Citrus Sinensis ID: 021140

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------
Protein Sequence
MDSQQRKRKRQPGGLQKKGAPILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Secondary Structure (PSIPRED)
ccHHHHHHHcccccccccccccHHcccccccccccccccccccHHHHHHHHcccccccccHHHHHccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHccHHHHHHHHHHcccHHHccccccccHHHHHHHHHcccccccEEEEccEEEccccccEEEEEccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccccEEc
Secondary Structure Prediction (SSPRO)
ccHHHHHHccccccccccccccHHccccccccccccEEEEEEccHHHEEEEEccccccEEEEccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHccccHHccccccccHHHHHHHHHHccccccEEEEccEEEEccHHHHHHHccccccccEcccccHHHHHHHHHHHcccccccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccHHccHEccHHHHHHccHHHHHHHHHHHHHHHHHHccccccccHHHHHEHHHHHHcccccEEc
Coil and Loop (DISEMBL)
mdsqqrkrkrqpgglqkkgapilrangqdavptsstygfvSYFNEEVKRLRSENSDLSVTLGLRKHIGktykelppeqkARYKkrdermgnsgnsnshsgdneivetkcvpERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKimgvkdggmaikingasdHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCpigsyistlflhpimdvssikslnwaTFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Flexible Loop (DISEMBL)
mdsqqrkrkrqpgglqkkgapilrangqdavptsstYGFVSYFNEEVKRlrsensdlsvTLGLrkhigktykelppeqkarykkrdermgnsgnsnshsgdneivETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQlklsicll
Low Complexity Region (SEG)
MDSQQRKRKRQPGGLQKKGAPILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMgnsgnsnshsgdnEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Disordered region (IsUnstruct)
***********************************TYGFVSYFNEEVK**********VTLGLRKHI************************************IVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICL*
Disordered Region (DISOPRED)
**************************************F*****************************************************************VETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Disordered Region (DISEMBL)
****************KKGAPILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKA*********************NEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Disordered Region (DISPRO)
****************************DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRK****************************************ETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSQQRKRKRQPGGLQKKGAPILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSYISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQVRPLLQLKLSICLL
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	317
296087190	766	unnamed protein product [Vitis vinifera]	0.826	0.342	0.337	8e-35
225453104	617	PREDICTED: uncharacterized protein LOC10	0.753	0.387	0.341	4e-34
147783848	708	hypothetical protein VITISV_032233 [Viti	0.753	0.337	0.341	6e-34
255583781	421	conserved hypothetical protein [Ricinus	0.835	0.629	0.308	1e-32
147795729	849	hypothetical protein VITISV_004916 [Viti	0.905	0.338	0.289	7e-32
224077245	628	predicted protein [Populus trichocarpa]	0.832	0.420	0.307	5e-30
147772140	637	hypothetical protein VITISV_026046 [Viti	0.785	0.390	0.292	8e-30
356533899	590	PREDICTED: uncharacterized protein LOC10	0.779	0.418	0.274	2e-23
147798273	326	hypothetical protein VITISV_001668 [Viti	0.684	0.665	0.302	1e-21
147856790	479	hypothetical protein VITISV_019328 [Viti	0.744	0.492	0.259	3e-21

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

 Score =  153 bits (387), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 91/270 (33%), Positives = 140/270 (51%), Gaps = 8/270 (2%)

Query: 42  YFNEEVKRLRSENSDLSVTL-GLRKHIGKTYKELPPEQKARYKKR-----DERMGNSGNS 95
           YF+ E  R  S +   S  L    K     +K +  E+KA+Y KR     D  +  +   
Sbjct: 169 YFSREFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPAR 228

Query: 96  NSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVN 155
                    + T+C P R   +++ L+ ++K A+R +GF SLL LRC  L+R LC WL+ 
Sbjct: 229 APKPRKQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLE 288

Query: 156 QFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIR 215
           +F   R  +E+ G+++ L PK    +MG+   G  +  +G  D I E+R  +  T  GI 
Sbjct: 289 RFNTARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGIS 348

Query: 216 IRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWAT 274
           +R LEE +    EA + FK +F L+A+ T+LCP     +S  FLH + ++ +I   NW  
Sbjct: 349 VRLLEERLAA-PEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGK 407

Query: 275 FCYDWLVKSICRFQNQQAAYIGGCLHFLQV 304
           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|225453104|ref|XP_002270459.1| PREDICTED: uncharacterized protein LOC100263780 [Vitis vinifera]

 Score =  151 bits (381), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 7/246 (2%)

Query: 65  KHIGKTYKELPPEQKARYKKR-----DERMGNSGNSNSHSGDNEIVETKCVPERFCALVK 119
           K     +K +  E+KA+Y KR     D  +  +            + T+C P R   +++
Sbjct: 55  KAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPARAPKPRKQTNLVTRCSPGRLFNVLQ 114

Query: 120 SLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFS 179
            L+ ++K A+R +GF SLL LRC  L+R LC WL+ +F   R  +E+ G+++ L PK   
Sbjct: 115 RLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLERFNTARRSLEICGERIPLSPKDVE 174

Query: 180 KIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTL 239
            +MG+   G  +  +G  D I E+R  +  T  GI +R LEE +    EA + FK +F L
Sbjct: 175 LVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGISVRLLEERLAA-PEAGEEFKRSFIL 233

Query: 240 FAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGC 298
           +A+ T+LCP     +S  FLH + ++ +I   NW  F  D LV+ + RF   +   +GGC
Sbjct: 234 YALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGKFLLDRLVREVSRFHQGKQRAVGGC 293

Query: 299 LHFLQV 304
           L FLQ+
Sbjct: 294 LLFLQL 299

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  150 bits (380), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 131/246 (53%), Gaps = 7/246 (2%)

Query: 65  KHIGKTYKELPPEQKARYKKR-----DERMGNSGNSNSHSGDNEIVETKCVPERFCALVK 119
           K     +K +  E+KA+Y KR     D  +  +            + T+C P R   +++
Sbjct: 109 KAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPARAPKPRKQTNLVTRCSPGRLFNVLQ 168

Query: 120 SLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFS 179
            L+ ++K A+R +GF SLL LRC  L+R LC WL+ +F   R  +E+ G+++ L PK   
Sbjct: 169 RLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLERFNTARRSLEICGERIPLSPKDVE 228

Query: 180 KIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTL 239
            +MG+   G  +  +G  D I E+R  +  T  GI +R LEE +    EA + FK +F L
Sbjct: 229 LVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGISVRLLEERLAA-PEAGEEFKRSFIL 287

Query: 240 FAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGC 298
           +A+ T+LCP     +S  FLH + ++ +I   NW  F  D LV+ + RF   +   +GGC
Sbjct: 288 YALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGKFLLDRLVREVSRFHQGKQRAVGGC 347

Query: 299 LHFLQV 304
           L FLQ+
Sbjct: 348 LLFLQL 353

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 =  146 bits (369), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 141/272 (51%), Gaps = 7/272 (2%)

Query: 39  FVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR-----DERMGNSG 93
           +V +  E +K   + + + S      K     +K +  E+KA+Y +R     D  +  + 
Sbjct: 41  WVHFSREFIKEYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTRRAREVWDNYLSTAP 100

Query: 94  NSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWL 153
                      + T+C P R   +++ L+ E+K A++++GF SLL LRC  L+R LC WL
Sbjct: 101 ARTPKPRKQTKLVTRCSPGRLFNVLQRLTPEQKDAVKDLGFGSLLGLRCRTLRRSLCLWL 160

Query: 154 VNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKG 213
           + +F      +E+ G ++ L PK    +MG+   G  +  +G  + I ++RR +  T +G
Sbjct: 161 LQRFNTTGRSLEICGDRIPLSPKDVEFVMGLAASGKDVVNSGPDNLILDLRRNYNATNRG 220

Query: 214 IRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNW 272
           I +  LEE + +  EA + FK +F L+A+ TLL P     +S  FLH + +V  +   NW
Sbjct: 221 ISVSLLEERL-KAPEAGEEFKRSFVLYALGTLLSPTARLDVSPSFLHFLTNVDVVHQYNW 279

Query: 273 ATFCYDWLVKSICRFQNQQAAYIGGCLHFLQV 304
             F  D LV+ + RF+  +   +GGCL FLQ+
Sbjct: 280 GKFLLDRLVREVARFRQGKQRAVGGCLLFLQL 311

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  144 bits (362), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 84/290 (28%), Positives = 147/290 (50%), Gaps = 3/290 (1%)

Query: 18  KGAPILRANGQDAV--PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELP 75
           KG  +   +G + V  P      ++ Y+N+++  ++ ++  + +   LRK +GK +  L 
Sbjct: 169 KGKKMSERDGLEVVRNPKRPIGAWIHYYNDQLAMMKEKDKGVKINDDLRKKLGKKWNALS 228

Query: 76  PEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFE 135
             +K  +  + +      +          ++T+C PER   +++ L  ++K AI EIGF 
Sbjct: 229 KVEKENFMAKSKESSKQYSLQKGVVPKLYLQTRCSPERVIRVIEKLEPKQKAAIXEIGFG 288

Query: 136 SLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKING 195
           SLL+LRC K+   LC  L+N F P   +++L+   ++L P     IMG++  G  I +N 
Sbjct: 289 SLLQLRCRKIDHGLCLXLINSFNPNTYMLQLYNTCIKLSPIDVEFIMGLRARGFKIGMNK 348

Query: 196 ASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCP-IGSYIS 254
              H  ++ + +      + +  LE  I +  E    FKV F LF +  LLCP +  +++
Sbjct: 349 DVXHKNDLCKKYCDKKGRLPLVMLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVN 408

Query: 255 TLFLHPIMDVSSIKSLNWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQV 304
             FLH + D+ SIK +NW  F   +LV  I  F+ +Q + + GCL FL +
Sbjct: 409 RSFLHLVEDIDSIKKMNWXEFVLSYLVHGIEEFKKKQQSGVCGCLLFLML 458

