Citrus Sinensis ID: 020237

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------33
Protein Sequence
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLCGM
Secondary Structure (PSIPRED)
cccccccccccccccccccEEEccccccccccccccccccccccHHHHHHHHcccccHHHHHHHHHHHccccccccHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHcHHHHHHHHHHccccccccccccccHHHHHHHHHcccccccEEEEccEEEEccccEEEEEEEEcccccccccccccHHHHHHHccccccccccHHHHHHHHHHHcccccHHHHHHHHHHHccEEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccEEEcHHHHHHHHHHHHcccccccccccccccccHHHccccc
Secondary Structure Prediction (SSPRO)
cEEEccccccccccccccEEEEEEccccccccccccccHEEEcHHHHHHcccccccccHHHHHHHHHHHHHHcccHHHHHHHHcccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHccccHcccccccccHHHHHHHHHHccccccEEEEccEEEEccHHHHHHHccccccccEEccccccccHHHHHHHccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccHHHHHHHccHHHHHHccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccccEEEccccHHHHHHccc
Coil and Loop (DISEMBL)
mkvvgtnkrkecdinrgtevvgvdasndggrkrqcrNGFIRYFGEVVRQIKANDGMACITKEIRKEIGstyknlppeekcrykseakrvgkskigkakfptrcapDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLngvevelspkSFSYVMgisdggkplqlegessevcayvdnftptsrgiNITVLAGILQKLKSADDQFKVTFMMFALCTilcppggvhissgflfslkdvesipkrnwaTFCFHRLIQGITRHKEEQVAYVGGCLLYLqcsfacrcctstllytESWRGIGQCVRLLCGM
Flexible Loop (DISEMBL)
mkvvgtnkrkecdinrgtevvgvdasndggrkrqcrNGFIRYFGEVVRQIKANDGMACITKEIRkeigstyknlppeekcrykseakrvgkskigkakfptrcapDRLAAAVLQLTDEQRVVVREMGfgsllqlncgRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLCGM
Low Complexity Region (SEG)
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLCGM
Disordered region (IsUnstruct)
*******************VV***********RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTY**************************KFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLE*ESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLC**
Disordered Region (DISOPRED)
****************************************************************************************************TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLCGM
Disordered Region (DISEMBL)
********RKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLCGM
Disordered Region (DISPRO)
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCR*****************FPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLCGM
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSFACRCCTSTLLYTESWRGIGQCVRLLCGM
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	329
296087190	766	unnamed protein product [Vitis vinifera]	0.787	0.338	0.330	1e-36
225453104	617	PREDICTED: uncharacterized protein LOC10	0.778	0.414	0.328	2e-36
147783848	708	hypothetical protein VITISV_032233 [Viti	0.778	0.361	0.328	2e-36
255583781	421	conserved hypothetical protein [Ricinus	0.796	0.622	0.313	7e-36
224077245	628	predicted protein [Populus trichocarpa]	0.787	0.412	0.309	3e-35
356533899	590	PREDICTED: uncharacterized protein LOC10	0.732	0.408	0.300	5e-30
147795729	849	hypothetical protein VITISV_004916 [Viti	0.790	0.306	0.278	9e-29
147772140	637	hypothetical protein VITISV_026046 [Viti	0.762	0.394	0.281	3e-27
147798273	326	hypothetical protein VITISV_001668 [Viti	0.683	0.690	0.277	3e-21
147856790	479	hypothetical protein VITISV_019328 [Viti	0.686	0.471	0.256	9e-21

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

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 90/272 (33%), Positives = 149/272 (54%), Gaps = 13/272 (4%)

Query: 42  YFG-EVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI--GKAK 98
           YF  E +R+  A+   +   K   K     +K++  EEK +Y   ++ V  + +    A+
Sbjct: 169 YFSREFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPAR 228

Query: 99  FP---------TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVE 149
            P         TRC+P RL   + +LT +Q+  VR MGFGSLL L C  L+R+LC WL+E
Sbjct: 229 APKPRKQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLE 288

Query: 150 KIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGIN 209
           + + AR  L++ G  + LSPK    VMG++  GK +   G    +    +++  T+ GI+
Sbjct: 289 RFNTARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGIS 348

Query: 210 ITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWAT 269
           + +L   L     A ++FK +F+++AL T+LCP   + +S  FL  L ++++I + NW  
Sbjct: 349 VRLLEERLAA-PEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGK 407

Query: 270 FCFHRLIQGITRHKEEQVAYVGGCLLYLQCSF 301
           F   RL++ ++R  + +   VGGCLL+LQ  +
Sbjct: 408 FLLDRLVREVSRFHQGKQRAVGGCLLFLQLFY 439

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 =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 88/268 (32%), Positives = 147/268 (54%), Gaps = 12/268 (4%)

Query: 45  EVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI--GKAKFP-- 100
           E +R+  A+   +   K   K     +K++  EEK +Y   ++ V  + +    A+ P  
Sbjct: 35  EFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPARAPKP 94

Query: 101 -------TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDI 153
                  TRC+P RL   + +LT +Q+  VR MGFGSLL L C  L+R+LC WL+E+ + 
Sbjct: 95  RKQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLERFNT 154

Query: 154 ARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVL 213
           AR  L++ G  + LSPK    VMG++  GK +   G    +    +++  T+ GI++ +L
Sbjct: 155 ARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGISVRLL 214

Query: 214 AGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFH 273
              L     A ++FK +F+++AL T+LCP   + +S  FL  L ++++I + NW  F   
Sbjct: 215 EERLAA-PEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGKFLLD 273

Query: 274 RLIQGITRHKEEQVAYVGGCLLYLQCSF 301
           RL++ ++R  + +   VGGCLL+LQ  +
Sbjct: 274 RLVREVSRFHQGKQRAVGGCLLFLQLFY 301

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 =  159 bits (401), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 88/268 (32%), Positives = 147/268 (54%), Gaps = 12/268 (4%)

Query: 45  EVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI--GKAKFP-- 100
           E +R+  A+   +   K   K     +K++  EEK +Y   ++ V  + +    A+ P  
Sbjct: 89  EFIREYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTKRSREVWDNYLTTAPARAPKP 148

Query: 101 -------TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDI 153
                  TRC+P RL   + +LT +Q+  VR MGFGSLL L C  L+R+LC WL+E+ + 
Sbjct: 149 RKQTNLVTRCSPGRLFNVLQRLTPDQKAAVRSMGFGSLLGLRCRTLRRSLCLWLLERFNT 208

Query: 154 ARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVL 213
           AR  L++ G  + LSPK    VMG++  GK +   G    +    +++  T+ GI++ +L
Sbjct: 209 ARRSLEICGERIPLSPKDVELVMGLAASGKDVVNSGPDDLIVELRNSYNATNHGISVRLL 268

Query: 214 AGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFH 273
              L     A ++FK +F+++AL T+LCP   + +S  FL  L ++++I + NW  F   
Sbjct: 269 EERLAA-PEAGEEFKRSFILYALGTVLCPTARLDVSPSFLHFLTNMDTIHQYNWGKFLLD 327

Query: 274 RLIQGITRHKEEQVAYVGGCLLYLQCSF 301
           RL++ ++R  + +   VGGCLL+LQ  +
Sbjct: 328 RLVREVSRFHQGKQRAVGGCLLFLQLFY 355

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 =  157 bits (396), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 150/274 (54%), Gaps = 12/274 (4%)

Query: 39  FIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKA- 97
           ++ +  E +++  A+   +   K   K     +K++  EEK +Y   A+ V  + +  A 
Sbjct: 41  WVHFSREFIKEYSASHPESSGLKAATKAASDAWKSMSLEEKAKYTRRAREVWDNYLSTAP 100

Query: 98  ----------KFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWL 147
                     K  TRC+P RL   + +LT EQ+  V+++GFGSLL L C  L+R+LC WL
Sbjct: 101 ARTPKPRKQTKLVTRCSPGRLFNVLQRLTPEQKDAVKDLGFGSLLGLRCRTLRRSLCLWL 160

Query: 148 VEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRG 207
           +++ +     L++ G  + LSPK   +VMG++  GK +   G  + +     N+  T+RG
Sbjct: 161 LQRFNTTGRSLEICGDRIPLSPKDVEFVMGLAASGKDVVNSGPDNLILDLRRNYNATNRG 220

Query: 208 INITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNW 267
           I++++L   L K   A ++FK +F+++AL T+L P   + +S  FL  L +V+ + + NW
Sbjct: 221 ISVSLLEERL-KAPEAGEEFKRSFVLYALGTLLSPTARLDVSPSFLHFLTNVDVVHQYNW 279

Query: 268 ATFCFHRLIQGITRHKEEQVAYVGGCLLYLQCSF 301
             F   RL++ + R ++ +   VGGCLL+LQ  +
Sbjct: 280 GKFLLDRLVREVARFRQGKQRAVGGCLLFLQLFY 313

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  155 bits (392), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 84/271 (30%), Positives = 148/271 (54%), Gaps = 12/271 (4%)

Query: 39  FIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKA- 97
           ++ +  E +++  A+   +C  K   K     +K++  EEK +Y  +A+ +  S +  A 
Sbjct: 47  WVHFSREFIKEYSASHPESCGLKAATKAASDAWKSMRVEEKAKYTKQARELWDSYLSTAP 106

Query: 98  ----------KFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWL 147
                     K  TRC+P RL   + +L+ EQ   V+ MGFGSLL L C  L+R+LC WL
Sbjct: 107 ARIPKPRKQTKLVTRCSPGRLFNVLQRLSPEQNAAVKSMGFGSLLGLRCRTLRRSLCLWL 166

Query: 148 VEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRG 207
           +E+ + A C L++ G+ + LSP+    V+G++  GK +   G    +     ++  T+ G
Sbjct: 167 LERFNTAGCSLEICGMCIPLSPRDVEIVLGLAASGKDVINSGPDDLIVDLRRSYNATNHG 226

Query: 208 INITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNW 267
           I++ +L   L   ++ +D FK +F+++AL T+L P   + +S  FL  L +++ + + NW
Sbjct: 227 ISVRLLEERLTAPEAGED-FKRSFVLYALGTLLSPTARLDVSPSFLHFLTNMDVVHQYNW 285

Query: 268 ATFCFHRLIQGITRHKEEQVAYVGGCLLYLQ 298
             F   RL++ ++R  + +   VGGCLL+LQ
Sbjct: 286 GKFLLDRLVREVSRFHQGKQRAVGGCLLFLQ 316

