Citrus Sinensis ID: 027215

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220------
Protein Sequence
MSSSTPAALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY
Secondary Structure (PSIPRED)
cccccccccccccccccccEEEEEcccccEEEEccccccccccccccccccEEEEEccccccccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccEEEEEEcccccEEEEEEEEEEEEEEcccccHccEEEEEccccccEEEEccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccccccccccccccccccHHccccccccccccccccHccccccc
Coil and Loop (DISEMBL)
mssstpaalspdhlssseqlcyvhctfcdtvlavpyhfifsvsvpctslfktvtvrcghctnlLSVNMRglllpaanqlhlghpfftpqNLLEEIrnvpanmlminppnpadqsvmpvrvvdhqeipkspvvnrppekrqrvpsaYNRFIKDEIQrikagnpdisHREAFSAAAKnwahfphihfglmpsdqpvkktSVRQQQEGedamikdgffapaanvgvtpy
Flexible Loop (DISEMBL)
mssstpaalspdhlsSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQeipkspvvnrppekrqrvpsaynrfIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEdamikdgffapaanvgvtpy
Low Complexity Region (SEG)
MSSSTPAALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY
Disordered region (IsUnstruct)
******************QLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMI******************************************RFIKDEIQRIK*****I*HREAFSAAAKNWAHFPHIHFGLM**************************************
Disordered Region (DISOPRED)
***************SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPA*************************************************************************FIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPH*******************************FFAPAANVGVTP*
Disordered Region (DISEMBL)
***************SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQ************GEDAMIKDGFFAPAANVGVTPY
Disordered Region (DISPRO)
*************LSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQ***************************************************PVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMP*************************F****NVGVTPY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSSTPAALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY
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	226	2.2.26 [Sep-21-2011]
O22152	229	Axial regulator YABBY 1 O	yes	no	0.933	0.921	0.669	1e-74
Q9XFB1	240	Axial regulator YABBY 3 O	no	no	0.911	0.858	0.628	6e-66
Q0JBF0	266	Protein YABBY 5 OS=Oryza	yes	no	0.960	0.815	0.505	4e-60
Q01JG2	266	Protein YABBY 5 OS=Oryza	N/A	no	0.960	0.815	0.505	4e-60
Q6H668	256	Protein YABBY 4 OS=Oryza	no	no	0.902	0.796	0.551	3e-56
A2X7Q3	256	Protein YABBY 4 OS=Oryza	N/A	no	0.902	0.796	0.551	3e-56
Q8GW46	164	Axial regulator YABBY 5 O	no	no	0.672	0.926	0.542	1e-43
Q2QM17	207	Protein YABBY 6 OS=Oryza	no	no	0.721	0.787	0.465	4e-41
Q9XFB0	184	Putative axial regulator	no	no	0.783	0.961	0.490	3e-40
Q10FZ7	186	Protein YABBY 2 OS=Oryza	no	no	0.663	0.806	0.529	1e-39

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

 Score =  279 bits (713), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 152/227 (66%), Positives = 176/227 (77%), Gaps = 16/227 (7%)

Query: 7   AALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSV 66
           A  SPDH S S+ LCYV C FC T+LAV        +VP TSLFKTVTVRCG CTNLLSV
Sbjct: 12  AVCSPDHFSPSDHLCYVQCNFCQTILAV--------NVPYTSLFKTVTVRCGCCTNLLSV 63

Query: 67  NMRGLLLPAANQLHLG---HPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDH 123
           NMR  +LPA+NQL L    H +F PQ++LEE+R+ P+NM M+        + +P  +  H
Sbjct: 64  NMRSYVLPASNQLQLQLGPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLH 123

Query: 124 Q--EIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181
           Q  EIPK+P VNRPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAAKNWAHFP
Sbjct: 124 QQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFP 183

Query: 182 HIHFGLMPSDQPVKKTSVRQQQEGEDAMI-KDGFFAP-AANVGVTPY 226
           HIHFGL+P +QPVKKT++  QQEGED M+ K+GF+AP AANVGVTPY
Sbjct: 184 HIHFGLVPDNQPVKKTNM-PQQEGEDNMVMKEGFYAPAAANVGVTPY 229

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|Q9XFB1|YAB3_ARATH Axial regulator YABBY 3 OS=Arabidopsis thaliana GN=YAB3 PE=1 SV=1

 Score =  250 bits (638), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 149/237 (62%), Positives = 171/237 (72%), Gaps = 31/237 (13%)

Query: 8   ALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSV- 66
           A  PDH SS++QLCYVHC+FCDTVLAV        SVP +SLFKTVTVRCGHC+NLLSV 
Sbjct: 13  AFPPDHFSSTDQLCYVHCSFCDTVLAV--------SVPPSSLFKTVTVRCGHCSNLLSVT 64