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 (346), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 140/273 (51%), Gaps = 9/273 (3%)

Query: 39  FVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH 98
           +V +  E +K   + + +        K     +K +  E+KA+Y K+   + +S  S + 
Sbjct: 47  WVHFSREFIKEYSASHPESCGLKAATKAASDAWKSMRVEEKAKYTKQARELWDSYLSTAP 106

Query: 99  S------GDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHW 152
           +         ++V T+C P R   +++ LS E+  A++ +GF SLL LRC  L+R LC W
Sbjct: 107 ARIPKPRKQTKLV-TRCSPGRLFNVLQRLSPEQNAAVKSMGFGSLLGLRCRTLRRSLCLW 165

Query: 153 LVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVK 212
           L+ +F      +E+ G  + L P+    ++G+   G  +  +G  D I ++RR +  T  
Sbjct: 166 LLERFNTAGCSLEICGMCIPLSPRDVEIVLGLAASGKDVINSGPDDLIVDLRRSYNATNH 225

Query: 213 GIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLN 271
           GI +R LEE +    EA + FK +F L+A+ TLL P     +S  FLH + ++  +   N
Sbjct: 226 GISVRLLEERLTA-PEAGEDFKRSFVLYALGTLLSPTARLDVSPSFLHFLTNMDVVHQYN 284

Query: 272 WATFCYDWLVKSICRFQNQQAAYIGGCLHFLQV 304
           W  F  D LV+ + RF   +   +GGCL FLQ+
Sbjct: 285 WGKFLLDRLVREVSRFHQGKQRAVGGCLLFLQL 317

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  137 bits (344), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 77/263 (29%), Positives = 132/263 (50%), Gaps = 14/263 (5%)

Query: 32  PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGN 91
           P      ++ Y+N+++  ++ ++  + +   LRK +GK +  L   +K  +  + +    
Sbjct: 47  PKRPIGAWIHYYNDQLAMMKEKDKGVKINDDLRKKLGKKWNALSKVEKENFMAKXKESSK 106

Query: 92  SGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCH 151
             +          ++T+C PER   ++++L  ++K AI EIGF SLL+LRC K+   LC 
Sbjct: 107 QYSLQKGVVPKLYLQTRCSPERVIRVIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCL 166

Query: 152 WLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTV 211
           WL+N F P   +++L+   ++L P     IMG++  G  I +N    H  +         
Sbjct: 167 WLINSFNPNTYMLQLYNTCIKLSPIDVEFIMGLRARGFKIGMNKDVGHKND--------- 217

Query: 212 KGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCP-IGSYISTLFLHPIMDVSSIKSL 270
               +  LE  I +  E    FKV F LF +  LLCP +  +++  FLH + D+ SIK +
Sbjct: 218 ----LLMLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKM 273

Query: 271 NWATFCYDWLVKSICRFQNQQAA 293
           NWA F   +LV  I  F+ +Q +
Sbjct: 274 NWAEFVLSYLVHGIEEFKKKQQS 296

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 =  116 bits (290), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 70/255 (27%), Positives = 124/255 (48%), Gaps = 8/255 (3%)

Query: 42  YFNEE-VKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR-----DERMGNSGNS 95
           YF++E +K   + + +        K     +K +  E+K +Y +      D  + +    
Sbjct: 37  YFSKEFIKEYIASHPESPGLKAATKAASNAWKSMSLEEKEKYARHAREVWDGYLSSGAAP 96

Query: 96  NSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVN 155
           N        + T+C P R   +++ L+ E+K+A++ +GF SLL LRC  L+R LC WL+ 
Sbjct: 97  NPKPRKQTKLVTRCSPGRLFKVLQRLTPEQKEAVKSMGFGSLLGLRCRTLRRSLCLWLLE 156

Query: 156 QFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIR 215
           +F      +E+    + L P     ++G+   G  +  +G  D I+++R  +     GI 
Sbjct: 157 RFDTTNCSLEICNVDVPLTPNDVEMVLGLSASGKEVVNSGPEDMISDLRNSYNAINHGIS 216

Query: 216 IRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWAT 274
           +R LEE +    E+   FK +F L+ + TLLCP     +S  FLH + ++  +   NW  
Sbjct: 217 VRLLEEQLATA-ESGDDFKRSFVLYVLGTLLCPTARLDVSPSFLHFLTNMDLVHQYNWGK 275

Query: 275 FCYDWLVKSICRFQN 289
           F  D LV+ +  ++N
Sbjct: 276 FLLDRLVRELFYYEN 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 =  110 bits (274), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 111/218 (50%), Gaps = 1/218 (0%)

Query: 57  LSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCA 116
           +S  + LRK +G  +  L   +K  +  + +      +          ++T+C  ER   
Sbjct: 106 ISPDVQLRKKLGIKWNALSKVEKENFMAKSKESSKQYSLQKGVVPKLYLQTRCSXERVIR 165

Query: 117 LVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPK 176
           ++++L  ++K AI EIGF SLL+LRC K+   LC WL+N F     +++L+   ++L P 
Sbjct: 166 VIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCLWLINSFNXNTYMLQLYNTCIKLSPI 225

Query: 177 MFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVKGIRIRTLEEVIEQLDEANKIFKVA 236
               IMG++  G  I +N    H  ++ + +      + +  LE  I +  E    FKV 
Sbjct: 226 DVEFIMGLRARGXKIGMNKDVGHKNDLCKKYCDKKGRLPLVMLENQIREDKEGGNDFKVR 285

Query: 237 FTLFAIATLLCP-IGSYISTLFLHPIMDVSSIKSLNWA 273
           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|147856790|emb|CAN83476.1| hypothetical protein VITISV_019328 [Vitis vinifera]

 Score =  108 bits (271), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 71/274 (25%), Positives = 124/274 (45%), Gaps = 38/274 (13%)

Query: 32  PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGN 91
           P      ++ Y+N+++  ++ ++  + +   LRK +GK + EL   +K  +  + +    
Sbjct: 22  PKRPIGXWIHYYNDQLXMIKEKDKGVKINDDLRKKLGKKWNELSKVEKXDFMAKSKESSK 81

Query: 92  SGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRKLCH 151
             +          ++T+C PER   +++ L  +++ AI EIGF SLL+LRC K+      
Sbjct: 82  QYSLQKGVVPKLYLQTRCSPERVIRVIEELEPKQRAAIEEIGFGSLLQLRCRKID----- 136

Query: 152 WLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTV 211
                          HG +                 G+ I +N    H  ++ + +    
Sbjct: 137 ---------------HGAR-----------------GLKIGMNKDVSHNNDLCKKYCDKK 164

Query: 212 KGIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCP-IGSYISTLFLHPIMDVSSIKSL 270
             + +  LE  I +  E    FKV F LF +  LLCP +  ++   FLH + D+ SIK +
Sbjct: 165 GQLPLVMLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVKRSFLHLVEDIDSIKKM 224

Query: 271 NWATFCYDWLVKSICRFQNQQAAYIGGCLHFLQV 304
           NWA F   +LV  I  F+ +Q + + GCL FL +
Sbjct: 225 NWAEFVLSYLVHGIEEFKMKQQSGVCGCLLFLML 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

No hits with e-value below 0.001 by BLAST

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00022339001 SubName- Full=Chromosome chr14 scaffold_26, whole genome shotgun sequence; (610 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

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	317
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	9e-05
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	0.001
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	0.001
smart00398	70	smart00398, HMG, high mobility group	0.003

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

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 4/58 (6%)

Query: 32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 89
          P S+   F  +  E+  +L++EN  L     + K +G+ +K L  E+K  Y+++ E+ 
Sbjct: 4  PLSA---FFLFSQEQRAKLKAENPGLKNA-EISKILGEKWKNLSEEEKKPYEEKAEKE 57

Length = 69

>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 14/51 (27%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDER 88
           +  +  E    +++EN  LSV   + K +G+ +K L  E+K +Y+++ E+
Sbjct: 7  AYFLFSQEHRAEVKAENPGLSVG-EISKILGEMWKSLSEEEKKKYEEKAEK 56

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 members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

>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 = 36.8 bits (86), Expect = 0.001
 Identities = 16/48 (33%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR 85
           +  +  E+  +L+ EN D SVT  + K +G+ +KEL  E+K +Y+++
Sbjct: 7  AYFLFSQEQRPKLKKENPDASVT-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

>gnl|CDD|197700 smart00398, HMG, high mobility group

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR 85
           F+ +  E   ++++EN DLS    + K +G+ +K L  E+KA Y+++
Sbjct: 8  AFMLFSQENRAKIKAENPDLSNAE-ISKKLGERWKLLSEEEKAPYEEK 54

Length = 70

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	317
PF10536	363	PMD: Plant mobile domain; InterPro: IPR019557 This	99.98
PTZ00199	94	high mobility group protein; Provisional	99.87
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.77
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.71
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.69
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.68
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	99.67
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.66
KOG0381	96	consensus HMG box-containing protein [General func	99.64
smart00398	70	HMG high mobility group.	99.64
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.63
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.61
KOG0527	331	consensus HMG-box transcription factor [Transcript	99.07
PF09331	142	DUF1985: Domain of unknown function (DUF1985); Int	98.89
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	98.7
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	98.55
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	98.14
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.32
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	97.27
KOG2746	683	consensus HMG-box transcription factor Capicua and	96.77
COG5648	211	NHP6B Chromatin-associated proteins containing the	96.7
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	96.56
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	93.66
PF03078	458	ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 A	91.3
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	87.27

>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=270.72  Aligned_cols=182  Identities=22%  Similarity=0.349  Sum_probs=158.1