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  137 bits (346), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 131/253 (51%), Gaps = 12/253 (4%)

Query: 38  GFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKA 97
            ++ +  E +++  A+   +   K   K   + +K++  EEK +Y   A+ V    +   
Sbjct: 34  SWVYFSKEFIKEYIASHPESPGLKAATKAASNAWKSMSLEEKEKYARHAREVWDGYLSSG 93

Query: 98  KFP-----------TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGW 146
             P           TRC+P RL   + +LT EQ+  V+ MGFGSLL L C  L+R+LC W
Sbjct: 94  AAPNPKPRKQTKLVTRCSPGRLFKVLQRLTPEQKEAVKSMGFGSLLGLRCRTLRRSLCLW 153

Query: 147 LVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSR 206
           L+E+ D   C L++  V+V L+P     V+G+S  GK +   G    +    +++   + 
Sbjct: 154 LLERFDTTNCSLEICNVDVPLTPNDVEMVLGLSASGKEVVNSGPEDMISDLRNSYNAINH 213

Query: 207 GINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRN 266
           GI++ +L   L   +S DD FK +F+++ L T+LCP   + +S  FL  L +++ + + N
Sbjct: 214 GISVRLLEEQLATAESGDD-FKRSFVLYVLGTLLCPTARLDVSPSFLHFLTNMDLVHQYN 272

Query: 267 WATFCFHRLIQGI 279
           W  F   RL++ +
Sbjct: 273 WGKFLLDRLVREL 285

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  133 bits (335), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 74/266 (27%), Positives = 134/266 (50%), Gaps = 6/266 (2%)

Query: 38  GFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK---- 93
            +I Y+ + +  +K  D    I  ++RK++G  +  L   EK  + +++K   K      
Sbjct: 191 AWIHYYNDQLAMMKEKDKGVKINDDLRKKLGKKWNALSKVEKENFMAKSKESSKQYSLQK 250

Query: 94  --IGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKI 151
             + K    TRC+P+R+   + +L  +Q+  + E+GFGSLLQL C ++   LC  L+   
Sbjct: 251 GVVPKLYLQTRCSPERVIRVIEKLEPKQKAAIXEIGFGSLLQLRCRKIDHGLCLXLINSF 310

Query: 152 DIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINIT 211
           +    +LQL    ++LSP    ++MG+   G  + +  +          +      + + 
Sbjct: 311 NPNTYMLQLYNTCIKLSPIDVEFIMGLRARGFKIGMNKDVXHKNDLCKKYCDKKGRLPLV 370

Query: 212 VLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFC 271
           +L   +++ K   + FKV F++F L  +LCP   + ++  FL  ++D++SI K NW  F 
Sbjct: 371 MLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKMNWXEFV 430

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

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  128 bits (322), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 76/270 (28%), Positives = 132/270 (48%), Gaps = 19/270 (7%)

Query: 38  GFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK---- 93
            +I Y+ + +  +K  D    I  ++RK++G  +  L   EK  + ++ K   K      
Sbjct: 53  AWIHYYNDQLAMMKEKDKGVKINDDLRKKLGKKWNALSKVEKENFMAKXKESSKQYSLQK 112

Query: 94  --IGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKI 151
             + K    TRC+P+R+   +  L  +Q+  + E+GFGSLLQL C ++   LC WL+   
Sbjct: 113 GVVPKLYLQTRCSPERVIRVIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCLWLINSF 172

Query: 152 DIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINIT 211
           +    +LQL    ++LSP    ++MG+   G  +   G + +V    D          + 
Sbjct: 173 NPNTYMLQLYNTCIKLSPIDVEFIMGLRARGFKI---GMNKDVGHKND----------LL 219

Query: 212 VLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFC 271
           +L   +++ K   + FKV F++F L  +LCP   + ++  FL  ++D++SI K NWA F 
Sbjct: 220 MLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKMNWAEFV 279

Query: 272 FHRLIQGITRHKEEQVAYVGGCLLYLQCSF 301
              L+ GI   K++Q + V   L+     F
Sbjct: 280 LSYLVHGIEEFKKKQQSGVXRLLIVFNEKF 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  108 bits (270), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 122/238 (51%), Gaps = 13/238 (5%)

Query: 40  IRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK------ 93
           +R  GEV  +I+  D ++    ++RK++G  +  L   EK  + +++K   K        
Sbjct: 90  LRIVGEVGAKIRVLDFISPDV-QLRKKLGIKWNALSKVEKENFMAKSKESSKQYSLQKGV 148

Query: 94  IGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDI 153
           + K    TRC+ +R+   +  L  +Q+  + E+GFGSLLQL C ++   LC WL+   + 
Sbjct: 149 VPKLYLQTRCSXERVIRVIENLEPKQKAAIEEIGFGSLLQLRCRKIDHGLCLWLINSFNX 208

Query: 154 ARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLE---GESSEVCAYVDNFTPTSRGINI 210
              +LQL    ++LSP    ++MG+   G  + +    G  +++C     +      + +
Sbjct: 209 NTYMLQLYNTCIKLSPIDVEFIMGLRARGXKIGMNKDVGHKNDLCK---KYCDKKGRLPL 265

Query: 211 TVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWA 268
            +L   +++ K   + FKV F++F L  +LCP   + ++  FL  ++D++SI K NWA
Sbjct: 266 VMLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVNRSFLHLVEDIDSIKKINWA 323

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  107 bits (266), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 123/269 (45%), Gaps = 43/269 (15%)

Query: 39  FIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK----- 93
           +I Y+ + +  IK  D    I  ++RK++G  +  L   EK  + +++K   K       
Sbjct: 29  WIHYYNDQLXMIKEKDKGVKINDDLRKKLGKKWNELSKVEKXDFMAKSKESSKQYSLQKG 88

Query: 94  -IGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKID 152
            + K    TRC+P+R+   + +L  +QR  + E+GFGSLLQL C ++     G  +    
Sbjct: 89  VVPKLYLQTRCSPERVIRVIEELEPKQRAAIEEIGFGSLLQLRCRKIDHGARGLKI---- 144

Query: 153 IARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITV 212
                    G+  ++S                      ++++C     +      + + +
Sbjct: 145 ---------GMNKDVS---------------------HNNDLCK---KYCDKKGQLPLVM 171

Query: 213 LAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCF 272
           L   +++ K   + FKV F++F L  +LCP   + +   FL  ++D++SI K NWA F  
Sbjct: 172 LENQIREDKEGGNDFKVRFVLFVLGALLCPTMKLFVKRSFLHLVEDIDSIKKMNWAEFVL 231

Query: 273 HRLIQGITRHKEEQVAYVGGCLLYLQCSF 301
             L+ GI   K +Q + V GCLL+L   +
Sbjct: 232 SYLVHGIEEFKMKQQSGVCGCLLFLMLFY 260

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	329
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	1e-06
smart00398	70	smart00398, HMG, high mobility group	4e-06
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	7e-06
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	1e-04
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	0.001
pfam09331	142	pfam09331, DUF1985, Domain of unknown function (DU	0.004

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 3/54 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + +  +  E   ++KA N G++    EI K +G  +K+L  EEK +Y+ +A++
Sbjct: 5  LSAYFLFSQEHRAEVKAENPGLS--VGEISKILGEMWKSLSEEEKKKYEEKAEK 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|197700 smart00398, HMG, high mobility group

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 3/54 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + F+ +  E   +IKA N  ++    EI K++G  +K L  EEK  Y+ +AK+
Sbjct: 6  MSAFMLFSQENRAKIKAENPDLS--NAEISKKLGERWKLLSEEEKAPYEEKAKK 57

Length = 70

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + F  +  E   ++KA N G+     EI K +G  +KNL  EEK  Y+ +A++
Sbjct: 5  LSAFFLFSQEQRAKLKAENPGLK--NAEISKILGEKWKNLSEEEKKPYEEKAEK 56

Length = 69

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

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 36 RNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + +  +  E   ++K  +       E+ K +G  +K L  EEK +Y+ +A++
Sbjct: 5  LSAYFLFSQEQRPKLKK-ENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEK 56

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|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 3/53 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAK 87
          RN FI Y  +   Q+K  N G+     EI + IG  +++  PE K  YK  A+
Sbjct: 6  RNAFILYRQDKHAQLKTENPGLT--NNEISRIIGRMWRSESPEVKAYYKELAE 56

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. Length = 77

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

 Score = 36.6 bits (85), Expect = 0.004
 Identities = 21/126 (16%), Positives = 51/126 (40%), Gaps = 7/126 (5%)

Query: 160 LNGVEVELSPKSFSYVMGISDGGKPLQLEGESS---EVCAYVDNFTPTSRGINITVLAGI 216
             G  +  S + F+ V G+  G  P + + +     +   + +      + + +  +   
Sbjct: 18  FAGKPIRFSLREFALVTGLPCGKYPKEKKVKKKGTLKKGPFWNKLFGLKKDVTVDDVEEK 77

Query: 217 LQKLK--SADDQFKVTFMMFALCTILCPP-GGVHISSGFLFSLKDVESIPKRNWATFCFH 273
           L+K K   ++D+ ++  ++F +  +L        I    L  ++D+E+     W    F 
Sbjct: 78  LKKKKKKDSEDRLRLALLLF-VDGVLLGTSKKTKIPKFHLEMVEDLEAFLTFPWGRLAFE 136

Query: 274 RLIQGI 279
            L++ I
Sbjct: 137 MLMKSI 142

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	329
PF10536	363	PMD: Plant mobile domain; InterPro: IPR019557 This	99.97
PF09331	142	DUF1985: Domain of unknown function (DUF1985); Int	98.92
PTZ00199	94	high mobility group protein; Provisional	98.71
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	98.51
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	98.51
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.37
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	98.32
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	98.29
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	98.28
smart00398	70	HMG high mobility group.	98.2
KOG0381	96	consensus HMG box-containing protein [General func	98.05
COG5648	211	NHP6B Chromatin-associated proteins containing the	97.74
KOG0527	331	consensus HMG-box transcription factor [Transcript	97.07
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	94.56
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	92.09
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	87.08
PF03078	458	ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 A	83.49
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	83.0

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

Probab=99.97  E-value=4.5e-33  Score=271.96  Aligned_cols=193  Identities=18%  Similarity=0.269  Sum_probs=164.5

