Citrus Sinensis ID: 019122

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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-------330-------340------
Protein Sequence
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDSKGGFDSHQVI
Secondary Structure (PSIPRED)
cccccccccccccccccccEEcccccccccccccccccccccccHHHHHHHcccccccHHHHHHHHHHccccccccHHHHHHHHHHccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHccccccccccccccHHHHHHHHHcccccccEEEEccEEEEcccccccEEEcccccccccccccccHHHHHHHHcccccccccHHHHHHHHHHHcccccHHHHHHHHHHHHcEEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHccccccccccccccccccHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEccccccccccccccEEEEEEcccccccccccccHHEEEcHHHHHHHccccccccHHHHHHHHHHHHHccccHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHccccHHccccccccHHHHHHHHHHccccccEEEEccEEEEccHHHHHHHccccccccEcccccccHHHHHHHHHHcccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccccccccHHHcHHHccHHHHHHccHHHHHHHHHHHHHHHHHHccccccccHHHHHEHHHHHHccccccccccccccEEEEcHHHHHHHHHHHHccccccccEEc
Coil and Loop (DISEMBL)
mkvvgtnkrkecdinrgtevvgvdasndggrkrqcrNGFIRYFGEVVRQIKANDGMACITKEIRKEIGstyknlppeekcrykseakrvgkskigkakfptrcapDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLngvevelspkSFSYVMgisdggkplqlegessevcayvdnftptsrgiNITVLAGILQKLKSADDQFKVTFMMFALCTilcppggvhissgflfslkdvesipkrnwaTFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVygklerdrsmcplALWNVNEIKKLMKWIdskggfdshqvi
Flexible Loop (DISEMBL)
mkvvgtnkrkecdinrgtevvgvdasndggrkrqcrNGFIRYFGEVVRQIKANDGMACITKEIRkeigstyknlppeekcrykseakrvgkskigkakfptrcapDRLAAAVLQLTDEQRVVVREMGfgsllqlncgRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDskggfdshqvi
Low Complexity Region (SEG)
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDSKGGFDSHQVI
Disordered region (IsUnstruct)
*******************VV***********RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTY**************************KFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLE*ESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDS**********
Disordered Region (DISOPRED)
****************************************************************************************************TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDSKGGFD*HQVI
Disordered Region (DISEMBL)
********RKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDSKGGFDSHQVI
Disordered Region (DISPRO)
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLP**E*********************PTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDSKGGFDS**VI
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKVVGTNKRKECDINRGTEVVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIKKLMKWIDSKGGFDSHQVI
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	346
296087190	766	unnamed protein product [Vitis vinifera]	0.869	0.392	0.319	2e-40
147783848	708	hypothetical protein VITISV_032233 [Viti	0.861	0.420	0.317	3e-40
255583781	421	conserved hypothetical protein [Ricinus	0.887	0.729	0.309	3e-40
225453104	617	PREDICTED: uncharacterized protein LOC10	0.861	0.482	0.317	3e-40
224077245	628	predicted protein [Populus trichocarpa]	0.887	0.488	0.311	3e-40
147795729	849	hypothetical protein VITISV_004916 [Viti	0.780	0.318	0.275	2e-30
356533899	590	PREDICTED: uncharacterized protein LOC10	0.696	0.408	0.312	7e-30
147772140	637	hypothetical protein VITISV_026046 [Viti	0.708	0.384	0.284	2e-26
147773967	535	hypothetical protein VITISV_035313 [Viti	0.679	0.439	0.293	1e-23
147820300	895	hypothetical protein VITISV_040636 [Viti	0.783	0.302	0.249	2e-23

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

 Score =  172 bits (436), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 103/322 (31%), Positives = 172/322 (53%), Gaps = 21/322 (6%)

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 FCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCP-----LALWNV 324
           F   RL++ ++R  + +   VGGCLL+LQ+ Y+ ++    +ER  S+ P     L+ W  
Sbjct: 408 FLLDRLVREVSRFHQGKQRAVGGCLLFLQLFYYETV---SVERPGSLVPGLGPCLSSWGE 464

Query: 325 NEIKKLMKWIDSKGGFDSHQVI 346
            EI +  K     GG+   +V+
Sbjct: 465 EEITEREKRERELGGYGFGEVL 486

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 =  172 bits (435), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 101/318 (31%), Positives = 170/318 (53%), Gaps = 20/318 (6%)

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 RLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCP-----LALWNVNEIK 328
           RL++ ++R  + +   VGGCLL+LQ+ Y+ ++    +ER  S+ P     L+ W   EI 
Sbjct: 328 RLVREVSRFHQGKQRAVGGCLLFLQLFYYETV---SVERPGSLVPGLGPCLSSWGEEEIT 384

Query: 329 KLMKWIDSKGGFDSHQVI 346
           +  K     GG+   +V+
Sbjct: 385 EREKRERELGGYGFGEVL 402

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 =  172 bits (435), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 100/323 (30%), Positives = 173/323 (53%), Gaps = 16/323 (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 ATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVY---GKLERDRSMCP-LALWN 323
             F   RL++ + R ++ +   VGGCLL+LQ+ Y+ ++     G LE D +  P L+ W 
Sbjct: 280 GKFLLDRLVREVARFRQGKQRAVGGCLLFLQLFYYETVSVEGPGSLEPDPASLPCLSSWG 339

Query: 324 VNEIKKLMKWIDSKGGFDSHQVI 346
             EI +  K     GG+   +V+
Sbjct: 340 EEEITEREKRERELGGYGFGEVM 362

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  172 bits (435), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 101/318 (31%), Positives = 170/318 (53%), Gaps = 20/318 (6%)

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 RLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCP-----LALWNVNEIK 328
           RL++ ++R  + +   VGGCLL+LQ+ Y+ ++    +ER  S+ P     L+ W   EI 
Sbjct: 274 RLVREVSRFHQGKQRAVGGCLLFLQLFYYETV---SVERPGSLVPGLGPCLSSWGEEEIT 330

Query: 329 KLMKWIDSKGGFDSHQVI 346
           +  K     GG+   +V+
Sbjct: 331 EREKRERELGGYGFGEVL 348

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  172 bits (435), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 100/321 (31%), Positives = 172/321 (53%), Gaps = 14/321 (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 ATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSI-VYGKLERDRSMCP-LALWNVN 325
             F   RL++ ++R  + +   VGGCLL+LQ+ Y+ SI V G    + S+ P L+ W   
Sbjct: 286 GKFLLDRLVREVSRFHQGKQRAVGGCLLFLQLFYYESISVEGSHSSNSSVVPCLSSWGEE 345

Query: 326 EIKKLMKWIDSKGGFDSHQVI 346
           EI +  K     GG+   +VI
Sbjct: 346 EISEREKRQRELGGYGFGEVI 366

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  139 bits (351), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 76/276 (27%), Positives = 138/276 (50%), Gaps = 6/276 (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 FHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVY 307
              L+ GI   K++Q + V GCLL+L + Y   I +
Sbjct: 431 LSYLVHGIEEFKKKQQSGVCGCLLFLMLFYHEHISF 466

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  137 bits (345), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 79/253 (31%), Positives = 133/253 (52%), Gaps = 12/253 (4%)

Query: 38  GFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRV--GKSKIG 95
            ++ +  E +++  A+   +   K   K   + +K++  EEK +Y   A+ V  G    G
Sbjct: 34  SWVYFSKEFIKEYIASHPESPGLKAATKAASNAWKSMSLEEKEKYARHAREVWDGYLSSG 93

Query: 96  KAKFP---------TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGW 146
            A  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|147772140|emb|CAN64547.1| hypothetical protein VITISV_026046 [Vitis vinifera]

 Score =  126 bits (316), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 75/264 (28%), Positives = 131/264 (49%), Gaps = 19/264 (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 FHRLIQGITRHKEEQVAYVGGCLL 295
              L+ GI   K++Q + V   L+
Sbjct: 280 LSYLVHGIEEFKKKQQSGVXRLLI 303

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147773967|emb|CAN67356.1| hypothetical protein VITISV_035313 [Vitis vinifera]

 Score =  117 bits (292), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 125/249 (50%), Gaps = 14/249 (5%)

Query: 95  GKAKFP-TRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKIDI 153
            + K P +RC+  +  + + +L D++R  + EMGFG LL L C  L+  LC W++   D 
Sbjct: 17  SQVKLPKSRCSGKKFISVIARLPDDKRDAITEMGFGGLLHLACRELRYELCSWIISNYDT 76

Query: 154 ARCILQL-NGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITV 212
           A   L +  GV V ++ +    +MGI   G+         E+  +    T ++R   I++
Sbjct: 77  AYHQLNMATGVVVPVTAQDVGNIMGIPCSGE---------EIVVHTRRGT-SNRTYTISL 126

