confidence            89999999999999999996 99999999999999999999999999999999987755

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

Probab=98.88  E-value=9.7e-10  Score=84.08  Aligned_cols=58  Identities=21%  Similarity=0.409  Sum_probs=54.2

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      |++|++++|..++++||+. ++.+|+|++|+.|++|++++|.+|..++.+.+.+|..+.
T Consensus        30 ~~~f~~~~~~~~k~~~p~~-~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~   87 (96)
T KOG0381|consen   30 FFLFSSEQRSKIKAENPGL-SVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKEL   87 (96)
T ss_pred             HHHHHHHHHHHHHHhCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            7899999999999999995 499999999999999999999999999999999997654

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

Probab=98.82  E-value=1.4e-09  Score=79.31  Aligned_cols=57  Identities=19%  Similarity=0.248  Sum_probs=49.4

Q ss_pred             cccchHHHHHHHHhh-CCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSE-NSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~-~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      |++|+.|.++.++.+ .|.. ....+.+.+|+.|++||++||++|.++|+..+.+|+.+
T Consensus        11 y~lF~~~~~~~~k~~G~~~~-~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e   68 (73)
T PF09011_consen   11 YNLFMKEMRKEVKEEGGQKQ-SFREVMKEISERWKSLSEEEKEPYEERAKEDKERYERE   68 (73)
T ss_dssp             HHHHHHHHHHHHHHHT-T-S-SHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcccCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHH
Confidence            889999999999999 7744 48899999999999999999999999999999988653

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 ....

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=98.45  E-value=8.6e-08  Score=88.73  Aligned_cols=59  Identities=19%  Similarity=0.321  Sum_probs=56.2

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||.++.+.|+.+-++||+.- ++.+-|.+|+.||.|+|+||.||++.|++.+++|.++-+
T Consensus        70 FMVWSq~~RRkma~qnP~mH-NSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehP  128 (331)
T KOG0527|consen   70 FMVWSQGQRRKLAKQNPKMH-NSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYP  128 (331)
T ss_pred             hhhhhHHHHHHHHHhCcchh-hHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCC
Confidence            89999999999999999996 999999999999999999999999999999999988763

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

Probab=98.07  E-value=6.9e-07  Score=85.73  Aligned_cols=55  Identities=11%  Similarity=0.235  Sum_probs=51.4

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|.+..|..+|++  +.+ ++.|+|.+|++||.||.  |.+|.+||+..+.||+.+++
T Consensus       543 ~m~w~~~~r~~ik~d--gi~-~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~  597 (615)
T KOG0526|consen  543 YMLWLNASRESIKED--GIS-VGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMK  597 (615)
T ss_pred             HHHHHHhhhhhHhhc--Cch-HHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHH
Confidence            899999999999999  554 99999999999999999  99999999999999988774

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=97.56  E-value=3.9e-05  Score=70.12  Aligned_cols=51  Identities=16%  Similarity=0.328  Sum_probs=47.2

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhc
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMG   53 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k   53 (280)
                      ||.||+|+|+.+-+|-- +|.-+++-+++|++|.+||-||.++|-+-|++.+
T Consensus       199 FmlyMKEmRa~vvaEct-lKeSAaiNqiLGrRWH~LSrEEQAKYyElArKer  249 (421)
T KOG3248|consen  199 FMLYMKEMRAKVVAECT-LKESAAINQILGRRWHALSREEQAKYYELARKER  249 (421)
T ss_pred             HHHHHHHHHHHHHHHhh-hhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHH
Confidence            79999999999999984 8889999999999999999999999998887766

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

Probab=97.36  E-value=4.6e-05  Score=69.06  Aligned_cols=59  Identities=22%  Similarity=0.273  Sum_probs=54.6

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||-|+.-.-..+|++||+++ .=.+||.+|.-|+.|+|+||..|+..-+.-|.+|+.+++
T Consensus        72 ymrySrkvWd~VkA~nPe~k-LWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smk  130 (410)
T KOG4715|consen   72 YMRYSRKVWDQVKASNPELK-LWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMK  130 (410)
T ss_pred             hhHHhhhhhhhhhccCcchH-HHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            77788888889999999999 888999999999999999999999999999999998874

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

Probab=95.83  E-value=0.0053  Score=44.67  Aligned_cols=53  Identities=6%  Similarity=0.072  Sum_probs=45.1

Q ss_pred             hHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            6 SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         6 ~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      .+..+..|-+.+|+.. ..+ -|+.+..|++|++.||.++.+||.+..++|+.+.
T Consensus        15 qq~vi~dYla~~~~dr-~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el   67 (85)
T PF14887_consen   15 QQSVIGDYLAKFRNDR-KKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYEREL   67 (85)
T ss_dssp             HHHHHHHHHHHTTSTH-HHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhHhH-HHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            4567788999999876 333 5699999999999999999999999999998755

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

Probab=95.47  E-value=0.0091  Score=57.37  Aligned_cols=58  Identities=14%  Similarity=0.299  Sum_probs=50.3