Query: 67  -NMRGLLLPAANQLHLGHPFFTPQ------NLLEEIR----NVPANMLM---INPPNPAD 112
            +MR LLLP+ + L  GH F  P       NLLEE+R    N+  NM+M    +  +P +
Sbjct: 65  VSMRALLLPSVSNL--GHSFLPPPPPPPPPNLLEEMRSGGQNINMNMMMSHHASAHHPNE 122

Query: 113 QSVMPVR---VVDH-QEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHRE 168
             VM  R    VDH QE+P+ P  NRPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHRE
Sbjct: 123 HLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHRE 182

Query: 169 AFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMI-KDGFFAPAANVGVT 224
           AFSAAAKNWAHFPHIHFGLM    P KK +VR QQEGED M+ ++GF+  AANVGV 
Sbjct: 183 AFSAAAKNWAHFPHIHFGLMADHPPTKKANVR-QQEGEDGMMGREGFYGSAANVGVA 238

Involved in the abaxial cell fate determination during embryogenesis and organogenesis. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  231 bits (588), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 139/275 (50%), Positives = 162/275 (58%), Gaps = 58/275 (21%)

Query: 1   MSSSTPAALSPDHLS-----------SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSL 49
           M SS P   S DHLS             EQLCYVHC FCDT+LAV         VPC+SL
Sbjct: 1   MMSSAPETFSLDHLSQHQQQQPPPLAEQEQLCYVHCNFCDTILAV--------GVPCSSL 52

Query: 50  FKTVTVRCGHCTNLLSVNMRGLLLPAA----NQLHLGHPFFTP---QNLLEEIRN--VPA 100
           FKTVTVRCGHC NLLSVN+RGLLLPAA    NQL  G    +P     LL+E+ +   PA
Sbjct: 53  FKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPFGQALLSPTSPHGLLDEVPSFQAPA 112

Query: 101 NMLMI------------------NPPNPADQSVMPVRVVDHQEIPK-SPVVNRPPEKRQR 141
           +++                    N P  +  S          + PK +P  NR  EKRQR
Sbjct: 113 SLMTEQASPNVSSITSSNSSCANNAPATSMASAANKATQREPQQPKNAPSANRTSEKRQR 172

Query: 142 VPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQ 201
           VPSAYNRFIKDEIQRIKA NPDI+HREAFSAAAKNWAHFPHIHFGLMP DQ +KKT ++ 
Sbjct: 173 VPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNWAHFPHIHFGLMP-DQGLKKTGIQS 231

Query: 202 QQ-EGEDAMIKDGFF---------APAANVGVTPY 226
           Q   GE  + KDG +           A+++GVTP+
Sbjct: 232 QDGAGECMLFKDGLYAAAAAAAAATAASSMGVTPF 266

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 =  231 bits (588), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 139/275 (50%), Positives = 162/275 (58%), Gaps = 58/275 (21%)

Query: 1   MSSSTPAALSPDHLS-----------SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSL 49
           M SS P   S DHLS             EQLCYVHC FCDT+LAV         VPC+SL
Sbjct: 1   MMSSAPETFSLDHLSQHQQQQPPPLAEQEQLCYVHCNFCDTILAV--------GVPCSSL 52

Query: 50  FKTVTVRCGHCTNLLSVNMRGLLLPAA----NQLHLGHPFFTP---QNLLEEIRN--VPA 100
           FKTVTVRCGHC NLLSVN+RGLLLPAA    NQL  G    +P     LL+E+ +   PA
Sbjct: 53  FKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPFGQALLSPTSPHGLLDEVPSFQAPA 112

Query: 101 NMLMI------------------NPPNPADQSVMPVRVVDHQEIPK-SPVVNRPPEKRQR 141
           +++                    N P  +  S          + PK +P  NR  EKRQR
Sbjct: 113 SLMTEQASPNVSSITSSNSSCANNAPATSMASAANKATQREPQQPKNAPSANRTSEKRQR 172

Query: 142 VPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQ 201
           VPSAYNRFIKDEIQRIKA NPDI+HREAFSAAAKNWAHFPHIHFGLMP DQ +KKT ++ 
Sbjct: 173 VPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNWAHFPHIHFGLMP-DQGLKKTGIQS 231

Query: 202 QQ-EGEDAMIKDGFF---------APAANVGVTPY 226
           Q   GE  + KDG +           A+++GVTP+
Sbjct: 232 QDGAGECMLFKDGLYAAAAAAAAATAASSMGVTPF 266

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

Oryza sativa subsp. indica (taxid: 39946)

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

 Score =  218 bits (554), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 140/254 (55%), Positives = 163/254 (64%), Gaps = 50/254 (19%)

Query: 12  DHLSS---SEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNM 68
           DHL++   +EQLCYVHC  CDT+LAV         VPC+SLFKTVTVRCGHC NLLSVN+
Sbjct: 14  DHLAAPSPTEQLCYVHCNCCDTILAV--------GVPCSSLFKTVTVRCGHCANLLSVNL 65

