Citrus Sinensis ID: 030615

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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----
Protein Sequence
MATNVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
Secondary Structure (PSIPRED)
cccccEEEEEEEEEEccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccEEEEEEEEEEcccccHHcEEEEEccccccEEEEccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccEEccccccccccccccHcccccccccHccccc
Coil and Loop (DISEMBL)
MATNVLVFLFFLGvsvpcsslfnivtvrcGHCANLLNVNMVSAlqavplqdpqkqhinledsitkdcgssskcnkfssafetaehetprmppirppekrqrvpsAYNRFIKEEIQRikasnpdishREAFSTAAknwahfphihfglkldgnkqaKLDKAAAYaegtqksngfy
Flexible Loop (DISEMBL)
MATNVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCNKFSSAfetaehetprmppirppekrqrvPSAYNRFIKEEIqrikasnpdiSHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAyaegtqksngfy
Low Complexity Region (SEG)
MATNvlvflfflgvSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
Disordered region (IsUnstruct)
***NVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPL*******************************************************************************AFSTAAKNWAHFPHIHFGLKLDG***********************
Disordered Region (DISOPRED)
*ATNVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMV******************************************************************RFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP******************************GFY
Disordered Region (DISEMBL)
MATNVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCNKFSSA**********MPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
Disordered Region (DISPRO)
**TNVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVP******************************************PPIRP*EKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD************************
Transmembrane Helix (TMHMM)
iiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooohhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MATNVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
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

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	174	2.2.26 [Sep-21-2011]
Q9XFB0	184	Putative axial regulator	yes	no	0.902	0.853	0.649	5e-52
Q8GW46	164	Axial regulator YABBY 5 O	no	no	0.867	0.920	0.609	5e-45
Q10FZ7	186	Protein YABBY 2 OS=Oryza	yes	no	0.919	0.860	0.553	8e-41
O22152	229	Axial regulator YABBY 1 O	no	no	0.942	0.716	0.510	4e-37
Q2QM17	207	Protein YABBY 6 OS=Oryza	no	no	0.925	0.777	0.478	1e-35
Q0JBF0	266	Protein YABBY 5 OS=Oryza	no	no	0.942	0.616	0.443	2e-35
Q01JG2	266	Protein YABBY 5 OS=Oryza	N/A	no	0.942	0.616	0.443	2e-35
Q7XIM7	169	Protein YABBY 1 OS=Oryza	no	no	0.798	0.822	0.532	4e-35
Q6H668	256	Protein YABBY 4 OS=Oryza	no	no	0.804	0.546	0.494	4e-34
A2X7Q3	256	Protein YABBY 4 OS=Oryza	N/A	no	0.804	0.546	0.494	4e-34

>sp|Q9XFB0|YAB2_ARATH Putative axial regulator YABBY 2 OS=Arabidopsis thaliana GN=YAB2 PE=2 SV=1

 Score =  203 bits (516), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 111/171 (64%), Positives = 126/171 (73%), Gaps = 14/171 (8%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQ---AVPL-QD--PQKQHINLEDSIT 64
            L VSVP +SLF +VTVRCGHC NLL++N+  +L    A P+ QD  P +QH        
Sbjct: 21  ILAVSVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAPPIHQDLQPHRQHTT-SLVTR 79

Query: 65  KDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDI 124
           KDC SSS+     S  E  + E PRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKA NP+I
Sbjct: 80  KDCASSSRSTNNLS--ENIDREAPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKACNPEI 137

Query: 125 SHREAFSTAAKNWAHFPHIHFGLKLDGNKQAK-LDKAAAYAEGTQKSNGFY 174
           SHREAFSTAAKNWAHFPHIHFGLKLDGNK+ K LD++ A     QKSNG+Y
Sbjct: 138 SHREAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLDQSVA----GQKSNGYY 184

Involved in the abaxial cell fate determination during embryogenesis and organogenesis.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8GW46|YAB5_ARATH Axial regulator YABBY 5 OS=Arabidopsis thaliana GN=YAB5 PE=2 SV=1

 Score =  180 bits (456), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 100/164 (60%), Positives = 115/164 (70%), Gaps = 13/164 (7%)

Query: 1   MATNVLVFL------FFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQK 54
           MAT  L ++        L V+VPCSSLF+IVTVRCGHC NL +VNM +ALQ+  L  P  
Sbjct: 6   MATEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQS--LSRPNF 63

Query: 55  QHINLEDSITKDCGSSSKCN-KFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEE 113
           Q  N       + GSSS+ + K  S   T      R+   RPPEKRQRVPSAYN+FIKEE
Sbjct: 64  QATNYA---VPEYGSSSRSHTKIPSRISTRTITEQRIVN-RPPEKRQRVPSAYNQFIKEE 119

Query: 114 IQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKL 157
           IQRIKA+NPDISHREAFSTAAKNWAHFPHIHFGL L+ NKQAK+
Sbjct: 120 IQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNKQAKI 163

Arabidopsis thaliana (taxid: 3702)

>sp|Q10FZ7|YAB2_ORYSJ Protein YABBY 2 OS=Oryza sativa subsp. japonica GN=YAB2 PE=2 SV=1

 Score =  166 bits (420), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 93/168 (55%), Positives = 112/168 (66%), Gaps = 8/168 (4%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVP----LQDPQKQHINLEDSITKD 66
              VSVP +S+ NIVTVRCGHC +LL+VN+   +QA+P    LQD  K H         +
Sbjct: 23  IFAVSVPSNSMLNIVTVRCGHCTSLLSVNLRGLVQALPAEDHLQDNLKMHNMSFRENYSE 82

Query: 67  CGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISH 126
            GSSS+  +    F  ++++T  M  +RPPEKRQRVPSAYNRFIKEEI+RIKA+NPDISH
Sbjct: 83  YGSSSRYGRVPMMF--SKNDTEHMLHVRPPEKRQRVPSAYNRFIKEEIRRIKANNPDISH 140

Query: 127 REAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           REAFSTAAKNWAHFP+IHFGL        KLD+A   A   QK    Y
Sbjct: 141 REAFSTAAKNWAHFPNIHFGLG-SHESSKKLDEAIG-APSPQKVQRLY 186

Oryza sativa subsp. japonica (taxid: 39947)

>sp|O22152|YAB1_ARATH Axial regulator YABBY 1 OS=Arabidopsis thaliana GN=YAB1 PE=1 SV=1

 Score =  154 bits (388), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 93/182 (51%), Positives = 107/182 (58%), Gaps = 18/182 (9%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVS----ALQAVPLQDPQKQHINLEDSIT-- 64
            L V+VP +SLF  VTVRCG C NLL+VNM S    A   + LQ     + N +D +   
Sbjct: 36  ILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYVLPASNQLQLQLGPHSYFNPQDILEEL 95

Query: 65  KDCGSSS---------KCNKFSSAFET-AEHETPRMPPI-RPPEKRQRVPSAYNRFIKEE 113
           +D  S+            N   S  +   +HE P+ PP+ RPPEKRQRVPSAYNRFIKEE
Sbjct: 96  RDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEE 155

Query: 114 IQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQ-KSNG 172
           IQRIKA NPDISHREAFS AAKNWAHFPHIHFGL  D     K +      E       G
Sbjct: 156 IQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDNQPVKKTNMPQQEGEDNMVMKEG 215

Query: 173 FY 174
           FY
Sbjct: 216 FY 217

Involved in the abaxial cell fate determination during embryogenesis and organogenesis. Required during flower formation and development, particularly for the patterning of floral organs. Positive regulator of class B (AP3 and PI) activity in whorls 2 and 3. Negative regulator of class B activity in whorl 1 and of SUP activity in whorl 3. Interacts with class A proteins (AP1, AP2 and LUG) to repress class C (AG) activity in whorls 1 and 2. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity. In vitro, can compete and displace the AP1 protein binding to DNA containing CArG box.

Arabidopsis thaliana (taxid: 3702)

>sp|Q2QM17|YAB6_ORYSJ Protein YABBY 6 OS=Oryza sativa subsp. japonica GN=YAB6 PE=2 SV=1

 Score =  149 bits (375), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/188 (47%), Positives = 108/188 (57%), Gaps = 27/188 (14%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVP-LQDPQKQHINLEDSITKDCGS 69
            L VSVP +S+ NIVTVRCGHC NLL+VN+   + + P LQD    H +L++S    C  
Sbjct: 22  ILAVSVPGNSMLNIVTVRCGHCTNLLSVNLRGLMHSAPALQD--HHHHHLQESGLSGCFR 79

Query: 70  SSKCNKFSSAFETAEHETPRMPPI--------------------RPPEKRQRVPSAYNRF 109
                        +     R+PP                     RPPEKRQRVPSAYNRF
Sbjct: 80  DQSGYPEFGFSAASSSSKLRLPPAAAAMVSYSQQNQQLEQALHARPPEKRQRVPSAYNRF 139

Query: 110 IKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLK---LDGNKQAKLDKAAAYAEG 166
           IKEEI+RIKA+NPDISHREAFSTAAKNWAH+P+IHFGL      G K   +D     A  
Sbjct: 140 IKEEIRRIKANNPDISHREAFSTAAKNWAHYPNIHFGLSPGHEGGKKLVDVDPIPT-APS 198

Query: 167 TQKSNGFY 174
           ++K  GFY
Sbjct: 199 SKKIQGFY 206

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q0JBF0|YAB5_ORYSJ Protein YABBY 5 OS=Oryza sativa subsp. japonica GN=YAB5 PE=2 SV=1