Query: 213 LAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFCF 272
           L   L+ L   DD F+ TF++FA  T+L P   +        ++ D +   ++NW+ F  
Sbjct: 127 LEQNLENLAIGDD-FRKTFLIFACATLLAPNSKLEGIHDLWDTIWDGDVGVQKNWSKFVL 185

Query: 273 HRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLALWNVNEIK-KLM 331
           H +  GI  +++ Q  Y+ GCL++LQ+ Y        +  D +M  LA W+ + IK +L 
Sbjct: 186 HYIEDGIREYQKNQPTYIRGCLIFLQLFYMTKFYLPSVTVDVTMPLLAAWSDDLIKRRLS 245

Query: 332 KWIDSKGGF 340
             I + GG+
Sbjct: 246 AEIATFGGY 254

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147820300|emb|CAN75849.1| hypothetical protein VITISV_040636 [Vitis vinifera]

 Score =  116 bits (290), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 79/317 (24%), Positives = 143/317 (45%), Gaps = 46/317 (14%)

Query: 38  GFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK---- 93
            +I Y+ + +  IK ND    I  ++RK++G  +  L   EK  + +++K   K      
Sbjct: 377 AWIHYYNDQLVMIKENDKGVKINDDLRKKLGKKWNELSKVEKXDFMAKSKESSKQYXLQK 436

Query: 94  --IGKAKFPTRCAPDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEKI 151
             + K    TRC+P+R+   + +L  +QR  + E+GFGSLLQL C ++     G  +   
Sbjct: 437 GVVPKLYLQTRCSPERVIRVIEELEPKQRAAIEEIGFGSLLQLRCRKIDHGARGLKI--- 493

Query: 152 DIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINIT 211
                     G+  ++S                      ++++C     +      + + 
Sbjct: 494 ----------GMNKDVS---------------------HNNDLCK---KYCDKKGQLPLV 519

Query: 212 VLAGILQKLKSADDQFKVTFMMFALCTILCPPGGVHISSGFLFSLKDVESIPKRNWATFC 271
           +L   +++ K   + FKV F++F L  +LCP     +   FL  ++D++SI K NWA F 
Sbjct: 520 MLENQIREDKEGGNDFKVRFVLFVLGALLCPTMKXFVKRSFLHLVEDIDSIKKMNWAEFV 579

Query: 272 FHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGK--LERDRSMCP-LALWNVNEIK 328
              L+ GI   K +Q + V GCLL+L + Y   I + +  L      CP +  W  +Z+ 
Sbjct: 580 LSYLVHGIEEFKMKQQSGVCGCLLFLMLFYHXHISFEEKFLXLYTRPCPXITAWGDDZVL 639

Query: 329 KLMKWIDSKGGFDSHQV 345
            + + +   GG+ +  V
Sbjct: 640 DMKRRLKKVGGYANDNV 656

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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

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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: eugene3.00040640 hypothetical protein (628 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

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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	346
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	4e-06
smart00398	70	smart00398, HMG, high mobility group	3e-05
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-05
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	4e-04
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	0.003

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

 Score = 43.4 bits (103), Expect = 4e-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 = 41.5 bits (98), Expect = 3e-05
 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 = 41.1 bits (97), Expect = 3e-05
 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 = 37.6 bits (88), Expect = 4e-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 = 35.7 bits (83), Expect = 0.003
 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	346
PF10536	363	PMD: Plant mobile domain; InterPro: IPR019557 This	100.0
PTZ00199	94	high mobility group protein; Provisional	99.28
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.12
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.06
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.04
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	98.98
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	98.96
KOG0381	96	consensus HMG box-containing protein [General func	98.96
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	98.94
PF09331	142	DUF1985: Domain of unknown function (DUF1985); Int	98.9
smart00398	70	HMG high mobility group.	98.88
COG5648	211	NHP6B Chromatin-associated proteins containing the	98.5
KOG0527	331	consensus HMG-box transcription factor [Transcript	98.19
KOG0526	615	consensus Nucleosome-binding factor SPN, POB3 subu	97.56
KOG3248	421	consensus Transcription factor TCF-4 [Transcriptio	95.29
KOG0528	511	consensus HMG-box transcription factor SOX5 [Trans	94.41
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	92.06
PF03078	458	ATHILA: ATHILA ORF-1 family; InterPro: IPR004312 A	89.58
KOG4715	410	consensus SWI/SNF-related matrix-associated actin-	87.56
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	84.06

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

Probab=100.00  E-value=1.1e-33  Score=277.94  Aligned_cols=198  Identities=18%  Similarity=0.303  Sum_probs=167.4

Q ss_pred             Ccccccccc--ccccchHHHHHHHhccccccceEEECCeEeecCHhHHHHHhcccCCCCcccccCChhhHHHHHhhcC--
Q 019122          127 GFGSLLQLN--CGRLKRNLCGWLVEKIDIARCILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFT--  202 (346)
Q Consensus       127 GFg~LL~i~--~~~l~~~L~~wL~~~~d~~t~~~~l~g~~i~it~~dV~~VLGLP~gG~~v~~~~~~~~~~~l~~~~~--  202 (346)
                      |||+|+.|.  ..++++.|+.+|+++|+++|++|+++++||+||++||.+|+|||+.|.+|......+ ..++.+.+.  
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 333333332  


Q ss_pred             ------CCCCCcchHHHHHHHhhccCC-CchHhHHHHHHhhhhhccCCCCC-cccccccccccccCCCCcccchHHHHHH
Q 019122          203 ------PTSRGINITVLAGILQKLKSA-DDQFKVTFMMFALCTILCPPGGV-HISSGFLFSLKDVESIPKRNWATFCFHR  274 (346)
Q Consensus       203 ------~~~~~i~i~~L~~~l~~~~~~-~d~f~r~Fll~~i~~~L~Pts~~-~vs~~yl~~l~D~d~i~~ynW~~~Vl~~  274 (346)
                            ..+..+.+++|++.+...+++ .+.+.||||++++|++|||+++. +|+..|++++.|++.+++||||++||++
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                  123456778898888655544 24899999999999999999988 8999999999999999999999999999


Q ss_pred             HHHHHHhhhccC--ccccchhHHHHHHHHHhhccCCCcC-----C----CCCCCCccccCHH
Q 019122          275 LIQGITRHKEEQ--VAYVGGCLLYLQMLYFNSIVYGKLE-----R----DRSMCPLALWNVN  325 (346)
Q Consensus       275 L~~~i~k~~~~k--~~~i~GCl~lLqi~Yld~l~~g~~~-----~----~~~~ppI~~w~~~  325 (346)
                      |++++.++..+.  ..+++||+.|||+|+|||++.+...     .    +...|++..|.+.
T Consensus       160 ly~~L~~~~~~~~~~~~~~g~~~llq~W~werf~~~rP~~~~~~~~~~~~~~~P~~~rW~~~  221 (363)
T PF10536_consen  160 LYRDLCKASRKSASQSNIGGPLWLLQLWAWERFPVGRPKLITAQKPNPIPDRPPRAARWCDR  221 (363)
T ss_pred             HHHHHHHHhhhcccccccccceeeeccchhheeecccccccccccccccccCCCeeeeeecc
Confidence            999999988776  7899999999999999999977541     1    1233349999873

>PTZ00199 high mobility group protein; Provisional

Probab=99.28  E-value=2.8e-12  Score=102.85  Aligned_cols=70  Identities=17%  Similarity=0.240  Sum_probs=64.6

Q ss_pred             cCCCCCCCccCCcchhhhhHHHHHHHHhcCCCcc-hHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           25 ASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMAC-ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      +..|||.||||+||||.|+.+.|.++++.||+.. .+.+|.+.+|+.|++||++||.+|.+.|.+....|.
T Consensus        16 ~~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~   86 (94)
T PTZ00199         16 KKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYE   86 (94)
T ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            3579999999999999999999999999999875 589999999999999999999999999999877764

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

Probab=99.12  E-value=3.8e-11  Score=89.04  Aligned_cols=62  Identities=19%  Similarity=0.305  Sum_probs=58.4

Q ss_pred             CccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      ||+|+|||+.|+.+++.++++.||+ ....++.+.+|..|++||+++|.+|.++|++...+|.
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~-~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~   62 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPD-ASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYE   62 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999998 6799999999999999999999999999999877764

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=99.06  E-value=6.4e-11  Score=90.37  Aligned_cols=66  Identities=23%  Similarity=0.333  Sum_probs=55.3

Q ss_pred             CCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      |++||||+|||+.|+.|.+.+.+..-.......++.+++|..|++||++||.+|.++|++.+.+|.
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~   66 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYE   66 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999999999999833366678999999999999999999999999999877663

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 ....

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

Probab=99.04  E-value=9.6e-11  Score=87.73  Aligned_cols=62  Identities=29%  Similarity=0.378  Sum_probs=56.3

Q ss_pred             CccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      ||||+|||+.|+++.+.++++.||+.. ..+|.+.+|..|++||+++|.+|.+.|.+....|.
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~-~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~   62 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLS-NKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYE   62 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTST-HHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhcccc-cccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999999999999877 99999999999999999999999999999877764

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 ....