Query: 69  RGLLLPAA-----NQLHLGHPFFTP---QNLLEEIRNVPANMLMINPPN----------- 109
           RGLLLPA      NQLH G    +P     LL+E+     ++LM    +           
Sbjct: 66  RGLLLPAPAPAPANQLHFGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSS 125

Query: 110 -------PADQSVMPVRVVDHQ-EIPKSP--VVNRPPEKRQRVPSAYNRFIKDEIQRIKA 159
                  PA Q + P + V  + E+PK+     NRPPEKRQRVPSAYNRFIKDEIQRIKA
Sbjct: 126 SSCASNAPAMQ-MPPAKPVQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKA 184

Query: 160 GNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFF---- 215
           GNPDISHREAFSAAAKNWAHFPHIHFGLMP DQ  KKT  + Q   ED ++KD  +    
Sbjct: 185 GNPDISHREAFSAAAKNWAHFPHIHFGLMP-DQGFKKT-FKPQDGSEDILLKDSLYAAAA 242

Query: 216 ---APAANVGVTPY 226
              A AAN+GVTP+
Sbjct: 243 AAAAAAANMGVTPF 256

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 =  218 bits (554), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 140/254 (55%), Positives = 163/254 (64%), Gaps = 50/254 (19%)

Query: 12  DHLSS---SEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNM 68
           DHL++   +EQLCYVHC  CDT+LAV         VPC+SLFKTVTVRCGHC NLLSVN+
Sbjct: 14  DHLAAPSPTEQLCYVHCNCCDTILAV--------GVPCSSLFKTVTVRCGHCANLLSVNL 65

Query: 69  RGLLLPAA-----NQLHLGHPFFTP---QNLLEEIRNVPANMLMINPPN----------- 109
           RGLLLPA      NQLH G    +P     LL+E+     ++LM    +           
Sbjct: 66  RGLLLPAPAPAPANQLHFGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSS 125

Query: 110 -------PADQSVMPVRVVDHQ-EIPKSP--VVNRPPEKRQRVPSAYNRFIKDEIQRIKA 159
                  PA Q + P + V  + E+PK+     NRPPEKRQRVPSAYNRFIKDEIQRIKA
Sbjct: 126 SSCASNAPAMQ-MPPAKPVQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKA 184

Query: 160 GNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFF---- 215
           GNPDISHREAFSAAAKNWAHFPHIHFGLMP DQ  KKT  + Q   ED ++KD  +    
Sbjct: 185 GNPDISHREAFSAAAKNWAHFPHIHFGLMP-DQGFKKT-FKPQDGSEDILLKDSLYAAAA 242

Query: 216 ---APAANVGVTPY 226
              A AAN+GVTP+
Sbjct: 243 AAAAAAANMGVTPF 256

Oryza sativa subsp. indica (taxid: 39946)

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

 Score =  176 bits (446), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 96/177 (54%), Positives = 114/177 (64%), Gaps = 25/177 (14%)

Query: 12  DHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGL 71
           + + ++EQLCY+ C FC+ +LAV        +VPC+SLF  VTVRCGHCTNL SVNM   
Sbjct: 3   NSVMATEQLCYIPCNFCNIILAV--------NVPCSSLFDIVTVRCGHCTNLWSVNM--- 51

Query: 72  LLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKSPV 131
              AA    L  P F   N       VP         +    + +P R+   + I +  +
Sbjct: 52  ---AAALQSLSRPNFQATNYA-----VPEY-----GSSSRSHTKIPSRI-STRTITEQRI 97

Query: 132 VNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLM 188
           VNRPPEKRQRVPSAYN+FIK+EIQRIKA NPDISHREAFS AAKNWAHFPHIHFGLM
Sbjct: 98  VNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLM 154

Arabidopsis thaliana (taxid: 3702)

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

 Score =  167 bits (424), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 95/204 (46%), Positives = 118/204 (57%), Gaps = 41/204 (20%)

Query: 13  HLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLL 72
            ++ +EQ+CYVHC FC+T+LAV        SVP  S+   VTVRCGHCTNLLSVN+RGL+
Sbjct: 4   QIAPAEQVCYVHCNFCNTILAV--------SVPGNSMLNIVTVRCGHCTNLLSVNLRGLM 55

Query: 73  ------------------LPAANQLHLGHP--FFTPQNLLEEIRNVPANMLMINPPNPAD 112
                             L    +   G+P   F+  +   ++R  PA   M++      
Sbjct: 56  HSAPALQDHHHHHLQESGLSGCFRDQSGYPEFGFSAASSSSKLRLPPAAAAMVSYSQQNQ 115

Query: 113 QSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSA 172
           Q    +               RPPEKRQRVPSAYNRFIK+EI+RIKA NPDISHREAFS 
Sbjct: 116 QLEQALHA-------------RPPEKRQRVPSAYNRFIKEEIRRIKANNPDISHREAFST 162