 Score =  147 bits (372), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/205 (44%), Positives = 106/205 (51%), Gaps = 41/205 (20%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNM--------VSALQAVP----LQDPQKQHIN 58
            L V VPCSSLF  VTVRCGHCANLL+VN+         S    +P    L  P   H  
Sbjct: 42  ILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPFGQALLSPTSPHGL 101

Query: 59  LED-----------------------SITKDCGSSSKCNKFSSAFETAEHETPRMPPIRP 95
           L++                       S    C +++     +SA   A    P+ P   P
Sbjct: 102 LDEVPSFQAPASLMTEQASPNVSSITSSNSSCANNAPATSMASAANKATQREPQQPKNAP 161

Query: 96  -----PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD 150
                 EKRQRVPSAYNRFIK+EIQRIKASNPDI+HREAFS AAKNWAHFPHIHFGL  D
Sbjct: 162 SANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNWAHFPHIHFGLMPD 221

Query: 151 -GNKQAKLDKAAAYAEGTQKSNGFY 174
            G K+  +       E     +G Y
Sbjct: 222 QGLKKTGIQSQDGAGECMLFKDGLY 246

May be involved in leaf cell growth and differentiation, rather than abaxial cell fate determination.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q01JG2|YAB5_ORYSI Protein YABBY 5 OS=Oryza sativa subsp. indica GN=YAB5 PE=2 SV=2

 Score =  147 bits (372), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/205 (44%), Positives = 106/205 (51%), Gaps = 41/205 (20%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNM--------VSALQAVP----LQDPQKQHIN 58
            L V VPCSSLF  VTVRCGHCANLL+VN+         S    +P    L  P   H  
Sbjct: 42  ILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPFGQALLSPTSPHGL 101

Query: 59  LED-----------------------SITKDCGSSSKCNKFSSAFETAEHETPRMPPIRP 95
           L++                       S    C +++     +SA   A    P+ P   P
Sbjct: 102 LDEVPSFQAPASLMTEQASPNVSSITSSNSSCANNAPATSMASAANKATQREPQQPKNAP 161

Query: 96  -----PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD 150
                 EKRQRVPSAYNRFIK+EIQRIKASNPDI+HREAFS AAKNWAHFPHIHFGL  D
Sbjct: 162 SANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNWAHFPHIHFGLMPD 221

Query: 151 -GNKQAKLDKAAAYAEGTQKSNGFY 174
            G K+  +       E     +G Y
Sbjct: 222 QGLKKTGIQSQDGAGECMLFKDGLY 246

May be involved in leaf cell growth and differentiation, rather than abaxial cell fate determination.

Oryza sativa subsp. indica (taxid: 39946)

>sp|Q7XIM7|YAB1_ORYSJ Protein YABBY 1 OS=Oryza sativa subsp. japonica GN=YAB1 PE=2 SV=1

 Score =  147 bits (370), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 74/139 (53%), Positives = 95/139 (68%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSS 70
            L V+VP +  +NIVTVRCGHC  +L++++    QA  +QD Q Q+   + +       +
Sbjct: 21  ILVVNVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQDHQVQNRGFQGNNFGSYDIA 80

Query: 71  SKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAF 130
           S+  + S+A         ++ PIRPPEKRQRVPSAYNRFIKEEIQRIK SNP+ISHREAF
Sbjct: 81  SRNQRTSTAMYPMPTSQQQVSPIRPPEKRQRVPSAYNRFIKEEIQRIKTSNPEISHREAF 140

Query: 131 STAAKNWAHFPHIHFGLKL 149
           S AAKNWAH P +HFGL +
Sbjct: 141 SAAAKNWAHLPRLHFGLSV 159

May play a role in floral meristem development and maintenance of stamens, rather than in determining polarity in floral organs.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6H668|YAB4_ORYSJ Protein YABBY 4 OS=Oryza sativa subsp. japonica GN=YAB4 PE=2 SV=1

 Score =  144 bits (362), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 89/180 (49%), Positives = 101/180 (56%), Gaps = 40/180 (22%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNM------------VSALQAVP-LQDPQKQHI 57
            L V VPCSSLF  VTVRCGHCANLL+VN+             + L   P L  P   H 
Sbjct: 36  ILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQLHFGPSLLSPTSPHG 95

Query: 58  NLEDS-------ITKDCGSSS----------KCNKFSSAFETA-------EHETPRMPPI 93
            L++        + +   S+S           C   + A +         E E P+  P 
Sbjct: 96  LLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAKPVQQEPELPKNAPA 155

Query: 94  ---RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD 150
              RPPEKRQRVPSAYNRFIK+EIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL  D
Sbjct: 156 SANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPD 215

Seems to be associated with phloem cell differentiation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|A2X7Q3|YAB4_ORYSI Protein YABBY 4 OS=Oryza sativa subsp. indica GN=YAB4 PE=2 SV=1

 Score =  144 bits (362), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 89/180 (49%), Positives = 101/180 (56%), Gaps = 40/180 (22%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNM------------VSALQAVP-LQDPQKQHI 57
            L V VPCSSLF  VTVRCGHCANLL+VN+             + L   P L  P   H 
Sbjct: 36  ILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQLHFGPSLLSPTSPHG 95

Query: 58  NLEDS-------ITKDCGSSS----------KCNKFSSAFETA-------EHETPRMPPI 93
            L++        + +   S+S           C   + A +         E E P+  P 
Sbjct: 96  LLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAKPVQQEPELPKNAPA 155

Query: 94  ---RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD 150
              RPPEKRQRVPSAYNRFIK+EIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL  D
Sbjct: 156 SANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPD 215

Oryza sativa subsp. indica (taxid: 39946)

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	174
427199347	181	YABBY2-like transcription factor YAB2 [M	0.908	0.872	0.830	5e-73
225436100	183	PREDICTED: putative axial regulator YABB	0.925	0.879	0.789	4e-68
118487174	191	unknown [Populus trichocarpa]	0.931	0.848	0.760	8e-66
224058941	185	predicted protein [Populus trichocarpa]	0.931	0.875	0.760	1e-65
351727853	183	uncharacterized protein LOC100500091 [Gl	0.913	0.868	0.730	2e-63
351724555	191	uncharacterized protein LOC100500026 [Gl	0.977	0.890	0.686	1e-60
41745658	186	YABBY2-like transcription factor YAB2 [A	0.919	0.860	0.711	3e-59
255549657	190	Axial regulator YABBY2, putative [Ricinu	0.936	0.857	0.757	1e-58
356543672	179	PREDICTED: putative axial regulator YABB	0.890	0.865	0.715	1e-58
255638173	181	unknown [Glycine max]	0.890	0.856	0.706	2e-58

>gi|427199347|gb|AFY26892.1| YABBY2-like transcription factor YAB2 [Morella rubra]

 Score =  278 bits (712), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 137/165 (83%), Positives = 145/165 (87%), Gaps = 7/165 (4%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSS 70
            L VSVPCSSLF IVTVRCGHCANLL+VNM ++LQAVP QD QKQH+     I++DCGSS
Sbjct: 23  ILAVSVPCSSLFTIVTVRCGHCANLLSVNMGASLQAVPPQDSQKQHV-----ISEDCGSS 77

Query: 71  SKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAF 130
           SKCNKFS AFET EHE PRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAF
Sbjct: 78  SKCNKFS-AFETVEHEQPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAF 136

Query: 131 STAAKNWAHFPHIHFGLKLDGNKQAKLDKA-AAYAEGTQKSNGFY 174
           STAAKNWAHFPHIHFGLKLDGNKQAKLD+  A   +GTQ SNGFY
Sbjct: 137 STAAKNWAHFPHIHFGLKLDGNKQAKLDQTLAGSDQGTQNSNGFY 181

Source: Morella rubra

Species: Morella rubra

Genus: Morella

Family: Myricaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436100|ref|XP_002277937.1| PREDICTED: putative axial regulator YABBY 2 [Vitis vinifera] gi|296084019|emb|CBI24407.3| unnamed protein product [Vitis vinifera]

 Score =  262 bits (669), Expect = 4e-68,   Method: Compositional matrix adjust.
 Identities = 131/166 (78%), Positives = 143/166 (86%), Gaps = 5/166 (3%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQD--PQKQHINLEDSITKDCG 68
            L VSVPC+SLF IVTVRCGHCANLL+VNM + LQ VP QD   QKQ ++  D  ++DCG
Sbjct: 21  ILAVSVPCTSLFTIVTVRCGHCANLLSVNMGALLQTVPTQDLQSQKQQLSCGDP-SEDCG 79

Query: 69  SSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHRE 128
           SSSKCNKFS AFE+AEHE PRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDI+HRE
Sbjct: 80  SSSKCNKFS-AFESAEHEQPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDITHRE 138

Query: 129 AFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           AFSTAAKNWAHFPHIHFGLKLDGNKQ KLD+A A  EG  K++GFY
Sbjct: 139 AFSTAAKNWAHFPHIHFGLKLDGNKQGKLDQAFA-GEGPHKAHGFY 183

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118487174|gb|ABK95415.1| unknown [Populus trichocarpa]

 Score =  254 bits (650), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 127/167 (76%), Positives = 138/167 (82%), Gaps = 5/167 (2%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQH---INLEDSITKDC 67
            L VSVP SSLFNIVTVRCGHC NLL+VNM ++LQ +PLQDPQ Q    IN ED + K+ 
Sbjct: 21  ILAVSVPSSSLFNIVTVRCGHCGNLLSVNMGASLQTLPLQDPQSQKLLLINSED-LNKNF 79