Q ss_pred             Ccccccccc--ccccchHHHHHHHhccccccceEEECCeEeeeCccchhhhhcccCCCccccccCChhHHHhHhhhcC--
Q 020237          127 GFGSLLQLN--CGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFT--  202 (329)
Q Consensus       127 GFggLL~i~--~~~l~~~L~~wL~er~d~~t~~~~l~g~~i~iT~~dV~~VLGLP~gG~~v~~~~~~~~~~~l~~~~g--  202 (329)
                      |||+|+.|.  ..++++.|+.+|+++|+++|+||+++++|++||++||.+++|||+.|.+|......+ ..++.+.+.  
T Consensus         1 ~~g~~~~i~~s~~~~~~~li~al~erW~~et~tF~~~~gEmtiTL~DV~~llGLpi~G~pv~~~~~~~-~~~~~~~ll~~   79 (363)
T PF10536_consen    1 GFGILDAIMASRITIDRSLISALVERWDPETNTFHFPWGEMTITLEDVAMLLGLPIDGRPVTGPLPPD-WRDLCEELLGV   79 (363)
T ss_pred             CchhHhhhhhhcCCCCHHHHHHHHHHhCcccCeeecccccccchhhhhhhccccccccccccCccccc-hhhHHHHHhcc
Confidence            899999999  899999999999999999999999999999999999999999999999998654433 223332222  


Q ss_pred             ------CCCCCccHHHHHHHHhhccCC-ChhHHHHHHHHHhhhhccCCCCC-cccccccccccccCCCCCccchHHHHHH
Q 020237          203 ------PTSRGINITVLAGILQKLKSA-DDQFKVTFMMFALCTILCPPGGV-HISSGFLFSLKDVESIPKRNWATFCFHR  274 (329)
Q Consensus       203 ------~~~~~isi~~L~e~l~~~~~~-~d~f~R~FiL~~~~~~L~Ptts~-~Vs~~yl~~l~D~d~I~~yNW~~~Vld~  274 (329)
                            ..+..+.+++|++.+.+.+++ ++.+.|||+++++|++|||+++. +|+..|++++.|++.+++||||++||++
T Consensus        80 ~~~~~~~~~~~~~~~wl~~~~~~~~~~d~~~~~rAFll~~lg~~lfp~~~~~~v~~~~l~~~~~l~~~~~~~wg~a~La~  159 (363)
T PF10536_consen   80 SPQIKSKKGSSIRLSWLEEFFSNRPEDDEEQYHRAFLLYWLGSFLFPDKSGDYVSPRYLPLAVDLARIKRYAWGSAVLAY  159 (363)
T ss_pred             cccccccccccchhhheeccccccccchHHHHHHHHHHHhhhceeccCCCcceeeeeEEeeeeccccccccccHHHHHHH
Confidence                  123456788898888665544 24899999999999999999988 8999999999999999999999999999


Q ss_pred             HHHHHHhhhccC--cceeeccHHHHHHHHHhhCCCCC---------------cchhhhhhchh
Q 020237          275 LIQGITRHKEEQ--VAYVGGCLLYLQCSFACRCCTST---------------LLYTESWRGIG  320 (329)
Q Consensus       275 L~~~i~k~~~~k--~~~I~GCl~lLqi~Yld~l~~~~---------------~~~~~~~~~~~  320 (329)
                      |++++.++..+.  ..+++||+.|||+|+++|++..-               +|+.-.|.+.+
T Consensus       160 ly~~L~~~~~~~~~~~~~~g~~~llq~W~werf~~~rP~~~~~~~~~~~~~~~P~~~rW~~~~  222 (363)
T PF10536_consen  160 LYRDLCKASRKSASQSNIGGPLWLLQLWAWERFPVGRPKLITAQKPNPIPDRPPRAARWCDRK  222 (363)
T ss_pred             HHHHHHHHhhhcccccccccceeeeccchhheeecccccccccccccccccCCCeeeeeeccc
Confidence            999999888776  78999999999999999999443               45666777743

>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=98.92  E-value=1.3e-09  Score=93.66  Aligned_cols=124  Identities=17%  Similarity=0.312  Sum_probs=92.1

Q ss_pred             ceEEECCeEeeeCccchhhhhcccCCCccccccCChhHH---HhHhhhcCCCCCCccHHHHHHHHhhc-cCCChhHHHHH
Q 020237          156 CILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEV---CAYVDNFTPTSRGINITVLAGILQKL-KSADDQFKVTF  231 (329)
Q Consensus       156 ~~~~l~g~~i~iT~~dV~~VLGLP~gG~~v~~~~~~~~~---~~l~~~~g~~~~~isi~~L~e~l~~~-~~~~d~f~R~F  231 (329)
                      .-+.++|..|.++..+.+.|+|||++..|-.........   ..+.+.+-..+..+++..+.++|+.. ..+.++-.|.-
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            568899999999999999999999998877654322111   13333332346789999999999885 23444444444


Q ss_pred             HHHHhhhhc-cCCCCCcccccccccccccCCCCCccchHHHHHHHHHHH
Q 020237          232 MMFALCTIL-CPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGI  279 (329)
Q Consensus       232 iL~~~~~~L-~Ptts~~Vs~~yl~~l~D~d~I~~yNW~~~Vld~L~~~i  279 (329)
                      +|+++..+| +++....|+..++..++|++...+|-||.+.++.++++|
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            455555445 444556899999999999999999999999999999864

>PTZ00199 high mobility group protein; Provisional

Probab=98.71  E-value=1.3e-08  Score=81.60  Aligned_cols=68  Identities=18%  Similarity=0.262  Sum_probs=61.0

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCcc-ccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMAC-ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      ..|+|.|+|++++|+.|+.+.+.++++.+|+.. .+.++.+.+|+.|++||++||.+|...|...-..|
T Consensus        17 ~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY   85 (94)
T PTZ00199         17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRY   85 (94)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            568899999999999999999999999999875 47899999999999999999999999888754444

>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=98.51  E-value=4.3e-08  Score=73.04  Aligned_cols=61  Identities=30%  Similarity=0.399  Sum_probs=54.3

Q ss_pred             CcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |+||+|+|+.|+++...++++.+|... ..++.+.+|..|++||++||.++...|......|
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~-~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y   61 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLS-NKEISKILAQMWKNLSEEEKAPYKEEAEEEKERY   61 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTST-HHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccc-cccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999877 8999999999999999999999999988866555

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 ....

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

Probab=98.51  E-value=7e-08  Score=71.15  Aligned_cols=61  Identities=20%  Similarity=0.325  Sum_probs=55.6

Q ss_pred             CcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |++|+++|+.|+.+++..+++.+|+ ....++.+.+|..|++||++||.++...|...-..|
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y   61 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERY   61 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999998 568899999999999999999999999888765555

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.

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

Probab=98.37  E-value=1.6e-07  Score=71.47  Aligned_cols=65  Identities=23%  Similarity=0.352  Sum_probs=52.9

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |+++++++++|+.|+.+.+.++++.-.......++.++++..|++||++||.+|...|+..-.+|
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y   65 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERY   65 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999983335567799999999999999999999999998755444

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 ....

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

Probab=98.32  E-value=7.1e-07  Score=68.54  Aligned_cols=61  Identities=28%  Similarity=0.366  Sum_probs=54.6

Q ss_pred             CcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .+||+|+||.|..+.+.++++.+|.. ...++.+.+|..|++||++||..|...|...-..|
T Consensus         2 ~kRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~   62 (77)
T cd01389           2 IPRPRNAFILYRQDKHAQLKTENPGL-TNNEISRIIGRMWRSESPEVKAYYKELAEEEKERH   62 (77)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999975 67899999999999999999999988887744444

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.

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

Probab=98.29  E-value=5.3e-07  Score=66.06  Aligned_cols=61  Identities=23%  Similarity=0.323  Sum_probs=54.8

Q ss_pred             CcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +++|+|+|+.|+.+++..+++.+|. ....++.+.+|..|++||+++|..+...|...-.+|
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y   61 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERY   61 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999987 457789999999999999999999999988865555

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

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

Probab=98.28  E-value=5.8e-07  Score=68.19  Aligned_cols=61  Identities=25%  Similarity=0.344  Sum_probs=54.2

Q ss_pred             CcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      -|||+|+||.|+.+.++++++.+|.. .+.++.|.+|..|++||++||.++...|...-.+|
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~-~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y   62 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLK-ENRAISKILGDRWKALSNEEKQPYYEEAKKLKELH   62 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            37899999999999999999999974 78899999999999999999999998887744443

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.

>smart00398 HMG high mobility group

Probab=98.20  E-value=1.2e-06  Score=64.96  Aligned_cols=62  Identities=27%  Similarity=0.388  Sum_probs=54.8

Q ss_pred             CCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           31 RKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .++++.++|+.|+.+++..+++.+|+.. ..++.+.+|..|++||+++|..+...|...-..|
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~-~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y   62 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLS-NAEISKKLGERWKLLSEEEKAPYEEKAKKDKERY   62 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            3789999999999999999999998754 7899999999999999999999998887754444

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

Probab=98.05  E-value=3.7e-06  Score=66.87  Aligned_cols=64  Identities=25%  Similarity=0.353  Sum_probs=56.5

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .+++++++++|+.|+.++...++..+|. .-+.++.|++|+.|++|+.++|.++..++...-..|
T Consensus        20 ~~~pkrp~sa~~~f~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y   83 (96)
T KOG0381|consen   20 AQAPKRPLSAFFLFSSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKY   83 (96)
T ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999999 778899999999999999999998877766644444

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

Probab=97.74  E-value=1.9e-05  Score=71.41  Aligned_cols=67  Identities=21%  Similarity=0.239  Sum_probs=61.9

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~   94 (329)
                      .|||+|+|+-++|+-|..+.+.++...+|.. -..+++|.+|++|++|+.+||.++-+.+...+..|-
T Consensus        66 ~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l-~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq  132 (211)
T COG5648          66 KDPNGPKRPLSAYFLYSAENRDEIRKENPKL-TFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQ  132 (211)
T ss_pred             cCCCCCCCchhHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHH
Confidence            5799999999999999999999999999988 678999999999999999999999999888777773

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=97.07  E-value=0.00039  Score=67.63  Aligned_cols=66  Identities=24%  Similarity=0.354  Sum_probs=58.9

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccC
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~   95 (329)
                      .++=||+-|+|+.+..+.+++|-+.+|.. -|-++-|.||..||.|+++||.+|...|++.-..+.+
T Consensus        60 ~~hIKRPMNAFMVWSq~~RRkma~qnP~m-HNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~Hmk  125 (331)
T KOG0527|consen   60 TDRIKRPMNAFMVWSQGQRRKLAKQNPKM-HNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMK  125 (331)
T ss_pred             ccccCCCcchhhhhhHHHHHHHHHhCcch-hhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHH
Confidence            34679999999999999999999999966 5679999999999999999999999999986666654