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||.+.+|.|.-+-.+.||-- +..+.|++|.+||+||..||+||-+.-...++.|--+-
T Consensus       333 FMVWAkDERRKILqA~PDMH-NSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~  390 (511)
T KOG0528|consen  333 FMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKY  390 (511)
T ss_pred             hhcccchhhhhhhhcCcccc-ccchhHHhcccccccccccccchHHHHHHHHHhhhccC
Confidence            78899999988889999986 88899999999999999999999888777777665443

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

Probab=93.33  E-value=0.058  Score=45.53  Aligned_cols=44  Identities=18%  Similarity=0.251  Sum_probs=35.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhh
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDE   50 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~   50 (280)
                      |+-|+.|||+    .|.+++ ..++...+.+.|..||++||.+|..++.
T Consensus        86 YLNFLReFRr----kh~~L~-p~dlI~~AAraW~rLSe~eK~rYrr~~~  129 (183)
T PF06382_consen   86 YLNFLREFRR----KHCGLS-PQDLIQRAARAWCRLSEAEKNRYRRMAP  129 (183)
T ss_pred             HHHHHHHHHH----HccCCC-HHHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence            5666666655    788887 6667777889999999999999999644

The function of this family is unknown.

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

Probab=90.59  E-value=0.085  Score=52.77  Aligned_cols=56  Identities=14%  Similarity=0.253  Sum_probs=50.5

Q ss_pred             cccchHHHH--HHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCC
Q 023605            2 LCFCSNEEV--KRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNS   58 (280)
Q Consensus         2 ~~~~~~~~~--~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~   58 (280)
                      +|+|.+..|  -.....||+.. +..|.|++|+.|-+|.+.||+.|.+-+.++|..|-+
T Consensus       189 f~ifskrhr~~g~vhq~~pn~D-NrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfk  246 (683)
T KOG2746|consen  189 FHIFSKRHRGEGRVHQRHPNQD-NRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFK  246 (683)
T ss_pred             HHHHHhhcCCccchhccCcccc-chhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhh
Confidence            578888888  88889999876 999999999999999999999999999999887765

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

Probab=90.49  E-value=0.1  Score=45.25  Aligned_cols=54  Identities=17%  Similarity=0.230  Sum_probs=43.5

Q ss_pred             hHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            6 SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         6 ~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ..+-|......+|+.. .-..+|++|+.|.+|++.-|++|.+.+++.+.+|++..
T Consensus       155 ~~~~r~~~~~~~~~~~-~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~  208 (211)
T COG5648         155 EPKIRPKVEGPSPDKA-LVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFY  208 (211)
T ss_pred             cHHhccccCCCCcchh-hhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhc
Confidence            3445555666666654 55569999999999999999999999999999998754

>PF03078 ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 ATHILA is a group of Arabidopsis thaliana retrotransposons [] belonging to the Ty3/gypsy family of the long terminal repeat (LTR) class of eukaryotic retrotransposons[, ]

Probab=85.01  E-value=4.3  Score=39.61  Aligned_cols=164  Identities=15%  Similarity=0.156  Sum_probs=94.0

Q ss_pred             cHHHHHHHHhhCCHHHHHHHHHcCChhhhcccccccCHHHHHHHhcc----c---CC--------CcceEEECCEEEEeC
Q 023605           73 VPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQ----F---KP--------ERNIIELHGQKLELC  137 (280)
Q Consensus        73 S~~~~~~~i~~Ls~~qk~~I~~~GFg~LL~i~~~~l~~~l~~wL~~~----~---d~--------~t~~~~i~g~~i~it  137 (280)
                      ++..+..+  .|.++-..+++.+|.+.|..++...-+...+.+|+.-    +   ++        ..-+|.|.|....+|
T Consensus        67 ~~etl~~L--Gl~~dV~~lf~~~gL~~f~~~~~~~Y~eet~qFLaTl~v~~~~~~~~~~~e~~glG~l~F~V~~~~y~ls  144 (458)
T PF03078_consen   67 DPETLQKL--GLLEDVEYLFKKCGLGTFMSYPYPTYPEETRQFLATLKVTFYNPSEPRAKELDGLGYLTFFVYGVEYSLS  144 (458)
T ss_pred             CHHHHHHh--ccHHHHHHHHHhcCchhhccCCCCCcHHHHHHhhheeeeeecccccchhhcccCcceEEEEEcceeeeee
Confidence            33444444  6778888999999999999888876665555555432    1   11        123577789999999


Q ss_pred             ccccceeeeecCCCcccccCCCchHHHHHHHHhCCCCCCcchhHHHHHHhhccccchhHHHHHHHhhhceeecccCCC--
Q 023605          138 PKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY--  215 (280)
Q Consensus       138 ~~dV~~VlGLP~~G~~i~~~~~~~~~~~l~~~~~~~~~~i~l~~L~~~l~~~~~~~d~f~r~Fll~~~~~~L~Ptt~~--  215 (280)
                      -.+...++|.|.++. +....+.+....+.+..|.+. .++...-...      ..-+=+.+++-=+++..|+|....  
T Consensus       145 i~~L~~i~GF~~~~~-i~~~~~~~el~~~W~~ig~~~-p~~~~~~ks~------~Ir~PviRy~hr~iA~tlf~R~~~~~  216 (458)
T PF03078_consen  145 IKHLERIFGFPSGDE-IKPDFDPEELNDFWATIGGGK-PFNSARSKSN------QIRSPVIRYFHRLIANTLFAREETGT  216 (458)
T ss_pred             HHHHHHHhCCCCccc-cCCCCCchHHHHHHHHhcCCC-cccccccccc------cccChHHHHHHHHHHhhhccccccCc
Confidence            999999999999844 333334444455655555321 1111111110      111223344444556666665533  