Query: 68  GSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR 127
           GSSSKCNK + A E+ EHE PRMP IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR
Sbjct: 80  GSSSKCNKVT-ASESTEHEPPRMPAIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR 138

Query: 128 EAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           EAFSTAAKNWAHFPHIHFGLKLD NK AKLD  +   EGTQK++G Y
Sbjct: 139 EAFSTAAKNWAHFPHIHFGLKLDSNKHAKLDHQSFAGEGTQKTSGLY 185

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224058941|ref|XP_002299655.1| predicted protein [Populus trichocarpa] gi|222846913|gb|EEE84460.1| predicted protein [Populus trichocarpa]

 Score =  254 bits (649), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 127/167 (76%), Positives = 138/167 (82%), Gaps = 5/167 (2%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQH---INLEDSITKDC 67
            L VSVP SSLFNIVTVRCGHC NLL+VNM ++LQ +PLQDPQ Q    IN ED + K+ 
Sbjct: 21  ILAVSVPSSSLFNIVTVRCGHCGNLLSVNMGASLQTLPLQDPQSQKLLLINSED-LNKNF 79

Query: 68  GSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR 127
           GSSSKCNK + A E+ EHE PRMP IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR
Sbjct: 80  GSSSKCNKVT-ASESTEHEPPRMPAIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR 138

Query: 128 EAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           EAFSTAAKNWAHFPHIHFGLKLD NK AKLD  +   EGTQK++G Y
Sbjct: 139 EAFSTAAKNWAHFPHIHFGLKLDSNKHAKLDHQSFAGEGTQKTSGLY 185

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351727853|ref|NP_001236663.1| uncharacterized protein LOC100500091 [Glycine max] gi|255629073|gb|ACU14881.1| unknown [Glycine max]

 Score =  246 bits (629), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 122/167 (73%), Positives = 137/167 (82%), Gaps = 8/167 (4%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSS 70
            L VSVP SSL  IVTVRCGHCANLL+VNM ++LQA P QDPQKQH++ ++  +K+ GSS
Sbjct: 22  ILAVSVPYSSLLTIVTVRCGHCANLLSVNMGASLQAFPPQDPQKQHLSFQEPSSKELGSS 81

Query: 71  SKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAF 130
           SKC+K +  FE  EHE PR+PPIRP EKR RVPSAYNRFIKEEIQRIKASNPDISHREAF
Sbjct: 82  SKCSKIA-PFEAVEHELPRIPPIRPTEKRHRVPSAYNRFIKEEIQRIKASNPDISHREAF 140

Query: 131 STAAKNWAHFPHIHFG---LKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           S+AAKNWAHFPHIHFG   LKLDGNKQ KLD+     EG +KSNGFY
Sbjct: 141 SSAAKNWAHFPHIHFGLKNLKLDGNKQEKLDQ----GEGAEKSNGFY 183

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724555|ref|NP_001235782.1| uncharacterized protein LOC100500026 [Glycine max] gi|255628597|gb|ACU14643.1| unknown [Glycine max]

 Score =  237 bits (605), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 127/185 (68%), Positives = 144/185 (77%), Gaps = 15/185 (8%)

Query: 1   MATNVLV----FLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQ--K 54
           ++ +VLV    FL ++ VSVP SSL  IVTVRCGHCANLL+VNM ++LQA P QDPQ  K
Sbjct: 11  ISESVLVLAFYFLVYILVSVPYSSLLTIVTVRCGHCANLLSVNMGASLQAFPPQDPQSQK 70

Query: 55  QHINLED-SITKDCGSSS-KCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKE 112
           Q ++ E+ S  K+ GSSS KCNK +   E  EHE PR+PPIRP EKR RVPSAYNRFIKE
Sbjct: 71  QLLSFEEPSSCKELGSSSSKCNKIAPFHEAVEHEQPRIPPIRPTEKRHRVPSAYNRFIKE 130

Query: 113 EIQRIKASNPDISHREAFSTAAKNWAHFPHIHFG---LKLDGNKQAKLDKAAAYAEGTQK 169
           EIQRIKASNPDISHREAFS+AAKNWAHFPHIHFG   LKLDGNKQ KLD+     EG +K
Sbjct: 131 EIQRIKASNPDISHREAFSSAAKNWAHFPHIHFGLKNLKLDGNKQEKLDQ----GEGAEK 186

Query: 170 SNGFY 174
           SNGFY
Sbjct: 187 SNGFY 191

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|41745658|gb|AAS10179.1| YABBY2-like transcription factor YAB2 [Antirrhinum majus]

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 121/170 (71%), Positives = 134/170 (78%), Gaps = 10/170 (5%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSS 70
            L VSVPCS++F IVTVRCGHCANLL+VNM + LQ+V LQD QKQ     ++  KD GSS
Sbjct: 21  ILAVSVPCSNMFTIVTVRCGHCANLLSVNMGALLQSVHLQDFQKQ--QHAEAAAKDNGSS 78

Query: 71  SKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAF 130
           SK N+++     AEHE P+MPPIRPPEKRQRVPSAYNRFIKEEIQRIKA NP+ISHREAF
Sbjct: 79  SKSNRYAPL--QAEHEQPKMPPIRPPEKRQRVPSAYNRFIKEEIQRIKAGNPEISHREAF 136

Query: 131 STAAKNWAHFPHIHFGLKLDGNKQAKL-DKAAAYAEGT-----QKSNGFY 174
           STAAKNWAHFPHIHFGLKLD NKQAKL D + A   GT     QKS GFY
Sbjct: 137 STAAKNWAHFPHIHFGLKLDSNKQAKLQDHSVAGGSGTTMARAQKSLGFY 186

Source: Antirrhinum majus

Species: Antirrhinum majus

Genus: Antirrhinum

Family: Plantaginaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549657|ref|XP_002515880.1| Axial regulator YABBY2, putative [Ricinus communis] gi|223545035|gb|EEF46549.1| Axial regulator YABBY2, putative [Ricinus communis]

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 125/165 (75%), Positives = 136/165 (82%), Gaps = 2/165 (1%)

Query: 11  FLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINL-EDSITKDCGS 69
            L VSVP S+L  IVTVRCGH ANLL+VNM  +LQ  PLQDPQ Q + L  + + KD GS
Sbjct: 21  ILAVSVPSSNLLTIVTVRCGHGANLLSVNMGGSLQTFPLQDPQSQKVQLNSEDLNKDTGS 80

Query: 70  SSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREA 129
           SSKCNK +S FE+A++E PRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREA
Sbjct: 81  SSKCNKVTS-FESADNEPPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREA 139

Query: 130 FSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           FSTAAKNWAHFPHIHFGLKLDGNK AK+D     AE TQKSNG Y
Sbjct: 140 FSTAAKNWAHFPHIHFGLKLDGNKHAKIDHQTFGAESTQKSNGLY 184

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543672|ref|XP_003540284.1| PREDICTED: putative axial regulator YABBY 2-like isoform 1 [Glycine max]

 Score =  230 bits (587), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 118/165 (71%), Positives = 133/165 (80%), Gaps = 10/165 (6%)

Query: 12  LGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDP-QKQHINLEDSITKDCGSS 70
           L VSVPCSSL  IVTVRCGHCANLL VNM ++LQ  P QD  Q+QH++++++ +K+ GSS
Sbjct: 23  LAVSVPCSSLLTIVTVRCGHCANLLTVNMGASLQTFPSQDTTQRQHLSVQEACSKELGSS 82

Query: 71  SKCNKFSSAFETAEHETPRMPPIRPP-EKRQRVPSAYNRFIKEEIQRIKASNPDISHREA 129
           SKC     +FET +HE     P   P EKRQRVPSAYNRFIKEEIQRIKASNPDISHREA
Sbjct: 83  SKCK----SFETVDHEQQPRIPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREA 138

Query: 130 FSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           FSTAAKNWAHFPHIHFGLKLDGNKQAKLD+     +GTQKSNGFY
Sbjct: 139 FSTAAKNWAHFPHIHFGLKLDGNKQAKLDQ----GDGTQKSNGFY 179

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638173|gb|ACU19400.1| unknown [Glycine max]

 Score =  229 bits (585), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 118/167 (70%), Positives = 133/167 (79%), Gaps = 12/167 (7%)

Query: 12  LGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDP---QKQHINLEDSITKDCG 68
           L VSVPCSSL  IVTVRCGHCANLL VNM ++LQ  P QD    Q+QH++++++ +K+ G
Sbjct: 23  LAVSVPCSSLLTIVTVRCGHCANLLTVNMGASLQTFPSQDTTQLQRQHLSVQEACSKELG 82

Query: 69  SSSKCNKFSSAFETAEHETPRMPPIRPP-EKRQRVPSAYNRFIKEEIQRIKASNPDISHR 127
           SSSKC     +FET +HE     P   P EKRQRVPSAYNRFIKEEIQRIKASNPDISHR
Sbjct: 83  SSSKCK----SFETVDHEQQPRIPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR 138

Query: 128 EAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY 174
           EAFSTAAKNWAHFPHIHFGLKLDGNKQAKLD+     +GTQKSNGFY
Sbjct: 139 EAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDQ----GDGTQKSNGFY 181