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

Probab=98.98  E-value=3.9e-10  Score=86.86  Aligned_cols=64  Identities=27%  Similarity=0.352  Sum_probs=59.3

Q ss_pred             CCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           31 RKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      ++|||+||||.|+.+++.++++.+|+ ....++.+.+|..|++||+++|.+|.+.|++....|..
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~-~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~   64 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPG-LTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAR   64 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHH
Confidence            47999999999999999999999997 47889999999999999999999999999998887754

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.

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

Probab=98.96  E-value=4.3e-10  Score=85.58  Aligned_cols=63  Identities=24%  Similarity=0.328  Sum_probs=58.3

Q ss_pred             CccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      -|||+||||.|+.+.+.++++.||+ ..+.++.|.+|..|++||+++|.+|.+.|++...+|..
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~-~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~   64 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPL-KENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMK   64 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999997 58899999999999999999999999999998877753

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

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

Probab=98.96  E-value=5.7e-10  Score=89.26  Aligned_cols=66  Identities=26%  Similarity=0.342  Sum_probs=61.3

Q ss_pred             CC--CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           28 DG--GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        28 ~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      ||  +.||||++|||.|+.+++..+++.||+ ..+.+|+|++|+.|++|++++|.+|.++|.+....|.
T Consensus        17 ~p~~~~pkrp~sa~~~f~~~~~~~~k~~~p~-~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~   84 (96)
T KOG0381|consen   17 DPNAQAPKRPLSAFFLFSSEQRSKIKAENPG-LSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYE   84 (96)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            55  599999999999999999999999999 8899999999999999999999999999988777764

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

Probab=98.94  E-value=6.2e-10  Score=82.13  Aligned_cols=62  Identities=23%  Similarity=0.303  Sum_probs=57.5

Q ss_pred             CccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      ||||+|||+.|+.+++..+++.+|+ ....++.+.+|..|++||+++|.+|.++|++...+|.
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~-~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~   62 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPG-LSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYE   62 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999988 5588999999999999999999999999999877764

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

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

Probab=98.90  E-value=2.3e-09  Score=92.30  Aligned_cols=124  Identities=17%  Similarity=0.311  Sum_probs=95.4

Q ss_pred             ceEEECCeEeecCHhHHHHHhcccCCCCcccccCChhhH---HHHHhhcCCCCCCcchHHHHHHHhhc-cCCCchHhHHH
Q 019122          156 CILQLNGVEVELSPKSFSYVMGISDGGKPLQLEGESSEV---CAYVDNFTPTSRGINITVLAGILQKL-KSADDQFKVTF  231 (346)
Q Consensus       156 ~~~~l~g~~i~it~~dV~~VLGLP~gG~~v~~~~~~~~~---~~l~~~~~~~~~~i~i~~L~~~l~~~-~~~~d~f~r~F  231 (346)
                      .-|.++|..|.++..+.+.|+|||++..|-.........   ..+.+.+-..+..+++..+.++|... ..+.++=+|..
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            568899999999999999999999998877654321111   13333333346779999999999886 23555666666


Q ss_pred             HHHhhhhhccCCC-CCcccccccccccccCCCCcccchHHHHHHHHHHH
Q 019122          232 MMFALCTILCPPG-GVHISSGFLFSLKDVESIPKRNWATFCFHRLIQGI  279 (346)
Q Consensus       232 ll~~i~~~L~Pts-~~~vs~~yl~~l~D~d~i~~ynW~~~Vl~~L~~~i  279 (346)
                      +|+++..+|+|++ +..|+..++..+.|++...+|-||.+.++.++++|
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            6666666666665 55899999999999999999999999999999864

>smart00398 HMG high mobility group

Probab=98.88  E-value=1.5e-09  Score=80.99  Aligned_cols=63  Identities=27%  Similarity=0.357  Sum_probs=57.5

Q ss_pred             CCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           31 RKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      +||+|+|||+.|+.+++..+++.+|+. ...++.+.+|..|++||+++|.+|.+.|++...+|.
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~-~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~   63 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDL-SNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYE   63 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            489999999999999999999999975 478999999999999999999999999998776663

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

Probab=98.50  E-value=6.8e-08  Score=86.78  Aligned_cols=68  Identities=21%  Similarity=0.236  Sum_probs=63.3

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      -.|||.||||-++||.|..+-|.++...+|+. -+.+++|.+|++|++||++||.+|-+.|..-+..|-
T Consensus        65 k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l-~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq  132 (211)
T COG5648          65 KKDPNGPKRPLSAYFLYSAENRDEIRKENPKL-TFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQ  132 (211)
T ss_pred             hcCCCCCCCchhHHHHHHHHHHHHHHHhCCCC-ChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHH
Confidence            35899999999999999999999999999988 889999999999999999999999999988777763

>KOG0527 consensus HMG-box transcription factor [Transcription]

Probab=98.19  E-value=9.5e-07  Score=85.74  Aligned_cols=64  Identities=25%  Similarity=0.371  Sum_probs=60.3

Q ss_pred             CCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           31 RKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      +=|||-|||.|+..+.|+.|-+.+|+- =+.++.|.+|..||.|+++||.+|.+.|+++..++++
T Consensus        62 hIKRPMNAFMVWSq~~RRkma~qnP~m-HNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~Hmk  125 (331)
T KOG0527|consen   62 RIKRPMNAFMVWSQGQRRKLAKQNPKM-HNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMK  125 (331)
T ss_pred             ccCCCcchhhhhhHHHHHHHHHhCcch-hhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHH
Confidence            449999999999999999999999965 6789999999999999999999999999999999987

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

Probab=97.56  E-value=3.9e-05  Score=77.41  Aligned_cols=69  Identities=12%  Similarity=0.223  Sum_probs=59.9

Q ss_pred             EeeccCCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           21 VGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .+.--.-|||.|||+-+||..|+++=|..+|+.   .-.+.+|+|.+|.+||.||.  |.++.++|+.-+.+|.
T Consensus       525 k~~kk~kdpnapkra~sa~m~w~~~~r~~ik~d---gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~  593 (615)
T KOG0526|consen  525 KKGKKKKDPNAPKRATSAYMLWLNASRESIKED---GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYE  593 (615)
T ss_pred             cCcccCCCCCCCccchhHHHHHHHhhhhhHhhc---CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHH
Confidence            566677899999999999999999999999994   88899999999999999999  7777777776665553

>KOG3248 consensus Transcription factor TCF-4 [Transcription]

Probab=95.29  E-value=0.013  Score=56.40  Aligned_cols=55  Identities=22%  Similarity=0.368  Sum_probs=47.4

Q ss_pred             ccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhh
Q 019122           33 RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR   88 (346)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~   88 (346)
                      |+|.+||.-||.|-|+..-+.-. .|--+++-|++|.+|+.||.||-+.|-.-|++
T Consensus       193 KKPLNAFmlyMKEmRa~vvaEct-lKeSAaiNqiLGrRWH~LSrEEQAKYyElArK  247 (421)
T KOG3248|consen  193 KKPLNAFMLYMKEMRAKVVAECT-LKESAAINQILGRRWHALSREEQAKYYELARK  247 (421)
T ss_pred             cccHHHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHH
Confidence            78999999999999998888553 45556899999999999999999998888775

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

Probab=94.41  E-value=0.021  Score=57.47  Aligned_cols=64  Identities=25%  Similarity=0.302  Sum_probs=56.3

Q ss_pred             ccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCC
Q 019122           33 RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKA   97 (346)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~   97 (346)
                      |||-+||.++-.|=|+.+-.+.|+-- +-++.|-+|..||+||..||.+|-..-.++++.++.+-
T Consensus       327 KRPMNAFMVWAkDERRKILqA~PDMH-NSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~  390 (511)
T KOG0528|consen  327 KRPMNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKY  390 (511)
T ss_pred             cCCcchhhcccchhhhhhhhcCcccc-ccchhHHhcccccccccccccchHHHHHHHHHhhhccC
Confidence            99999999999999999999998432 23578899999999999999999999999999888753

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

Probab=92.06  E-value=0.1  Score=46.20  Aligned_cols=47  Identities=19%  Similarity=0.355  Sum_probs=34.5

Q ss_pred             cchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhh
Q 019122           37 NGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR   88 (346)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~   88 (346)
                      +||+.||.+|++.    |.+ ....++-..+...|..||+.+|..|...+-.
T Consensus        84 naYLNFLReFRrk----h~~-L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~  130 (183)
T PF06382_consen   84 NAYLNFLREFRRK----HCG-LSPQDLIQRAARAWCRLSEAEKNRYRRMAPS  130 (183)
T ss_pred             hHHHHHHHHHHHH----ccC-CCHHHHHHHHHHHHHhCCHHHHHHHHhhcch
Confidence            5788887776654    433 5556666777778999999999999875443

The function of this family is unknown.