Q ss_pred             CCccccccc-----------ccc----CCCccccchHHHHHHHHHH
Q 023605          216 ISTLFLHPI-----------MDV----SSIKSLNWATFCYDWLVKS  246 (280)
Q Consensus       216 vs~~yl~~l-----------~D~----~~i~~ynW~~~Vl~~L~~~  246 (280)
                      |..+-|..+           .|-    .+..+.|=+...++||...
T Consensus       217 v~~~El~~l~~~L~~~Lr~~~~g~~l~~d~~dt~~~~vl~~hL~~y  262 (458)
T PF03078_consen  217 VRNDELEMLDQALKHLLRRTKDGKLLRGDLNDTNVSMVLLDHLCSY  262 (458)
T ss_pred             eechhHHHHHHHHHHHHHhcCCCccccCcccccchhHHHHHHHHhh
Confidence            655543321           111    1235666777777777654

The central region of ATHILA retrotransposons contains two or three open reading frames (ORFs). This family represents the ORF1 product. The function of ORF1 is unknown.

---

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	280
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	4e-04

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92

 Score = 37.7 bits (88), Expect = 4e-04
 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 6  SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDER 51
           NE  +++R+ + DL     + K +G  + +L P +K RY    E+
Sbjct: 19 LNERREQIRTRHPDLPFP-EITKMLGAEWSKLQPAEKQRYLDEAEK 63

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	280
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.36
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.33
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.29
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.27
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.25
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.25
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.23
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.23
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.23
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.22
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.21
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.2
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.2
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.17
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.16
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.16
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.15
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.15
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.14
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.14
2cto_A	93	Novel protein; high mobility group box domain, hel	99.13
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.13
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.12
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.11
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.09
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.07
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.06
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.01
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	98.99
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	98.89
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	98.85
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.82
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.81
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.78
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	98.77
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	98.74
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	98.6
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	98.42
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.37

>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=99.36  E-value=1.2e-13  Score=103.54  Aligned_cols=57  Identities=7%  Similarity=0.025  Sum_probs=54.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      |++|++++|..|+++||+  .+++|+|.+|++|++||++||+||.++|.+.+.+|+.++
T Consensus        12 y~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm   68 (91)
T 1l8y_A           12 EEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYEREL   68 (91)
T ss_dssp             HHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999999  589999999999999999999999999999999998866

>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=99.33  E-value=6.1e-13  Score=98.07  Aligned_cols=58  Identities=16%  Similarity=0.197  Sum_probs=52.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|+++.|..++++||+.+.+..|+|.+|++|++||++||++|.++|+....+-..+
T Consensus        13 y~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~~~~~~e   70 (81)
T 2d7l_A           13 FQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGETASEGTE   70 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSSSSSCCC
T ss_pred             HHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhhhhh
Confidence            8999999999999999999658999999999999999999999999999987554333

>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=99.29  E-value=6e-13  Score=95.33  Aligned_cols=58  Identities=12%  Similarity=0.202  Sum_probs=54.5

Q ss_pred             cccchHHHHHHHHhhCCCChh-hhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSV-TLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~-~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|+++.|..++++||+.+. +..|+|.+|+.|++||++||++|.++|++.+.+|..+
T Consensus         9 y~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e   67 (71)
T 1ckt_A            9 YAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYERE   67 (71)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999873 7999999999999999999999999999999998754

>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=99.27  E-value=1.5e-12  Score=97.76  Aligned_cols=59  Identities=24%  Similarity=0.467  Sum_probs=56.8

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++|.|.+++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..+..
T Consensus        28 y~lF~~~~r~~~k~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A           28 MFIFSEEKRRQLQEERPELS-ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             HHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 999999999999999999999999999999999998874

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

Probab=99.25  E-value=1.2e-12  Score=93.52  Aligned_cols=59  Identities=27%  Similarity=0.416  Sum_probs=56.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++++|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|.+.+.+|..+.+
T Consensus        10 f~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~   68 (71)
T 4a3n_A           10 FMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHP   68 (71)
T ss_dssp             HHHHHHHHHHHHHTTCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            89999999999999999997 999999999999999999999999999999999987654

>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=99.25  E-value=2e-12  Score=95.27  Aligned_cols=59  Identities=15%  Similarity=0.249  Sum_probs=56.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++++|..++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..+.+
T Consensus        15 f~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~   73 (82)
T 1wz6_A           15 FLLFCKRHRSLVRQEHPRLD-NRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANP   73 (82)
T ss_dssp             HHHHHHHHHHHHHHHCSSSC-TTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCS
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhH
Confidence            89999999999999999986 899999999999999999999999999999999998874