Query: 173 AAKNWAHFPHIHFGLMPSDQPVKK 196
           AAKNWAH+P+IHFGL P  +  KK
Sbjct: 163 AAKNWAHYPNIHFGLSPGHEGGKK 186

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  164 bits (416), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 99/202 (49%), Positives = 124/202 (61%), Gaps = 25/202 (12%)

Query: 16  SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPA 75
           SSE++CYVHC+FC T+LAV        SVP  SLF  VTVRCGHCTNLLS+N+ G+ L  
Sbjct: 6   SSERVCYVHCSFCTTILAV--------SVPYASLFTLVTVRCGHCTNLLSLNI-GVSL-- 54

Query: 76  ANQLHLGHPFFTP--QNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVN 133
                  H    P     L+  R    +++       + +S   +     +E P+ P + 
Sbjct: 55  -------HQTSAPPIHQDLQPHRQHTTSLVTRKDCASSSRSTNNLSENIDREAPRMPPI- 106

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQP 193
           RPPEKRQRVPSAYNRFIK+EIQRIKA NP+ISHREAFS AAKNWAHFPHIHFGL   D  
Sbjct: 107 RPPEKRQRVPSAYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKL-DGN 165

Query: 194 VKKTSVRQQQEGEDAMIKDGFF 215
            K   + Q   G+ +   +G++
Sbjct: 166 KKGKQLDQSVAGQKS---NGYY 184

Involved in the abaxial cell fate determination during embryogenesis and organogenesis.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  162 bits (411), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 91/172 (52%), Positives = 108/172 (62%), Gaps = 22/172 (12%)

Query: 18  EQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLL--LPA 75
           E +CYVHC FC+T        IF+VSVP  S+   VTVRCGHCT+LLSVN+RGL+  LPA
Sbjct: 10  EHVCYVHCNFCNT--------IFAVSVPSNSMLNIVTVRCGHCTSLLSVNLRGLVQALPA 61

Query: 76  ANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVNRP 135
            + L          NL     +   N       +   +  M     D + +    +  RP
Sbjct: 62  EDHLQ--------DNLKMHNMSFRENYSEYGSSSRYGRVPMMFSKNDTEHM----LHVRP 109

Query: 136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 187
           PEKRQRVPSAYNRFIK+EI+RIKA NPDISHREAFS AAKNWAHFP+IHFGL
Sbjct: 110 PEKRQRVPSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHFPNIHFGL 161

Oryza sativa subsp. japonica (taxid: 39947)

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	226
225453975	210	PREDICTED: axial regulator YABBY 1 [Viti	0.924	0.995	0.801	9e-92
147839790	210	hypothetical protein VITISV_031595 [Viti	0.924	0.995	0.797	2e-91
444247303	210	transcription factor YABBY1 [Vitis pseud	0.924	0.995	0.797	2e-90
41745624	211	YABBY-like transcription factor GRAMINIF	0.924	0.990	0.776	6e-89
224129954	212	predicted protein [Populus trichocarpa]	0.924	0.985	0.783	1e-88
356496338	215	PREDICTED: axial regulator YABBY 1-like	0.902	0.948	0.779	9e-88
356506384	216	PREDICTED: axial regulator YABBY 1-like	0.893	0.935	0.767	1e-86
224067680	210	predicted protein [Populus trichocarpa]	0.924	0.995	0.763	2e-86
255646070	216	unknown [Glycine max]	0.893	0.935	0.762	1e-85
225426944	211	PREDICTED: axial regulator YABBY 1 [Viti	0.929	0.995	0.731	2e-81

>gi|225453975|ref|XP_002280334.1| PREDICTED: axial regulator YABBY 1 [Vitis vinifera] gi|296089181|emb|CBI38884.3| unnamed protein product [Vitis vinifera]

 Score =  342 bits (876), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 182/227 (80%), Positives = 197/227 (86%), Gaps = 18/227 (7%)

Query: 1   MSSSTPAALSPDHLS-SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGH 59
           MSSS+  A SPDHLS +S+QLCYVHC FCDTVLAV        SVPCTSLFKTVTVRCGH
Sbjct: 1   MSSSS--AFSPDHLSPTSDQLCYVHCNFCDTVLAV--------SVPCTSLFKTVTVRCGH 50

Query: 60  CTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVR 119
           CTNLLSVNMRGLLLPAANQLHLGH  F+P N+LEEIR+ P++ML IN PNP +++VMPVR
Sbjct: 51  CTNLLSVNMRGLLLPAANQLHLGHSLFSPHNILEEIRSPPSSML-INQPNP-NEAVMPVR 108

Query: 120 VVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAH 179
            VD  EIPK PVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNP ISHREAFSAAAKNWAH
Sbjct: 109 GVD--EIPKPPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPGISHREAFSAAAKNWAH 166

Query: 180 FPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           FPHIHFGLMP DQPVKK +VR QQEGED ++KDGFFAP ANVGV+PY
Sbjct: 167 FPHIHFGLMP-DQPVKKANVR-QQEGEDMLMKDGFFAP-ANVGVSPY 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147839790|emb|CAN70458.1| hypothetical protein VITISV_031595 [Vitis vinifera]