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	174
TAIR|locus:2826731	184	YAB2 "YABBY2" [Arabidopsis tha	0.873	0.826	0.672	1.5e-49
TAIR|locus:2066311	164	YAB5 "YABBY5" [Arabidopsis tha	0.787	0.835	0.652	5.2e-42
TAIR|locus:2126931	240	YAB3 "YABBY3" [Arabidopsis tha	0.511	0.370	0.703	6.4e-37
UNIPROTKB|Q7XIM7	169	YAB1 "Protein YABBY 1" [Oryza	0.787	0.810	0.536	1.2e-33
TAIR|locus:2005492	229	AFO "AT2G45190" [Arabidopsis t	0.522	0.397	0.677	3.8e-31
TAIR|locus:2028020	231	INO "INNER NO OUTER" [Arabidop	0.741	0.558	0.431	2.2e-25
TAIR|locus:2026418	181	CRC "AT1G69180" [Arabidopsis t	0.666	0.640	0.457	1.1e-23
UNIPROTKB|Q76EJ0	194	DL "Protein DROOPING LEAF" [Or	0.678	0.608	0.467	1.6e-22

TAIR|locus:2826731 YAB2 "YABBY2" [Arabidopsis thaliana (taxid:3702)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 113/168 (67%), Positives = 128/168 (76%)

Query:    15 SVPCSSLFNIVTVRCGHCANLLNVNM-VSALQ--AVPL-QD--PQKQHINLEDSIT-KDC 67
             SVP +SLF +VTVRCGHC NLL++N+ VS  Q  A P+ QD  P +QH      +T KDC
Sbjct:    25 SVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAPPIHQDLQPHRQHTT--SLVTRKDC 82

Query:    68 GSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHR 127
              SSS+     S  E  + E PRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKA NP+ISHR
Sbjct:    83 ASSSRSTNNLS--ENIDREAPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKACNPEISHR 140

Query:   128 EAFSTAAKNWAHFPHIHFGLKLDGNKQAK-LDKAAAYAEGTQKSNGFY 174
             EAFSTAAKNWAHFPHIHFGLKLDGNK+ K LD++ A   G QKSNG+Y
Sbjct:   141 EAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLDQSVA---G-QKSNGYY 184

GO:0005634 "nucleus" evidence=ISM

GO:0010158 "abaxial cell fate specification" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

TAIR|locus:2066311 YAB5 "YABBY5" [Arabidopsis thaliana (taxid:3702)]

 Score = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 94/144 (65%), Positives = 107/144 (74%)

Query:    15 SVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCN 74
             +VPCSSLF+IVTVRCGHC NL +VNM +ALQ+  L  P  Q  N       + GSSS+ +
Sbjct:    26 NVPCSSLFDIVTVRCGHCTNLWSVNMAAALQS--LSRPNFQATNYA---VPEYGSSSRSH 80

Query:    75 -KFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTA 133
              K  S   T      R+   RPPEKRQRVPSAYN+FIKEEIQRIKA+NPDISHREAFSTA
Sbjct:    81 TKIPSRISTRTITEQRIVN-RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTA 139

Query:   134 AKNWAHFPHIHFGLKLDGNKQAKL 157
             AKNWAHFPHIHFGL L+ NKQAK+
Sbjct:   140 AKNWAHFPHIHFGLMLESNKQAKI 163

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0006417 "regulation of translation" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

TAIR|locus:2126931 YAB3 "YABBY3" [Arabidopsis thaliana (taxid:3702)]

 Score = 313 (115.2 bits), Expect = 6.4e-37, Sum P(2) = 6.4e-37
 Identities = 64/91 (70%), Positives = 65/91 (71%)

Query:    86 ETPRMPPI-RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIH 144
             E PR PP  RPPEKRQRVPSAYNRFIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIH
Sbjct:   139 EMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIH 198

Query:   145 FGLKLDGNKQAKLDKAAAYAE-GTQKSNGFY 174
             FGL  D     K +      E G     GFY
Sbjct:   199 FGLMADHPPTKKANVRQQEGEDGMMGREGFY 229

GO:0005634 "nucleus" evidence=ISM

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

GO:0010158 "abaxial cell fate specification" evidence=IGI

UNIPROTKB|Q7XIM7 YAB1 "Protein YABBY 1" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 366 (133.9 bits), Expect = 1.2e-33, P = 1.2e-33
 Identities = 74/138 (53%), Positives = 95/138 (68%)

Query:    15 SVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCN 74
             +VP +  +NIVTVRCGHC  +L++++    QA  +QD Q Q+   + +       +S+  
Sbjct:    25 NVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQDHQVQNRGFQGNNFGSYDIASRNQ 84

Query:    75 KFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAA 134
             + S+A         ++ PIRPPEKRQRVPSAYNRFIKEEIQRIK SNP+ISHREAFS AA
Sbjct:    85 RTSTAMYPMPTSQQQVSPIRPPEKRQRVPSAYNRFIKEEIQRIKTSNPEISHREAFSAAA 144

Query:   135 KNWAHFPHIHFGLKL-DG 151
             KNWAH P +HFGL + DG
Sbjct:   145 KNWAHLPRLHFGLSVADG 162

GO:0005634 "nucleus" evidence=IDA

GO:0048833 "specification of floral organ number" evidence=IMP

TAIR|locus:2005492 AFO "AT2G45190" [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 3.8e-31, Sum P(2) = 3.8e-31
 Identities = 63/93 (67%), Positives = 67/93 (72%)

Query:    84 EHETPRMPPI-RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 142
             +HE P+ PP+ RPPEKRQRVPSAYNRFIKEEIQRIKA NPDISHREAFS AAKNWAHFPH
Sbjct:   125 QHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPH 184

Query:   143 IHFGLKLDGNKQAKLDKAAAYAEGTQ-KSNGFY 174
             IHFGL  D     K +      E       GFY
Sbjct:   185 IHFGLVPDNQPVKKTNMPQQEGEDNMVMKEGFY 217

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;TAS

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=ISS

GO:0009909 "regulation of flower development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

GO:0010158 "abaxial cell fate specification" evidence=IGI

GO:0010159 "specification of organ position" evidence=IMP

GO:0010093 "specification of floral organ identity" evidence=IMP

GO:0010450 "inflorescence meristem growth" evidence=IMP

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0009737 "response to abscisic acid stimulus" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0016226 "iron-sulfur cluster assembly" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=IMP

GO:0045165 "cell fate commitment" evidence=IMP

TAIR|locus:2028020 INO "INNER NO OUTER" [Arabidopsis thaliana (taxid:3702)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 63/146 (43%), Positives = 91/146 (62%)

Query:    15 SVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ---------DPQKQHINLEDSITK 65
             SVP +SL  +VTVRCGHC +LL+VN++ A   +PL          +  K+ +   D + +
Sbjct:    36 SVPFTSLSMVVTVRCGHCTSLLSVNLMKA-SFIPLHLLASLSHLDETGKEEVAATDGVEE 94

Query:    66 DCG--SSSKCNKFSSAFETAEHETPRMPPI-----RPPEKRQRVPSAYNRFIKEEIQRIK 118
             +    +  K N  ++   ++++E   +  +     +PPEKRQR PSAYN FIKEEI+R+K
Sbjct:    95 EAWKVNQEKENSPTTLVSSSDNEDEDVSRVYQVVNKPPEKRQRAPSAYNCFIKEEIRRLK 154

Query:   119 ASNPDISHREAFSTAAKNWAHFPHIH 144
             A NP ++H+EAFS AAKNWAHFP  H
Sbjct:   155 AQNPSMAHKEAFSLAAKNWAHFPPAH 180

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=IDA

GO:0048481 "ovule development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

TAIR|locus:2026418 CRC "AT1G69180" [Arabidopsis thaliana (taxid:3702)]

 Score = 272 (100.8 bits), Expect = 1.1e-23, P = 1.1e-23
 Identities = 59/129 (45%), Positives = 82/129 (63%)

Query:    16 VPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSS-SKCN 74
             +P   + + VTV+CGHC NL      S L   P   P + H++L   +    GS   K +
Sbjct:    37 IPLKRMLDTVTVKCGHCGNL------SFLTTTP---PLQGHVSLTLQMQSFGGSDYKKGS 87

Query:    75 KFSSAFETAEHETPR-MPP--IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFS 131
               SS+  T+  + P   PP  ++PPEK+QR+PSAYNRF+++EIQRIK++NP+I HREAFS
Sbjct:    88 SSSSSSSTSSDQPPSPSPPFVVKPPEKKQRLPSAYNRFMRDEIQRIKSANPEIPHREAFS 147

Query:   132 TAAKNWAHF 140
              AAKNWA +
Sbjct:   148 AAAKNWAKY 156

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS;TAS

GO:0005634 "nucleus" evidence=ISM

GO:0010254 "nectary development" evidence=IMP

GO:0048440 "carpel development" evidence=RCA;IMP

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0009944 "polarity specification of adaxial/abaxial axis" evidence=TAS

GO:0010582 "floral meristem determinacy" evidence=IGI

GO:0048479 "style development" evidence=IMP

GO:0006333 "chromatin assembly or disassembly" evidence=RCA

GO:0009827 "plant-type cell wall modification" evidence=RCA

GO:0009860 "pollen tube growth" evidence=RCA

GO:0009886 "post-embryonic morphogenesis" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0010093 "specification of floral organ identity" evidence=RCA

GO:0031540 "regulation of anthocyanin biosynthetic process" evidence=RCA

GO:0048441 "petal development" evidence=RCA

GO:0048443 "stamen development" evidence=RCA

GO:0048481 "ovule development" evidence=RCA

GO:0048507 "meristem development" evidence=RCA

UNIPROTKB|Q76EJ0 DL "Protein DROOPING LEAF" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 261 (96.9 bits), Expect = 1.6e-22, P = 1.6e-22
 Identities = 58/124 (46%), Positives = 74/124 (59%)