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

Probab=94.56  E-value=0.02  Score=58.43  Aligned_cols=54  Identities=11%  Similarity=0.291  Sum_probs=48.4

Q ss_pred             eeccCCCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChh
Q 020237           21 VGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPE   77 (329)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~   77 (329)
                      .+.--.-|||.|||+-++|+-++++-+..||+.   ...+.++.|.+|.+|+.||.+
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d---gi~~~dv~kk~g~~wk~ms~k  578 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED---GISVGDVAKKAGEKWKQMSAK  578 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc---CchHHHHHHHHhHHHhhhccc
Confidence            555567799999999999999999999999995   677789999999999999994

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=92.09  E-value=0.11  Score=50.48  Aligned_cols=55  Identities=22%  Similarity=0.368  Sum_probs=44.2

Q ss_pred             cccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhh
Q 020237           33 RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR   88 (329)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~   88 (329)
                      |.+.|+|.-|+.|-++..-+.-. .+-..+++|.+|.+|++||.||-++|-.-|++
T Consensus       193 KKPLNAFmlyMKEmRa~vvaEct-lKeSAaiNqiLGrRWH~LSrEEQAKYyElArK  247 (421)
T KOG3248|consen  193 KKPLNAFMLYMKEMRAKVVAECT-LKESAAINQILGRRWHALSREEQAKYYELARK  247 (421)
T ss_pred             cccHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHH
Confidence            45678998888888777777444 45556999999999999999999988777766

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

Probab=87.08  E-value=0.36  Score=48.93  Aligned_cols=62  Identities=26%  Similarity=0.303  Sum_probs=53.7

Q ss_pred             CcccccchhhhhHHHHHHHHhhCC---CccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCC
Q 020237           32 KRQCRNGFIRYFGEVVRQIKANDG---MACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKA   97 (329)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~   97 (329)
                      -|||-|+|..+-+|=++.|-.+.|   +++|    -|-+|++||+||..||.+|-......|+.+..+-
T Consensus       326 IKRPMNAFMVWAkDERRKILqA~PDMHNSnI----SKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~  390 (511)
T KOG0528|consen  326 IKRPMNAFMVWAKDERRKILQAFPDMHNSNI----SKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKY  390 (511)
T ss_pred             ccCCcchhhcccchhhhhhhhcCccccccch----hHHhcccccccccccccchHHHHHHHHHhhhccC
Confidence            478999999999999999999988   4444    5789999999999999999999999898887754

>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=83.49  E-value=9.4  Score=39.06  Aligned_cols=184  Identities=15%  Similarity=0.190  Sum_probs=105.5

Q ss_pred             CHHHHHHHHHhCCHHHHHHHHHcCccccccccccccchHHHHHHHhc----c---cc--------ccceEEECCeEeeeC
Q 020237          104 APDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEK----I---DI--------ARCILQLNGVEVELS  168 (329)
Q Consensus       104 Sp~~~~~~i~~Ls~~qk~~I~~~GFggLL~i~~~~l~~~L~~wL~er----~---d~--------~t~~~~l~g~~i~iT  168 (329)
                      ++..+..+  .|.++-..+++.+|.+.|..++...-+...+.+|+.-    +   ++        ..-+|.|.+.+..+|
T Consensus        67 ~~etl~~L--Gl~~dV~~lf~~~gL~~f~~~~~~~Y~eet~qFLaTl~v~~~~~~~~~~~e~~glG~l~F~V~~~~y~ls  144 (458)
T PF03078_consen   67 DPETLQKL--GLLEDVEYLFKKCGLGTFMSYPYPTYPEETRQFLATLKVTFYNPSEPRAKELDGLGYLTFFVYGVEYSLS  144 (458)
T ss_pred             CHHHHHHh--ccHHHHHHHHHhcCchhhccCCCCCcHHHHHHhhheeeeeecccccchhhcccCcceEEEEEcceeeeee
Confidence            44555555  7788888999999999999888866554444444321    1   11        234677889999999


Q ss_pred             ccchhhhhcccCCCccccccCChhHHHhHhhhcCCCCCCccHHHHHHHHhhccCCChhHHHHHHHHHhhhhccCCCC-Cc
Q 020237          169 PKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGG-VH  247 (329)
Q Consensus       169 ~~dV~~VLGLP~gG~~v~~~~~~~~~~~l~~~~g~~~~~isi~~L~e~l~~~~~~~d~f~R~FiL~~~~~~L~Ptts-~~  247 (329)
                      -.+...++|.|.+.. +.......+...|....|.+ ..++...-...      ..-+-+.+|+-=+++..|||... ..
T Consensus       145 i~~L~~i~GF~~~~~-i~~~~~~~el~~~W~~ig~~-~p~~~~~~ks~------~Ir~PviRy~hr~iA~tlf~R~~~~~  216 (458)
T PF03078_consen  145 IKHLERIFGFPSGDE-IKPDFDPEELNDFWATIGGG-KPFNSARSKSN------QIRSPVIRYFHRLIANTLFAREETGT  216 (458)
T ss_pred             HHHHHHHhCCCCccc-cCCCCCchHHHHHHHHhcCC-Ccccccccccc------cccChHHHHHHHHHHhhhccccccCc
Confidence            999999999999854 33333445555666666642 11121111111      11222444455556666666654 36


Q ss_pred             ccccccccc-----------ccc----CCCCCccchHHHHHHHHHHHHhhhcc--C---cceeeccHHHH
Q 020237          248 ISSGFLFSL-----------KDV----ESIPKRNWATFCFHRLIQGITRHKEE--Q---VAYVGGCLLYL  297 (329)
Q Consensus       248 Vs~~yl~~l-----------~D~----d~I~~yNW~~~Vld~L~~~i~k~~~~--k---~~~I~GCl~lL  297 (329)
                      |..+-|.++           .|.    .+..+.+-+...++||+..=......  +   .-.+||=+.-+
T Consensus       217 v~~~El~~l~~~L~~~Lr~~~~g~~l~~d~~dt~~~~vl~~hL~~yk~wa~~~~~~~~~~l~vGgviTpI  286 (458)
T PF03078_consen  217 VRNDELEMLDQALKHLLRRTKDGKLLRGDLNDTNVSMVLLDHLCSYKGWAKTNKKKARGSLCVGGVITPI  286 (458)
T ss_pred             eechhHHHHHHHHHHHHHhcCCCccccCcccccchhHHHHHHHHhhhHHHhhcCCCCCceeeecchhhhH
Confidence            665554331           121    12356677777777777552211111  2   34677755443

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.

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

Probab=83.00  E-value=0.95  Score=40.34  Aligned_cols=48  Identities=17%  Similarity=0.372  Sum_probs=35.6

Q ss_pred             ccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhh
Q 020237           36 RNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR   88 (329)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~   88 (329)
                      .++||.|    +++|+++|.+ ....|+-+.+...|..||+.+|..|.+.+-.
T Consensus        83 nnaYLNF----LReFRrkh~~-L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~  130 (183)
T PF06382_consen   83 NNAYLNF----LREFRRKHCG-LSPQDLIQRAARAWCRLSEAEKNRYRRMAPS  130 (183)
T ss_pred             chHHHHH----HHHHHHHccC-CCHHHHHHHHHHHHHhCCHHHHHHHHhhcch
Confidence            3567666    5556666654 5567788888899999999999999775443

The function of this family is unknown.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	329
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-09
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	2e-07
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	2e-06
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	8e-06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-05
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	7e-05
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	1e-05
2lhj_A	97	High mobility group protein homolog NHP1; structur	5e-05
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	6e-05
1ckt_A	71	High mobility group 1 protein; high-mobility group	7e-05
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	8e-05
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	9e-05
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	9e-05
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	9e-05
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-04
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	1e-04
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-04
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	2e-04
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	2e-04
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	2e-04
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-04
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	4e-04
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	5e-04
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	6e-04

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

 Score = 57.2 bits (137), Expect = 4e-09
 Identities = 51/305 (16%), Positives = 97/305 (31%), Gaps = 77/305 (25%)

Query: 8   KRKECD--INRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRK 65
            ++E D  I     V G          +Q      ++  EV+R    N     +   I+ 
Sbjct: 47  SKEEIDHIIMSKDAVSGTLRLFWTLLSKQ-EEMVQKFVEEVLRI---NYKF--LMSPIKT 100

Query: 66  EIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFP-TRCAP-DRLAAAVLQLTDEQRVVV 123
           E     +  P      Y  +  R+       AK+  +R  P  +L  A+L+L   + V++
Sbjct: 101 E-----QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLI 155

Query: 124 REM-GFG-SLLQLN-C--GRLKRNLCG---WLVEKIDIARC------ILQLNGVEVELSP 169
             + G G + + L+ C   +++  +     W    +++  C      +  L  +  ++ P
Sbjct: 156 DGVLGSGKTWVALDVCLSYKVQCKMDFKIFW----LNLKNCNSPETVLEMLQKLLYQIDP 211

Query: 170 KSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADD-QFK 228
              S     SD    ++L   S +  A +      S+     +L  +L       + Q  
Sbjct: 212 NWTSR----SDHSSNIKLRIHSIQ--AELRRLL-KSKPYENCLL--VL------LNVQNA 256

Query: 229 VTFMMFAL-CTIL-----------------CPPGGVHISSGF-------LFSLK---DVE 260
             +  F L C IL                       H S          L         +
Sbjct: 257 KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316

Query: 261 SIPKR 265
            +P+ 
Sbjct: 317 DLPRE 321

>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 Length = 101

 Score = 48.0 bits (114), Expect = 2e-07
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 25 ASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKS 84
          +S   G K+   NG+ ++  E++   + N       KE   EIGS ++ +   +K  YK 
Sbjct: 2  SSGSSGPKKPPMNGYQKFSQELLSNGELNHLPL---KERMVEIGSRWQRISQSQKEHYKK 58

Query: 85 EAKR 88
           A+ 
Sbjct: 59 LAEE 62

>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 = 44.3 bits (105), Expect = 2e-06
 Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 25 ASNDGGRKRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYK 83
           S+     +    G++R+  E   QI+  +  +     EI K +G+ +  L P EK RY 
Sbjct: 1  GSSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP--FPEITKMLGAEWSKLQPAEKQRYL 58