 Score =  340 bits (873), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 181/227 (79%), Positives = 196/227 (86%), Gaps = 18/227 (7%)

Query: 1   MSSSTPAALSPDHLS-SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGH 59
           MSSS+  A SPDHLS +S+QLCYVHC FCDTVLAV        SVPCTSLFKTVTVRCGH
Sbjct: 1   MSSSS--AFSPDHLSPTSDQLCYVHCNFCDTVLAV--------SVPCTSLFKTVTVRCGH 50

Query: 60  CTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVR 119
           CTNLLSVNMRGLLLPAANQLHLGH  F+P NJLEEIR+ P++ML  N PNP +++VMPVR
Sbjct: 51  CTNLLSVNMRGLLLPAANQLHLGHSLFSPHNJLEEIRSPPSSML-TNQPNP-NEAVMPVR 108

Query: 120 VVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAH 179
            VD  EIPK PVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNP ISHREAFSAAAKNWAH
Sbjct: 109 GVD--EIPKPPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPGISHREAFSAAAKNWAH 166

Query: 180 FPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           FPHIHFGLMP DQPVKK +VR QQEGED ++KDGFFAP ANVGV+PY
Sbjct: 167 FPHIHFGLMP-DQPVKKANVR-QQEGEDMLMKDGFFAP-ANVGVSPY 210

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|444247303|gb|AGD94962.1| transcription factor YABBY1 [Vitis pseudoreticulata]

 Score =  337 bits (865), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 181/227 (79%), Positives = 195/227 (85%), Gaps = 18/227 (7%)

Query: 1   MSSSTPAALSPDHLS-SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGH 59
           MSSS+  A SPDHLS +S+QLCYVHC FCDT LAV        SVPCTSLFKTVTVRCGH
Sbjct: 1   MSSSS--AFSPDHLSPTSDQLCYVHCNFCDTALAV--------SVPCTSLFKTVTVRCGH 50

Query: 60  CTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVR 119
           CTNLLSVNMRGLLLPAANQLHLGH  F+P NLLEEIR+ P++ML  N PNP +++VMPVR
Sbjct: 51  CTNLLSVNMRGLLLPAANQLHLGHSPFSPHNLLEEIRSPPSSML-TNQPNP-NEAVMPVR 108

Query: 120 VVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAH 179
            VD  EIPK PVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNP ISHREAFSAAAKNWAH
Sbjct: 109 GVD--EIPKPPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPGISHREAFSAAAKNWAH 166

Query: 180 FPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           FPHIHFGLMP DQPVKK +VR QQEGED ++KDGFFAP ANVGV+PY
Sbjct: 167 FPHIHFGLMP-DQPVKKANVR-QQEGEDMLMKDGFFAP-ANVGVSPY 210

Source: Vitis pseudoreticulata

Species: Vitis pseudoreticulata

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|41745624|gb|AAS10177.1| YABBY-like transcription factor GRAMINIFOLIA [Antirrhinum majus]

 Score =  332 bits (851), Expect = 6e-89,   Method: Compositional matrix adjust.
 Identities = 177/228 (77%), Positives = 193/228 (84%), Gaps = 19/228 (8%)

Query: 1   MSSSTPAALSPDH--LSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCG 58
           MSSS+  A +PDH  ++ SEQLCYVHC FCDTVLAV        SVPCTSL KTVTVRCG
Sbjct: 1   MSSSS--AFAPDHHHITPSEQLCYVHCNFCDTVLAV--------SVPCTSLIKTVTVRCG 50

Query: 59  HCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPV 118
           HCTNLLSVNMRGLLLPAANQLHLGH FF+PQNLLEEIRN P+N+LM N PNP D S+MPV
Sbjct: 51  HCTNLLSVNMRGLLLPAANQLHLGHSFFSPQNLLEEIRNSPSNLLM-NQPNPND-SMMPV 108

Query: 119 RVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWA 178
           R +D  E+PK PV NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWA
Sbjct: 109 RGLD--ELPKPPVANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWA 166

Query: 179 HFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           HFPHIHFGLMP DQPVKK +V  +Q G+D ++KDGF AP ANVGV+PY
Sbjct: 167 HFPHIHFGLMP-DQPVKKPNV-CRQHGDDVLMKDGFLAP-ANVGVSPY 211

Source: Antirrhinum majus

Species: Antirrhinum majus

Genus: Antirrhinum

Family: Plantaginaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224129954|ref|XP_002320712.1| predicted protein [Populus trichocarpa] gi|222861485|gb|EEE99027.1| predicted protein [Populus trichocarpa]

 Score =  331 bits (849), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 177/226 (78%), Positives = 192/226 (84%), Gaps = 17/226 (7%)

Query: 3   SSTPAALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTN 62
           +S+ AA SPDHLSSS+QLCYVHC FCDTVLAV        SVPC+SLFKTVTVRCGHCTN
Sbjct: 2   ASSSAAFSPDHLSSSDQLCYVHCNFCDTVLAV--------SVPCSSLFKTVTVRCGHCTN 53