Query:    16 VPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHINLEDSITKDCGSSSKCNK 75
             VPC  L + VTV+CGHC NL  ++    +   PL  P    +        DC  +     
Sbjct:    26 VPCKRLMDTVTVKCGHCNNLSFLSPRPPM-VQPLS-PTDHPLGPFQGPCTDCRRNQPLPL 83

Query:    76 FSSAFETAEHETPRMP-PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAA 134
              S    T+   +PR P  ++PPEK+ R+PSAYNRF++EEIQRIKA+ PDI HREAFS AA
Sbjct:    84 VSP---TSNEGSPRAPFVVKPPEKKHRLPSAYNRFMREEIQRIKAAKPDIPHREAFSMAA 140

Query:   135 KNWA 138
             KNWA
Sbjct:   141 KNWA 144


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.316   0.129   0.386    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      174       164   0.00088  107 3  11 22  0.39    32
                                                     30  0.45    34


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  8
  No. of states in DFA:  600 (64 KB)
  Total size of DFA:  156 KB (2093 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  18.14u 0.20s 18.34t   Elapsed:  00:00:00
  Total cpu time:  18.14u 0.20s 18.34t   Elapsed:  00:00:00
  Start:  Sat May 11 07:41:49 2013   End:  Sat May 11 07:41:49 2013

GO:0010022 "meristem determinacy" evidence=IGI;IMP

GO:0048366 "leaf development" evidence=IMP

GO:0048440 "carpel development" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9XFB0	YAB2_ARATH	No assigned EC number	0.6491	0.9022	0.8532	yes	no
Q10FZ7	YAB2_ORYSJ	No assigned EC number	0.5535	0.9195	0.8602	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	174
pfam04690	170	pfam04690, YABBY, YABBY protein	2e-62
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	4e-04
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	6e-04

>gnl|CDD|113458 pfam04690, YABBY, YABBY protein

 Score =  190 bits (483), Expect = 2e-62
 Identities = 86/152 (56%), Positives = 97/152 (63%), Gaps = 19/152 (12%)

Query: 12  LGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQD---------------PQKQH 56
           L VSVP +SLFNIVTVRCGHC NLL+VN++     +P                     Q+
Sbjct: 22  LAVSVPYTSLFNIVTVRCGHCTNLLSVNLMMRSHLLPALSHLDETGKPELLQNLGVHGQN 81

Query: 57  INLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPP-IRPPEKRQRVPSAYNRFIKEEIQ 115
            N    +     S+S  +   S  +    E PR+PP  RPPEKRQRVPSAYNRFIKEEIQ
Sbjct: 82  FNSNM-MKSHSASTSVSSYMMSDNQD--EEMPRVPPVNRPPEKRQRVPSAYNRFIKEEIQ 138

Query: 116 RIKASNPDISHREAFSTAAKNWAHFPHIHFGL 147
           RIKA NPDISHREAFS AAKNWAHFPHIHFGL
Sbjct: 139 RIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 170

YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs. Length = 170

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

 Score = 36.8 bits (86), Expect = 4e-04
 Identities = 13/37 (35%), Positives = 18/37 (48%)

Query: 101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 137
           R  SAY  F +E+  ++K  NPD S  E      + W
Sbjct: 3   RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKW 39

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

 Score = 36.4 bits (85), Expect = 6e-04
 Identities = 13/37 (35%), Positives = 17/37 (45%)

Query: 101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 137
           R  SAY  F +E    +KA NP +S  E      + W
Sbjct: 3   RPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMW 39

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	174
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	100.0
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.25
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	97.8
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	97.74
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	97.71
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.7
smart00398	70	HMG high mobility group.	97.6
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	97.55
PTZ00199	94	high mobility group protein; Provisional	97.47
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	96.74
KOG0381	96	consensus HMG box-containing protein [General func	96.34
KOG3223	221	consensus Uncharacterized conserved protein [Funct	95.12
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	87.52

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

Probab=100.00  E-value=9.8e-72  Score=454.69  Aligned_cols=144  Identities=60%  Similarity=0.939  Sum_probs=111.4

Q ss_pred             ccceeeeeeeecccCCCCcceeeeecCCCCCccccccccccCCCCCCCcccccc--------CC-CCcccCcCC---CCC
Q 030615            4 NVLVFLFFLGVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQKQHI--------NL-EDSITKDCG---SSS   71 (174)
Q Consensus         4 ~~~~C~TILaVsVPcssL~~~VTVRCGHCtnLlsVNm~~llqs~~~q~~~~~~~--------~~-~~~~~~~~~---sss   71 (174)
                      .||||||||||||||+|||+|||||||||+|||||||++++++++.|++..+..        .. .+.......   +++
T Consensus        14 hCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (170)
T PF04690_consen   14 HCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPENFGSNSSSSSSSS   93 (170)
T ss_pred             EcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhccccccccccccccccccccccccCCCcc
Confidence            699999999999999999999999999999999999999999988766411110        00 111111111   111


Q ss_pred             cCCCCCCccccCCCCCCCCC-CCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccccc
Q 030615           72 KCNKFSSAFETAEHETPRMP-PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL  147 (174)
Q Consensus        72 ~~~~~~~~~~~~~~~~p~~~-~~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~PhihfGl  147 (174)
                      ++..........+++.|+++ ++||||||||+|||||+||||||||||++||||+|||||++|||||||+|||||||
T Consensus        94 ~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~phihfgl  170 (170)
T PF04690_consen   94 SSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFPHIHFGL  170 (170)
T ss_pred             ccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCcccccCC
Confidence            11110011233455667654 68999999999999999999999999999999999999999999999999999997

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

Probab=98.25  E-value=1.7e-06  Score=60.12  Aligned_cols=46  Identities=35%  Similarity=0.624  Sum_probs=38.5

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhccCC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKAS-NPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~-~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |.|-.|.+|||+.||++.+.+++.. .+.++++|++..++..|+..+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls   47 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLS   47 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcC
Confidence            5677899999999999999999999 888999999999999999754

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 ....

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

Probab=97.80  E-value=4.9e-05  Score=50.22  Aligned_cols=41  Identities=32%  Similarity=0.487  Sum_probs=38.7

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       101 RvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |-+|||..||++....+++.+|+++..|....++..|+..+
T Consensus         3 rp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls   43 (66)
T cd01390           3 RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS   43 (66)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            56899999999999999999999999999999999999765

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

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

Probab=97.74  E-value=6.4e-05  Score=52.05  Aligned_cols=42  Identities=17%  Similarity=0.284  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|-++||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus         3 KrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls   44 (72)
T cd01388           3 KRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALS   44 (72)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            367899999999999999999999999999999999999754

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

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

Probab=97.71  E-value=6.5e-05  Score=50.18  Aligned_cols=42  Identities=33%  Similarity=0.624  Sum_probs=37.3

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|-+|||..|+++....||+++|+++..|.-+.+++.|+..+
T Consensus         2 krP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~   43 (69)
T PF00505_consen    2 KRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLS   43 (69)
T ss_dssp             SSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCC
Confidence            467899999999999999999999999999999999999753

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

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

Probab=97.70  E-value=9e-05  Score=48.38  Aligned_cols=43  Identities=30%  Similarity=0.422  Sum_probs=39.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .|-+|+|..|++++...+++.+|+++..|....+++.|+..+.
T Consensus         2 krp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~   44 (66)
T cd00084           2 KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE   44 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence            3568999999999999999999999999999999999997654

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

>smart00398 HMG high mobility group

Probab=97.60  E-value=0.00017  Score=47.55  Aligned_cols=43  Identities=33%  Similarity=0.511  Sum_probs=39.5

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .|-+|+|..|+++....+++++|+++..|....++..|+..+.
T Consensus         3 krp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~   45 (70)
T smart00398        3 KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSE   45 (70)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCH
Confidence            4678999999999999999999999999999999999997653

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

Probab=97.55  E-value=0.0002  Score=50.07  Aligned_cols=43  Identities=16%  Similarity=0.348  Sum_probs=40.2

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .|-++||-.|+++....|+++||++++.|.-+.++..|+..+.
T Consensus         3 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~   45 (77)
T cd01389           3 PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESP   45 (77)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCH
Confidence            4789999999999999999999999999999999999998654

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.