>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=99.23  E-value=1.9e-12  Score=94.97  Aligned_cols=59  Identities=15%  Similarity=0.284  Sum_probs=56.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|+++.|..++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..+.+
T Consensus        10 f~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~   68 (80)
T 1gt0_D           10 FMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHP   68 (80)
T ss_dssp             HHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            89999999999999999986 999999999999999999999999999999999987763

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

Probab=99.23  E-value=2.2e-12  Score=95.95  Aligned_cols=58  Identities=10%  Similarity=0.207  Sum_probs=54.7

Q ss_pred             cccchHHHHHHHHhhCCCChh-hhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSV-TLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~-~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|++|.|.+++++||+.+. +..|+|.+|+.|++||++||++|.++|++.+.+|..+
T Consensus        23 y~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e   81 (86)
T 2eqz_A           23 YAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDRE   81 (86)
T ss_dssp             HHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999974 7999999999999999999999999999999998754

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

Probab=99.23  E-value=2.7e-12  Score=96.78  Aligned_cols=58  Identities=19%  Similarity=0.210  Sum_probs=55.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+++.|.+++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..++
T Consensus        15 y~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~   72 (92)
T 2cs1_A           15 SALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQM   72 (92)
T ss_dssp             HHHHHHHHHHHHHHHCCSSC-HHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999996 89999999999999999999999999999999997654

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

Probab=99.22  E-value=1.2e-12  Score=96.76  Aligned_cols=60  Identities=12%  Similarity=0.209  Sum_probs=56.4

Q ss_pred             cccchHHHHHHHHhhCCCChh-hhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSV-TLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~-~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++++|.+++++||+.+. +..|+|.+|+.|++||++||++|.++|++.+.+|..+++
T Consensus        15 y~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~   75 (83)
T 1aab_A           15 YAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK   75 (83)
T ss_dssp             HHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999873 799999999999999999999999999999999987764

>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=99.21  E-value=3.7e-12  Score=93.66  Aligned_cols=59  Identities=14%  Similarity=0.283  Sum_probs=56.2

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++|+|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|++.+.+|..+.+
T Consensus        12 f~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p   70 (81)
T 1i11_A           12 FMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYP   70 (81)
T ss_dssp             HHHHHHHHHHHHHTTCSSCC-HHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            89999999999999999987 999999999999999999999999999999999988764

>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=99.20  E-value=3.3e-12  Score=92.68  Aligned_cols=58  Identities=14%  Similarity=0.275  Sum_probs=54.9

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++|+|..++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..+.
T Consensus        12 f~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   69 (76)
T 1hry_A           12 FIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY   69 (76)
T ss_dssp             HHHHHHHHHHHHHHHCSCCS-SSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHCcCCC-HHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            89999999999999999986 89999999999999999999999999999999987655

>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=99.20  E-value=3.4e-12  Score=94.73  Aligned_cols=59  Identities=14%  Similarity=0.264  Sum_probs=55.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++|+|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|++.+.+|..+.+
T Consensus        12 f~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~   70 (85)
T 1j46_A           12 FIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYP   70 (85)
T ss_dssp             HHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            89999999999999999986 999999999999999999999999999999999977663

>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=99.17  E-value=7.9e-12  Score=92.92  Aligned_cols=58  Identities=12%  Similarity=0.189  Sum_probs=54.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++++|..++++||+.+ +..|+|.+|+.|++||++||++|.+.|+..+.+|..+.
T Consensus        10 f~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~   67 (86)
T 2lef_A           10 FMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLY   67 (86)
T ss_dssp             HHHHHHHHHHHHHHHSSCCC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            89999999999999999985 99999999999999999999999999999999886655

>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=99.16  E-value=6.7e-12  Score=91.26  Aligned_cols=59  Identities=15%  Similarity=0.337  Sum_probs=55.3

Q ss_pred             CcccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            1 MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         1 ~~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      .||+|+.+.|..++++||+.+ +..|+|.+|+.|++||++||++|.++|+..+.+|..+.
T Consensus        13 af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~   71 (77)
T 1hme_A           13 AFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI   71 (77)
T ss_dssp             TTHHHHHHHHHHHHHHCTTCC-HHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            389999999999999999986 99999999999999999999999999999999987654

>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=99.16  E-value=5.7e-12  Score=93.98  Aligned_cols=58  Identities=7%  Similarity=0.151  Sum_probs=54.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++|+|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|++.+.+|..+.
T Consensus        25 f~lf~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~   82 (87)
T 2e6o_A           25 FMLFAKKYRVEYTQMYPGKD-NRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLN   82 (87)
T ss_dssp             HHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            89999999999999999986 99999999999999999999999999999999886544

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

Probab=99.15  E-value=8.8e-12  Score=93.91  Aligned_cols=58  Identities=22%  Similarity=0.341  Sum_probs=54.9

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++++|..++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..+.
T Consensus        15 f~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~   72 (92)
T 2crj_A           15 YVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKEL   72 (92)
T ss_dssp             HHHHHHHHHHHHHHHCTTCC-HHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999987 99999999999999999999999999999999987654