Q ss_pred             Ccchhhccc--cccccHHHHHHHHhcccCCcceEEEcCEEeeeChhhhhhhhcccCCCcccccCCCh---hHHHHHHHHh
Q 021140          133 GFESLLELR--CGKLKRKLCHWLVNQFKPERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGAS---DHIAEVRRIF  207 (317)
Q Consensus       133 GFg~LL~i~--~~~l~~~L~~wL~~~~d~~t~~~~l~g~~i~it~~dV~~VLGLP~gG~~v~~~~~~---~~~~~l~~~~  207 (317)
                      |||+|+.|.  ..++++.|+.+|+++|+++|++|++++++++||++||.+|+|||+.|.+|......   +.++++.+..
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  89999999999999999999999999999999999999999999999999875432   3344443332


Q ss_pred             CC----CCCCcchHHHHHHHhhcccc-cchhhhhHHhhhhcceecccCCC--CCcccccccccccccccccchHHHHHHH
Q 021140          208 QP----TVKGIRIRTLEEVIEQLDEA-NKIFKVAFTLFAIATLLCPIGSY--ISTLFLHPIMDVSSIKSLNWATFCYDWL  280 (317)
Q Consensus       208 ~~----~~~~i~l~~L~~~l~~~~~~-~d~f~r~Fll~~i~~~L~Ptts~--vs~~yl~~l~D~~~i~~yNW~~~Vld~L  280 (317)
                      ..    .+..+.++++++.+.+.+++ .+.+.||||++.+|++|||+++.  |+..|++++.|++.+++||||.+||++|
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            21    24566788999888544333 24899999999999999999877  9999999999999999999999999999


Q ss_pred             HHHHHHHhhcC--CccccccHHHHHHHHHhcCCCcc
Q 021140          281 VKSICRFQNQQ--AAYIGGCLHFLQVRPLLQLKLSI  314 (317)
Q Consensus       281 ~~~i~k~~~~~--~~~i~GCl~lLqi~Yld~l~~~~  314 (317)
                      +++|++++.+.  ..+++||+.|||+|+||||+++.
T Consensus       161 y~~L~~~~~~~~~~~~~~g~~~llq~W~werf~~~r  196 (363)
T PF10536_consen  161 YRDLCKASRKSASQSNIGGPLWLLQLWAWERFPVGR  196 (363)
T ss_pred             HHHHHHHhhhcccccccccceeeeccchhheeeccc
Confidence            99999998877  78999999999999999999763

>PTZ00199 high mobility group protein; Provisional

Probab=99.87  E-value=8.5e-23  Score=161.37  Aligned_cols=76  Identities=18%  Similarity=0.314  Sum_probs=71.1

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCc-hhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLS-VTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~-~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +.|+.+|||+||||+||||+|++++|.+++++||+++ .+++|++++|++|++||++||++|+++|++++.+|..++
T Consensus        13 ~~k~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~   89 (94)
T PTZ00199         13 NKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEK   89 (94)
T ss_pred             cCCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4577899999999999999999999999999999986 238999999999999999999999999999999998775

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

Probab=99.77  E-value=9e-20  Score=160.09  Aligned_cols=76  Identities=21%  Similarity=0.312  Sum_probs=73.3

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      .+|+++|||+||||.||||+|+++.|.+++++||+++| ++|||.+|++||+|+|+||+||.+.|..++.||..+++
T Consensus        61 ~~r~k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~-~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~  136 (211)
T COG5648          61 LVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTF-GEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKE  136 (211)
T ss_pred             HHHHhcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCCh-HHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHH
Confidence            67889999999999999999999999999999999999 99999999999999999999999999999999998863

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

Probab=99.71  E-value=5.1e-18  Score=124.46  Aligned_cols=65  Identities=26%  Similarity=0.458  Sum_probs=62.7

Q ss_pred             CCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        32 pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ||||+||||+|++++|..++++||++++ .+|++.+|+.|++||++||++|.++|++++.+|..++
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~-~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASV-TEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999999999988 9999999999999999999999999999999998653

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.

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

Probab=99.69  E-value=2e-17  Score=125.76  Aligned_cols=66  Identities=23%  Similarity=0.350  Sum_probs=63.7

Q ss_pred             CCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           31 VPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        31 ~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .||||++|||+|++++|.+++++||+.++ .+|++++|+.|+.||++||++|.++|++++.+|..+.
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~-~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~   66 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTN-NEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREY   66 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            38999999999999999999999999998 9999999999999999999999999999999999776

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.

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

Probab=99.68  E-value=1.2e-17  Score=125.68  Aligned_cols=68  Identities=19%  Similarity=0.293  Sum_probs=59.8

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhh-CCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSE-NSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~-~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ||+||||+|||++|+.+++.+++++ ++...+ .++.+.+|+.|++||++||++|.++|++++.+|+.++
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~-~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~   69 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSF-REVMKEISERWKSLSEEEKEPYEERAKEDKERYEREM   69 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSH-HHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCH-HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999 887778 8999999999999999999999999999999998654

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 ....

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

Probab=99.67  E-value=1.1e-17  Score=163.24  Aligned_cols=73  Identities=12%  Similarity=0.272  Sum_probs=69.9

Q ss_pred             chhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           21 PILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        21 ~~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      ++.|++|||||||||.||||+|+|..|..+|++  +.++ ++|+|.+|++||+||.  |++|+++|+.+|.||+.++.
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~-~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~  597 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED--GISV-GDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMK  597 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc--CchH-HHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHH
Confidence            477899999999999999999999999999999  9988 9999999999999998  99999999999999999884

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

Probab=99.66  E-value=9.5e-17  Score=120.53  Aligned_cols=65  Identities=14%  Similarity=0.192  Sum_probs=62.3

Q ss_pred             CCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        32 pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      -|||+||||+|++++|.+++++||++++ .+|+|.+|++|+.||++||++|.++|+.++++|..+.
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~~~-~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~   66 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLKEN-RAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLY   66 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            4899999999999999999999999998 8999999999999999999999999999999998665

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.

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

Probab=99.64  E-value=1.9e-16  Score=125.05  Aligned_cols=70  Identities=21%  Similarity=0.404  Sum_probs=66.6

Q ss_pred             CCC--CCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           28 QDA--VPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        28 ~~~--~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      ||+  +||||+||||+|++++|..++++||++++ .+|+|++|+.|+.|+++||.+|..++..++.+|..++.
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~-~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~   88 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPGLSV-GEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELA   88 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            885  99999999999999999999999999888 99999999999999999999999999999999987653

>smart00398 HMG high mobility group

Probab=99.64  E-value=1.5e-16  Score=117.51  Aligned_cols=66  Identities=24%  Similarity=0.428  Sum_probs=63.3

Q ss_pred             CCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           31 VPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        31 ~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +||||+|||++|++++|..++++||++++ ++|++.+|+.|+.||++||++|.++|++++.+|..+.
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~-~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~   66 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSN-AEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEM   66 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999999998 9999999999999999999999999999999998654

>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=99.63  E-value=2.2e-16  Score=116.81  Aligned_cols=64  Identities=28%  Similarity=0.449  Sum_probs=59.9

Q ss_pred             CCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCC
Q 021140           32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   96 (317)
Q Consensus        32 pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~   96 (317)
                      ||||+|||++|++++|..++++||+.+. .+|++.+|+.|++||++||++|.+.|++.+.+|..+
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~-~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~   64 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSN-KEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKE   64 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTH-HHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhccccc-ccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999997 999999999999999999999999999999998754

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 ....

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

Probab=99.61  E-value=5.4e-16  Score=113.20  Aligned_cols=64  Identities=23%  Similarity=0.420  Sum_probs=61.6

Q ss_pred             CCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCC
Q 021140           32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   96 (317)
Q Consensus        32 pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~   96 (317)
                      ||||+|||+.|++++|..++++||+.+. .+|.+.+|++|+.||++||++|.++|++.+.+|..+
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~-~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~   64 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSV-GEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKE   64 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHh
Confidence            8999999999999999999999999988 899999999999999999999999999999998754

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

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=99.07  E-value=5.9e-11  Score=112.98  Aligned_cols=71  Identities=15%  Similarity=0.261  Sum_probs=64.9

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ++....=|||..|||++.+.+|..+-++||+..- +||.|.+|+.||.|+|+||.||.+.|++.+..|.++=
T Consensus        57 k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHN-SEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~Hmkeh  127 (331)
T KOG0527|consen   57 KTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHN-SEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEY  127 (331)
T ss_pred             CCCccccCCCcchhhhhhHHHHHHHHHhCcchhh-HHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhC
Confidence            4444555999999999999999999999999966 9999999999999999999999999999999988763

>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=98.89  E-value=2.8e-09  Score=90.43  Aligned_cols=123  Identities=14%  Similarity=0.265  Sum_probs=90.5

Q ss_pred             ceEEEcCEEeeeChhhhhhhhcccCCCcccccCCChh---HHHHHHHHhCCCCCCcchHHHHHHHhhc--ccccchhhhh
Q 021140          162 NIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASD---HIAEVRRIFQPTVKGIRIRTLEEVIEQL--DEANKIFKVA  236 (317)
Q Consensus       162 ~~~~l~g~~i~it~~dV~~VLGLP~gG~~v~~~~~~~---~~~~l~~~~~~~~~~i~l~~L~~~l~~~--~~~~d~f~r~  236 (317)
                      ..|.++|..|.++..+.+.|+|||++..+-.......   ....+.+.+-..+..+++.++.++|...  .+.++.+.-+
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            4678899999999999999999999887766542111   0113333322345679999999999865  2234445555


Q ss_pred             HHhhhhcceecccCCC-CCcccccccccccccccccchHHHHHHHHHHH
Q 021140          237 FTLFAIATLLCPIGSY-ISTLFLHPIMDVSSIKSLNWATFCYDWLVKSI  284 (317)
Q Consensus       237 Fll~~i~~~L~Ptts~-vs~~yl~~l~D~~~i~~yNW~~~Vld~L~~~i  284 (317)
                      +++++.|.+++++.+. |+..++..+.|++.+.+|-||.+.++.++++|
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