>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=89.58  E-value=3.5  Score=42.20  Aligned_cols=187  Identities=15%  Similarity=0.191  Sum_probs=106.8

Q ss_pred             ccc-CHHHHHHHHhhCCHHHHHHHHHcCccccccccccccchHHHHHHHhc----c---cc--------ccceEEECCeE
Q 019122          101 TRC-APDRLAAAVLQLTDEQRVVVREMGFGSLLQLNCGRLKRNLCGWLVEK----I---DI--------ARCILQLNGVE  164 (346)
Q Consensus       101 tRc-S~~~~~~~i~~Ls~~qk~~I~~~GFg~LL~i~~~~l~~~L~~wL~~~----~---d~--------~t~~~~l~g~~  164 (346)
                      ||. ++..+..+  .|.++-..+++.+|.+.|..++...-+...+.+|+..    +   ++        ..-+|.|.+.+
T Consensus        63 TRyp~~etl~~L--Gl~~dV~~lf~~~gL~~f~~~~~~~Y~eet~qFLaTl~v~~~~~~~~~~~e~~glG~l~F~V~~~~  140 (458)
T PF03078_consen   63 TRYPDPETLQKL--GLLEDVEYLFKKCGLGTFMSYPYPTYPEETRQFLATLKVTFYNPSEPRAKELDGLGYLTFFVYGVE  140 (458)
T ss_pred             cccCCHHHHHHh--ccHHHHHHHHHhcCchhhccCCCCCcHHHHHHhhheeeeeecccccchhhcccCcceEEEEEccee
Confidence            443 45555555  7888889999999999999888865554444444321    1   11        22467778999


Q ss_pred             eecCHhHHHHHhcccCCCCcccccCChhhHHHHHhhcCCCCCCcchHHHHHHHhhccCCCchHhHHHHHHhhhhhccCCC
Q 019122          165 VELSPKSFSYVMGISDGGKPLQLEGESSEVCAYVDNFTPTSRGINITVLAGILQKLKSADDQFKVTFMMFALCTILCPPG  244 (346)
Q Consensus       165 i~it~~dV~~VLGLP~gG~~v~~~~~~~~~~~l~~~~~~~~~~i~i~~L~~~l~~~~~~~d~f~r~Fll~~i~~~L~Pts  244 (346)
                      ..+|-.+.+.++|.|.++. +......++...|....|.+. .++...-...      ..-+-+.+|+-=+++..|+|..
T Consensus       141 y~lsi~~L~~i~GF~~~~~-i~~~~~~~el~~~W~~ig~~~-p~~~~~~ks~------~Ir~PviRy~hr~iA~tlf~R~  212 (458)
T PF03078_consen  141 YSLSIKHLERIFGFPSGDE-IKPDFDPEELNDFWATIGGGK-PFNSARSKSN------QIRSPVIRYFHRLIANTLFARE  212 (458)
T ss_pred             eeeeHHHHHHHhCCCCccc-cCCCCCchHHHHHHHHhcCCC-cccccccccc------cccChHHHHHHHHHHhhhcccc
Confidence            9999999999999999854 333444455566666666321 1111111111      1122234444455565566555


Q ss_pred             CC-ccccccccc-----------cccc----CCCCcccchHHHHHHHHHHHHhhhcc--C---ccccchhHHHH
Q 019122          245 GV-HISSGFLFS-----------LKDV----ESIPKRNWATFCFHRLIQGITRHKEE--Q---VAYVGGCLLYL  297 (346)
Q Consensus       245 ~~-~vs~~yl~~-----------l~D~----d~i~~ynW~~~Vl~~L~~~i~k~~~~--k---~~~i~GCl~lL  297 (346)
                      .+ .|...-|.+           ..|.    .+..+.+-+...++||...=..+...  +   .-.+||=+.-+
T Consensus       213 ~~~~v~~~El~~l~~~L~~~Lr~~~~g~~l~~d~~dt~~~~vl~~hL~~yk~wa~~~~~~~~~~l~vGgviTpI  286 (458)
T PF03078_consen  213 ETGTVRNDELEMLDQALKHLLRRTKDGKLLRGDLNDTNVSMVLLDHLCSYKGWAKTNKKKARGSLCVGGVITPI  286 (458)
T ss_pred             ccCceechhHHHHHHHHHHHHHhcCCCccccCcccccchhHHHHHHHHhhhHHHhhcCCCCCceeeecchhhhH
Confidence            33 555444332           1221    12366777777788877553222111  2   34677766544

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.

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

Probab=87.56  E-value=0.52  Score=45.37  Aligned_cols=63  Identities=29%  Similarity=0.294  Sum_probs=51.6

Q ss_pred             CCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           31 RKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      -|.+|.-++.+|..-.-.+.|++||+.+. =++||.+|.-|.-|+++||..|+..=.--+.+|-
T Consensus        64 ppekpl~pymrySrkvWd~VkA~nPe~kL-WeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~  126 (410)
T KOG4715|consen   64 PPEKPLMPYMRYSRKVWDQVKASNPELKL-WEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYN  126 (410)
T ss_pred             CCCcccchhhHHhhhhhhhhhccCcchHH-HHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHH
Confidence            45677788889988888999999999874 4899999999999999999988776555445553

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

Probab=84.06  E-value=0.82  Score=35.18  Aligned_cols=60  Identities=12%  Similarity=0.046  Sum_probs=45.2

Q ss_pred             ccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           33 RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      ..|-+|-=.+....+.-|-+.+++.....  -+++..+|++|++++|.+--++|.+.-+.|.
T Consensus         5 E~PKt~qe~Wqq~vi~dYla~~~~dr~K~--~kam~~~W~~me~Kekl~WIkKA~EdqKrYE   64 (85)
T PF14887_consen    5 ETPKTAQEIWQQSVIGDYLAKFRNDRKKA--LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYE   64 (85)
T ss_dssp             ----THHHHHHHHHHHHHHHHTTSTHHHH--HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhhHhHHHH--HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHH
Confidence            34455555667888888998888765443  5688999999999999999999998777664

---

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	346
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-09
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	5e-07
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	8e-06
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	4e-05
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	5e-05
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	7e-05
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	4e-04
2lhj_A	97	High mobility group protein homolog NHP1; structur	2e-04
1ckt_A	71	High mobility group 1 protein; high-mobility group	2e-04
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	2e-04
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	2e-04
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	2e-04
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	3e-04
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	4e-04
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	4e-04
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	6e-04
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	5e-04
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	5e-04
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	6e-04
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	6e-04
1wgf_A	90	Upstream binding factor 1; transcription factor, D	7e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	8e-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 = 56.8 bits (136), Expect = 5e-09
 Identities = 59/370 (15%), Positives = 109/370 (29%), Gaps = 89/370 (24%)

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-SLLQLNCGRLKRNLCG------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 SIPKRNWATFCFHRLIQGITRHKEEQVAYVGGCLLYLQMLYFNSIVYGKLERDRSMCPLA 320
            +P+         R +  I     + +A             +  +   KL          
Sbjct: 317 DLPRE--VLTTNPRRLSIIAESIRDGLA---------TWDNWKHVNCDKLTTIIESSLNV 365

Query: 321 LWNVNEIKKL 330
           L    E +K+
Sbjct: 366 L-EPAEYRKM 374

>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 = 46.5 bits (110), Expect = 5e-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 = 42.7 bits (101), Expect = 8e-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 = 41.2 bits (97), Expect = 4e-05
 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

>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 = 41.1 bits (96), Expect = 5e-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

>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 = 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 = 40.1 bits (93), Expect = 4e-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: 113 GKPKRPRSAYNVYVAERFQEAKGDS-----PQEKLKTVKENWKNLSDSEKELYIQHAKE 166

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

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 36 RNGFIRYFGEVVRQIKA-NDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + ++ +  E   +I A N  +A     I K IG+ +  L  EEK  Y+  +  
Sbjct: 27 LSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDE 80

>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 = 38.1 bits (89), Expect = 2e-04
 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

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

 Score = 39.3 bits (92), Expect = 2e-04
 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

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

 Score = 38.5 bits (90), Expect = 2e-04
 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 = 38.0 bits (89), Expect = 2e-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: 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 = 38.4 bits (90), Expect = 3e-04
 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

>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A 1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A Length = 77

 Score = 37.6 bits (88), Expect = 4e-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

>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 = 40.2 bits (93), Expect = 4e-04
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

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

Query: 87 KR 88
          + 
Sbjct: 96 RA 97

>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 = 39.8 bits (92), Expect = 6e-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

>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 = 37.5 bits (88), Expect = 5e-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

>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 = 39.2 bits (91), Expect = 5e-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

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

 Score = 37.8 bits (88), Expect = 6e-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