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

Probab=99.15  E-value=9.9e-12  Score=94.98  Aligned_cols=56  Identities=25%  Similarity=0.316  Sum_probs=53.1

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNS   58 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~   58 (280)
                      ||+|++|.|.+++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..
T Consensus        18 f~lF~~~~r~~ik~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~   73 (99)
T 1k99_A           18 YFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFER   73 (99)
T ss_dssp             HHHHHHHHHHHHHTTCTTSC-SHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 999999999999999999999999999999999543

>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=99.14  E-value=9.8e-12  Score=90.77  Aligned_cols=59  Identities=19%  Similarity=0.310  Sum_probs=55.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|+++.|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|++.+.+|..+.+
T Consensus        10 f~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p   68 (79)
T 3u2b_C           10 FMVWSQIERRKIMEQSPDMH-NAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYP   68 (79)
T ss_dssp             HHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            89999999999999999987 899999999999999999999999999999999877663

>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=99.14  E-value=1e-11  Score=91.59  Aligned_cols=59  Identities=27%  Similarity=0.416  Sum_probs=56.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++++|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|++.+.+|..+.+
T Consensus        14 f~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~   72 (83)
T 3f27_D           14 FMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHP   72 (83)
T ss_dssp             HHHHHHHHHHHHHHHCSSSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            89999999999999999997 999999999999999999999999999999999987663

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

Probab=99.13  E-value=4.7e-12  Score=95.58  Aligned_cols=63  Identities=16%  Similarity=0.294  Sum_probs=54.3

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhh---hhcccCCChhhhhhhhhhhhhhcccCCCCCCCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHI---GKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEI   67 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~---g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~~~k~~~   67 (280)
                      ||+|++|+|.+++.+  ++. +.+|+|.+   |++|++|+++||+||.++|.+.+.+|++..++..+++
T Consensus        18 f~lF~~e~R~~ik~e--~~~-~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~~~~~~~   83 (93)
T 2cto_A           18 YYFFVQEKIPELRRR--GLP-VARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGPSEKQK   83 (93)
T ss_dssp             HHHHHHTTHHHHHHH--TCC-CSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSSCCCCCC
T ss_pred             HHHHHHHHHHHHHHc--CCC-HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcccccccccc
Confidence            899999999999999  443 77788887   9999999999999999999999999988875444433

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

Probab=99.13  E-value=1.7e-11  Score=94.17  Aligned_cols=58  Identities=17%  Similarity=0.207  Sum_probs=54.9

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++++|..++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..+.
T Consensus        25 y~lF~~~~r~~i~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~   82 (102)
T 2co9_A           25 YALFFRDTQAAIKGQNPNAT-FGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQL   82 (102)
T ss_dssp             HHHTHHHHHHHHHHHCTTSC-HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 99999999999999999999999999999999997644

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

Probab=99.12  E-value=9.7e-12  Score=96.18  Aligned_cols=59  Identities=17%  Similarity=0.307  Sum_probs=56.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|+.++|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|++.+.+|..+.+
T Consensus        37 f~lF~~~~r~~~k~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   95 (106)
T 4euw_A           37 FMVWAQAARRKLADQYPHLH-NAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHP   95 (106)
T ss_dssp             HHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            89999999999999999987 899999999999999999999999999999999987764

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

Probab=99.11  E-value=1.4e-11  Score=88.77  Aligned_cols=57  Identities=16%  Similarity=0.317  Sum_probs=54.1

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|+++.|.+++++||+.+ +..|+|.+|+.|++|  +||++|.++|++.+.+|..+.+
T Consensus        11 y~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~   67 (73)
T 1wxl_A           11 FMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMR   67 (73)
T ss_dssp             HHHHHHHHHHHHHHHSTTCC-HHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTG
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 899999999999999  8899999999999999998764

>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=99.09  E-value=9.1e-12  Score=94.04  Aligned_cols=58  Identities=29%  Similarity=0.456  Sum_probs=55.1

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++|+|..++++||+.+ +..|+|.+|+.|++||++||++|.++|+..+.+|..+.
T Consensus        28 f~lF~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~   85 (93)
T 1cg7_A           28 YMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEK   85 (93)
T ss_dssp             HHHHHHHHTSTTTTTCTTSC-HHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999996 99999999999999999999999999999999998653

>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=99.07  E-value=2.3e-11  Score=87.64  Aligned_cols=55  Identities=11%  Similarity=0.274  Sum_probs=52.2

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|++|.|..++++||+.+ +.+|+|.+|+.|++||+  |++|.++|.+.+.+|..+
T Consensus        11 y~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~   65 (73)
T 3nm9_A           11 YALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRA   65 (73)
T ss_dssp             HHHHHHHHHHHHHHHSSSCC-HHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHH
Confidence            89999999999999999997 89999999999999998  999999999999998754

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

Probab=99.06  E-value=2.1e-11  Score=86.30  Aligned_cols=53  Identities=11%  Similarity=0.176  Sum_probs=49.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|+++.|..++.+||     .+++|.+|+.|++||++||++|.++|.+.+.+|..+
T Consensus        10 y~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e   62 (67)
T 3fgh_A           10 YNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNE   62 (67)
T ss_dssp             HHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999998     489999999999999999999999999999998654