Query: 84 SEAKR 88
           EA++
Sbjct: 59 DEAEK 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 = 43.2 bits (102), Expect = 8e-06
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 3/53 (5%)

Query: 37 NGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
            + R+F E   +    +  M+    ++ K +   YK LP ++K +Y  + +R
Sbjct: 16 TPYFRFFMEKRAKYAKLHPEMS--NLDLTKILSKKYKELPEKKKMKYIQDFQR 66

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 44.7 bits (105), Expect = 1e-05
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 3/65 (4%)

Query: 25 ASNDGGRKRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYK 83
          +S      ++  + ++R+  E +   KA N      T E+ + I   ++ LP  +K  Y+
Sbjct: 3  SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK--TTELIRRIAQRWRELPDSKKKIYQ 60

Query: 84 SEAKR 88
             + 
Sbjct: 61 DAYRA 65

>3tq6_A Transcription factor A, mitochondrial; transcription, transcription regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo sapiens} Length = 214

 Score = 42.4 bits (99), Expect = 7e-05
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 30  GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           G+ ++ R+ +  Y  E  ++ K +       +E  K +   +KNL   EK  Y   AK 
Sbjct: 113 GKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKE 166

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108

 Score = 42.7 bits (100), Expect = 1e-05
 Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 5/57 (8%)

Query: 32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           +   N +  Y  E++  +K        + E        +K L  +EK  Y  +  +
Sbjct: 18 TKPPPNSYSLYCAELMANMKDVP-----STERMVLCSQQWKLLSQKEKDAYHKKCDQ 69

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 32 KRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
          KR   + ++ +  E   +I A N  +A     I K IG+ +  L  EEK  Y+  +  
Sbjct: 24 KR-ALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDE 80

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

 Score = 40.5 bits (95), Expect = 6e-05
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + +  +F +    IK  N        E+ K + S +  L  E+K  YK + + 
Sbjct: 22 VSAYALFFRDTQAAIKGQNPNAT--FGEVSKIVASMWDGLGEEQKQVYKKKTEA 73

>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 Length = 71

 Score = 39.7 bits (93), Expect = 7e-05
 Identities = 8/54 (14%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + +  +      + K  +   +    E  K+    +K +  +EK +++  AK 
Sbjct: 6  MSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKA 59

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 1/54 (1%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + +  +      + K  N  +     E  K+    +K +  +EK ++   AK 
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKA 73

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67

 Score = 39.2 bits (92), Expect = 9e-05
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
          G+ ++ R+ +  Y  E  ++ K +       +E  K +   +KNL   EK  Y   AK 
Sbjct: 1  GKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKE 54

>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 Length = 86

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 3/55 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRV 89
           N F+ Y  E+   + A +      +  I + +G  +  L  EE+ +Y   A++ 
Sbjct: 7  LNAFMLYMKEMRANVVAESTLKE--SAAINQILGRRWHALSREEQAKYYELARKE 59

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238

 Score = 42.1 bits (98), Expect = 9e-05
 Identities = 18/122 (14%), Positives = 40/122 (32%), Gaps = 4/122 (3%)

Query: 28  DGGRKRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEA 86
                ++  + ++R+  E +   KA N      T E+ + I   ++ LP  +K  Y+   
Sbjct: 38  LASCPKKPVSSYLRFSKEQLPIFKAQNPDAK--TTELIRRIAQRWRELPDSKKKIYQDAY 95

Query: 87  KRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGW 146
           +        +     +          L+     + + R+           G+ KR    +
Sbjct: 96  RA-EWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAY 154

Query: 147 LV 148
            V
Sbjct: 155 NV 156

>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group, transcription, LSP1, mitochon transcription-DNA complex; HET: DNA; 2.50A {Homo sapiens} Length = 238

 Score = 41.7 bits (97), Expect = 1e-04
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 30  GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           G+ ++ R+ +  Y  E  ++ K +       +E  K +   +KNL   EK  Y   AK 
Sbjct: 145 GKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKE 198

>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 = 39.2 bits (92), Expect = 1e-04
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 32 KRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
          KR   + F  +  E   +IK  + G++    ++ K++G  + N   ++K  Y+ +A +
Sbjct: 8  KR-PPSAFFLFCSEYRPKIKGEHPGLS--IGDVAKKLGEMWNNTAADDKQPYEKKAAK 62

>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 = 41.1 bits (96), Expect = 1e-04
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 32  KRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           KR   + F  +  E   +IK  + G++    ++ K++G  + N   ++K  Y+ +A +
Sbjct: 103 KR-PPSAFFLFCSEYRPKIKGEHPGLS--IGDVAKKLGEMWNNTAADDKQPYEKKAAK 157

>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* Length = 76

 Score = 38.7 bits (91), Expect = 2e-04
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRV 89
           N FI +  +  R++   N  M     EI K++G  +K L   EK  +  EA+++
Sbjct: 9  MNAFIVWSRDQRRKMALENPRMR--NSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 11/65 (16%), Positives = 26/65 (40%), Gaps = 3/65 (4%)

Query: 25 ASNDGGRKRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYK 83
           S+     ++  +    +  +   Q    N   +   ++   +I   +K L  EEK +Y+
Sbjct: 1  GSSGSSGIKKPMSASALFVQDHRPQFLIENPKTS--LEDATLQIEELWKTLSEEEKLKYE 58

Query: 84 SEAKR 88
           +A +
Sbjct: 59 EKATK 63

>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 = 38.8 bits (91), Expect = 2e-04
 Identities = 12/54 (22%), Positives = 29/54 (53%), Gaps = 3/54 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + ++ +  E    +++ N  +     ++ K++G  +K L PEEK  Y+++A+ 
Sbjct: 25 LSAYMFFANENRDIVRSENPDIT--FGQVGKKLGEKWKALTPEEKQPYEAKAQA 76

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83

 Score = 38.4 bits (90), Expect = 2e-04
 Identities = 10/62 (16%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 28 DGGRKRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEA 86
          D  + R   + +  +      + K  +   +    E  K+    +K +  +EK +++  A
Sbjct: 4  DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63

Query: 87 KR 88
          K 
Sbjct: 64 KA 65

>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 Length = 90

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 8/53 (15%), Positives = 23/53 (43%), Gaps = 3/53 (5%)

Query: 37 NGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
          +    +  E  RQ++     ++    E+ + +   + +L  ++K +YK+    
Sbjct: 26 SAMFIFSEEKRRQLQEERPELS--ESELTRLLARMWNDLSEKKKAKYKAREAA 76

>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 Length = 85

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRV 89
           N FI +  +  R++   N  M     EI K++G  +K L   EK  +  EA+++
Sbjct: 9  MNAFIVWSRDQRRKMALENPRMR--NSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Length = 82

 Score = 37.2 bits (87), Expect = 5e-04
 Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 3/55 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRV 89
           N F+ +       ++  +  +    +   K +   +  L P+EK +Y   AK  
Sbjct: 12 MNAFLLFCKRHRSLVRQEHPRLD--NRGATKILADWWAVLDPKEKQKYTDMAKEY 64

>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 Length = 81

 Score = 37.2 bits (87), Expect = 6e-04
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRV 89
           N F+ +  +  R+I      M      I K +GS +K +   EK  Y  E  R+
Sbjct: 9  MNAFMVWAKDERRKILQAFPDMH--NSNISKILGSRWKAMTNLEKQPYYEEQARL 61

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	329
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	98.78
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	98.77
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	98.73
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	98.68
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	98.68
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	98.66
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	98.64
1wgf_A	90	Upstream binding factor 1; transcription factor, D	98.63
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	98.63
1ckt_A	71	High mobility group 1 protein; high-mobility group	98.61
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	98.6
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	98.6
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	98.59
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	98.57
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	98.56
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	98.55
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	98.53
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	98.53
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	98.49
2lhj_A	97	High mobility group protein homolog NHP1; structur	98.46
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	98.46
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	98.45
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	98.43
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	98.4
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	98.39
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	98.37
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	98.37
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	98.34
2cto_A	93	Novel protein; high mobility group box domain, hel	98.33
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	98.32
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.23
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	98.21
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	98.19
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.17
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.12
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	98.06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	97.84
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	97.73
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.63

>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=98.78  E-value=4.7e-09  Score=80.81  Aligned_cols=62  Identities=21%  Similarity=0.240  Sum_probs=58.0

Q ss_pred             CCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhc
Q 020237           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRV   89 (329)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~   89 (329)
                      ++|.+||+.++|+.|+.+.+.++++.||....+.++.|.+|..|++||++||.+|...|+..
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            46789999999999999999999999998876889999999999999999999999988874

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

Probab=98.77  E-value=2.9e-09  Score=82.45  Aligned_cols=67  Identities=13%  Similarity=0.176  Sum_probs=60.6

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccc-cHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACI-TKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .||+.++||.++|+.|+.+.+.++++.+|...+ ..++.|.+|..|++||++||.+|...|...-..|
T Consensus        11 kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   78 (86)
T 2eqz_A           11 GDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRY   78 (86)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999998875 7899999999999999999999999888744444

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

Probab=98.73  E-value=2.4e-09  Score=82.27  Aligned_cols=67  Identities=16%  Similarity=0.207  Sum_probs=60.5

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccc-cHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACI-TKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .||+.++|+.++|+.|+.+.+.++++.+|...+ ..++.|.+|..|++||++||.+|...|...-..|
T Consensus         3 kdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   70 (83)
T 1aab_A            3 GDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARY   70 (83)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999998875 7899999999999999999999999888754444

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

Probab=98.68  E-value=9.9e-09  Score=80.46  Aligned_cols=67  Identities=15%  Similarity=0.168  Sum_probs=60.6

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +.+++.+||+.++|+.|+.+.+.++++.+|... +.++.|.+|..|++||++||.+|...|...-..|
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y   68 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPKTS-LEDATLQIEELWKTLSEEEKLKYEEKATKDLERY   68 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSC-HHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            567889999999999999999999999999864 6799999999999999999999999888755555

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

Probab=98.68  E-value=8.1e-09  Score=80.96  Aligned_cols=67  Identities=27%  Similarity=0.417  Sum_probs=60.2

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +.||+.++||.++|+.|+.+.+.++++.+|... +.++.|.+|..|++||++||.+|...|...-..|
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y   68 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDLP-FPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQY   68 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCC-HHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            568999999999999999999999999999854 7899999999999999999999998888744444

>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=98.66  E-value=8.7e-09  Score=77.65  Aligned_cols=65  Identities=23%  Similarity=0.314  Sum_probs=56.7