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

Probab=98.70  E-value=9.9e-09  Score=95.27  Aligned_cols=74  Identities=19%  Similarity=0.290  Sum_probs=70.1

Q ss_pred             hcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           24 RANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        24 ~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      +..+-|.+|-+|+-.||-|+...+.++|++||+++. =+|||++|..|+-|+|+||..|+.-.+..|.+|+..++
T Consensus        57 t~pkpPkppekpl~pymrySrkvWd~VkA~nPe~kL-WeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smk  130 (410)
T KOG4715|consen   57 TRPKPPKPPEKPLMPYMRYSRKVWDQVKASNPELKL-WEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMK  130 (410)
T ss_pred             cCCCCCCCCCcccchhhHHhhhhhhhhhccCcchHH-HHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            447789999999999999999999999999999999 89999999999999999999999999999999998873

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=98.55  E-value=6.5e-08  Score=90.64  Aligned_cols=59  Identities=17%  Similarity=0.350  Sum_probs=53.7

Q ss_pred             CCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccC
Q 021140           33 TSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNS   92 (317)
Q Consensus        33 kr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~   92 (317)
                      |.|+.|||.||+|+|+.+-+|-- ++-.++|-+++|.+|-+||-||.++|-+.|++++.-
T Consensus       193 KKPLNAFmlyMKEmRa~vvaEct-lKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerql  251 (421)
T KOG3248|consen  193 KKPLNAFMLYMKEMRAKVVAECT-LKESAAINQILGRRWHALSREEQAKYYELARKERQL  251 (421)
T ss_pred             cccHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHH
Confidence            88999999999999999999986 544499999999999999999999999999988653

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

Probab=98.14  E-value=1e-06  Score=86.41  Aligned_cols=61  Identities=15%  Similarity=0.312  Sum_probs=52.6

Q ss_pred             CCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCC
Q 021140           33 TSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGN   94 (317)
Q Consensus        33 kr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~   94 (317)
                      |||.+|||++.+|.|..+-...||.-- ..+.|++|.+||+||..||+||-+--....+.|-
T Consensus       327 KRPMNAFMVWAkDERRKILqA~PDMHN-SnISKILGSRWKaMSN~eKQPYYEEQaRLSk~Hl  387 (511)
T KOG0528|consen  327 KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMSNTEKQPYYEEQARLSKLHL  387 (511)
T ss_pred             cCCcchhhcccchhhhhhhhcCccccc-cchhHHhcccccccccccccchHHHHHHHHHhhh
Confidence            999999999999999999999999977 7899999999999999999988444333444444

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

Probab=97.32  E-value=0.00043  Score=60.10  Aligned_cols=46  Identities=17%  Similarity=0.382  Sum_probs=41.2

Q ss_pred             hhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhh
Q 021140           37 YGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDE   87 (317)
Q Consensus        37 ~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~   87 (317)
                      .||+.|+.|||.    .|.+++. .++-..++..|..||++||.+|..++.
T Consensus        84 naYLNFLReFRr----kh~~L~p-~dlI~~AAraW~rLSe~eK~rYrr~~~  129 (183)
T PF06382_consen   84 NAYLNFLREFRR----KHCGLSP-QDLIQRAARAWCRLSEAEKNRYRRMAP  129 (183)
T ss_pred             hHHHHHHHHHHH----HccCCCH-HHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence            699999999886    5889998 799999999999999999999988654

The function of this family is unknown.

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

Probab=97.27  E-value=0.00015  Score=54.51  Aligned_cols=64  Identities=6%  Similarity=0.066  Sum_probs=52.7

Q ss_pred             CCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        32 pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |..|-+|==.+.+.-+..|-+.+|+... .+ -++.+.+|+.|++.||.++.++|.++.++|+.++
T Consensus         4 PE~PKt~qe~Wqq~vi~dYla~~~~dr~-K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el   67 (85)
T PF14887_consen    4 PETPKTAQEIWQQSVIGDYLAKFRNDRK-KA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYEREL   67 (85)
T ss_dssp             S----THHHHHHHHHHHHHHHHTTSTHH-HH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhhHhHH-HH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            4444455567788999999999999987 44 6699999999999999999999999999999775

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

Probab=96.77  E-value=0.00057  Score=69.85  Aligned_cols=62  Identities=13%  Similarity=0.219  Sum_probs=58.3

Q ss_pred             CCCchhhHHHHHHHH--HHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCC
Q 021140           33 TSSTYGFVSYFNEEV--KRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNS   95 (317)
Q Consensus        33 kr~~~~~~~f~~~~r--~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~   95 (317)
                      .||.+||++|++..|  ..+...||+..- ..|.|++|+.|-+|-+.||+.|.+.|.+.|.-+-+
T Consensus       183 rrPMnaf~ifskrhr~~g~vhq~~pn~DN-rtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfk  246 (683)
T KOG2746|consen  183 RRPMNAFHIFSKRHRGEGRVHQRHPNQDN-RTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFK  246 (683)
T ss_pred             hhhhHHHHHHHhhcCCccchhccCccccc-hhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhh
Confidence            799999999999999  999999999988 89999999999999999999999999998877765

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

Probab=96.70  E-value=0.00066  Score=60.47  Aligned_cols=68  Identities=15%  Similarity=0.182  Sum_probs=63.0

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .-+|++|+.+|..+..+-|......+|+... .+.+|.+|+.|++|++.-|++|.+.+.+++.+|++..
T Consensus       141 k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~-~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~  208 (211)
T COG5648         141 KLPNKAPIGPFIENEPKIRPKVEGPSPDKAL-VEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFY  208 (211)
T ss_pred             ccCCCCCCchhhhccHHhccccCCCCcchhh-hHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhc
Confidence            3467999999999999999999999999988 7999999999999999999999999999999998764

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

Probab=96.56  E-value=0.0036  Score=54.51  Aligned_cols=49  Identities=20%  Similarity=0.373  Sum_probs=43.7

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELP   75 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~   75 (317)
                      .+-|-+..|-||||-.||+|.-.++|++||+++- .|.=+++++.|+-.+
T Consensus       116 ~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ish-keaFs~aAknW~h~p  164 (170)
T PF04690_consen  116 NKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISH-KEAFSAAAKNWAHFP  164 (170)
T ss_pred             cCCccccCCCchhHHHHHHHHHHHHHhcCCCCCH-HHHHHHHHHhhhhCc
Confidence            4556666799999999999999999999999999 899999999998755

>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases []

Probab=93.66  E-value=0.088  Score=37.31  Aligned_cols=39  Identities=10%  Similarity=0.146  Sum_probs=35.6

Q ss_pred             chhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCC
Q 021140           36 TYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELP   75 (317)
Q Consensus        36 ~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~   75 (317)
                      .|.|=.|.+-.|..+.++||++.. ..+-.+++.+|++-+
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~~~-sKl~~l~~AKwrEF~   51 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKAPM-SKLMMLLQAKWREFQ   51 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCcH-HHHHHHHHHHHHHHH
Confidence            577889999999999999999998 899999999998744

; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>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=91.30  E-value=5  Score=40.45  Aligned_cols=189  Identities=15%  Similarity=0.118  Sum_probs=108.4

Q ss_pred             hhhcCCChHHhhhhhhhhhhhccCCCCCCCCCCCCcceeeechhHHHHHhhcCCHHHHHHHHHhCcchhhccccccccHH
Q 021140           69 KTYKELPPEQKARYKKRDERMGNSGNSNSHSGDNEIVETKCVPERFCALVKSLSEEKKKAIREIGFESLLELRCGKLKRK  148 (317)
Q Consensus        69 ~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~~~k~~~~~~RcS~~~~~~~i~~Ls~~qk~~I~~~GFg~LL~i~~~~l~~~  148 (317)
                      .+|+..+++|--.|.+.-+--..||-               ++..+..+  .|.++-..+++.+|.+.|..++...-+..
T Consensus        41 ~k~~~~t~~eyy~~l~~~~~~~TRyp---------------~~etl~~L--Gl~~dV~~lf~~~gL~~f~~~~~~~Y~ee  103 (458)
T PF03078_consen   41 KKKDKLTPSEYYQLLKKIEFAPTRYP---------------DPETLQKL--GLLEDVEYLFKKCGLGTFMSYPYPTYPEE  103 (458)
T ss_pred             cccccCChHHHHHHHhhccccccccC---------------CHHHHHHh--ccHHHHHHHHHhcCchhhccCCCCCcHHH
Confidence            35566666665555555444444443               34445555  67888899999999999998887655544


Q ss_pred             HHHHHHhcccC----------------CcceEEEcCEEeeeChhhhhhhhcccCCCcccccCCChhHHHHHHHHhCCCCC
Q 021140          149 LCHWLVNQFKP----------------ERNIIELHGQKLELCPKMFSKIMGVKDGGMAIKINGASDHIAEVRRIFQPTVK  212 (317)
Q Consensus       149 L~~wL~~~~d~----------------~t~~~~l~g~~i~it~~dV~~VLGLP~gG~~v~~~~~~~~~~~l~~~~~~~~~  212 (317)
                      .+..|+.. ..                ..-+|.|.|....+|-.+...++|.|.|+. +....+.+....|++..|.+. 
T Consensus       104 t~qFLaTl-~v~~~~~~~~~~~e~~glG~l~F~V~~~~y~lsi~~L~~i~GF~~~~~-i~~~~~~~el~~~W~~ig~~~-  180 (458)
T PF03078_consen  104 TRQFLATL-KVTFYNPSEPRAKELDGLGYLTFFVYGVEYSLSIKHLERIFGFPSGDE-IKPDFDPEELNDFWATIGGGK-  180 (458)
T ss_pred             HHHhhhee-eeeecccccchhhcccCcceEEEEEcceeeeeeHHHHHHHhCCCCccc-cCCCCCchHHHHHHHHhcCCC-
Confidence            44444432 21                123577789999999999999999998743 434444444566777665431 