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

Probab=99.01  E-value=3e-11  Score=91.86  Aligned_cols=59  Identities=19%  Similarity=0.311  Sum_probs=54.5

Q ss_pred             CcccchHHHHHHHHhhCCCCh-hhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            1 MLCFCSNEEVKRLRSENSDLS-VTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         1 ~~~~~~~~~~~~~~~~~p~~~-~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      .||+|++|+|..++++||+.+ .+..|+|.+|+.|++||++||++|.++|++.+.+|..+
T Consensus        29 ay~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e   88 (97)
T 2lhj_A           29 SYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYERE   88 (97)
T ss_dssp             SSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            389999999999999999974 28899999999999999999999999999999998754

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

Probab=98.99  E-value=2.4e-11  Score=90.95  Aligned_cols=55  Identities=15%  Similarity=0.218  Sum_probs=49.5

Q ss_pred             cccchHHHHHHHHhhCCCCh-hhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLS-VTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~-~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++|+|..++++||+.+ .+++|+    +.|++|+++||+||.++|++.+.+|...+
T Consensus        30 f~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~~~   85 (90)
T 2yuk_A           30 PVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRINK   85 (90)
T ss_dssp             HHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             HHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHhhH
Confidence            89999999999999999975 266666    99999999999999999999999987654

>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=98.89  E-value=3.3e-10  Score=93.42  Aligned_cols=57  Identities=16%  Similarity=0.363  Sum_probs=54.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|++|.|..++.+||+.+ +.+|+|.+|+.|++||++||++|.++|.+.+.+|..+
T Consensus        96 y~lf~~~~r~~~~~~~p~~~-~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~  152 (159)
T 2gzk_A           96 FFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD  152 (159)
T ss_dssp             HHHHHHHHHHHHHHHCSCCC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchhhHhhHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 9999999999999999999999999999999998754

>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=98.85  E-value=7.3e-10  Score=84.83  Aligned_cols=57  Identities=21%  Similarity=0.169  Sum_probs=47.7

Q ss_pred             CcccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            1 MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         1 ~~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      .||+|++|++.  ..++|+++ +..++|.+|++|++|+++||+||.++|++.+.+|..+.
T Consensus        15 ay~lF~~e~~~--~p~~~~~~-~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~   71 (101)
T 1v63_A           15 GYQKFSQELLS--NGELNHLP-LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHL   71 (101)
T ss_dssp             SHHHHHHHHHH--HCTTTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            38999999974  22333343 78999999999999999999999999999999998764

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

Probab=98.82  E-value=1.1e-09  Score=91.68  Aligned_cols=59  Identities=10%  Similarity=0.160  Sum_probs=54.4

Q ss_pred             cccchHHHHHHHHhhCCCCh-hhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLS-VTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~-~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+.+.|.+++++||+.+ .+..|+|.+|+.|++||++||++|.+.|.+.+.+|..+.
T Consensus        23 y~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~   82 (173)
T 2yrq_A           23 YAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREM   82 (173)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            89999999999999999963 599999999999999999999999999999999886543

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

Probab=98.81  E-value=9.7e-10  Score=91.95  Aligned_cols=57  Identities=16%  Similarity=0.363  Sum_probs=54.2

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|+++.|..++.+||+.+ +.+|+|.+|+.|++||++||++|.++|++.+.+|..+
T Consensus       109 f~lf~~~~r~~~~~~~p~~~-~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~  165 (173)
T 2yrq_A          109 FFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD  165 (173)
T ss_dssp             HHHHHHHHHHHHHHHCSSSC-HHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 9999999999999999999999999999999998754

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

Probab=98.78  E-value=1.4e-09  Score=95.68  Aligned_cols=58  Identities=21%  Similarity=0.274  Sum_probs=55.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+.+.|..++++||+.+ +..|.|.+|++|++||++||++|.++|.+.+.+|+.++
T Consensus        49 y~lF~~e~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~  106 (238)
T 3tmm_A           49 YLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEI  106 (238)
T ss_dssp             HHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999997 99999999999999999999999999999999998764

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

Probab=98.77  E-value=1.5e-09  Score=93.90  Aligned_cols=58  Identities=21%  Similarity=0.274  Sum_probs=55.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+.+.|..++++||+.+ +..|.|.+|++|++||++||++|.++|.+.+.+|+.+.
T Consensus        17 y~lF~~~~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~   74 (214)
T 3tq6_A           17 YLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEI   74 (214)
T ss_dssp             HHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHh
Confidence            89999999999999999997 99999999999999999999999999999999998653

>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=98.74  E-value=1.5e-09  Score=84.11  Aligned_cols=54  Identities=13%  Similarity=0.183  Sum_probs=49.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++|+|.+++    ++ .+..++|.+|+.|++||++||++|.++|+..+.+|..+.
T Consensus        25 y~lF~~e~r~~~k----~~-~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~   78 (108)
T 1v64_A           25 YSLYCAELMANMK----DV-PSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVEL   78 (108)
T ss_dssp             HHHHHHHHHHHCT----TS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh----CC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999988    44 489999999999999999999999999999999998653