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

 Score = 37.3 bits (87), Expect = 6e-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 = 37.4 bits (87), Expect = 7e-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

>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA recognition, chromatin, DNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A 1lwm_A Length = 93

 Score = 37.3 bits (87), Expect = 8e-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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	346
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.37
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.31
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.29
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.28
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.26
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.26
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.25
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.25
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.25
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.22
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.22
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.21
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.2
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.19
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.19
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.18
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.17
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.15
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.15
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.12
2cto_A	93	Novel protein; high mobility group box domain, hel	99.12
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.12
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.1
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.1
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.09
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.08
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.07
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.06
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.06
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.04
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.04
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	98.99
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.95
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.9
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	98.88
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.86
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	98.75
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.68
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	98.58

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

Probab=99.37  E-value=1.6e-13  Score=107.79  Aligned_cols=65  Identities=15%  Similarity=0.036  Sum_probs=60.5

Q ss_pred             CCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      .|.||||+||||.|+.+||+.|++.+|+  .+.+|+|++|+.|++||++||.+|.+.|++.+..|..
T Consensus         2 ~~kPKrP~SAy~lf~~~~r~~~k~~~p~--~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYek   66 (91)
T 1l8y_A            2 GKLPESPKRAEEIWQQSVIGDYLARFKN--DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYER   66 (91)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHHTTS--THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCC--CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999998  6799999999999999999999999999998877754

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

Probab=99.31  E-value=7.5e-13  Score=103.08  Aligned_cols=69  Identities=13%  Similarity=0.153  Sum_probs=64.1

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcch-HHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACI-TKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      -.||++||||++||+.|+.+.|.++++.||+..+ ..++.|.+|+.|++||++||.+|.+.|++...+|.
T Consensus        10 ~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   79 (86)
T 2eqz_A           10 KGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD   79 (86)
T ss_dssp             SCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999999999875 79999999999999999999999999999877764

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

Probab=99.29  E-value=2.5e-12  Score=99.26  Aligned_cols=63  Identities=21%  Similarity=0.230  Sum_probs=59.5

Q ss_pred             CCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcc
Q 019122           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVG   90 (346)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~   90 (346)
                      ++|+||||.+|||.|+.+.|.++++.||+...+.+|.|.+|+.|++||++||.+|.+.|+...
T Consensus         2 ~~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A            2 SSGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            689999999999999999999999999987658999999999999999999999999999864

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

Probab=99.28  E-value=5e-13  Score=103.31  Aligned_cols=69  Identities=16%  Similarity=0.183  Sum_probs=63.9

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcch-HHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACI-TKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      .|||+||||.+||+.|+.++|.++++.||+..+ ..++.|.+|+.|++||++||.+|.+.|++.+.+|..
T Consensus         3 kdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~   72 (83)
T 1aab_A            3 GDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYER   72 (83)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999998764 789999999999999999999999999998877743

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

Probab=99.26  E-value=1.6e-12  Score=98.94  Aligned_cols=67  Identities=16%  Similarity=0.297  Sum_probs=62.4

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .|||+||||+|||+.|+.+.|.++++.+|+ ..+.+|.+.+|..|++||++||.+|.+.|++...+|.
T Consensus         2 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   68 (77)
T 1hme_A            2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE   68 (77)
T ss_dssp             CCSSCCCCCCCTTHHHHHHHHHHHHHHCTT-CCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            489999999999999999999999999997 4688999999999999999999999999999877764

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

Probab=99.26  E-value=1.4e-12  Score=99.04  Aligned_cols=66  Identities=23%  Similarity=0.297  Sum_probs=59.8

Q ss_pred             CCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      |||++|||+|||+.|+.+.|.++++.+|+. .+.++.|.+|..|++||+++|.+|.++|++.+.+|.
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   66 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHR   66 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCC-SSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999974 577999999999999999999999999999877764

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

Probab=99.25  E-value=2.5e-12  Score=101.38  Aligned_cols=68  Identities=26%  Similarity=0.427  Sum_probs=63.4

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      +.||+.||||++||+.|+.+.|.++++.||+. .+.+|.|.+|..|++||+++|.+|.+.|++...+|.
T Consensus         2 ~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   69 (92)
T 2crj_A            2 SSGSSGPKAPVTGYVRFLNERREQIRTRHPDL-PFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYL   69 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTC-CHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            57999999999999999999999999999985 588999999999999999999999999999877764

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

Probab=99.25  E-value=3.3e-12  Score=100.71  Aligned_cols=69  Identities=14%  Similarity=0.142  Sum_probs=64.1

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      +.||+.||||.+||+.|+.+.|.++++.||+. .+.++.|.+|+.|++||++||.+|.+.|++.+.+|..
T Consensus         2 ~~~p~~pKrP~say~lF~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~   70 (92)
T 2cs1_A            2 SSGSSGIKKPMSASALFVQDHRPQFLIENPKT-SLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNS   70 (92)
T ss_dssp             CCCCSSSCCCCCHHHHHHHHHHHHHHHHCCSS-CHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999986 5789999999999999999999999999998887753

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

Probab=99.25  E-value=2.5e-12  Score=101.07  Aligned_cols=70  Identities=13%  Similarity=0.239  Sum_probs=65.6

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCC
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGK   96 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~   96 (346)
                      -.|||+||||++|||.|+.+.|.++++.||+ ..+.++.|.+|+.|++||++||.+|.+.|++.+.+|...
T Consensus        15 ~kdp~~pKrP~say~lF~~~~r~~~k~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e   84 (90)
T 1wgf_A           15 KGGSEKPKRPVSAMFIFSEEKRRQLQEERPE-LSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             SSCCCCCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4699999999999999999999999999998 568899999999999999999999999999999998654

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

Probab=99.22  E-value=2.9e-12  Score=100.01  Aligned_cols=68  Identities=16%  Similarity=0.193  Sum_probs=62.9

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      ..|||+||||++|||.|+.++|.++++.+|+ ..+.+|.|.+|+.|++||++||.+|.++|++.+.+|.
T Consensus        12 ~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~-~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~   79 (87)
T 2e6o_A           12 ATSPNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQK   79 (87)
T ss_dssp             CCCCSSCCCCCCHHHHHHHHTHHHHHHHCTT-SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999997 4688999999999999999999999999999877764

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

Probab=99.22  E-value=4.8e-12  Score=97.54  Aligned_cols=70  Identities=17%  Similarity=0.213  Sum_probs=64.5

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCC
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGK   96 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~   96 (346)
                      +.|+++||||++||+.|+.++|.++++.+|+ ..+.+|.|.+|..|++||++||.+|.+.|++.+.+|...
T Consensus         2 ~~~~~~pkrP~~af~lf~~~~r~~~~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~   71 (82)
T 1wz6_A            2 SSGSSGARRPMNAFLLFCKRHRSLVRQEHPR-LDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKA   71 (82)
T ss_dssp             CSSCCCSCCCCCHHHHHHHHHHHHHHHHCSS-SCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999997 457899999999999999999999999999988888653

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

Probab=99.21  E-value=4.4e-12  Score=94.89  Aligned_cols=64  Identities=16%  Similarity=0.165  Sum_probs=59.4

Q ss_pred             CCccCCcchhhhhHHHHHHHHhcCCCcc-hHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           31 RKRQCRNGFIRYFGEVVRQIKANDGMAC-ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      +||||+|||+.|+.+.|.++++.||+.. ...++.|.+|+.|++||+++|.+|.+.|++.+.+|.
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   65 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE   65 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999877 479999999999999999999999999999877663

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

Probab=99.20  E-value=8.6e-12  Score=100.25  Aligned_cols=67  Identities=21%  Similarity=0.310  Sum_probs=62.9

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .|||+||||++|||.|+.++|.++++.||+. .+.+|.|.+|..|++||+++|.+|.+.|++.+.+|.
T Consensus        13 kdp~~pKrP~say~lF~~~~r~~i~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   79 (102)
T 2co9_A           13 KDPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYL   79 (102)
T ss_dssp             CCCCSCCCCCCHHHHTHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999986 588999999999999999999999999999887764

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

Probab=99.19  E-value=4.4e-12  Score=94.74  Aligned_cols=65  Identities=22%  Similarity=0.345  Sum_probs=56.9

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      |++|||+|||+.|+.++|.++++.+|+.. +.++.|.+|..|++||+++|.+|.++|++.+.+|..
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~   65 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQ   65 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999865 789999999999999999999999999998877653

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

Probab=99.19  E-value=1.1e-11  Score=96.12  Aligned_cols=67  Identities=22%  Similarity=0.289  Sum_probs=62.0

Q ss_pred             CCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      .||.||||+||||.|+.+++.++++.+|+. .+.+|.|.+|..|++||++||.+|.+.|++...+|..
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~   67 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHRE   67 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Confidence            488999999999999999999999999975 6889999999999999999999999999998877754