Query: 63  LLSVNMRGLLLPAANQLHLGHPFFTPQ-NLLEEIRNVPAN-MLMINPPNPADQSVMPVRV 120
           L SVNMR LL PAANQ +LGH FF PQ N+LE +R+  A   LMIN PNP ++SVMP+R 
Sbjct: 54  LFSVNMRSLL-PAANQFYLGHGFFNPQINILEGMRSTGAPPSLMINQPNP-NESVMPIRG 111

Query: 121 VDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 180
           V  +EIPK PVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF
Sbjct: 112 V--EEIPKPPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 169

Query: 181 PHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           PHIHFGLMP DQPVKKT+VR QQEGED ++KDGFFAP ANVGVTPY
Sbjct: 170 PHIHFGLMP-DQPVKKTNVR-QQEGEDVLMKDGFFAP-ANVGVTPY 212

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496338|ref|XP_003517025.1| PREDICTED: axial regulator YABBY 1-like [Glycine max]

 Score =  328 bits (841), Expect = 9e-88,   Method: Compositional matrix adjust.
 Identities = 170/218 (77%), Positives = 180/218 (82%), Gaps = 14/218 (6%)

Query: 11  PD-HLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMR 69
           PD HLS S+QLCYVHC FCDTVLA        VSVPCTSLFKTVTVRCGHCTNLLSVNMR
Sbjct: 10  PDQHLSPSDQLCYVHCNFCDTVLA--------VSVPCTSLFKTVTVRCGHCTNLLSVNMR 61

Query: 70  GLLLPAANQLHLGHPFFTPQNLLEEIRNVPA-NMLMINPPNPADQSVMPVRVVDHQEIPK 128
           GLLLP+ANQLHLGH FFTPQNLLEEIRN P+ NM+M   PNP D  VM       +E PK
Sbjct: 62  GLLLPSANQLHLGHSFFTPQNLLEEIRNAPSTNMMMNQLPNPNDL-VMSTMRGGPEETPK 120

Query: 129 SPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLM 188
            P  NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLM
Sbjct: 121 PPSANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLM 180

Query: 189 PSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           P +QPVKK +VR  QE ED ++KDGFFAP ANVGV+PY
Sbjct: 181 PDNQPVKKANVR--QEAEDVLMKDGFFAP-ANVGVSPY 215

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356506384|ref|XP_003521963.1| PREDICTED: axial regulator YABBY 1-like [Glycine max]

 Score =  325 bits (832), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 165/215 (76%), Positives = 177/215 (82%), Gaps = 13/215 (6%)

Query: 13  HLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLL 72
           HLS S+QLCYVHC FCDTVLA        VSVPCTSLFK VTVRCGHCTNLLSVNMRGLL
Sbjct: 14  HLSPSDQLCYVHCNFCDTVLA--------VSVPCTSLFKNVTVRCGHCTNLLSVNMRGLL 65

Query: 73  LPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINP-PNPADQSVMPVRVVDHQEIPKSPV 131
           LP+ANQLHLGH FFTPQNL+EEIRN P+  +M+N  PNP D  VM       +E PK P 
Sbjct: 66  LPSANQLHLGHTFFTPQNLMEEIRNAPSTNIMMNQLPNPNDL-VMSTMRGGPEETPKPPS 124

Query: 132 VNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSD 191
            NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMP +
Sbjct: 125 ANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDN 184

Query: 192 QPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           QPVKK +VR  QE ED ++KDGFFAP ANVGV+PY
Sbjct: 185 QPVKKANVR--QEAEDVLMKDGFFAP-ANVGVSPY 216

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067680|ref|XP_002302524.1| predicted protein [Populus trichocarpa] gi|222844250|gb|EEE81797.1| predicted protein [Populus trichocarpa]

 Score =  324 bits (830), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 171/224 (76%), Positives = 186/224 (83%), Gaps = 15/224 (6%)

Query: 3   SSTPAALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTN 62
           SS+ AA  PDHLSSSEQLCYVHC FCDTVLAV        SVPCTSL+KTV VRCGHCTN
Sbjct: 2   SSSSAAFGPDHLSSSEQLCYVHCNFCDTVLAV--------SVPCTSLYKTVAVRCGHCTN 53

Query: 63  LLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVD 122
           LLSV+M GLL PAANQ +LGH FF PQN+LEEIRN     L+IN P+P ++SV+P R V 
Sbjct: 54  LLSVSMHGLL-PAANQFYLGHGFFNPQNILEEIRNGAPPNLLINQPHP-NESVIPFRGV- 110

Query: 123 HQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPH 182
            +EIPK P+VNRPPEKR RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPH
Sbjct: 111 -EEIPKPPMVNRPPEKRHRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPH 169