>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=98.60  E-value=1e-08  Score=84.38  Aligned_cols=58  Identities=14%  Similarity=0.275  Sum_probs=53.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+.+.|..++++||++. +..|+|.+|+.|++||++||++|.+.|...+.+|..+.
T Consensus        12 f~~~~~~~~~ki~~~~P~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   69 (159)
T 2gzk_A           12 FIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY   69 (159)
T ss_dssp             HHHHHHHHHHHHHHHCSSCC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHh
Confidence            78999999999999999976 99999999999999999999999999999998876544

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

Probab=98.42  E-value=1.4e-08  Score=87.88  Aligned_cols=53  Identities=11%  Similarity=0.192  Sum_probs=49.8

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|++|.|..++.+||+     .|+|.+|+.|++||++||+||.++|.+.+.+|..+
T Consensus       122 y~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e  174 (214)
T 3tq6_A          122 YNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNE  174 (214)
T ss_dssp             HHHHHHHHTTTSSCSSHH-----HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhHHHHHHhhccCCHH-----HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999986     69999999999999999999999999999999764

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

Probab=98.37  E-value=1.9e-08  Score=88.44  Aligned_cols=54  Identities=11%  Similarity=0.180  Sum_probs=50.3

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++|.|..++.+||+     .|+|.+|+.|++|+++||+||.++|.+.+.+|+.+.
T Consensus       154 y~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~  207 (238)
T 3tmm_A          154 YNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEM  207 (238)
T ss_dssp             HHHHHHHHTTTSCCSSHH-----HHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCHH-----HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999986     699999999999999999999999999999997643

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	280
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	0.002

>d1hsma_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Hamster (Cricetulus griseus) [TaxId: 10029]} Length = 79

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]

 Score = 34.0 bits (78), Expect = 0.002
 Identities = 9/47 (19%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 6  SNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 52
           +E   +++ E+  LS+   + K +G+ +     + K  Y+K+  ++
Sbjct: 14 CSEYRPKIKGEHPGLSIG-DVAKKLGEMWNNTAADDKQPYEKKAAKL 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	280
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.31
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.26
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.21
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.2
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.19
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.18
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.18
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.03
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.95
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	98.94
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	98.84
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	98.5
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	87.05

>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=99.31  E-value=2.2e-13  Score=95.99  Aligned_cols=58  Identities=14%  Similarity=0.295  Sum_probs=54.7

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+++.|+.++++||+.+ +..|+|.+|+.|++||++||++|.++|++.+.+|..+.
T Consensus        10 y~lf~~~~r~~i~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~   67 (70)
T d1i11a_          10 FMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKY   67 (70)
T ss_dssp             HHHHHHHHHHHHHTTCSSCC-HHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHhccCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            89999999999999999987 89999999999999999999999999999999986553

>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=99.26  E-value=5.9e-13  Score=96.15  Aligned_cols=59  Identities=15%  Similarity=0.284  Sum_probs=56.2

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|+++.|.+++++||+.+ +.+|+|.+|+.|++||++||++|.++|.+.+.+|..+.+
T Consensus        10 y~lF~~~~r~~~~~~~p~~~-~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p   68 (80)
T d1gt0d_          10 FMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHP   68 (80)
T ss_dssp             HHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            89999999999999999986 999999999999999999999999999999999988764

>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=99.21  E-value=9.6e-13  Score=96.07  Aligned_cols=59  Identities=14%  Similarity=0.264  Sum_probs=56.0

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   61 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~   61 (280)
                      ||+|++|+|..++++||+.+ +.+|+|.+|+.|++||++||++|.++|.+.+.+|....+
T Consensus        12 y~lF~~~~r~~i~~~~p~~~-~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~   70 (85)
T d1j46a_          12 FIVWSRDQRRKMALENPRMR-NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYP   70 (85)
T ss_dssp             HHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHHhccCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhH
Confidence            89999999999999999997 899999999999999999999999999999999987663

>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=99.20  E-value=3.2e-12  Score=94.08  Aligned_cols=60  Identities=23%  Similarity=0.461  Sum_probs=57.1

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHS   62 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k~~   62 (280)
                      |++|+.|.|.+++++||+.+ +.+|.+.+|+.|++|+++||++|.++|.+.+.+|+.+.++
T Consensus        28 y~lF~~e~r~~~~~~~p~~~-~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~~~~   87 (90)
T d1wgfa_          28 MFIFSEEKRRQLQEERPELS-ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGP   87 (90)
T ss_dssp             HHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSS
T ss_pred             HHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            89999999999999999987 8899999999999999999999999999999999988753

>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=99.19  E-value=2e-12  Score=91.02  Aligned_cols=59  Identities=12%  Similarity=0.191  Sum_probs=54.3

Q ss_pred             cccchHHHHHHHHhhCCCChh-hhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSV-TLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~-~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+++.|..++++||+.+. +..|+|.+|+.|++||++||++|.++|.+.+.+|..++
T Consensus         9 y~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~   68 (71)
T d1ckta_           9 YAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREM   68 (71)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999998654 67999999999999999999999999999999986543