Q ss_pred             CcchHHHHHHHhhcccccchhhhhHHhhhhcceecccCCC--CCcccccc-----------cccc----cccccccchHH
Q 021140          213 GIRIRTLEEVIEQLDEANKIFKVAFTLFAIATLLCPIGSY--ISTLFLHP-----------IMDV----SSIKSLNWATF  275 (317)
Q Consensus       213 ~i~l~~L~~~l~~~~~~~d~f~r~Fll~~i~~~L~Ptts~--vs~~yl~~-----------l~D~----~~i~~yNW~~~  275 (317)
                      .++...-....      .-+=+.+++--+++..|+|.+..  |..+-|.+           ..|.    .+..+.|-+..
T Consensus       181 p~~~~~~ks~~------Ir~PviRy~hr~iA~tlf~R~~~~~v~~~El~~l~~~L~~~Lr~~~~g~~l~~d~~dt~~~~v  254 (458)
T PF03078_consen  181 PFNSARSKSNQ------IRSPVIRYFHRLIANTLFAREETGTVRNDELEMLDQALKHLLRRTKDGKLLRGDLNDTNVSMV  254 (458)
T ss_pred             ccccccccccc------ccChHHHHHHHHHHhhhccccccCceechhHHHHHHHHHHHHHhcCCCccccCcccccchhHH
Confidence            11111111111      11223344444566666664433  55544332           1121    12356667777


Q ss_pred             HHHHHHHH
Q 021140          276 CYDWLVKS  283 (317)
Q Consensus       276 Vld~L~~~  283 (317)
                      .++||+..
T Consensus       255 l~~hL~~y  262 (458)
T PF03078_consen  255 LLDHLCSY  262 (458)
T ss_pred             HHHHHHhh
Confidence            77777654

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.

>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function

Probab=87.27  E-value=0.89  Score=37.60  Aligned_cols=49  Identities=12%  Similarity=0.220  Sum_probs=43.9

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELP   75 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~   75 (317)
                      ..|.++-+|---||--|-...-.++|++||++.. .++--++-+.|+--|
T Consensus        67 ~~drHPErR~KAAy~afeE~~Lp~lK~E~PgLrl-sQ~kq~l~K~w~KSP  115 (122)
T PF06244_consen   67 PIDRHPERRMKAAYKAFEERRLPELKEENPGLRL-SQYKQMLWKEWQKSP  115 (122)
T ss_pred             CCCCCcchhHHHHHHHHHHHHhHHHHhhCCCchH-HHHHHHHHHHHhcCC
Confidence            5577788888899999999999999999999999 899999999997644

---

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	317
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	7e-05
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	2e-04
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-04
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	5e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	5e-04
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	7e-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 = 40.1 bits (94), Expect = 7e-05
 Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDER 88
          G+V + NE  +++R+ + DL     + K +G  + +L P +K RY    E+
Sbjct: 14 GYVRFLNERREQIRTRHPDLPFP-EITKMLGAEWSKLQPAEKQRYLDEAEK 63

>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding protein; NMR {Homo sapiens} SCOP: a.21.1.1 Length = 99

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDER 88
           +  +F E+  +    + ++S    L K + K YKELP ++K +Y +  +R
Sbjct: 17 PYFRFFMEKRAKYAKLHPEMSNL-DLTKILSKKYKELPEKKKMKYIQDFQR 66

>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box domain, structural genomics, NPPSFA; NMR {Mus musculus} Length = 102

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDER 88
           +  +F +    ++ +N + +    + K +   +  L  EQK  YKK+ E 
Sbjct: 24 AYALFFRDTQAAIKGQNPNATFG-EVSKIVASMWDGLGEEQKQVYKKKTEA 73

>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 Length = 77

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDER 88
           F  + +E   +++ E+  LS+   + K +G+ +     + K  Y+K+  +
Sbjct: 13 AFFLFCSEYRPKIKGEHPGLSIG-DVAKKLGEMWNNTAADDKQPYEKKAAK 62

>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 Length = 93

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKR 85
           ++ + NE    +RSEN D++    + K +G+ +K L PE+K  Y+ +
Sbjct: 27 AYMFFANENRDIVRSENPDITFG-QVGKKLGEKWKALTPEEKQPYEAK 73

>2yrq_A High mobility group protein B1; HMG box domain, DNA binding, helix-turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 173

 Score = 38.8 bits (90), Expect = 7e-04
 Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 38  GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDER 88
            F  + +E   +++ E+  LS+   + K +G+ +     + K  Y+K+  +
Sbjct: 108 AFFLFCSEYRPKIKGEHPGLSIG-DVAKKLGEMWNNTAADDKQPYEKKAAK 157

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	317
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.88
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.86
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.85
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.85
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.85
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.84
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.84
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.83
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.83
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.83
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.82
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.81
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.81
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.81
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.81
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.8
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.79
2cto_A	93	Novel protein; high mobility group box domain, hel	99.78
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.78
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.77
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.77
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.76
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.75
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.75
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.75
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.74
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.74
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.73
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.73
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.72
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.71
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.71
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.7
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.67
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.66
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.6
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.6
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.57
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.51

>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=99.88  E-value=3.6e-23  Score=161.07  Aligned_cols=76  Identities=20%  Similarity=0.374  Sum_probs=73.1

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      +.|+++|||+||||+||||+|++++|.+++++||++++ .+|+|.+|+.|++||++||++|+++|++++.+|..++.
T Consensus        11 ~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A           11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSE-SELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             cCcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            55778999999999999999999999999999999999 99999999999999999999999999999999999875

>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=99.86  E-value=5.6e-23  Score=160.89  Aligned_cols=85  Identities=22%  Similarity=0.333  Sum_probs=76.8

Q ss_pred             CCCCccccCcchhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhc
Q 021140           11 QPGGLQKKGAPILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMG   90 (317)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~   90 (317)
                      |.+.+..+++ +.|+.+|||+||||+||||+|++++|.+++++||++++ ++|+|++|+.|++||++||++|.++|++++
T Consensus         1 ~~~~~~~k~~-~~k~~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k   78 (93)
T 1cg7_A            1 MVTPREPKKR-TTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITF-GQVGKKLGEKWKALTPEEKQPYEAKAQADK   78 (93)
T ss_dssp             CCCCCCCCCC-CCCCCCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCH-HHHTTTHHHHHHTTHHHHHHHHHHHHTTHH
T ss_pred             CCCCCCCCcc-cCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            4455555554 56778999999999999999999999999999999998 999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 021140           91 NSGNSNS   97 (317)
Q Consensus        91 ~~y~~~k   97 (317)
                      .+|..++
T Consensus        79 ~~y~~e~   85 (93)
T 1cg7_A           79 KRYESEK   85 (93)
T ss_dssp             HHTTHHH
T ss_pred             HHHHHHH
Confidence            9998764

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

Probab=99.85  E-value=1.8e-22  Score=155.71  Aligned_cols=75  Identities=11%  Similarity=0.198  Sum_probs=69.8

Q ss_pred             hhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCch-hhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           23 LRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSV-TLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        23 ~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~-~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .++++|||+||||+||||+|++++|.+++++||+.+. ..+|+|.+|++|++||++||++|+++|++++.+|..++
T Consensus         7 ~~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~   82 (86)
T 2eqz_A            7 GMAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREM   82 (86)
T ss_dssp             SCSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3568999999999999999999999999999999973 38999999999999999999999999999999998664

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

Probab=99.85  E-value=1.2e-22  Score=160.18  Aligned_cols=86  Identities=17%  Similarity=0.321  Sum_probs=76.8

Q ss_pred             CCCCccccCcc-hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCc--hhhhhhhHHhhhhcCCChHHhhhhhhhhh
Q 021140           11 QPGGLQKKGAP-ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLS--VTLGLRKHIGKTYKELPPEQKARYKKRDE   87 (317)
Q Consensus        11 ~~~~~~~~~~~-~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~--~~~~~~k~~g~~wk~l~~~ek~~y~~~a~   87 (317)
                      |||+..++.++ +.++.+|||+||||+||||+|++++|.+++++||+++  + ++|+|++|+.|++||++||++|+++|+
T Consensus         1 ~~~~~~~~~k~~~~k~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~-~eisk~lg~~Wk~ls~eeK~~Y~~~A~   79 (97)
T 2lhj_A            1 MAGASDRTGVRRPRKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDV-AAIGKMIGAAWNALSDEEKKPYERMSD   79 (97)
T ss_dssp             CCCCSSSSSCCCTTCTTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCS-SHHHHHHHHTSSSSCSTTTSSSSHHHH
T ss_pred             CCCccccccccccccCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccH-HHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            56554444444 6677899999999999999999999999999999998  7 999999999999999999999999999


Q ss_pred             hhccCCCCCC
Q 021140           88 RMGNSGNSNS   97 (317)
Q Consensus        88 ~~~~~y~~~k   97 (317)
                      +++.+|..++
T Consensus        80 ~~k~~y~~e~   89 (97)
T 2lhj_A           80 EDRVRYEREK   89 (97)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999998664

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

Probab=99.85  E-value=9.4e-23  Score=161.48  Aligned_cols=73  Identities=23%  Similarity=0.373  Sum_probs=69.6

Q ss_pred             hcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           24 RANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        24 ~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |+++|||+||||+||||+|++++|.+++++||++++ ++|+|++|+.|++||++||++|+++|++++.+|..++
T Consensus         3 kk~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~   75 (99)
T 1k99_A            3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSN-LDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNL   75 (99)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCS-HHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            568999999999999999999999999999999998 9999999999999999999999999999999977665

>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=99.84  E-value=3.8e-21  Score=146.75  Aligned_cols=67  Identities=18%  Similarity=0.280  Sum_probs=63.4