Q ss_pred             CCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |++.++|+.++|+.|..+.+.++++.+|+. .+.++.|.+|..|++||++||.++...|...-..|
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   65 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH   65 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCC-SSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999975 46789999999999999999999999888754444

>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=98.64  E-value=9.4e-09  Score=77.66  Aligned_cols=66  Identities=17%  Similarity=0.316  Sum_probs=59.0

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .||+.++||.++|+.|+.+.+.++++.+|.. .+.++.+.+|..|++||++||.+|...|...-..|
T Consensus         2 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   67 (77)
T 1hme_A            2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY   67 (77)
T ss_dssp             CCSSCCCCCCCTTHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999974 57899999999999999999999999888754444

>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=98.63  E-value=1.7e-08  Score=78.92  Aligned_cols=69  Identities=12%  Similarity=0.227  Sum_probs=62.9

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccC
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~   95 (329)
                      -.|++.++||.++|+.|+.+.+.++++.+|. ..+.++.|.+|..|++||++||.+|...|...-..|..
T Consensus        15 ~kdp~~pKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~   83 (90)
T 1wgf_A           15 KGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER   83 (90)
T ss_dssp             SSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            3588999999999999999999999999998 45789999999999999999999999999987777754

>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=98.63  E-value=1.1e-08  Score=80.40  Aligned_cols=63  Identities=14%  Similarity=0.008  Sum_probs=56.9

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~   94 (329)
                      +.|+||+++|+.|+++|++.|++.+|+  ...++.|.+|..|++||.+||.+|...|...-..|.
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYe   65 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYE   65 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            469999999999999999999999998  679999999999999999999999988887655553

>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=98.61  E-value=1.3e-08  Score=75.68  Aligned_cols=63  Identities=16%  Similarity=0.212  Sum_probs=56.3

Q ss_pred             CCcccccchhhhhHHHHHHHHhhCCCccc-cHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           31 RKRQCRNGFIRYFGEVVRQIKANDGMACI-TKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +||||.++|+.|+.+.+.++++.+|...+ ..++.|.+|..|++||++||.++...|+..-..|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   64 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARY   64 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHH
Confidence            48999999999999999999999998774 6899999999999999999999998887744443

>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=98.60  E-value=2.3e-08  Score=76.54  Aligned_cols=69  Identities=17%  Similarity=0.220  Sum_probs=61.2

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccC
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~   95 (329)
                      +.|++.++|+.++|+.|..+.+.++++.+|.. .+.++.|.+|..|++||++||.+|...|...-..|..
T Consensus         2 ~~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~   70 (82)
T 1wz6_A            2 SSGSSGARRPMNAFLLFCKRHRSLVRQEHPRL-DNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMK   70 (82)
T ss_dssp             CSSCCCSCCCCCHHHHHHHHHHHHHHHHCSSS-CTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHH
Confidence            45688999999999999999999999999974 5679999999999999999999999998886666643

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

Probab=98.60  E-value=1.1e-08  Score=75.95  Aligned_cols=63  Identities=22%  Similarity=0.348  Sum_probs=54.0

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |+++||.++|+.|..+++.++++.+|... ..++.|.+|..|++||++||.+|...|...-..|
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   63 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQH   63 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999876 7899999999999999999999999888755554

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

Probab=98.59  E-value=2.5e-08  Score=79.74  Aligned_cols=66  Identities=21%  Similarity=0.301  Sum_probs=59.6

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .|++.++||.++|+.|+.+.+.++++.+|.. .+.++.|.+|..|++||++||.+|...|...-..|
T Consensus        13 kdp~~pKrP~say~lF~~~~r~~i~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y   78 (102)
T 2co9_A           13 KDPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEY   78 (102)
T ss_dssp             CCCCSCCCCCCHHHHTHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999986 47899999999999999999999999888754444

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

Probab=98.57  E-value=1.4e-08  Score=74.86  Aligned_cols=59  Identities=25%  Similarity=0.358  Sum_probs=53.1

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |+||||.++|+.|+.+.+.++++.+|     .++.|.+|..|++||++||.+|...|...-..|
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y   59 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRY   59 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHH
Confidence            67999999999999999999998877     599999999999999999999998888754444

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

Probab=98.56  E-value=1.7e-08  Score=80.32  Aligned_cols=65  Identities=17%  Similarity=0.273  Sum_probs=59.4

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKS   92 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~   92 (329)
                      .|++.++||.++|+.|+.+.+.++++.+|+. .+.++.|.+|..|++||++||.+|...|...-..
T Consensus         6 kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~   70 (99)
T 1k99_A            6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQREKQE   70 (99)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence            5788999999999999999999999999986 4789999999999999999999999988875555

>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=98.55  E-value=1.9e-08  Score=77.98  Aligned_cols=66  Identities=17%  Similarity=0.214  Sum_probs=58.7

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccc
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKS   92 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~   92 (329)
                      ..|++.++||.++||.|+.+.+.++++.+|.. .+.++.|.+|..|++||++||.+|...|...-..
T Consensus        12 ~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~   77 (87)
T 2e6o_A           12 ATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGK-DNRAISVILGDRWKKMKNEERRMYTLEAKALAEE   77 (87)
T ss_dssp             CCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999974 5779999999999999999999999988774433

>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=98.53  E-value=4.3e-08  Score=74.81  Aligned_cols=65  Identities=23%  Similarity=0.279  Sum_probs=56.8

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccccc
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~   94 (329)
                      ++.++||.++|+.|..+.+.++++.+|+.. +.++.|.+|..|++||++||.+|...|...-..|.
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~   66 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHL   66 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCC-HHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHH
Confidence            467999999999999999999999999764 78999999999999999999999888777555543

>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=98.53  E-value=4.9e-08  Score=75.32  Aligned_cols=64  Identities=23%  Similarity=0.334  Sum_probs=57.8

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |+.++||.++|+.|+.+.+.++++.+|+. .+.++.|.+|..|++||++||.+|...|...-..|
T Consensus         2 p~~pKRP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y   65 (85)
T 1j46_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH   65 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
Confidence            68899999999999999999999999975 57799999999999999999999999888755444

>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=98.49  E-value=3.6e-08  Score=75.49  Aligned_cols=65  Identities=22%  Similarity=0.303  Sum_probs=55.9

Q ss_pred             CCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .++.++||+++||.|..+.+.++++.+|+.. ..++.|.+|..|++||++||.+|...|...-..|
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   67 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQH   67 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999866 7899999999999999999999999888755554

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

Probab=98.46  E-value=3.1e-08  Score=78.34  Aligned_cols=68  Identities=19%  Similarity=0.220  Sum_probs=59.7

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCcc-ccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMAC-ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      -.|++.++||.++|+.|+.+.+.++++.+|... .+.++.|.+|..|++||++||.+|...|...-..|
T Consensus        17 ~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y   85 (97)
T 2lhj_A           17 KKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRY   85 (97)
T ss_dssp             TSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999764 47899999999999999999999988887744444

>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=98.46  E-value=9.1e-08  Score=72.76  Aligned_cols=63  Identities=25%  Similarity=0.349  Sum_probs=56.2

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +.++||.++|+.|..+.+.++++.+|.. .+.++.+.+|..|++||++||.+|...|...-..|
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y   63 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALH   63 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999975 47899999999999999999999999888754444

>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=98.45  E-value=9.8e-08  Score=73.70  Aligned_cols=63  Identities=19%  Similarity=0.329  Sum_probs=56.6

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |.++||.++|+.|+.+.+.++++.+|+. .+.++.+.+|..|++||++||.+|...|...-..|
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y   63 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKERQLH   63 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999985 57899999999999999999999998888754444

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

Probab=98.43  E-value=1.2e-07  Score=76.37  Aligned_cols=73  Identities=18%  Similarity=0.246  Sum_probs=57.9

Q ss_pred             eeccCCCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccccc
Q 020237           21 VGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (329)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~   94 (329)
                      +.....-|++.++||+++|+.|..+.++++++.+|... +.++.|.+|..|++||++||.+|...|...-..|.
T Consensus        19 ~~~~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   91 (106)
T 4euw_A           19 LYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLH-NAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHK   91 (106)
T ss_dssp             ---------CCCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            33445667899999999999999999999999999754 57999999999999999999999998887655553

>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=98.40  E-value=2.1e-08  Score=78.74  Aligned_cols=67  Identities=19%  Similarity=0.339  Sum_probs=60.0

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      -.|++.++||.++|+.|+.+.+.++++.+|... +.++.|.+|..|++||++||.+|...|...-..|
T Consensus        15 ~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~-~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y   81 (93)
T 1cg7_A           15 KKDPNAPKRALSAYMFFANENRDIVRSENPDIT-FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRY   81 (93)
T ss_dssp             CCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSC-HHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            357889999999999999999999999999865 7899999999999999999999999888755555

>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=98.39  E-value=9.7e-08  Score=72.29  Aligned_cols=63  Identities=24%  Similarity=0.316  Sum_probs=56.4

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |..+||+++|+.|..+.+.++++.+|+.. +.++.|.+|..|++||++||.+|...|...-..|
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   63 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMH-NAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKH   63 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999764 6799999999999999999999999888755444

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

Probab=98.37  E-value=1.5e-07  Score=70.46  Aligned_cols=63  Identities=17%  Similarity=0.304  Sum_probs=56.0

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccccc
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~   94 (329)
                      ||.++||.++|+.|+.+.+.++++.+|... +.++.|.+|..|++|  +||.+|...|...-..|.
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~   63 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYH   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCC-HHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHH
Confidence            688999999999999999999999999854 689999999999999  889999988887555553

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

Probab=98.37  E-value=4.1e-07  Score=72.61  Aligned_cols=83  Identities=25%  Similarity=0.344  Sum_probs=65.5

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCcc--ccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCCCcccccC
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMAC--ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCA  104 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~~l~tRcS  104 (329)
                      -.++.+|||.++|+.|+.+++.     +|+..  ...++.|.+|..|++||++||.+|...|...-..|.          
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~-----~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~----------   68 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS-----NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK----------   68 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH-----HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH----------
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh-----CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH----------
Confidence            3456799999999999999753     55543  357999999999999999999999999988666663          