>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=99.18  E-value=1.9e-12  Score=93.10  Aligned_cols=59  Identities=15%  Similarity=0.337  Sum_probs=55.2

Q ss_pred             CcccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            1 MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         1 ~~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      .|++|++|.|+.++++||+.+ +.+|+|.+|+.|++||++||++|.+++.+.+.+|..++
T Consensus         9 ay~~f~~~~r~~i~~~~p~~~-~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~   67 (79)
T d1hsma_           9 AFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI   67 (79)
T ss_dssp             SHHHHHHHHHHHHHHHCTTCC-TTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCC-HHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            389999999999999999986 89999999999999999999999999999999997654

>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=99.18  E-value=3.2e-12  Score=93.41  Aligned_cols=58  Identities=12%  Similarity=0.189  Sum_probs=53.9

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|+++.|..++++||+.+ +.+|++.+|+.|++||++||++|.++|++.+.+|....
T Consensus        10 f~lF~~~~r~~~~~~~P~~~-~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~   67 (86)
T d2lefa_          10 FMLYMKEMRANVVAESTLKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLY   67 (86)
T ss_dssp             HHHHHHHHHHHHHHHSSCCC-HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            89999999999999999996 88999999999999999999999999999998875543

>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=99.03  E-value=3.2e-11  Score=89.22  Aligned_cols=57  Identities=30%  Similarity=0.463  Sum_probs=53.9

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      |++|++|.|..++++||+.+ +.+|++.+|+.|++||++||++|.+++.+.+.+|..+
T Consensus        28 f~lF~~e~r~~ik~~~p~~~-~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e   84 (93)
T d1lwma_          28 YMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE   84 (93)
T ss_dssp             HHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCc-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 8899999999999999999999999999999988654

>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=98.95  E-value=5.6e-11  Score=87.46  Aligned_cols=58  Identities=26%  Similarity=0.315  Sum_probs=54.3

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      |++|+.+.|..++++||+.+ +..|++.+|..|++||++||++|.+++...+.+|..+.
T Consensus        18 y~lf~~~~r~~~~~~~p~~~-~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~   75 (91)
T d1k99a_          18 YFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNL   75 (91)
T ss_dssp             HHHHHHHHHHHHHTTCTTSC-SHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCC-HHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999987 99999999999999999999999999999998886543

>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=98.94  E-value=7e-11  Score=83.41  Aligned_cols=56  Identities=11%  Similarity=0.265  Sum_probs=51.4

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ||+|++|.|..++++||+.+ +.+|+|.+|+.|++|+  ||++|.+++.+.+.+|+.++
T Consensus        11 y~lf~~~~r~~~k~~~p~~~-~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~   66 (73)
T d1qrva_          11 YMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAV   66 (73)
T ss_dssp             HHHHHHHHHHHHHHTSTTCC-HHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCC-HHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999986 8999999999999986  49999999999999987643

>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=98.84  E-value=3.3e-10  Score=84.77  Aligned_cols=57  Identities=18%  Similarity=0.090  Sum_probs=52.2

Q ss_pred             CcccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605            1 MLCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus         1 ~~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      .||+|++|.|+.++.+||+   +.+++|.+|+.|++||++||++|.++|.+.+.+|..++
T Consensus        15 ay~~F~~e~r~~~~~~~~~---~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~   71 (101)
T d1v63a_          15 GYQKFSQELLSNGELNHLP---LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHL   71 (101)
T ss_dssp             SHHHHHHHHHHHCTTTTSC---HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCC---HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3899999999999988875   67999999999999999999999999999999997653

>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=98.50  E-value=9.6e-09  Score=77.57  Aligned_cols=53  Identities=13%  Similarity=0.166  Sum_probs=47.5

Q ss_pred             cccchHHHHHHHHhhCCCChhhhhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCC
Q 023605            2 LCFCSNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   59 (280)
Q Consensus         2 ~~~~~~~~~~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~   59 (280)
                      ||+|+.|+|++    +|+.. +.++.+.+|+.|++||++||++|.++|++.+.+|..+
T Consensus        25 y~lF~~~~r~~----~~~~~-~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~   77 (108)
T d1v64a_          25 YSLYCAELMAN----MKDVP-STERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVE   77 (108)
T ss_dssp             HHHHHHHHHHH----CTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH----ccCCC-HHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHH
Confidence            89999998875    46664 7889999999999999999999999999999999765

>d1l8ya_ 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=87.05  E-value=0.028  Score=37.72  Aligned_cols=37  Identities=11%  Similarity=0.122  Sum_probs=31.9

Q ss_pred             hhhhhhhhhcccCCChhhhhhhhhhhhhhcccCCCCC
Q 023605           24 LGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   60 (280)
Q Consensus        24 ~~~~k~~g~~wk~l~~~~k~~~~~~~~~~k~~~~~~k   60 (280)
                      ...-|+-...|++|...||.++.+||.++.+||+.+.
T Consensus        31 ~KaqkaMeatW~~meKkEki~wikkaaedqkryerel   67 (84)
T d1l8ya_          31 VKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYEREL   67 (84)
T ss_dssp             HHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            3456777789999999999999999999999998754