>PTZ00199 high mobility group protein; Provisional

Probab=97.47  E-value=0.00033  Score=51.64  Aligned_cols=50  Identities=26%  Similarity=0.422  Sum_probs=42.8

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCc
Q 030615           93 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDIS--HREAFSTAAKNWAHFPH  142 (174)
Q Consensus        93 ~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~--HkEaFs~aAknW~~~Ph  142 (174)
                      .+.|.+-.|-+|||..|+++.-..|+++||+++  -.|.-+.++..|+..+.
T Consensus        17 ~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~   68 (94)
T PTZ00199         17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSE   68 (94)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCH
Confidence            355666678899999999999999999999987  57888899999998663

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

Probab=96.74  E-value=0.0025  Score=50.45  Aligned_cols=54  Identities=28%  Similarity=0.510  Sum_probs=48.3

Q ss_pred             CCCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCccccc
Q 030615           91 PPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFG  146 (174)
Q Consensus        91 ~~~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~PhihfG  146 (174)
                      .+-|.||||-+  -||..|--.+|.+||++||++.+-+-=-..=|.|..+|...|-
T Consensus        67 ~~drHPErR~K--AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeNP~N  120 (122)
T PF06244_consen   67 PIDRHPERRMK--AAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPENPFN  120 (122)
T ss_pred             CCCCCcchhHH--HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCCCcc
Confidence            45688999864  6999999999999999999999999888999999999998763

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

Probab=96.34  E-value=0.0088  Score=42.67  Aligned_cols=45  Identities=29%  Similarity=0.429  Sum_probs=40.2

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615           98 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus        98 KRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .-+|-+|||..|+.+.-.+||++||+++..|.=+.+...|.....
T Consensus        22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~   66 (96)
T KOG0381|consen   22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAE   66 (96)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCH
Confidence            456778899999999999999999999999999999999987543

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.12  E-value=0.01  Score=51.14  Aligned_cols=53  Identities=30%  Similarity=0.508  Sum_probs=47.5

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccccc
Q 030615           93 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL  147 (174)
Q Consensus        93 ~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~PhihfGl  147 (174)
                      -|-||||-|.  ||--|=..+|-|||.++|+++|-+-=-..-|.|..+|...|.-
T Consensus       161 drHPEkRmrA--A~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~Nq  213 (221)
T KOG3223|consen  161 DRHPEKRMRA--AFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFNQ  213 (221)
T ss_pred             ccChHHHHHH--HHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhhH
Confidence            3899998774  9999999999999999999999988778889999999988853

>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function

Probab=87.52  E-value=0.24  Score=33.56  Aligned_cols=36  Identities=19%  Similarity=0.454  Sum_probs=25.8

Q ss_pred             ccceeeeeeeecccCCCCcc---eeeeecCCCCCccccccc
Q 030615            4 NVLVFLFFLGVSVPCSSLFN---IVTVRCGHCANLLNVNMV   41 (174)
Q Consensus         4 ~~~~C~TILaVsVPcssL~~---~VTVRCGHCtnLlsVNm~   41 (174)
                      .|.-|..+|  .+|-+.++.   .-.+|||.|+.++++.++
T Consensus         8 ~C~~C~~lL--qlP~~~~~~~k~~~klrCGaCs~vl~~s~~   46 (46)
T PF11331_consen    8 VCSSCFELL--QLPAKFSLSKKNQQKLRCGACSEVLSFSLP   46 (46)
T ss_pred             ECccHHHHH--cCCCccCCCccceeEEeCCCCceeEEEecC
Confidence            477775554  457775443   568999999999988653

---

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	174
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	7e-06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	8e-06
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-05
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	4e-04
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	3e-04
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	8e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	8e-04

>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 = 43.7 bits (102), Expect = 7e-06
 Identities = 16/54 (29%), Positives = 22/54 (40%)

Query: 88  PRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 141
            R          ++  S+Y RF KE++   KA NPD    E     A+ W   P
Sbjct: 31  GRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 84

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

 Score = 43.2 bits (101), Expect = 8e-06
 Identities = 16/52 (30%), Positives = 22/52 (42%)

Query: 90  MPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 141
           M         ++  S+Y RF KE++   KA NPD    E     A+ W   P
Sbjct: 1   MGSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 52

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

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 15/78 (19%), Positives = 26/78 (33%)

Query: 60  EDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKA 119
           E    +D   + K             +       + P   +R PSA+  F  E   +IK 
Sbjct: 63  EKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKG 122

Query: 120 SNPDISHREAFSTAAKNW 137
            +P +S  +      + W
Sbjct: 123 EHPGLSIGDVAKKLGEMW 140

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

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 94  RPPEKRQRVPSAYNRFIKEEIQRIKASNPD--ISHREAFSTAAKNWAHFP 141
             P+K +   S+Y  F++   +  K  +PD  ++  E     ++ W    
Sbjct: 11  GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 60

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

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 8/44 (18%), Positives = 22/44 (50%)

Query: 94  RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 137
           + P+  ++  + Y RF  E+  +    +P++S+ +     +K +
Sbjct: 6   KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKY 49

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

 Score = 36.2 bits (84), Expect = 8e-04
 Identities = 13/46 (28%), Positives = 20/46 (43%)

Query: 92  PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 137
             + P + Q+  SAY  F ++    IK  NP+ +  E     A  W
Sbjct: 11  KKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMW 56

>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 = 36.1 bits (84), Expect = 8e-04
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 11/59 (18%)

Query: 90  MPPIRPPEKRQ-----------RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 137
           M   R P+KR            R  SAY  F  E    +++ NPDI+  +      + W
Sbjct: 1   MVTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	174
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	97.94
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	97.86
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	97.78
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	97.76
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	97.76
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	97.75
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	97.75
1wgf_A	90	Upstream binding factor 1; transcription factor, D	97.73
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	97.71
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	97.7
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	97.69
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	97.63
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	97.62
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	97.6
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	97.59
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	97.59
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	97.55
1ckt_A	71	High mobility group 1 protein; high-mobility group	97.52
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	97.49
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.45
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	97.44
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	97.38
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.38
2lhj_A	97	High mobility group protein homolog NHP1; structur	97.36
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	97.31
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	97.28
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	97.24
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.19
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	96.87
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	96.82
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	96.69
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	96.31
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	96.26
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	95.25
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	95.25
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	94.25
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	94.17
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	93.46
2cto_A	93	Novel protein; high mobility group box domain, hel	90.41

>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=97.94  E-value=1.7e-05  Score=53.97  Aligned_cols=47  Identities=26%  Similarity=0.432  Sum_probs=42.7

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           95 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        95 PPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      -|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         3 dp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   49 (77)
T 1hme_A            3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA   49 (77)
T ss_dssp             CSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            46666788999999999999999999999999999999999999754

>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=97.86  E-value=2.2e-05  Score=54.19  Aligned_cols=48  Identities=21%  Similarity=0.308  Sum_probs=43.4

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .+|.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLD   50 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            356666788999999999999999999999999999999999999754

>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=97.78  E-value=3.5e-05  Score=52.23  Aligned_cols=43  Identities=26%  Similarity=0.405  Sum_probs=40.1

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           99 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        99 RQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      -.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         4 PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   46 (73)
T 3nm9_A            4 PKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK   46 (73)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            3578999999999999999999999999999999999999865

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

Probab=97.76  E-value=5.8e-05  Score=53.44  Aligned_cols=48  Identities=19%  Similarity=0.433  Sum_probs=43.3

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +-|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus         3 kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (92)
T 2crj_A            3 SGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQ   50 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            446666788999999999999999999999999999999999999754

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

Probab=97.76  E-value=5.4e-05  Score=53.62  Aligned_cols=47  Identities=17%  Similarity=0.241  Sum_probs=42.0

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           95 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        95 PPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus         4 ~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (92)
T 2cs1_A            4 GSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLS   50 (92)
T ss_dssp             CCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            34555678999999999999999999999999999999999999754

>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=97.75  E-value=3.4e-05  Score=52.26  Aligned_cols=46  Identities=13%  Similarity=0.346  Sum_probs=41.3

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |.+-.|-+|||..|+++.-+.|++++|+++..|.-+.++..|+..+
T Consensus         2 p~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   47 (76)
T 1hry_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (76)
T ss_dssp             -CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCC
Confidence            4555678999999999999999999999999999999999999754

>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=97.75  E-value=4.3e-05  Score=53.62  Aligned_cols=48  Identities=19%  Similarity=0.271  Sum_probs=43.7

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +-|.+-.|-++||..|+++.-++|++++|++++.|.-+.++..|+..+
T Consensus        13 kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   60 (87)
T 2e6o_A           13 TSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMK   60 (87)
T ss_dssp             CCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            456677788999999999999999999999999999999999999754

>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=97.73  E-value=4.1e-05  Score=54.16  Aligned_cols=48  Identities=25%  Similarity=0.379  Sum_probs=43.4

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +.|.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus        16 kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   63 (90)
T 1wgf_A           16 GGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLS   63 (90)
T ss_dssp             SCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            456666788999999999999999999999999999999999999754

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

Probab=97.71  E-value=5.8e-05  Score=54.60  Aligned_cols=48  Identities=27%  Similarity=0.472  Sum_probs=43.6

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +.|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus        13 kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls   60 (102)
T 2co9_A           13 KDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLG   60 (102)
T ss_dssp             CCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCC
Confidence            456666788999999999999999999999999999999999999764

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

Probab=97.70  E-value=6.4e-05  Score=50.93  Aligned_cols=45  Identities=20%  Similarity=0.412  Sum_probs=40.9

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF  140 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  140 (174)
                      |.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   45 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL   45 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh
Confidence            344567899999999999999999999999999999999999975

>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=97.69  E-value=7.1e-05  Score=52.17  Aligned_cols=46  Identities=13%  Similarity=0.346  Sum_probs=41.5

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |.+-.|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+
T Consensus         2 p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   47 (85)
T 1j46_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSC
T ss_pred             cCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC
Confidence            4455678999999999999999999999999999999999999754

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

Probab=97.63  E-value=7.4e-05  Score=54.01  Aligned_cols=48  Identities=19%  Similarity=0.407  Sum_probs=43.3

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +.|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         6 kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls   53 (99)
T 1k99_A            6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP   53 (99)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            456666788999999999999999999999999999999999999654

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

Probab=97.62  E-value=9.3e-05  Score=54.08  Aligned_cols=49  Identities=14%  Similarity=0.249  Sum_probs=42.3

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           93 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        93 ~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .+.|.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus        24 ~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   72 (106)
T 4euw_A           24 SKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLN   72 (106)
T ss_dssp             ----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             cCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            3667777889999999999999999999999999999999999998754

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

Probab=97.60  E-value=0.0001  Score=51.42  Aligned_cols=47  Identities=23%  Similarity=0.405  Sum_probs=41.0