Q ss_pred             HHHHHHHHHhCCHHHHHHHHH
Q 020237          105 PDRLAAAVLQLTDEQRVVVRE  125 (329)
Q Consensus       105 p~~~~~~i~~Ls~~qk~~I~~  125 (329)
                       ..+......++++++..+.+
T Consensus        69 -~e~~~Y~~~~~~~~~~~~~~   88 (101)
T 1v63_A           69 -VHLDLWVKSLSPQDRAAYKE   88 (101)
T ss_dssp             -HHHHHHHHHSCTTHHHHHHH
T ss_pred             -HHHHHHHhhCCHHHHHHHHH
Confidence             34455567888888876654

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

Probab=98.34  E-value=2.8e-07  Score=74.47  Aligned_cols=81  Identities=21%  Similarity=0.230  Sum_probs=67.9

Q ss_pred             CCCCCC-cccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCCCcccccCH
Q 020237           27 NDGGRK-RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAP  105 (329)
Q Consensus        27 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~~l~tRcSp  105 (329)
                      .|+|+| |||.++|+.|+.+.+.+++     ...+.++.|.+|..|++||++||.+|...|...-..|.           
T Consensus        12 kd~~~P~KrP~say~lF~~e~r~~~k-----~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~-----------   75 (108)
T 1v64_A           12 KFDGRPTKPPPNSYSLYCAELMANMK-----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYE-----------   75 (108)
T ss_dssp             CTTTSCCCCCSSHHHHHHHHHHHHCT-----TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH-----------
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHh-----CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH-----------
Confidence            478889 9999999999999999988     35678999999999999999999999999988666663           


Q ss_pred             HHHHHHHHhCCHHHHHHH
Q 020237          106 DRLAAAVLQLTDEQRVVV  123 (329)
Q Consensus       106 ~~~~~~i~~Ls~~qk~~I  123 (329)
                      ..+......+++++++.+
T Consensus        76 ~e~~~Y~~~~~~~~r~~~   93 (108)
T 1v64_A           76 VELLRFLESLPEEEQQRV   93 (108)
T ss_dssp             HHHHHHHHHSCHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHH
Confidence            344555568888888765

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

Probab=98.33  E-value=7.1e-08  Score=76.12  Aligned_cols=67  Identities=18%  Similarity=0.263  Sum_probs=59.0

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHh---cCCCCCCChhhhhhhhhhhhhccccccC
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEI---GSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~---~~~~~sls~~ek~~~~~~~~~~~~~~~~   95 (329)
                      +.+++++||++++|+.|+.++++++++.   ...+.++.|.+   |..|++||++||.+|...|...-..|.+
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e---~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~k   74 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR---GLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGK   74 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH---TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhc
Confidence            5677899999999999999999999987   45678899999   9999999999999999998876666655

>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=98.32  E-value=1.5e-07  Score=70.39  Aligned_cols=61  Identities=11%  Similarity=0.241  Sum_probs=54.0

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +.||||+++|+.|+.+.+.++++.+|+.. +.++.|.+|..|++||+  |.+|...|...-..|
T Consensus         2 ~~PKrP~say~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y   62 (73)
T 3nm9_A            2 DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDY   62 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSSCC-HHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHH
Confidence            57999999999999999999999999875 68999999999999997  888888887754444

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

Probab=98.23  E-value=4.1e-07  Score=79.00  Aligned_cols=67  Identities=16%  Similarity=0.182  Sum_probs=60.2

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCc-cccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMA-CITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .|++.++|+.++|+.|+.+.+.++++.+|.. ..+.++.|.+|..|++||++||.+|...|...-..|
T Consensus        11 ~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y   78 (173)
T 2yrq_A           11 GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARY   78 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999987 468899999999999999999999998887744444

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

Probab=98.21  E-value=4.4e-07  Score=77.62  Aligned_cols=66  Identities=17%  Similarity=0.316  Sum_probs=58.9

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .|++.++||+++|+.|+.+.+.++++.+|+. .+.++.|.+|..|++||++||.+|...|...-..|
T Consensus        84 kdp~~pKrp~say~lf~~~~r~~~~~~~p~~-~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y  149 (159)
T 2gzk_A           84 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY  149 (159)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHHHHCSCC-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhhHhhHHHHHHhCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999984 57899999999999999999999998887744444

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

Probab=98.19  E-value=6.6e-07  Score=80.65  Aligned_cols=85  Identities=20%  Similarity=0.219  Sum_probs=71.2

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCCCcccccCH
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAP  105 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~~l~tRcSp  105 (329)
                      +.+++.++||.++|+.|+.+.+.++++.+|+.. +.++.|.+|..|++||++||.+|...|+..-..|.           
T Consensus         4 ~~~p~~PKrP~say~lF~~~~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~-----------   71 (214)
T 3tq6_A            4 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK-----------   71 (214)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH-----------
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHH-----------
Confidence            445778999999999999999999999999877 89999999999999999999999998888555553           


Q ss_pred             HHHHHHHHhCCHHHHHH
Q 020237          106 DRLAAAVLQLTDEQRVV  122 (329)
Q Consensus       106 ~~~~~~i~~Ls~~qk~~  122 (329)
                      ..+......++|.|+..
T Consensus        72 ~e~~~y~~~~tp~q~~~   88 (214)
T 3tq6_A           72 EEISRFKEQLTPSQIMS   88 (214)
T ss_dssp             HHHHHHHHHCCHHHHHH
T ss_pred             HHhhhhcccCCHHHHHH
Confidence            34455666778877543

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

Probab=98.17  E-value=8.8e-07  Score=81.05  Aligned_cols=84  Identities=20%  Similarity=0.226  Sum_probs=71.1

Q ss_pred             CCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCCCcccccCH
Q 020237           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAP  105 (329)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~~l~tRcSp  105 (329)
                      +.|++.++|+.++|+.|+.+.++++++.+|+.. +.++.|.+|..|++||++||.+|...|+.....|.           
T Consensus        36 ~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~-----------  103 (238)
T 3tmm_A           36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK-----------  103 (238)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH-----------
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH-----------
Confidence            456778999999999999999999999999887 79999999999999999999999999888555553           


Q ss_pred             HHHHHHHHhCCHHHHH
Q 020237          106 DRLAAAVLQLTDEQRV  121 (329)
Q Consensus       106 ~~~~~~i~~Ls~~qk~  121 (329)
                      ..+......++|.|+.
T Consensus       104 ~e~~~y~~~~~p~~~~  119 (238)
T 3tmm_A          104 EEISRFKEQLTPSQIM  119 (238)
T ss_dssp             HHHHHHHHHCCHHHHH
T ss_pred             HHHHHHHhcCCHHHHH
Confidence            3455566677887743

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

Probab=98.12  E-value=8.4e-07  Score=77.03  Aligned_cols=66  Identities=17%  Similarity=0.315  Sum_probs=59.0

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .|++.++||+++|+.|+.+.+.++++.+|. ..+.++.|.+|..|++||++||.+|...|...-..|
T Consensus        97 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y  162 (173)
T 2yrq_A           97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY  162 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHH
T ss_pred             cCCccccCcccHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999998 457899999999999999999999998887754444

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

Probab=98.06  E-value=1.6e-07  Score=73.69  Aligned_cols=62  Identities=11%  Similarity=0.089  Sum_probs=51.9

Q ss_pred             CCCCCcccccchhhhhHHHHHHHHhhCCCcc-ccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMAC-ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      ||+.|+|++++||.|.+++++++++.||+.. .+.++.    ..|++||++||.+|..+|...-..|
T Consensus        19 DpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h   81 (90)
T 2yuk_A           19 EEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAAL   81 (90)
T ss_dssp             HHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            6788999999999999999999999999754 234444    9999999999999998887744333

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

Probab=97.84  E-value=1.2e-06  Score=78.81  Aligned_cols=62  Identities=24%  Similarity=0.285  Sum_probs=54.9

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .|+|.|+||+++|+.|+.+.+.++++.+|.     ++.|.+|..|++||++||.+|...|...-..|
T Consensus       110 kdp~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y  171 (214)
T 3tq6_A          110 TLLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRY  171 (214)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSSCSSHH-----HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCcccccchhhhhHHHHHHhhccCCHH-----HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence            368899999999999999999999887764     89999999999999999999999888855555

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

Probab=97.73  E-value=2.1e-06  Score=78.55  Aligned_cols=62  Identities=24%  Similarity=0.285  Sum_probs=55.1

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .|+|.++||+++|+.|+.|.+.++++.+|.     ++.|.+|..|++||++||.+|...|...-..|
T Consensus       142 kdp~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y  203 (238)
T 3tmm_A          142 TLLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRY  203 (238)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSCCSSHH-----HHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCcHHHHHHHHHHHHHhccCHH-----HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            368899999999999999999999887765     89999999999999999999999888855555

>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=97.63  E-value=1.9e-05  Score=67.36  Aligned_cols=63  Identities=24%  Similarity=0.335  Sum_probs=55.9

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccc
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKS   92 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~   92 (329)
                      +++++|+.++||.|..+.+.++++.+|. ..+.++.|.+|..|++||++||.+|...|...-..
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~   64 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM   64 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSS-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHH
Confidence            5689999999999999999999999998 56789999999999999999999998887764333

---

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	329
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-08
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-07
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	2e-06
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-06
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	8e-06
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	9e-06
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	1e-05
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-05
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	3e-05
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	1e-04
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-04

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101

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]

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 3/63 (4%)

Query: 26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSE 85
          S   G K+   NG+ ++  E++   + N       KE   EIGS ++ +   +K  YK  
Sbjct: 3  SGSSGPKKPPMNGYQKFSQELLSNGELNH---LPLKERMVEIGSRWQRISQSQKEHYKKL 59

Query: 86 AKR 88
          A+ 
Sbjct: 60 AEE 62

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108

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]

 Score = 45.7 bits (108), Expect = 4e-07
 Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 5/61 (8%)

Query: 28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAK 87
          DG   +   N +  Y  E++  +K        + E        +K L  +EK  Y  +  
Sbjct: 14 DGRPTKPPPNSYSLYCAELMANMKD-----VPSTERMVLCSQQWKLLSQKEKDAYHKKCD 68

Query: 88 R 88
          +
Sbjct: 69 Q 69

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
          KR   N FI +  +  R++   +       EI K++G  +K L   EK  +  EA++
Sbjct: 6  KR-PMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQK 60

>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 = 42.1 bits (99), Expect = 3e-06
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 32 KRQCRNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
          KR   + F  +  E   +IK  + G++    ++ K++G  + N   ++K  Y+ +A +
Sbjct: 4  KR-PPSAFFLFCSEYRPKIKGEHPGLSI--GDVAKKLGEMWNNTAADDKQPYEKKAAK 58