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

Probab=99.18  E-value=4.8e-12  Score=101.24  Aligned_cols=67  Identities=16%  Similarity=0.249  Sum_probs=62.5

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSK   93 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~   93 (346)
                      -.||+.||||+||||.|+.+.|.++++.+|+. .+.+|.|.+|..|++||++||.+|.++|++...+|
T Consensus         5 ~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y   71 (99)
T 1k99_A            5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEF   71 (99)
T ss_dssp             CSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            36899999999999999999999999999985 58899999999999999999999999999988874

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

Probab=99.17  E-value=5.7e-12  Score=93.36  Aligned_cols=60  Identities=25%  Similarity=0.340  Sum_probs=55.9

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      |+||||+|||+.|+.+.|.++++.||     .++.|.+|+.|++||++||.+|.+.|++.+.+|.
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p-----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~   60 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP-----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYH   60 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH-----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH-----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999887     5999999999999999999999999999877763

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

Probab=99.15  E-value=9.6e-12  Score=95.92  Aligned_cols=68  Identities=21%  Similarity=0.301  Sum_probs=58.9

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      ..++++|||++|||.|+.++|.++++.||+.. ..+|.|.+|..|++||++||.+|.+.|++.+..|..
T Consensus         2 ~~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~   69 (83)
T 3f27_D            2 SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLH-NAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQ   69 (83)
T ss_dssp             -----CCCCCCHHHHHHHHHHHHHHHHCSSSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999865 789999999999999999999999999998877753

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

Probab=99.15  E-value=1.7e-11  Score=94.13  Aligned_cols=66  Identities=23%  Similarity=0.266  Sum_probs=60.3

Q ss_pred             CCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      +|.+|||++|||.|+.+++.++++.+|+. .+.+|.|.+|..|++||++||.+|.+.|++...+|..
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~   67 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDM-HNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLE   67 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSC-CHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHT
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999975 4889999999999999999999999999998877754

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

Probab=99.12  E-value=2.6e-11  Score=98.09  Aligned_cols=75  Identities=17%  Similarity=0.220  Sum_probs=60.7

Q ss_pred             eEeeccCCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           20 VVGVDASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      -+-....-||++||||++|||.|+.++|+++++.+|+. .+.+|.|.+|..|++||++||.+|.+.|++.+.+|..
T Consensus        18 ~~~~~~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~   92 (106)
T 4euw_A           18 NLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHL-HNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKK   92 (106)
T ss_dssp             ----------CCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhhhccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence            34455667899999999999999999999999999975 5679999999999999999999999999998887754

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

Probab=99.12  E-value=5.7e-12  Score=99.65  Aligned_cols=68  Identities=18%  Similarity=0.262  Sum_probs=62.2

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHh---ccCCCCCChhhhhhhhHHhhhccccccCC
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEI---GSTYKNLPPEEKCRYKSEAKRVGKSKIGK   96 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~---~~~~~sl~~~~k~~~~~~a~~~~~~~~~~   96 (346)
                      +.++|+||||++|||.|+.|+|+++++.   +..+.+|.|.+   |+.|++||++||.+|.+.|++.+..|.+.
T Consensus         5 ~~~~~~PKRP~sAf~lF~~e~R~~ik~e---~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd   75 (93)
T 2cto_A            5 SSGMPNRKASRNAYYFFVQEKIPELRRR---GLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKD   75 (93)
T ss_dssp             CCCCCCCCSSCCHHHHHHHTTHHHHHHH---TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcc
Confidence            5688999999999999999999999997   56678899998   99999999999999999999998888764

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

Probab=99.12  E-value=3.1e-11  Score=92.45  Aligned_cols=65  Identities=25%  Similarity=0.345  Sum_probs=59.9

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      |+||||++||+.|+.+.+.++++.+|+. .+.+|.|.+|..|++||++||.+|.+.|++...+|..
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~   65 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMK   65 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999974 5789999999999999999999999999998877754

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

Probab=99.10  E-value=3.9e-11  Score=93.24  Aligned_cols=65  Identities=18%  Similarity=0.327  Sum_probs=60.3

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      |++|||+||||.|+.+++.++++.+|+. .+.++.+.+|..|++||++||.+|.+.|++...+|..
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~   65 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKERQLHMQ   65 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999985 6889999999999999999999999999998877753

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

Probab=99.10  E-value=1.1e-11  Score=98.59  Aligned_cols=69  Identities=19%  Similarity=0.203  Sum_probs=63.0

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcc-hHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMAC-ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      -.|||+||||++||+.|+.++|.++++.||+.. .+.++.|.+|..|++||++||.+|.+.|++...+|.
T Consensus        17 ~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~   86 (97)
T 2lhj_A           17 KKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYE   86 (97)
T ss_dssp             TSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999863 378999999999999999999999999999877764

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

Probab=99.09  E-value=7.4e-12  Score=98.90  Aligned_cols=68  Identities=19%  Similarity=0.321  Sum_probs=63.2

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      -.|||.||||+|||+.|+.++|.++++.||+. .+.++.|.+|..|++||++||.+|.+.|++...+|.
T Consensus        15 ~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~-~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~   82 (93)
T 1cg7_A           15 KKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYE   82 (93)
T ss_dssp             CCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTS-CHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999999986 488999999999999999999999999999887774

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

Probab=99.08  E-value=3.8e-11  Score=90.41  Aligned_cols=64  Identities=17%  Similarity=0.303  Sum_probs=59.4

Q ss_pred             CCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      ||+||||+|||+.|+.+.|.++++.||+. .+.++.|.+|+.|++|  +||.+|.+.|++.+.+|..
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~   64 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGI-KVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHD   64 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTC-CHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHT
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999985 5789999999999999  8899999999998888754

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

Probab=99.07  E-value=4.9e-12  Score=99.32  Aligned_cols=64  Identities=11%  Similarity=0.050  Sum_probs=57.3

Q ss_pred             CCCCCccCCcchhhhhHHHHHHHHhcCCCcc-hHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMAC-ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      |||.||||++|||.|+.++|.++++.||+.. .+.+|.    +.|++||++||.+|.++|++.+..|.-
T Consensus        19 DpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~   83 (90)
T 2yuk_A           19 EEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRI   83 (90)
T ss_dssp             HHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            8899999999999999999999999999754 266666    889999999999999999998887753

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

Probab=99.06  E-value=4.2e-11  Score=90.18  Aligned_cols=63  Identities=11%  Similarity=0.215  Sum_probs=57.9

Q ss_pred             CCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .|+||||++|||.|+.+.|.++++.||+.. +.+|.|.+|+.|++||+  |.+|.++|++.+.+|.
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~-~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~   63 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYD   63 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCC-HHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCC-HHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999864 79999999999999998  9999999999877764

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

Probab=99.06  E-value=5.3e-11  Score=90.78  Aligned_cols=65  Identities=23%  Similarity=0.317  Sum_probs=59.9

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      |.+|||+|||+.|+.+.|.++++.+|+. .+.++.|.+|..|++||++||.+|.+.|++.+.+|..
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~-~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~   65 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDM-HNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMA   65 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999975 5779999999999999999999999999998877753

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

Probab=99.04  E-value=2e-10  Score=92.18  Aligned_cols=84  Identities=26%  Similarity=0.349  Sum_probs=68.2

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcc--hHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCCCccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMAC--ITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRC  103 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~~~~tRc  103 (346)
                      +-.+++||||++|||.|+.+++.     +|+..  .+.++.|.+|+.|++||++||.+|.+.|++.+.+|.         
T Consensus         3 s~~~~~PKrP~say~lF~~e~~~-----~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~---------   68 (101)
T 1v63_A            3 SGSSGPKKPPMNGYQKFSQELLS-----NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK---------   68 (101)
T ss_dssp             CCCCSSCCCCSSSHHHHHHHHHH-----HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH---------
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHh-----CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH---------
Confidence            44667899999999999999853     56543  468999999999999999999999999999888874         


Q ss_pred             CHHHHHHHHhhCCHHHHHHHHH
Q 019122          104 APDRLAAAVLQLTDEQRVVVRE  125 (346)
Q Consensus       104 S~~~~~~~i~~Ls~~qk~~I~~  125 (346)
                        ..+..-...++++++..+.+
T Consensus        69 --~e~~~Y~~~~~~~~~~~~~~   88 (101)
T 1v63_A           69 --VHLDLWVKSLSPQDRAAYKE   88 (101)
T ss_dssp             --HHHHHHHHHSCTTHHHHHHH
T ss_pred             --HHHHHHHhhCCHHHHHHHHH
Confidence              44455556788888776544

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

Probab=99.04  E-value=1.1e-10  Score=94.68  Aligned_cols=81  Identities=21%  Similarity=0.230  Sum_probs=70.2