Q ss_pred             CCCCCCCCCchhhHHHHHHHHHHHHhhCCCCc-hhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCC
Q 021140           27 GQDAVPTSSTYGFVSYFNEEVKRLRSENSDLS-VTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGN   94 (317)
Q Consensus        27 ~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~-~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~   94 (317)
                      ++||+||||+||||+|++++|.+++++||+++ + ++|+|.+|++|++||++||+||+++|+.+..+-.
T Consensus         1 ~~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~-~eisK~lge~Wk~ls~eeK~~y~~~A~~d~~~~~   68 (81)
T 2d7l_A            1 GSSGSSGRPKTGFQMWLEENRSNILSDNPDFSDE-ADIIKEGMIRFRVLSTEERKVWANKAKGETASEG   68 (81)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSH-HHHHHHHHHHHSSSCHHHHHHHHHHTTSSSSSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchh-HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhhh
Confidence            58999999999999999999999999999998 7 9999999999999999999999999999976543

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

Probab=99.84  E-value=1.9e-21  Score=154.66  Aligned_cols=75  Identities=16%  Similarity=0.254  Sum_probs=71.1

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +.|+.+|||+||||+||||+|++++|.+++++||++++ .+|+|++|++|++||++||++|+++|++++.+|..++
T Consensus         8 ~kk~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~   82 (102)
T 2co9_A            8 KKKKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATF-GEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQL   82 (102)
T ss_dssp             SCSSCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCH-HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44668999999999999999999999999999999998 9999999999999999999999999999999998765

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

Probab=99.83  E-value=5.8e-22  Score=151.74  Aligned_cols=73  Identities=11%  Similarity=0.232  Sum_probs=69.1

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCch-hhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSV-TLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~-~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      ++|||+||||+||||+|++++|.+++++||+.+. +++|+|.+|++|++||++||++|+++|++++.+|..++.
T Consensus         2 kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~   75 (83)
T 1aab_A            2 KGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK   75 (83)
T ss_dssp             CCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999873 389999999999999999999999999999999998874

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

Probab=99.83  E-value=7.8e-23  Score=158.62  Aligned_cols=80  Identities=19%  Similarity=0.241  Sum_probs=71.4

Q ss_pred             CCccccCcchhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCc--hhhhhhhHHhhhhcCCChHHhhhhhhhhhhhc
Q 021140           13 GGLQKKGAPILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLS--VTLGLRKHIGKTYKELPPEQKARYKKRDERMG   90 (317)
Q Consensus        13 ~~~~~~~~~~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~--~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~   90 (317)
                      |+.+...+...|+++|||+||||+||||+|++++|..++++||+++  + ++|+    ++|+.|+++||+||+++|++++
T Consensus         4 ~~~~~~~~~~~k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~-~eIs----e~Wk~ls~eeK~pY~~kA~~~K   78 (90)
T 2yuk_A            4 GSSGNAQRSTLKWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRV-KQIA----KLWRKASSQERAPYVQKARDNR   78 (90)
T ss_dssp             SSCCCCCCCHHHHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHH-HHHH----HHHHHSCHHHHHHHHHHHHHHH
T ss_pred             CCccccHHHHhhccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchH-HHHH----HHHHcCCHHHHHHHHHHHHHHH
Confidence            3344444446788999999999999999999999999999999998  7 8888    9999999999999999999999


Q ss_pred             cCCCCCC
Q 021140           91 NSGNSNS   97 (317)
Q Consensus        91 ~~y~~~k   97 (317)
                      ++|..++
T Consensus        79 ~~h~~~~   85 (90)
T 2yuk_A           79 AALRINK   85 (90)
T ss_dssp             HHHHHSS
T ss_pred             HHHHhhH
Confidence            9998765

>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=99.83  E-value=2.6e-21  Score=145.92  Aligned_cols=71  Identities=15%  Similarity=0.344  Sum_probs=68.5

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ++|||+||||+||||+|++++|.+++++||++++ ++|+|.+|+.|++||++||++|.++|++++.+|..++
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~   71 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSI-GDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI   71 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCH-HHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4799999999999999999999999999999998 9999999999999999999999999999999998765

>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=99.82  E-value=1e-20  Score=146.20  Aligned_cols=73  Identities=7%  Similarity=0.094  Sum_probs=69.1

Q ss_pred             hcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           24 RANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        24 ~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ++.+|||+||||+||||+|++++|.+++++||++++ .+|+|++|+.|++||++||++|+++|++++.+|..+.
T Consensus        10 ~~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~   82 (87)
T 2e6o_A           10 VSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDN-RAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLN   82 (87)
T ss_dssp             CCCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            457899999999999999999999999999999998 9999999999999999999999999999999987543

>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=99.81  E-value=3.9e-21  Score=149.06  Aligned_cols=67  Identities=9%  Similarity=0.078  Sum_probs=64.4

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .|.||||+||||+|++++|.+++++||+ .+ ++|+|.+|++|++||++||+||+++|++++.+|+.++
T Consensus         2 ~~kPKrP~SAy~lf~~~~r~~~k~~~p~-~~-~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm   68 (91)
T 1l8y_A            2 GKLPESPKRAEEIWQQSVIGDYLARFKN-DR-VKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYEREL   68 (91)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHHTTS-TH-HHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCC-CH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3799999999999999999999999999 66 9999999999999999999999999999999999887

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

Probab=99.81  E-value=1.1e-20  Score=147.40  Aligned_cols=71  Identities=23%  Similarity=0.449  Sum_probs=68.5

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .+|||+||||+||||+|++++|.+++++||++++ .+|+|++|+.|++||++||++|.++|++++.+|..++
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~   72 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPF-PEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKEL   72 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCH-HHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999999998 9999999999999999999999999999999998765

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

Probab=99.81  E-value=6.5e-21  Score=148.77  Aligned_cols=71  Identities=15%  Similarity=0.170  Sum_probs=68.4

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ..+||+||||+||||+|++++|.+++++||++++ .+|+|++|++|++||++||++|.++|++++.+|..++
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~   72 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPKTSL-EDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQM   72 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCH-HHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999998 8999999999999999999999999999999999776

>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=99.81  E-value=1.4e-20  Score=141.43  Aligned_cols=69  Identities=12%  Similarity=0.230  Sum_probs=65.1

Q ss_pred             CCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           28 QDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        28 ~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |||+||||+||||+|++++|.+++++||++++ ++|+|++|+.|++||++||++|.++|++++.+|..+.
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   69 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY   69 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSS-SHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCH-HHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            79999999999999999999999999999998 8999999999999999999999999999999998765

>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=99.80  E-value=2.9e-20  Score=141.92  Aligned_cols=72  Identities=14%  Similarity=0.222  Sum_probs=69.3

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      ..||++||||+||||+|++++|.+++++||++++ .+|+|++|+.|++||++||++|.++|++++.+|..+..
T Consensus         2 ~~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~   73 (82)
T 1wz6_A            2 SSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDN-RGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANP   73 (82)
T ss_dssp             CSSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCT-THHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhH
Confidence            4689999999999999999999999999999999 99999999999999999999999999999999998874

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

Probab=99.79  E-value=3.9e-20  Score=138.17  Aligned_cols=67  Identities=19%  Similarity=0.404  Sum_probs=65.1

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      ||+||||+||||+|++++|.+++++||++++ ++|+|.+|+.|++|  +||++|+++|++++.+|..++.
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~   67 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKV-TEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMR   67 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCH-HHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTG
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999999999999999998 99999999999999  8999999999999999998874

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

Probab=99.78  E-value=3.8e-20  Score=144.61  Aligned_cols=76  Identities=14%  Similarity=0.252  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHH---hhhhcCCChHHhhhhhhhhhhhccCCCCCCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHI---GKTYKELPPEQKARYKKRDERMGNSGNSNSHSGDN  102 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~---g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~~~k~  102 (317)
                      .+++|+||||+||||+|++++|.+++.+  ++++ ++|+|.+   |++|+.||++||+||+++|++++.+|+++.++..+
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~~~-~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~~~~~   81 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR--GLPV-ARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGPSEK   81 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH--TCCC-SSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSSCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc--CCCH-HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcccccccc
Confidence            6799999999999999999999999999  7877 8999999   99999999999999999999999999998865444


Q ss_pred             Cc
Q 021140          103 EI  104 (317)
Q Consensus       103 ~~  104 (317)
                      .+
T Consensus        82 ~~   83 (93)
T 2cto_A           82 QK   83 (93)
T ss_dssp             CC
T ss_pred             cc
Confidence            44

>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=99.78  E-value=1.5e-19  Score=139.01  Aligned_cols=70  Identities=11%  Similarity=0.224  Sum_probs=67.2

Q ss_pred             CCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           28 QDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        28 ~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      .||+||||+||||+|++++|.+++++||++++ ++|+|++|+.|++||++||++|.++|++++.+|..+..
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~   70 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYP   70 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSCH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            48999999999999999999999999999998 99999999999999999999999999999999987763

>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=99.77  E-value=4.9e-20  Score=136.65  Aligned_cols=67  Identities=10%  Similarity=0.198  Sum_probs=63.1

Q ss_pred             CCCCCchhhHHHHHHHHHHHHhhCCCCch-hhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           31 VPTSSTYGFVSYFNEEVKRLRSENSDLSV-TLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        31 ~pkr~~~~~~~f~~~~r~~~~~~~p~~~~-~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +||||+||||+|++++|.+++++||+.+. +++|+|.+|++|++||++||++|.++|++++.+|..++
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~   68 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREM   68 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            69999999999999999999999999863 48999999999999999999999999999999998665

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

Probab=99.77  E-value=1.5e-19  Score=144.70  Aligned_cols=76  Identities=14%  Similarity=0.263  Sum_probs=66.0