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

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]

 Score = 41.4 bits (97), Expect = 8e-06
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 36 RNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           N F+ Y  E+   + A   +      I + +G  +  L  EE+ +Y   A++
Sbjct: 7  LNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARK 58

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

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]

 Score = 40.6 bits (95), Expect = 9e-06
 Identities = 8/54 (14%), Positives = 21/54 (38%), Gaps = 1/54 (1%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + +  +      + K  +   +    E  K+    +K +  +EK +++  AK 
Sbjct: 6  MSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKA 59

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70

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

 Score = 40.6 bits (95), Expect = 1e-05
 Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
          KR   N F+ +  +  R+I            I K +GS +K +   EK  Y  E  R
Sbjct: 4  KR-PMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQAR 58

>d1wgfa_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 90

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]

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 7/64 (10%), Positives = 23/64 (35%), Gaps = 1/64 (1%)

Query: 25 ASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKS 84
                + ++  +    +  E  R+    +       E+ + +   + +L  ++K +YK+
Sbjct: 14 GKGGSEKPKRPVSAMFIFSEEK-RRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKA 72

Query: 85 EAKR 88
              
Sbjct: 73 REAA 76

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

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

 Score = 39.4 bits (92), Expect = 3e-05
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 36 RNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           N F+ +     R++   +       EI K +G+ +K L   EK  +  EAKR
Sbjct: 7  MNAFMVWSRGQRRKMAQENPKMH-NSEISKRLGAEWKLLSETEKRPFIDEAKR 58

>d1lwma_ a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 93

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

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEA 86
           D    ++  + ++ +  E    +++ +       ++ K++G  +K L PEEK  Y+++A
Sbjct: 16 KDPNAPKRALSAYMFFANENRDIVRSENPDITF-GQVGKKLGEKWKALTPEEKQPYEAKA 74

Query: 87 KR 88
          + 
Sbjct: 75 QA 76

>d1k99a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]} Length = 91

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]

 Score = 38.0 bits (88), Expect = 1e-04
 Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAK 87
               ++    + R+F E   +            ++ K +   YK LP ++K +Y  + +
Sbjct: 7  HPDFPKKPLTPYFRFFMEKRAKYAKLHPE-MSNLDLTKILSKKYKELPEKKKMKYIQDFQ 65

Query: 88 R 88
          R
Sbjct: 66 R 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	329
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	98.67
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.61
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	98.6
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	98.57
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	98.44
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	98.43
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	98.39
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	98.39
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.35
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	98.28
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	98.13
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	98.1

>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=98.67  E-value=3.5e-09  Score=77.29  Aligned_cols=63  Identities=16%  Similarity=0.212  Sum_probs=56.6

Q ss_pred             CCcccccchhhhhHHHHHHHHhhCCCccc-cHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           31 RKRQCRNGFIRYFGEVVRQIKANDGMACI-TKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +|+||+++|+.|+.+.+.++++.+|...+ ..++.|.+|..|++||++||.++...|+....+|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y   64 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARY   64 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence            48999999999999999999999997665 4799999999999999999999999998865555

>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=98.61  E-value=1.4e-08  Score=77.37  Aligned_cols=73  Identities=12%  Similarity=0.241  Sum_probs=64.8

Q ss_pred             CCCCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCCC
Q 020237           25 ASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAK   98 (329)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~~   98 (329)
                      ...|+++++||+++|+.|+.+.+.++++.+|+.. ..++.+.++..|++||++||.+|...|...-.+|..+..
T Consensus        14 ~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~-~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~~~   86 (90)
T d1wgfa_          14 GKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             CSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3457788999999999999999999999999765 578999999999999999999999999998888876544

>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=98.60  E-value=8.7e-09  Score=79.20  Aligned_cols=66  Identities=20%  Similarity=0.343  Sum_probs=59.7

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      .|++.+++|+++|+.|+.+.+.++++.+|+. ...++.+.+|..|++||++||..|...|.....+|
T Consensus        16 k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~-~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y   81 (93)
T d1lwma_          16 KDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRY   81 (93)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCcCCCCCCCCHHHHHHHHHHHHHHHhCCCC-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            4677899999999999999999999999985 56799999999999999999999999998866555

>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=98.57  E-value=7.1e-09  Score=77.20  Aligned_cols=63  Identities=16%  Similarity=0.321  Sum_probs=56.6

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      |.||||+++|+.|+.+.+.++++.+|... ..++.|.+|..|++||++||..+.+.|......|
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~-~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y   63 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLS-IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY   63 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCC-TTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999854 5789999999999999999999999988755555

>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=98.44  E-value=5e-08  Score=73.60  Aligned_cols=63  Identities=24%  Similarity=0.345  Sum_probs=56.8

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      ++.+||+|+||.|+.+.+.++++.+|.. ...++.|.+|..|++||++||.+|...|...-..|
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~-~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y   65 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMH   65 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999975 46789999999999999999999999888755554

>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=98.43  E-value=5.7e-08  Score=72.62  Aligned_cols=64  Identities=25%  Similarity=0.357  Sum_probs=56.6

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhcccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~   94 (329)
                      ++.+||+|+||.|+.+.++++++.+|.. ...++.|.+|..|++||++||..+...|...-..|.
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~-~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~   64 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHM   64 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999975 567899999999999999999999998887555553

>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=98.39  E-value=6.2e-08  Score=70.45  Aligned_cols=61  Identities=25%  Similarity=0.280  Sum_probs=54.3

Q ss_pred             CcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      -+||.|+|+.|+.+.+.++++.+|.. ...++.|.+|..|++||++||.+|...|...-..|
T Consensus         3 iKRP~nay~lf~~~~r~~i~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~   63 (70)
T d1i11a_           3 IKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQH   63 (70)
T ss_dssp             SCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999964 46789999999999999999999999998755554

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

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

Probab=98.39  E-value=1.4e-07  Score=72.97  Aligned_cols=80  Identities=25%  Similarity=0.299  Sum_probs=65.1

Q ss_pred             CCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCCCcccccCHHHH
Q 020237           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRL  108 (329)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~~l~tRcSp~~~  108 (329)
                      .|.+|+|.++|+.|+.|.+..++..++   ...++.|.+|..|++||++||.+|...|.....+|.           ..+
T Consensus         6 ~~p~KrP~~ay~~F~~e~r~~~~~~~~---~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~-----------~e~   71 (101)
T d1v63a_           6 SGPKKPPMNGYQKFSQELLSNGELNHL---PLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK-----------VHL   71 (101)
T ss_dssp             CSSCCCCSSSHHHHHHHHHHHCTTTTS---CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH-----------HHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHhcCC---CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH-----------HHH
Confidence            346899999999999999999987775   467999999999999999999999999999777763           234


Q ss_pred             HHHHHhCCHHHHHH
Q 020237          109 AAAVLQLTDEQRVV  122 (329)
Q Consensus       109 ~~~i~~Ls~~qk~~  122 (329)
                      ......+++.++..
T Consensus        72 ~~y~~~~~~~~~~~   85 (101)
T d1v63a_          72 DLWVKSLSPQDRAA   85 (101)
T ss_dssp             HHHHHHSCTTHHHH
T ss_pred             HHHHhcCCHHHHHH
Confidence            45556677766553

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

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

Probab=98.35  E-value=5.8e-08  Score=73.96  Aligned_cols=66  Identities=17%  Similarity=0.262  Sum_probs=59.7

Q ss_pred             CCCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      -||+.|++|.++|+.|+.+.+..+++.+|... ..++.+.+|..|++||++||..+...|......|
T Consensus         6 k~p~~PKrP~say~lf~~~~r~~~~~~~p~~~-~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y   71 (91)
T d1k99a_           6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMS-NLDLTKILSKKYKELPEKKKMKYIQDFQREKQEF   71 (91)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSC-SHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999754 7899999999999999999999999998866555

>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=98.28  E-value=2.6e-07  Score=69.71  Aligned_cols=60  Identities=20%  Similarity=0.373  Sum_probs=53.1

Q ss_pred             cccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           33 RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      +||.|+||.|+.+.+.++++.+|.. ...++.+.+|..|++||++||.+|...|...-..|
T Consensus         4 kRP~naf~lF~~~~r~~~~~~~P~~-~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~   63 (86)
T d2lefa_           4 KKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKERQLH   63 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999975 56689999999999999999999998887754433

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

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

Probab=98.13  E-value=6.7e-07  Score=70.11  Aligned_cols=81  Identities=21%  Similarity=0.231  Sum_probs=65.2

Q ss_pred             CCCCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccccCCCCcccccCHHH
Q 020237           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDR  107 (329)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~~~k~~l~tRcSp~~  107 (329)
                      |+..+|+|.++|+.|+.|++.+++.     ...+++.+++|..|++||++||.+|...|......|.           ..
T Consensus        14 ~~~p~K~P~~ay~lF~~~~r~~~~~-----~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~-----------~~   77 (108)
T d1v64a_          14 DGRPTKPPPNSYSLYCAELMANMKD-----VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYE-----------VE   77 (108)
T ss_dssp             TTSCCCCCSSHHHHHHHHHHHHCTT-----SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH-----------HH
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHccC-----CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHH-----------HH
Confidence            4455788899999999998877654     4557999999999999999999999999999777773           24


Q ss_pred             HHHHHHhCCHHHHHHHH
Q 020237          108 LAAAVLQLTDEQRVVVR  124 (329)
Q Consensus       108 ~~~~i~~Ls~~qk~~I~  124 (329)
                      +......+++++++.+.
T Consensus        78 ~~~y~~~~~~~~k~~~~   94 (108)
T d1v64a_          78 LLRFLESLPEEEQQRVL   94 (108)
T ss_dssp             HHHHHHHSCHHHHHHHH
T ss_pred             HHHHHhhCCHHHHHHHH
Confidence            45556788888876553

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

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

Probab=98.10  E-value=3.9e-07  Score=66.51  Aligned_cols=61  Identities=11%  Similarity=0.281  Sum_probs=51.1

Q ss_pred             CCCcccccchhhhhHHHHHHHHhhCCCccccHHHHHHhcCCCCCCChhhhhhhhhhhhhccccc
Q 020237           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (329)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sls~~ek~~~~~~~~~~~~~~   93 (329)
                      ++||||+++|+.|+.+.+.++++.+|+. ...++.|.+|..|++|+  ||.++...|...-..|
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~~-~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y   62 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPGI-KVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDY   62 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTTC-CHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHH
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999975 46799999999999986  4777777776644433