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 030615           95 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISH--REAFSTAAKNWAHFP  141 (174)
Q Consensus        95 PPEKRQRvpSayN~fmK~ei~riK~~~P~i~H--kEaFs~aAknW~~~P  141 (174)
                      -|.+-.|-+|||..|+++.-..|++++|+++.  .|.-+.++..|+..+
T Consensus        12 dp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   60 (86)
T 2eqz_A           12 DPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMS   60 (86)
T ss_dssp             CSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCC
Confidence            44555678899999999999999999999974  999999999998754

>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=97.59  E-value=8.6e-05  Score=51.03  Aligned_cols=45  Identities=24%  Similarity=0.461  Sum_probs=39.9

Q ss_pred             CCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           97 EKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        97 EKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         5 ~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   49 (83)
T 3f27_D            5 SRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   49 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            344678999999999999999999999999999999999998754

>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=97.59  E-value=0.00013  Score=50.18  Aligned_cols=44  Identities=18%  Similarity=0.342  Sum_probs=40.1

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           98 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        98 KRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +-.|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+
T Consensus         4 ~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   47 (81)
T 1i11_A            4 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMT   47 (81)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCC
Confidence            34577999999999999999999999999999999999999754

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

Probab=97.55  E-value=0.0001  Score=48.85  Aligned_cols=42  Identities=26%  Similarity=0.490  Sum_probs=38.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         4 krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (71)
T 4a3n_A            4 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   45 (71)
T ss_dssp             -CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            577899999999999999999999999999999999998744

>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=97.52  E-value=0.00015  Score=48.33  Aligned_cols=42  Identities=21%  Similarity=0.342  Sum_probs=38.3

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISH--REAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~H--kEaFs~aAknW~~~P  141 (174)
                      .|-+|||..|+++.-+.|++++|+++.  .|.-+.++..|+..+
T Consensus         3 KrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls   46 (71)
T 1ckt_A            3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   46 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCC
Confidence            577999999999999999999999976  999999999998643

>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=97.49  E-value=0.00019  Score=49.14  Aligned_cols=43  Identities=14%  Similarity=0.332  Sum_probs=39.6

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           99 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        99 RQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      -.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         3 pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (80)
T 1gt0_D            3 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            3567999999999999999999999999999999999999754

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

Probab=97.45  E-value=0.0002  Score=54.41  Aligned_cols=48  Identities=25%  Similarity=0.441  Sum_probs=42.7

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +-|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus        84 kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls  131 (159)
T 2gzk_A           84 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA  131 (159)
T ss_dssp             CCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSC
T ss_pred             cccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            345555678999999999999999999999999999999999999754

>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=97.44  E-value=0.00017  Score=49.03  Aligned_cols=42  Identities=21%  Similarity=0.375  Sum_probs=39.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (79)
T 3u2b_C            4 KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLK   45 (79)
T ss_dssp             CCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            477899999999999999999999999999999999998644

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

Probab=97.38  E-value=0.00014  Score=50.24  Aligned_cols=47  Identities=23%  Similarity=0.402  Sum_probs=41.0

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 030615           95 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISH--REAFSTAAKNWAHFP  141 (174)
Q Consensus        95 PPEKRQRvpSayN~fmK~ei~riK~~~P~i~H--kEaFs~aAknW~~~P  141 (174)
                      -|.+-.|-+|||..|+++.-..|++++|+++.  .|.-+.++..|+..+
T Consensus         4 dp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls   52 (83)
T 1aab_A            4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMS   52 (83)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCC
Confidence            45555788999999999999999999999975  999999999998643

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

Probab=97.38  E-value=0.00026  Score=54.78  Aligned_cols=48  Identities=25%  Similarity=0.441  Sum_probs=42.8

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +-|.+-.|-+|||..|+++...+|++++|+++..|.-+.++..|+..+
T Consensus        97 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls  144 (173)
T 2yrq_A           97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA  144 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             cCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            345556778999999999999999999999999999999999999754

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

Probab=97.36  E-value=9.2e-05  Score=52.87  Aligned_cols=50  Identities=26%  Similarity=0.381  Sum_probs=44.8

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCc
Q 030615           93 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDIS--HREAFSTAAKNWAHFPH  142 (174)
Q Consensus        93 ~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~--HkEaFs~aAknW~~~Ph  142 (174)
                      .+.|.+-.|-+|||..|+++.-.+|++++|+++  ..|.-+.++..|+..+.
T Consensus        17 ~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~   68 (97)
T 2lhj_A           17 KKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSD   68 (97)
T ss_dssp             TSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCH
Confidence            456777788999999999999999999999999  99999999999997543

>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=97.31  E-value=6.2e-05  Score=53.53  Aligned_cols=48  Identities=25%  Similarity=0.477  Sum_probs=43.3

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +.|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus        16 kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   63 (93)
T 1cg7_A           16 KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALT   63 (93)
T ss_dssp             CCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            456666788999999999999999999999999999999999999753

>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=97.28  E-value=0.00047  Score=47.95  Aligned_cols=42  Identities=12%  Similarity=0.204  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   45 (86)
T 2lef_A            4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALS   45 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            467999999999999999999999999999999999999754

>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=97.24  E-value=0.00061  Score=48.12  Aligned_cols=43  Identities=16%  Similarity=0.345  Sum_probs=39.1

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCC-HHHHHHHHHHhhccCC
Q 030615           99 RQRVPSAYNRFIKEEIQRIKASNPDIS-HREAFSTAAKNWAHFP  141 (174)
Q Consensus        99 RQRvpSayN~fmK~ei~riK~~~P~i~-HkEaFs~aAknW~~~P  141 (174)
                      -.|-+|||..|+++.-..||++||+++ ..|.-+.++..|+..+
T Consensus         6 PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls   49 (81)
T 2d7l_A            6 SGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLS   49 (81)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCC
Confidence            356799999999999999999999998 9999999999998653

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

Probab=97.19  E-value=0.00057  Score=52.82  Aligned_cols=48  Identities=21%  Similarity=0.396  Sum_probs=42.6

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPD--ISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~--i~HkEaFs~aAknW~~~P  141 (174)
                      +-|.+-.|-+|||..|+++....|++++|+  ++-.|..+.++..|+..+
T Consensus        11 ~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   60 (173)
T 2yrq_A           11 GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   60 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCC
Confidence            456666788999999999999999999999  689999999999998754

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

Probab=96.87  E-value=0.0008  Score=54.53  Aligned_cols=46  Identities=33%  Similarity=0.550  Sum_probs=41.3

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |.+-.|-+|||..|+++....|++++|+++..|..+.++..|+..+
T Consensus         7 p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   52 (214)
T 3tq6_A            7 ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   52 (214)
T ss_dssp             HHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccC
Confidence            3444578999999999999999999999999999999999999765

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

Probab=96.82  E-value=0.00088  Score=55.09  Aligned_cols=48  Identities=31%  Similarity=0.497  Sum_probs=43.1

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           94 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        94 KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      +-|.+-.|-+|||..|+++....|+++||+++..|..+.++..|+..+
T Consensus        37 ~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   84 (238)
T 3tmm_A           37 VLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   84 (238)
T ss_dssp             HHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            345666788999999999999999999999999999999999999754

>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=96.69  E-value=0.0024  Score=48.43  Aligned_cols=46  Identities=13%  Similarity=0.346  Sum_probs=42.0

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |++..|-++||-.|++++-.+|+.++|+++..|.-+.++..|+..+
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls   47 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhh
Confidence            5666788999999999999999999999999999999999998654

>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=96.31  E-value=0.0056  Score=44.92  Aligned_cols=41  Identities=12%  Similarity=0.155  Sum_probs=37.3

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 030615           99 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF  140 (174)
Q Consensus        99 RQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~  140 (174)
                      .-|-+|||+.|+.+...++++++|+ +..|.-+.+...|+..
T Consensus         5 PKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~l   45 (91)
T 1l8y_A            5 PESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNM   45 (91)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcC
Confidence            3467999999999999999999999 9999999999999974

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

Probab=96.26  E-value=0.0034  Score=41.51  Aligned_cols=38  Identities=34%  Similarity=0.675  Sum_probs=34.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|-+|||..|+++.-..|+..+|    .|..+.++..|+..+
T Consensus         4 KrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls   41 (67)
T 3fgh_A            4 KRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLS   41 (67)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCC
Confidence            56789999999999999999887    599999999999754

>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=95.25  E-value=0.021  Score=41.86  Aligned_cols=39  Identities=18%  Similarity=0.488  Sum_probs=35.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .|-+|||..|+++.-..||    +++..|.-+.++..|+..+.
T Consensus        19 KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~   57 (108)
T 1v64_A           19 KPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQ   57 (108)
T ss_dssp             CCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCH
Confidence            5678999999999999988    89999999999999998654

>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=95.25  E-value=0.029  Score=40.55  Aligned_cols=40  Identities=13%  Similarity=0.341  Sum_probs=31.8

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       101 RvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      |-+|||..|+++.++  +..+++++..|.-+.++..|+..+.
T Consensus        11 rP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~   50 (101)
T 1v63_A           11 PPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQ   50 (101)
T ss_dssp             CCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCH
Confidence            358999999999964  3445557889999999999997543

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

Probab=94.25  E-value=0.012  Score=48.39  Aligned_cols=42  Identities=33%  Similarity=0.600  Sum_probs=36.7