Q ss_pred             CCCCCC-ccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCCCcccccCH
Q 019122           27 NDGGRK-RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAP  105 (346)
Q Consensus        27 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~~~~tRcS~  105 (346)
                      .|+|+| |||.+|||.|+.++|.+++     +..+.++.|.+|+.|++||++||.+|.+.|++.+.+|.           
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            589999 9999999999999999988     45789999999999999999999999999999888874           


Q ss_pred             HHHHHHHhhCCHHHHHHH
Q 019122          106 DRLAAAVLQLTDEQRVVV  123 (346)
Q Consensus       106 ~~~~~~i~~Ls~~qk~~I  123 (346)
                      ..+..-...+++++++.+
T Consensus        76 ~e~~~Y~~~~~~~~r~~~   93 (108)
T 1v64_A           76 VELLRFLESLPEEEQQRV   93 (108)
T ss_dssp             HHHHHHHHHSCHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHH
Confidence            344455567888887765

>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=98.99  E-value=1.4e-10  Score=100.15  Aligned_cols=68  Identities=16%  Similarity=0.279  Sum_probs=63.1

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      ..|||.||||++|||.|+.+.+.++++.||+ ..+.+|.|.+|..|++||+++|.+|.+.|++....|.
T Consensus        83 ~kdp~~pKrp~say~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~  150 (159)
T 2gzk_A           83 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE  150 (159)
T ss_dssp             SCCTTCCCCCCCHHHHHHHHHHHHHHHHCSC-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccchhhHhhHHHHHHhCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999997 5688999999999999999999999999999877764

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

Probab=98.95  E-value=2.3e-10  Score=100.13  Aligned_cols=68  Identities=16%  Similarity=0.166  Sum_probs=63.5

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCc-chHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMA-CITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .||++||||.+||+.|+.+.|.++++.||+. ..+.++.|.+|+.|++||++||.+|.+.|++.+..|.
T Consensus        11 ~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   79 (173)
T 2yrq_A           11 GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE   79 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999997 5789999999999999999999999999999777664

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

Probab=98.90  E-value=4.1e-10  Score=98.52  Aligned_cols=67  Identities=16%  Similarity=0.297  Sum_probs=62.6

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .|||.||||++||+.|+.+.+.++++.||+ ..+.++.|.+|..|++||+++|.+|.+.|.+...+|.
T Consensus        97 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~-~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~  163 (173)
T 2yrq_A           97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE  163 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCSS-SCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHH
T ss_pred             cCCccccCcccHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            489999999999999999999999999998 5688999999999999999999999999999887764

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

Probab=98.88  E-value=7.6e-10  Score=100.28  Aligned_cols=85  Identities=20%  Similarity=0.227  Sum_probs=72.6

Q ss_pred             cCCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCCCcccccC
Q 019122           25 ASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCA  104 (346)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~~~~tRcS  104 (346)
                      .+.+|++||||.+||+.|+.+.|.++++.||+.. +.++.|.+|+.|++||++||.+|.+.|+..+..|.          
T Consensus         3 s~~~p~~PKrP~say~lF~~~~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~----------   71 (214)
T 3tq6_A            3 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK----------   71 (214)
T ss_dssp             -CHHHHSCCCCCCHHHHHHHHHHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH----------
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHH----------
Confidence            3556899999999999999999999999999876 89999999999999999999999999999888774          


Q ss_pred             HHHHHHHHhhCCHHHHH
Q 019122          105 PDRLAAAVLQLTDEQRV  121 (346)
Q Consensus       105 ~~~~~~~i~~Ls~~qk~  121 (346)
                       ..+......++|.|..
T Consensus        72 -~e~~~y~~~~tp~q~~   87 (214)
T 3tq6_A           72 -EEISRFKEQLTPSQIM   87 (214)
T ss_dssp             -HHHHHHHHHCCHHHHH
T ss_pred             -HHhhhhcccCCHHHHH
Confidence             3444555667777653

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

Probab=98.86  E-value=1e-09  Score=100.94  Aligned_cols=84  Identities=20%  Similarity=0.224  Sum_probs=72.9

Q ss_pred             cCCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCCCcccccC
Q 019122           25 ASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCA  104 (346)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~~~~tRcS  104 (346)
                      .+.||++||||.+||+.|+.+.|.++++.||+.. +.++.|.+|+.|++||++||.+|.+.|+..+..|.          
T Consensus        35 s~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~-~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~----------  103 (238)
T 3tmm_A           35 SSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAK-TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYK----------  103 (238)
T ss_dssp             CCHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH----------
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH----------
Confidence            3568899999999999999999999999999876 89999999999999999999999999999888774          


Q ss_pred             HHHHHHHHhhCCHHHH
Q 019122          105 PDRLAAAVLQLTDEQR  120 (346)
Q Consensus       105 ~~~~~~~i~~Ls~~qk  120 (346)
                       ..+......++|.|.
T Consensus       104 -~e~~~y~~~~~p~~~  118 (238)
T 3tmm_A          104 -EEISRFKEQLTPSQI  118 (238)
T ss_dssp             -HHHHHHHHHCCHHHH
T ss_pred             -HHHHHHHhcCCHHHH
Confidence             344455566777664

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

Probab=98.75  E-value=5.8e-10  Score=101.06  Aligned_cols=63  Identities=24%  Similarity=0.269  Sum_probs=58.7

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .|||.||||++|||.|+.+++.+++..+|.     ++.|++|..|++||+++|.+|.++|.+.+..|.
T Consensus       110 kdp~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~  172 (214)
T 3tq6_A          110 TLLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYH  172 (214)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSSCSSHH-----HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCcccccchhhhhHHHHHHhhccCCHH-----HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999999988875     899999999999999999999999999888874

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

Probab=98.68  E-value=1.1e-09  Score=100.75  Aligned_cols=63  Identities=24%  Similarity=0.269  Sum_probs=58.7

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      .|||.||||++|||.|+.|.+.+++..||.     ++.|.+|+.|++||+++|.+|.++|++.+..|.
T Consensus       142 kdp~~PKrP~say~lF~~e~r~~~k~~~p~-----ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~  204 (238)
T 3tmm_A          142 TLLGKPKRPRSAYNVYVAERFQEAKGDSPQ-----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYH  204 (238)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSCCSSHH-----HHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCcHHHHHHHHHHHHHhccCHH-----HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            479999999999999999999999988875     799999999999999999999999999888875

>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=98.58  E-value=1.7e-08  Score=86.89  Aligned_cols=65  Identities=23%  Similarity=0.316  Sum_probs=60.3

Q ss_pred             CCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           29 GGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      |+++|||.++||.|..+.+.+++..||+ ..+.++.|.+|..|++||++||.+|.+.|+.....|.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~   66 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPR-MRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHR   66 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSS-CCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHH
Confidence            6799999999999999999999999998 6788999999999999999999999999998776654

---

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	346
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-07
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-06
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	8e-06
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	1e-05
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	3e-05
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-05
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-05
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	4e-05
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	9e-05
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	5e-04
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	6e-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 = 47.2 bits (112), Expect = 1e-07
 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 = 43.8 bits (103), Expect = 2e-06
 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 = 41.4 bits (97), Expect = 8e-06
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 36 RNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           N FI +  +  R++   +       EI K++G  +K L   EK  +  EA++
Sbjct: 9  MNAFIVWSRDQRRKMALENPRMRN-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 = 40.6 bits (95), Expect = 1e-05
 Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 36 RNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           + F  +  E   +IK       I  ++ K++G  + N   ++K  Y+ +A +
Sbjct: 7  PSAFFLFCSEYRPKIKGEHPGLSIG-DVAKKLGEMWNNTAADDKQPYEKKAAK 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 = 39.8 bits (93), Expect = 3e-05
 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 = 39.5 bits (92), Expect = 3e-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

>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 = 39.9 bits (93), Expect = 4e-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

>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 = 39.0 bits (91), Expect = 4e-05
 Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 1/53 (1%)

Query: 36 RNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKR 88
           N F+ +  +  R+I            I K +GS +K +   EK  Y  E  R
Sbjct: 7  MNAFMVWAKDERRKILQAFPDMH-NSNISKILGSRWKAMTNLEKQPYYEEQAR 58

>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 = 38.2 bits (89), Expect = 9e-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 = 36.8 bits (85), Expect = 5e-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 = 36.5 bits (84), Expect = 6e-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	346
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.19
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.19
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.14
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.13
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.12
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.12
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.06
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.03
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	98.96
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	98.93
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	98.92
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	98.77

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

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

Probab=99.19  E-value=2.7e-12  Score=94.50  Aligned_cols=64  Identities=16%  Similarity=0.195  Sum_probs=59.2

Q ss_pred             CCccCCcchhhhhHHHHHHHHhcCCCcch-HHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           31 RKRQCRNGFIRYFGEVVRQIKANDGMACI-TKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      +||||+||||.|+.+.|.++++.||+... ..+|.|.+|..|++||+++|.+|.++|++.+.+|.
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~   65 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE   65 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999998655 57999999999999999999999999999887764