Query: 183 IHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           IHFGLMP DQPVKK +VR QQEGED ++ D FFA AANVGVTPY
Sbjct: 170 IHFGLMP-DQPVKKANVR-QQEGEDVLMTDEFFA-AANVGVTPY 210

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255646070|gb|ACU23522.1| unknown [Glycine max]

 Score =  322 bits (824), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 164/215 (76%), Positives = 176/215 (81%), Gaps = 13/215 (6%)

Query: 13  HLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLL 72
           HLS S+QLCYVHC FCDTVLA        VSVPCTSLFK VTVRCGHCTNLLSVNMRGLL
Sbjct: 14  HLSPSDQLCYVHCNFCDTVLA--------VSVPCTSLFKNVTVRCGHCTNLLSVNMRGLL 65

Query: 73  LPAANQLHLGHPFFTPQNLLEEIRNVPANMLMINP-PNPADQSVMPVRVVDHQEIPKSPV 131
           LP+ANQLHLGH FFTPQNL+EEIRN P+  +M+N  PNP D  VM       +E PK P 
Sbjct: 66  LPSANQLHLGHTFFTPQNLMEEIRNAPSTNIMMNQLPNPNDL-VMNTMRGGPEETPKPPS 124

Query: 132 VNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSD 191
            NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMP +
Sbjct: 125 ANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPDN 184

Query: 192 QPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           Q VKK +VR  QE ED ++KDGFFAP ANVGV+PY
Sbjct: 185 QSVKKANVR--QEAEDVLMKDGFFAP-ANVGVSPY 216

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225426944|ref|XP_002266233.1| PREDICTED: axial regulator YABBY 1 [Vitis vinifera] gi|297741152|emb|CBI31883.3| unnamed protein product [Vitis vinifera]

 Score =  307 bits (787), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 166/227 (73%), Positives = 182/227 (80%), Gaps = 17/227 (7%)

Query: 1   MSSSTPAALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHC 60
           MSSS+   LS DHL  SEQLCYVHC  CDTVLAV        SVPCTSLFKTVTVRCGHC
Sbjct: 1   MSSSS--TLSLDHLPPSEQLCYVHCNICDTVLAV--------SVPCTSLFKTVTVRCGHC 50

Query: 61  TNLLSVNMRGLLLPAANQLHLGHPFFTP-QNLLEEIRNVPANMLMINPPNPADQSVMPVR 119
           TNLL VN+RGLLLP+ANQLHLGH FF+P  NLLEEI N P+   +IN     D SV    
Sbjct: 51  TNLLPVNLRGLLLPSANQLHLGHAFFSPSHNLLEEIPN-PSPNFLINQTTANDFSVSARG 109

Query: 120 VVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAH 179
             D  E+P+ PV+NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDI+HREAFSAAAKNWAH
Sbjct: 110 GAD--ELPRPPVINRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDITHREAFSAAAKNWAH 167

Query: 180 FPHIHFGLMPSDQPVKKTSVRQQQEGEDAMIKDGFFAPAANVGVTPY 226
           FPHIHFGLMP DQ +KKT+VR QQEGED ++KDGFFA +ANVGV+PY
Sbjct: 168 FPHIHFGLMP-DQTMKKTNVR-QQEGEDVLMKDGFFA-SANVGVSPY 211

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	226
TAIR|locus:2005492	229	AFO "AT2G45190" [Arabidopsis t	0.955	0.943	0.670	3.5e-75
TAIR|locus:2126931	240	YAB3 "YABBY3" [Arabidopsis tha	0.942	0.887	0.570	3.2e-58
TAIR|locus:2066311	164	YAB5 "YABBY5" [Arabidopsis tha	0.318	0.439	0.767	1.8e-42
TAIR|locus:2826731	184	YAB2 "YABBY2" [Arabidopsis tha	0.619	0.760	0.543	2.5e-33
TAIR|locus:2028020	231	INO "INNER NO OUTER" [Arabidop	0.730	0.714	0.460	6e-32
UNIPROTKB|Q7XIM7	169	YAB1 "Protein YABBY 1" [Oryza	0.610	0.816	0.487	1e-27
TAIR|locus:2026418	181	CRC "AT1G69180" [Arabidopsis t	0.261	0.325	0.677	1.1e-27
UNIPROTKB|Q76EJ0	194	DL "Protein DROOPING LEAF" [Or	0.548	0.639	0.442	1.8e-23

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

 Score = 758 (271.9 bits), Expect = 3.5e-75, P = 3.5e-75
 Identities = 157/234 (67%), Positives = 183/234 (78%)

Query:     1 MSSSTPAALSPDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHC 60
             MSS + A  SPDH S S+ LCYV C FC T+LAV        +VP TSLFKTVTVRCG C
Sbjct:     6 MSSPSSAVCSPDHFSPSDHLCYVQCNFCQTILAV--------NVPYTSLFKTVTVRCGCC 57