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |.+-.|-+|||+.|+++...+|+.++|+    |..+.++..|+..+
T Consensus       144 p~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls  185 (238)
T 3tmm_A          144 LGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLS  185 (238)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSCCSSHH----HHHHHHHHHHHTCC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHhccCHH----HHHHHHHHHHHhCC
Confidence            4555788999999999999999988876    89999999999864

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

Probab=94.17  E-value=0.012  Score=47.53  Aligned_cols=42  Identities=33%  Similarity=0.600  Sum_probs=36.4

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           96 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        96 PEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |.+-.|-+|||..|+++...+|+.++|+    |..+.++..|+..+
T Consensus       112 p~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls  153 (214)
T 3tq6_A          112 LGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLS  153 (214)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSSCSSHH----HHHHHHHHHHHTCC
T ss_pred             ccCcccccchhhhhHHHHHHhhccCCHH----HHHHHHHHHHHcCC
Confidence            4445678999999999999999988876    99999999999865

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

Probab=93.46  E-value=0.0086  Score=43.67  Aligned_cols=41  Identities=17%  Similarity=0.216  Sum_probs=33.6

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           99 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        99 RQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      -.|-||||-.|+.++-.+||++||+++  +.|..+|+.|+..+
T Consensus        23 PKRp~sAf~lf~~e~R~kik~enP~~s--~~~~eIse~Wk~ls   63 (90)
T 2yuk_A           23 GEMATVAPVLYTNINFPNLKEEFPDWT--TRVKQIAKLWRKAS   63 (90)
T ss_dssp             GGGCSSSHHHHHHHHCTTHHHHCCSHH--HHHHHHHHHHHHSC
T ss_pred             CCCCccHHHHHHHHhHHHHHHHCcCcc--chHHHHHHHHHcCC
Confidence            367899999999999999999999985  33555669998743

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

Probab=90.41  E-value=0.13  Score=37.24  Aligned_cols=39  Identities=18%  Similarity=0.429  Sum_probs=33.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHH---HHhhccC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTA---AKNWAHF  140 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~a---AknW~~~  140 (174)
                      .|-+|||..|+++.-.+||.+  +++-.|.=+..   ...|+..
T Consensus        12 KRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~l   53 (93)
T 2cto_A           12 KASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWALL   53 (93)
T ss_dssp             CSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHcC
Confidence            467999999999999999998  78888877777   9999874

---

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	174
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-04
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	0.001
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	0.003
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	0.004

>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 = 37.2 bits (86), Expect = 1e-04
 Identities = 9/48 (18%), Positives = 23/48 (47%)

Query: 94  RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 141
           + P+  ++  + Y RF  E+  +    +P++S+ +     +K +   P
Sbjct: 6   KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP 53

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

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

 Score = 34.0 bits (78), Expect = 0.001
 Identities = 11/41 (26%), Positives = 18/41 (43%)

Query: 101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 141
           R PSA+  F  E   +IK  +P +S  +      + W +  
Sbjct: 5   RPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 45

>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 = 33.3 bits (76), Expect = 0.003
 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 6/57 (10%)

Query: 87  TPRMP------PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 137
           TPR P        + P   +R  SAY  F  E    +++ NPDI+  +      + W
Sbjct: 3   TPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]} Length = 73

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

 Score = 32.4 bits (74), Expect = 0.004
 Identities = 11/37 (29%), Positives = 15/37 (40%)

Query: 101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 137
           R  SAY  ++    + IK  NP I   E      + W
Sbjct: 6   RPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELW 42

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	174
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.07
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.0
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	97.89
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	97.84
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.7
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	97.63
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.42
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.42
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	97.19
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	97.11
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	96.6
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	95.79

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

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

Probab=98.07  E-value=4.9e-06  Score=57.01  Aligned_cols=48  Identities=25%  Similarity=0.389  Sum_probs=42.3

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615           95 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus        95 PPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .|.+..|-+|||..||++..++|++++|++++.|.-..++..|+..+.
T Consensus        17 ~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~   64 (90)
T d1wgfa_          17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSE   64 (90)
T ss_dssp             CCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCH
Confidence            344445778999999999999999999999999999999999998643

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

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

Probab=98.00  E-value=4.5e-06  Score=57.28  Aligned_cols=49  Identities=18%  Similarity=0.385  Sum_probs=44.6

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           93 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        93 ~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      .|.|++-.|-+|+|..|+++....|++.+|+++..|.-+.++..|+..+
T Consensus         5 kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls   53 (91)
T d1k99a_           5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP   53 (91)
T ss_dssp             CSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCC
Confidence            3567777888999999999999999999999999999999999999754

>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=97.89  E-value=9.3e-06  Score=56.34  Aligned_cols=50  Identities=24%  Similarity=0.437  Sum_probs=44.9

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615           93 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus        93 ~KPPEKRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .+.|.+..|-+|||..|+++....||+++|++++.|.-..++..|+..+.
T Consensus        15 ~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~   64 (93)
T d1lwma_          15 KKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTP   64 (93)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCH
T ss_pred             CCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCH
Confidence            45666777889999999999999999999999999999999999998653

>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=97.84  E-value=6.8e-06  Score=55.15  Aligned_cols=41  Identities=27%  Similarity=0.430  Sum_probs=38.6

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       101 RvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |-+|||..|+++....|++++|++++.|..+.++..|+..+
T Consensus         5 rP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls   45 (79)
T d1hsma_           5 RPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA   45 (79)
T ss_dssp             CCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSC
T ss_pred             CCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCC
Confidence            45799999999999999999999999999999999999865

>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=97.70  E-value=2.7e-05  Score=51.62  Aligned_cols=40  Identities=28%  Similarity=0.419  Sum_probs=37.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhcc
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAH  139 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~  139 (174)
                      .|-+|||..||++.-+.|++++|++++.|.-+.++..|+.
T Consensus         5 KrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~   44 (73)
T d1qrva_           5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA   44 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcC
Confidence            4569999999999999999999999999999999999984

>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=97.63  E-value=4.6e-05  Score=49.90  Aligned_cols=42  Identities=19%  Similarity=0.377  Sum_probs=37.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCC
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPD--ISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~--i~HkEaFs~aAknW~~~P  141 (174)
                      .|-+|||..|+++.-++||+++|+  +++.|.-+.++..|+..+
T Consensus         3 KrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls   46 (71)
T d1ckta_           3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   46 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCC
Confidence            467899999999999999999997  667899999999999865

>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=97.42  E-value=0.00011  Score=50.17  Aligned_cols=43  Identities=14%  Similarity=0.349  Sum_probs=39.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          100 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       100 QRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      .|-+|||..|+++.-..|++++|++++.|.=+.++..|+..+.
T Consensus         6 KRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~   48 (85)
T d1j46a_           6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTE   48 (85)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCH
Confidence            5778999999999999999999999999999999999998653

>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=97.42  E-value=0.00012  Score=49.81  Aligned_cols=44  Identities=14%  Similarity=0.345  Sum_probs=40.6

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615           98 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus        98 KRQRvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |-.|-+|||-.|+++.-++|++++|++++.|.=+.++..|+..+
T Consensus         2 kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~   45 (80)
T d1gt0d_           2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCC
Confidence            44578899999999999999999999999999999999999865

>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=97.19  E-value=0.00029  Score=46.34  Aligned_cols=42  Identities=19%  Similarity=0.370  Sum_probs=38.7

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       101 RvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      |-+|||-.|+++.-++|++++|++++.|.=+.++..|+..+.
T Consensus         5 RP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~   46 (70)
T d1i11a_           5 RPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTN   46 (70)
T ss_dssp             CSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCS
T ss_pred             CCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCH
Confidence            557999999999999999999999999999999999997543

>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=97.11  E-value=0.00034  Score=47.62  Aligned_cols=41  Identities=12%  Similarity=0.197  Sum_probs=38.0

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 030615          101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  141 (174)
Q Consensus       101 RvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~P  141 (174)
                      |-+|||-.|+++.-++|++++|+++..|.=..++..|+..+
T Consensus         5 RP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls   45 (86)
T d2lefa_           5 KPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALS   45 (86)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            45699999999999999999999999999999999999754

>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=96.60  E-value=0.0012  Score=46.35  Aligned_cols=38  Identities=16%  Similarity=0.419  Sum_probs=32.2

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          101 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       101 RvpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      |-++||..|+++..+    ..|+++.+|.+..+++.|+..+.
T Consensus        20 ~P~~ay~lF~~~~r~----~~~~~~~~e~~k~ig~~W~~Ls~   57 (108)
T d1v64a_          20 PPPNSYSLYCAELMA----NMKDVPSTERMVLCSQQWKLLSQ   57 (108)
T ss_dssp             CCSSHHHHHHHHHHH----HCTTSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCcHHHHHHHHHHH----HccCCCHHHHHHHHHHHHccCCH
Confidence            447999999998655    45899999999999999998664

>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=95.79  E-value=0.0047  Score=42.26  Aligned_cols=39  Identities=13%  Similarity=0.357  Sum_probs=34.0

Q ss_pred             CchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 030615          102 VPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  142 (174)
Q Consensus       102 vpSayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~Ph  142 (174)
                      -++||..|+++.++.|+..+  ++.+|.-+.++..|+..+.
T Consensus        12 P~~ay~~F~~e~r~~~~~~~--~~~~ei~k~~g~~Wk~ls~   50 (101)
T d1v63a_          12 PMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQ   50 (101)
T ss_dssp             CSSSHHHHHHHHHHHCTTTT--SCHHHHHHHHHHHHTTSCH
T ss_pred             CCCHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHhhCCH
Confidence            47999999999999998766  5689999999999998654