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      .....+||++||||+||||+|++++|.+++++||++++ .+|+|++|+.|++||++||++|.++|++++.+|..+..
T Consensus        20 ~~~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   95 (106)
T 4euw_A           20 YFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHN-AELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHP   95 (106)
T ss_dssp             --------CCCCCCCCHHHHHHHHHHHHHHHHCTTSCH-HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             hhhccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            34557899999999999999999999999999999999 89999999999999999999999999999999997763

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

Probab=99.76  E-value=4.7e-19  Score=151.31  Aligned_cols=85  Identities=16%  Similarity=0.329  Sum_probs=75.0

Q ss_pred             CCCCccccCcchhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhc
Q 021140           11 QPGGLQKKGAPILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMG   90 (317)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~   90 (317)
                      |+.-...+++ +.++.+|||+||||+||||+|++++|..++++||++++ ++|+|.+|+.|++||++||++|.++|++++
T Consensus        69 ~~~y~~~k~~-~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~-~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k  146 (159)
T 2gzk_A           69 YPNYKYRKGE-TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSI-GDVAKKLGEMWNNTAADDKQPYEKKAAKLK  146 (159)
T ss_dssp             CSSCSCCCCC-CGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHH
T ss_pred             hhcccccccc-ccccccccccccccccccchhhHhhHHHHHHhCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHH
Confidence            4433333333 45678999999999999999999999999999999998 999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 021140           91 NSGNSNS   97 (317)
Q Consensus        91 ~~y~~~k   97 (317)
                      .+|..++
T Consensus       147 ~~y~~~~  153 (159)
T 2gzk_A          147 EKYEKDI  153 (159)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9998664

>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=99.75  E-value=3.4e-19  Score=133.06  Aligned_cols=66  Identities=12%  Similarity=0.309  Sum_probs=63.1

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .|+||||+||||+|++++|.+++++||++++ ++|+|.+|+.|++||+  |++|+++|++++.+|..++
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~   66 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIKV-TEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAV   66 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCCH-HHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999999998 9999999999999998  9999999999999998664

>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=99.75  E-value=4.7e-19  Score=134.49  Aligned_cols=68  Identities=13%  Similarity=0.239  Sum_probs=65.4

Q ss_pred             CCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           30 AVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        30 ~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      +.||||+||||+|++++|.+++++||++++ ++|+|++|+.|++||++||++|.++|++++.+|..+..
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~   68 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHP   68 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            579999999999999999999999999998 99999999999999999999999999999999998773

>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=99.75  E-value=6.1e-19  Score=134.20  Aligned_cols=69  Identities=13%  Similarity=0.245  Sum_probs=65.5

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      +++||||+||||+|++++|..++++||++++ ++|+|++|+.|++||++||++|.++|++++.+|..+..
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p   70 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYP   70 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCH-HHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCS
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            6899999999999999999999999999998 99999999999999999999999999999999987763

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

Probab=99.74  E-value=5.4e-19  Score=130.84  Aligned_cols=68  Identities=25%  Similarity=0.365  Sum_probs=61.8

Q ss_pred             CCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           30 AVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        30 ~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      +.||||+||||+|++++|.+++++||++++ ++|+|.+|+.|++||++||++|.++|++++.+|..+..
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~   68 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHP   68 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            469999999999999999999999999998 99999999999999999999999999999999987753

>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=99.74  E-value=4.9e-19  Score=135.23  Aligned_cols=71  Identities=24%  Similarity=0.338  Sum_probs=63.9

Q ss_pred             CCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           27 GQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        27 ~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      ..++.||||+||||+|++++|..++++||++++ ++|+|++|+.|++||++||++|.++|++++.+|..+..
T Consensus         2 ~~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~   72 (83)
T 3f27_D            2 SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHP   72 (83)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHHHHCSSSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            357899999999999999999999999999998 99999999999999999999999999999999987763

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

Probab=99.73  E-value=3e-19  Score=131.08  Aligned_cols=63  Identities=13%  Similarity=0.237  Sum_probs=59.8

Q ss_pred             CCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           30 AVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        30 ~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |+||||+||||+|++++|.+++.+||     ++|+|.+|+.|++||++||++|.++|++++.+|..++
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~   63 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEM   63 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999987     5899999999999999999999999999999998664

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

Probab=99.73  E-value=5.4e-19  Score=141.98  Aligned_cols=69  Identities=14%  Similarity=0.210  Sum_probs=65.0

Q ss_pred             hcCCCCCCC-CCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           24 RANGQDAVP-TSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        24 ~~~~~~~~p-kr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ++.+|||+| |||+||||+|++++|.+++    ++++ ++|+|.+|++|++||++||++|+++|++++.+|..++
T Consensus         9 kk~kd~~~P~KrP~say~lF~~e~r~~~k----~~~~-~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~   78 (108)
T 1v64_A            9 LKDKFDGRPTKPPPNSYSLYCAELMANMK----DVPS-TERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVEL   78 (108)
T ss_dssp             SSCCTTTSCCCCCSSHHHHHHHHHHHHCT----TSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCCCCCCHHHHHHHHHHHHHh----CCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            457899999 9999999999999999988    7888 9999999999999999999999999999999999775

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

Probab=99.72  E-value=4.6e-18  Score=147.21  Aligned_cols=73  Identities=8%  Similarity=0.199  Sum_probs=69.0

Q ss_pred             hcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCC--chhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           24 RANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDL--SVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        24 ~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~--~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ++++|||+||||+||||+|++++|.+++++||+.  ++ ++|+|.+|++|++||++||++|.++|++++.+|..++
T Consensus         8 ~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~   82 (173)
T 2yrq_A            8 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNF-SEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREM   82 (173)
T ss_dssp             SSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999999994  66 9999999999999999999999999999999998765

>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=99.71  E-value=6.6e-18  Score=129.96  Aligned_cols=66  Identities=14%  Similarity=0.196  Sum_probs=63.7

Q ss_pred             CCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           31 VPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        31 ~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .||||+||||+|++++|.+++++||++++ ++|+|++|+.|++||++||++|.++|++++.+|..+.
T Consensus         2 ~pKRP~naf~lf~~~~r~~~~~~~P~~~~-~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~   67 (86)
T 2lef_A            2 HIKKPLNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARKERQLHMQLY   67 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            59999999999999999999999999998 9999999999999999999999999999999998765

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

Probab=99.71  E-value=4.6e-18  Score=147.16  Aligned_cols=74  Identities=15%  Similarity=0.331  Sum_probs=70.0

Q ss_pred             hhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           23 LRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        23 ~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .|+.+|||+||||+||||+|+++.|.+++++||++++ .+|+|.+|+.|++||++||++|.++|++++.+|..++
T Consensus        93 kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~-~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~  166 (173)
T 2yrq_A           93 KKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSI-GDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI  166 (173)
T ss_dssp             SCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCH-HHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3557899999999999999999999999999999999 9999999999999999999999999999999998664

>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=99.70  E-value=7.6e-18  Score=127.33  Aligned_cols=68  Identities=16%  Similarity=0.262  Sum_probs=64.8

Q ss_pred             CCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           30 AVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        30 ~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      +.||||+||||+|+++.|.+++++||++++ ++|+|++|+.|++||++||++|.++|++++.+|..+..
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p   68 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHN-AEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYP   68 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            469999999999999999999999999998 89999999999999999999999999999999987763

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

Probab=99.67  E-value=1.5e-17  Score=131.99  Aligned_cols=69  Identities=19%  Similarity=0.278  Sum_probs=61.0

Q ss_pred             CCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           26 NGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        26 ~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .+..++||||+||||+|+++++.  ..++|++++ ++|+|.+|++|+.||++||+||+++|++++.+|..++
T Consensus         3 s~~~~~PKrP~say~lF~~e~~~--~p~~~~~~~-~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~   71 (101)
T 1v63_A            3 SGSSGPKKPPMNGYQKFSQELLS--NGELNHLPL-KERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHL   71 (101)
T ss_dssp             CCCCSSCCCCSSSHHHHHHHHHH--HCTTTTSCH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHh--CCCCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            35678999999999999999975  334555777 8999999999999999999999999999999999775

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

Probab=99.66  E-value=6.2e-18  Score=153.72  Aligned_cols=75  Identities=15%  Similarity=0.245  Sum_probs=69.4

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +....+|||+||||+||||+|+++.|.+++++||++++ ++|+|.+|++|+.||++||++|+++|++++.+|+.++
T Consensus        32 ~~~s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~-~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~  106 (238)
T 3tmm_A           32 RGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKT-TELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEI  106 (238)
T ss_dssp             ---CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            33446799999999999999999999999999999998 9999999999999999999999999999999999775

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

Probab=99.60  E-value=2e-16  Score=141.51  Aligned_cols=69  Identities=16%  Similarity=0.306  Sum_probs=66.8

Q ss_pred             CCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           28 QDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        28 ~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +||+||||+||||+|+++.|.+++++||++++ ++|+|.+|++|++||++||++|+++|++++.+|+.++
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~~~-~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~   74 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKT-TELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEI   74 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHh
Confidence            58999999999999999999999999999998 9999999999999999999999999999999999765

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

Probab=99.60  E-value=1.3e-17  Score=149.24  Aligned_cols=70  Identities=11%  Similarity=0.182  Sum_probs=65.2

Q ss_pred             hhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           23 LRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        23 ~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .|..+|||+||||+||||+|++|+|..++.+||+     +|+|.+|+.|++||++||+||+++|++++.+|..++
T Consensus       106 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~  175 (214)
T 3tq6_A          106 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEM  175 (214)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSSCSSHH-----HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccccCcccccchhhhhHHHHHHhhccCCHH-----HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556899999999999999999999999988875     899999999999999999999999999999999775

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

Probab=99.57  E-value=2.6e-17  Score=149.59  Aligned_cols=70  Identities=11%  Similarity=0.182  Sum_probs=65.4