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

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

Probab=99.19  E-value=6.3e-12  Score=96.76  Aligned_cols=74  Identities=12%  Similarity=0.221  Sum_probs=67.4

Q ss_pred             cCCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCCCc
Q 019122           25 ASNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKF   99 (346)
Q Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~~~   99 (346)
                      +..|+++||||++||+.|+.+.|.++++.||+.. ..+|.+.+|..|++||++||.+|.++|++...+|..+..-
T Consensus        14 ~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~-~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~~~~   87 (90)
T d1wgfa_          14 GKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS-ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGP   87 (90)
T ss_dssp             CSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSC-HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSS
T ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCC-HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4578999999999999999999999999999764 5799999999999999999999999999999999876544

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

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

Probab=99.14  E-value=8.1e-12  Score=96.85  Aligned_cols=68  Identities=19%  Similarity=0.321  Sum_probs=62.7

Q ss_pred             CCCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           26 SNDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      -.||+.||||++||+.|+.+.+.++++.+|+. ...++.+++|..|++||+++|.+|.++|++...+|.
T Consensus        15 ~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~-~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~   82 (93)
T d1lwma_          15 KKDPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYE   82 (93)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTS-CHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCC-cHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999985 678999999999999999999999999999887764

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

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

Probab=99.13  E-value=4.9e-12  Score=95.06  Aligned_cols=64  Identities=16%  Similarity=0.292  Sum_probs=59.1

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      |.||||+||||.|+.+.|.++++.||+. ...+|.|.+|..|++||++||.+|.++|++...+|.
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~-~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~   64 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYE   64 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTC-CTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence            6799999999999999999999999985 567999999999999999999999999999877764

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

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

Probab=99.12  E-value=1.3e-11  Score=94.07  Aligned_cols=65  Identities=23%  Similarity=0.318  Sum_probs=60.4

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      |++|||+||||.|+.|.|.++++.+|+. ...+|.|.+|..|++||++||.+|.+.|.+...+|..
T Consensus         3 ~~iKRP~nay~lF~~~~r~~i~~~~p~~-~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~   67 (85)
T d1j46a_           3 DRVKRPMNAFIVWSRDQRRKMALENPRM-RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHRE   67 (85)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHhccC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999975 5779999999999999999999999999998887754

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

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

Probab=99.12  E-value=1.4e-11  Score=92.94  Aligned_cols=65  Identities=25%  Similarity=0.345  Sum_probs=60.2

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      +++|||+||||.|+.|.|+++++.||+. ...+|.|.+|..|++||++||.+|.+.|++...+|..
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~-~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~   65 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKM-HNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMK   65 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTS-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCC-CHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999999975 6789999999999999999999999999998887754

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

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

Probab=99.06  E-value=3.2e-11  Score=88.54  Aligned_cols=62  Identities=24%  Similarity=0.289  Sum_probs=57.4

Q ss_pred             CccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           32 KRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      -|||.|||+.|+.+.|.++++.||+ ....+|.|.+|+.|++||+++|.+|.+.|++...+|.
T Consensus         3 iKRP~nay~lf~~~~r~~i~~~~p~-~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~   64 (70)
T d1i11a_           3 IKRPMNAFMVWAKDERRKILQAFPD-MHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHL   64 (70)
T ss_dssp             SCCSCCHHHHHHHHHHHHHHTTCSS-CCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHhcc-CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            4899999999999999999999995 5678899999999999999999999999999887764

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

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

Probab=99.03  E-value=2.6e-11  Score=93.39  Aligned_cols=68  Identities=16%  Similarity=0.227  Sum_probs=62.7

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      .||+.||||+|||+.|+.+.+..+++.||+. .+.+|.+++|..|++||+++|.+|.++|.+...+|..
T Consensus         6 k~p~~PKrP~say~lf~~~~r~~~~~~~p~~-~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~   73 (91)
T d1k99a_           6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFER   73 (91)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTS-CSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999965 4789999999999999999999999999998877743

>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=98.96  E-value=2.9e-10  Score=89.01  Aligned_cols=81  Identities=25%  Similarity=0.297  Sum_probs=66.2

Q ss_pred             CCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCCCcccccCHHH
Q 019122           28 DGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPDR  107 (346)
Q Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~~~~tRcS~~~  107 (346)
                      ..|.+|||+||||.|+.|.+.+++..|+   ...++.|++|..|++||++||.+|.++|++...+|.           ..
T Consensus         5 ~~~p~KrP~~ay~~F~~e~r~~~~~~~~---~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~-----------~e   70 (101)
T d1v63a_           5 SSGPKKPPMNGYQKFSQELLSNGELNHL---PLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK-----------VH   70 (101)
T ss_dssp             CCSSCCCCSSSHHHHHHHHHHHCTTTTS---CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH-----------HH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHhcCC---CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHH-----------HH
Confidence            3456799999999999999999988776   467999999999999999999999999999888874           33


Q ss_pred             HHHHHhhCCHHHHHH
Q 019122          108 LAAAVLQLTDEQRVV  122 (346)
Q Consensus       108 ~~~~i~~Ls~~qk~~  122 (346)
                      +......+++.++..
T Consensus        71 ~~~y~~~~~~~~~~~   85 (101)
T d1v63a_          71 LDLWVKSLSPQDRAA   85 (101)
T ss_dssp             HHHHHHHSCTTHHHH
T ss_pred             HHHHHhcCCHHHHHH
Confidence            344445666666543

>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=98.93  E-value=2.1e-10  Score=87.43  Aligned_cols=62  Identities=19%  Similarity=0.369  Sum_probs=56.9

Q ss_pred             ccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccC
Q 019122           33 RQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIG   95 (346)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~   95 (346)
                      |||+||||.|+.+.|.++++.||+. ...+|.+.+|..|++||++||.+|.+.|++...+|..
T Consensus         4 kRP~naf~lF~~~~r~~~~~~~P~~-~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~   65 (86)
T d2lefa_           4 KKPLNAFMLYMKEMRANVVAESTLK-ESAAINQILGRRWHALSREEQAKYYELARKERQLHMQ   65 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCC-CHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence            7999999999999999999999975 6778999999999999999999999999998777643

>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=98.92  E-value=1.3e-10  Score=85.76  Aligned_cols=62  Identities=11%  Similarity=0.254  Sum_probs=55.7

Q ss_pred             CCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhcccccc
Q 019122           30 GRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKI   94 (346)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~   94 (346)
                      |+||||+||||.|+.|.|.++++.||+ ....+|.|.+|..|++|+  ||.+|.++|++...+|.
T Consensus         2 n~PKrP~say~lf~~~~r~~~k~~~p~-~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~   63 (73)
T d1qrva_           2 DKPKRPLSAYMLWLNSARESIKRENPG-IKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYD   63 (73)
T ss_dssp             CSCCCCCCHHHHHHHHHHHHHHHTSTT-CCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCcHHHHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999997 567899999999999986  48899999988777663

>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=98.77  E-value=1.6e-09  Score=85.88  Aligned_cols=82  Identities=21%  Similarity=0.216  Sum_probs=66.3

Q ss_pred             CCCCCCccCCcchhhhhHHHHHHHHhcCCCcchHHHHHHHhccCCCCCChhhhhhhhHHhhhccccccCCCCcccccCHH
Q 019122           27 NDGGRKRQCRNGFIRYFGEVVRQIKANDGMACITKEIRKEIGSTYKNLPPEEKCRYKSEAKRVGKSKIGKAKFPTRCAPD  106 (346)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~sl~~~~k~~~~~~a~~~~~~~~~~~~~~tRcS~~  106 (346)
                      .|+..+|+|++||+.|+.|++.+++.     ....++.+++|..|++||++||.+|.++|++.+.+|.           .
T Consensus        13 ~~~~p~K~P~~ay~lF~~~~r~~~~~-----~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~-----------~   76 (108)
T d1v64a_          13 FDGRPTKPPPNSYSLYCAELMANMKD-----VPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYE-----------V   76 (108)
T ss_dssp             TTTSCCCCCSSHHHHHHHHHHHHCTT-----SCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHH-----------H
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHccC-----CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHH-----------H
Confidence            34555688899999999999987754     4568999999999999999999999999999988884           3


Q ss_pred             HHHHHHhhCCHHHHHHHH
Q 019122          107 RLAAAVLQLTDEQRVVVR  124 (346)
Q Consensus       107 ~~~~~i~~Ls~~qk~~I~  124 (346)
                      .+......+++.+++.+.
T Consensus        77 ~~~~y~~~~~~~~k~~~~   94 (108)
T d1v64a_          77 ELLRFLESLPEEEQQRVL   94 (108)
T ss_dssp             HHHHHHHHSCHHHHHHHH
T ss_pred             HHHHHHhhCCHHHHHHHH
Confidence            445555678887776553