Q ss_pred             hhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           23 LRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        23 ~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .|..+|||+||||+||||+|++|+|..++.+||+     +|+|.+|+.|+.||++||+||+++|++++.+|+.++
T Consensus       138 kk~~kdp~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~  207 (238)
T 3tmm_A          138 KKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEM  207 (238)
T ss_dssp             HHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSSHH-----HHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhcccCCCCCCCcHHHHHHHHHHHHHhccCHH-----HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556899999999999999999999999988876     799999999999999999999999999999999775

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

Probab=99.51  E-value=5.2e-15  Score=126.12  Aligned_cols=68  Identities=12%  Similarity=0.240  Sum_probs=65.6

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |+.||||++|||+|+++.|..++++||++++ ++|+|.+|+.|+.||++||++|.+.|+.++.+|..+.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   69 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY   69 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999998 9999999999999999999999999999999988765

---

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	317
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-04

>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 = 37.1 bits (86), Expect = 2e-04
 Identities = 10/52 (19%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 38 GFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERM 89
           F  + +E   +++ E+  LS+   + K +G+ +     + K  Y+K+  ++
Sbjct: 9  AFFLFCSEYRPKIKGEHPGLSIG-DVAKKLGEMWNNTAADDKQPYEKKAAKL 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	317
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.82
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.81
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.79
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.76
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.75
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.74
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.72
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.72
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.65
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.56
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.56
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	93.54

>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=99.82  E-value=8.7e-21  Score=145.57  Aligned_cols=76  Identities=20%  Similarity=0.374  Sum_probs=72.4

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      ...+++||++||||+||||+|++++|.+++++||+.++ .+|.+.+|+.|+.||++||++|.++|++++.+|+.+.+
T Consensus        11 ~~~~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~-~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~~~   86 (90)
T d1wgfa_          11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSE-SELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             SCCCSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             ccCCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45567899999999999999999999999999999999 89999999999999999999999999999999998875

>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=99.81  E-value=3.8e-21  Score=148.62  Aligned_cols=75  Identities=24%  Similarity=0.400  Sum_probs=71.5

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      ..|+.+||++||||+||||+|++|+|.+++++||+.++ .+|++.+|+.|++||++||++|.++|++++.+|..++
T Consensus        11 ~~k~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~-~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~   85 (93)
T d1lwma_          11 TTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITF-GQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEK   85 (93)
T ss_dssp             CCSCCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCH-HHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            56778999999999999999999999999999999999 8999999999999999999999999999999998664

>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=99.79  E-value=4.9e-21  Score=143.52  Aligned_cols=67  Identities=16%  Similarity=0.384  Sum_probs=65.2

Q ss_pred             CCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           30 AVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        30 ~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |+||||+||||+|+++.|.+++++||+.++ .+|+|.+|+.|++||++||++|.++|++++.+|..++
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~~-~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~   67 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSI-GDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI   67 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCT-TTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999999 8999999999999999999999999999999998765

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

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

Probab=99.76  E-value=8.1e-20  Score=140.34  Aligned_cols=73  Identities=23%  Similarity=0.373  Sum_probs=69.9

Q ss_pred             hcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           24 RANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        24 ~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |+++||++||||+||||+|+++.|..++++||++++ .+|++.+|+.|++||++||++|.++|++++.+|..+.
T Consensus         3 k~kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~-~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~   75 (91)
T d1k99a_           3 KLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSN-LDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNL   75 (91)
T ss_dssp             CCCSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCS-HHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            568999999999999999999999999999999999 8999999999999999999999999999999997665

>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=99.75  E-value=1.4e-19  Score=135.87  Aligned_cols=68  Identities=13%  Similarity=0.239  Sum_probs=65.6

Q ss_pred             CCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           30 AVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        30 ~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      |.||||+||||+|+++.|.+++++||+.++ ++|+|++|+.|++||++||++|+++|++++++|..+.+
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~-~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p   68 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHP   68 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCH-HHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            689999999999999999999999999999 99999999999999999999999999999999998864

>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=99.75  E-value=2.8e-19  Score=135.76  Aligned_cols=68  Identities=12%  Similarity=0.231  Sum_probs=65.9

Q ss_pred             CCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCCC
Q 021140           30 AVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNSH   98 (317)
Q Consensus        30 ~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k~   98 (317)
                      |.||||+||||+|++++|.+++++||+.++ ++|+|.+|+.|++||++||++|+++|++++.+|..++.
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~~~-~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~   70 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYP   70 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTSCH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccCCH-HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhH
Confidence            789999999999999999999999999999 89999999999999999999999999999999998874

>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=99.74  E-value=1.6e-19  Score=132.35  Aligned_cols=67  Identities=10%  Similarity=0.212  Sum_probs=62.2

Q ss_pred             CCCCCchhhHHHHHHHHHHHHhhCCCCchh-hhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           31 VPTSSTYGFVSYFNEEVKRLRSENSDLSVT-LGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        31 ~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~-~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +||||+||||+|++++|.+++++||+.+.. ++|+|.+|+.|++||++||++|+++|++++.+|..++
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~   68 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREM   68 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            599999999999999999999999986532 7999999999999999999999999999999998665

>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=99.72  E-value=1.1e-18  Score=127.76  Aligned_cols=64  Identities=14%  Similarity=0.285  Sum_probs=61.6

Q ss_pred             CCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCC
Q 021140           32 PTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSN   96 (317)
Q Consensus        32 pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~   96 (317)
                      .|||+||||+|+++.|..++++||+.++ ++|+|.+|+.|++||++||++|.++|++++++|..+
T Consensus         3 iKRP~nay~lf~~~~r~~i~~~~p~~~~-~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~   66 (70)
T d1i11a_           3 IKRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK   66 (70)
T ss_dssp             SCCSCCHHHHHHHHHHHHHHTTCSSCCH-HHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhccCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999 999999999999999999999999999999999755

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

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

Probab=99.72  E-value=3.8e-19  Score=131.17  Aligned_cols=66  Identities=12%  Similarity=0.325  Sum_probs=62.2

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      .|+||||+||||+|+++.|.+++++||+.++ .+|+|.+|+.|++|+  ||++|+++|++++.+|..++
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~~~-~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~   66 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGIKV-TEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAV   66 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTCCH-HHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCCCH-HHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999999999 899999999999986  59999999999999998665

>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=99.65  E-value=3e-17  Score=124.64  Aligned_cols=64  Identities=14%  Similarity=0.226  Sum_probs=61.3

Q ss_pred             CCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           33 TSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        33 kr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |||+||||+|+++.|.+++++||++++ ++|++++|+.|++||++||++|.++|++++.+|..+.
T Consensus         4 kRP~naf~lF~~~~r~~~~~~~P~~~~-~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~   67 (86)
T d2lefa_           4 KKPLNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARKERQLHMQLY   67 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCCCH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCH-HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            799999999999999999999999999 9999999999999999999999999999999887654

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

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

Probab=99.56  E-value=6.8e-16  Score=121.82  Aligned_cols=71  Identities=13%  Similarity=0.131  Sum_probs=64.4

Q ss_pred             hhhcCCCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           22 ILRANGQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        22 ~~~~~~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +.|.+.|+.+||||+||||+|++|+|.+    +|+.++ .++.+.+|+.|++||++||++|+++|++++.+|..++
T Consensus         8 ~~k~~~~~~p~K~P~~ay~lF~~~~r~~----~~~~~~-~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~   78 (108)
T d1v64a_           8 QLKDKFDGRPTKPPPNSYSLYCAELMAN----MKDVPS-TERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVEL   78 (108)
T ss_dssp             CSSCCTTTSCCCCCSSHHHHHHHHHHHH----CTTSCH-HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccCCCCCCCCCCcHHHHHHHHHHHH----ccCCCH-HHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455788999999999999999999865    688888 8999999999999999999999999999999998764

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

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

Probab=99.56  E-value=7e-16  Score=120.16  Aligned_cols=68  Identities=16%  Similarity=0.217  Sum_probs=61.6

Q ss_pred             CCCCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           27 GQDAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        27 ~~~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      +...+||||+||||+|++|+|..++.+||  ++ .+|+|.+|+.|++||++||++|.++|++++.+|..++
T Consensus         4 ~~~~p~KrP~~ay~~F~~e~r~~~~~~~~--~~-~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~   71 (101)
T d1v63a_           4 GSSGPKKPPMNGYQKFSQELLSNGELNHL--PL-KERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHL   71 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHHHCTTTTS--CH-HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHhcCC--CH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44567999999999999999999987765  56 7999999999999999999999999999999998765

>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=93.54  E-value=0.021  Score=39.68  Aligned_cols=64  Identities=9%  Similarity=0.055  Sum_probs=45.2

Q ss_pred             CCCCCCCchhhHHHHHHHHHHHHhhCCCCchhhhhhhHHhhhhcCCChHHhhhhhhhhhhhccCCCCCC
Q 021140           29 DAVPTSSTYGFVSYFNEEVKRLRSENSDLSVTLGLRKHIGKTYKELPPEQKARYKKRDERMGNSGNSNS   97 (317)
Q Consensus        29 ~~~pkr~~~~~~~f~~~~r~~~~~~~p~~~~~~~~~k~~g~~wk~l~~~ek~~y~~~a~~~~~~y~~~k   97 (317)
                      |..||.   |==.+.+.---.|-+...+-..  ...|+.-..|++|...||.++.++|.+|.+||+.+.
T Consensus         4 petpkt---aeeiWQqsvIgdYlA~fk~DR~--KaqkaMeatW~~meKkEki~wikkaaedqkryerel   67 (84)
T d1l8ya_           4 PESPKR---AEEIWQQSVIGDYLARFKNDRV--KALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYEREL   67 (84)
T ss_dssp             CCCCCH---HHHHHHHHHHHHHHHHTTSTHH--HHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCC---HHHHHHHHHHHHHHHHHHhhHH--HHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence            444544   4444455555556555544433  345677779999999999999999999999999663