Query:    61 TNLLSVNMRGLLLPAANQLHL--G-HPFFTPQNLLEEIRNVPANM-LMINPPNPADQSVM 116
             TNLLSVNMR  +LPA+NQL L  G H +F PQ++LEE+R+ P+NM +M+   +P    + 
Sbjct:    58 TNLLSVNMRSYVLPASNQLQLQLGPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDI- 116

Query:   117 PVRVVDHQ--EIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAA 174
             P  +  HQ  EIPK+P VNRPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAA
Sbjct:   117 PSFMDLHQQHEIPKAPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAA 176

Query:   175 KNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMI-KDGFFAPAA-NVGVTPY 226
             KNWAHFPHIHFGL+P +QPVKKT++  QQEGED M+ K+GF+APAA NVGVTPY
Sbjct:   177 KNWAHFPHIHFGLVPDNQPVKKTNM-PQQEGEDNMVMKEGFYAPAAANVGVTPY 229

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

 Score = 598 (215.6 bits), Expect = 3.2e-58, P = 3.2e-58
 Identities = 138/242 (57%), Positives = 166/242 (68%)

Query:     1 MSSSTPAALSPDHLSSSEQLCYVHCTFCDTVLAV--PYHFIF-SVSVPCTSLFKTVTVRC 57
             MSSS+  A  PDH SS++QLCYVHC+FCDTVLAV  P   +F +V+V C          C
Sbjct:     6 MSSSSAPAFPPDHFSSTDQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCG--------HC 57

Query:    58 GHCTNLLSVNMRGLLLPAANQL-HL---GHPFFTPQNLLEEIR----NVPANMLM---IN 106
              +  ++ +V+MR LLLP+ + L H      P   P NLLEE+R    N+  NM+M    +
Sbjct:    58 SNLLSV-TVSMRALLLPSVSNLGHSFLPPPPPPPPPNLLEEMRSGGQNINMNMMMSHHAS 116

Query:   107 PPNPADQSVMPVR---VVDH-QEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNP 162
               +P +  VM  R    VDH QE+P+ P  NRPPEKRQRVPSAYNRFIK+EIQRIKAGNP
Sbjct:   117 AHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNP 176

Query:   163 DISHREAFSAAAKNWAHFPHIHFGLMPSDQPVKKTSVRQQQEGEDAMI-KDGFFAPAANV 221
             DISHREAFSAAAKNWAHFPHIHFGLM    P KK +VRQQ EGED M+ ++GF+  AANV
Sbjct:   177 DISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQ-EGEDGMMGREGFYGSAANV 235

Query:   222 GV 223
             GV
Sbjct:   236 GV 237

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

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

 Score = 299 (110.3 bits), Expect = 1.8e-42, Sum P(2) = 1.8e-42
 Identities = 56/73 (76%), Positives = 63/73 (86%)

Query:   116 MPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAK 175
             +P R+   + I +  +VNRPPEKRQRVPSAYN+FIK+EIQRIKA NPDISHREAFS AAK
Sbjct:    83 IPSRI-STRTITEQRIVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAK 141

Query:   176 NWAHFPHIHFGLM 188
             NWAHFPHIHFGLM
Sbjct:   142 NWAHFPHIHFGLM 154

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

 Score = 363 (132.8 bits), Expect = 2.5e-33, P = 2.5e-33
 Identities = 81/149 (54%), Positives = 98/149 (65%)

Query:    39 IFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNV 98
             I +VSVP  SLF  VTVRCGHCTNLLS+N+ G+ L   +   + H    P       R  
Sbjct:    21 ILAVSVPYASLFTLVTVRCGHCTNLLSLNI-GVSLHQTSAPPI-HQDLQPH------RQH 72

Query:    99 PANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIK 158
               +++       + +S   +     +E P+ P + RPPEKRQRVPSAYNRFIK+EIQRIK
Sbjct:    73 TTSLVTRKDCASSSRSTNNLSENIDREAPRMPPI-RPPEKRQRVPSAYNRFIKEEIQRIK 131

Query:   159 AGNPDISHREAFSAAAKNWAHFPHIHFGL 187
             A NP+ISHREAFS AAKNWAHFPHIHFGL
Sbjct:   132 ACNPEISHREAFSTAAKNWAHFPHIHFGL 160

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

 Score = 350 (128.3 bits), Expect = 6.0e-32, P = 6.0e-32
 Identities = 82/178 (46%), Positives = 103/178 (57%)

Query:    19 QLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVN-MRGLLLPAAN 77
             Q+C+V C FC T+L V        SVP TSL   VTVRCGHCT+LLSVN M+   +P   
Sbjct:    20 QICHVQCGFCTTILLV--------SVPFTSLSMVVTVRCGHCTSLLSVNLMKASFIPLHL 71

Query:    78 QLHLGHPFFTPQNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPKS---PVVNR 134
                L H   T +  +     V      +N       + + V   D+++   S    VVN+
Sbjct:    72 LASLSHLDETGKEEVAATDGVEEEAWKVNQEKENSPTTL-VSSSDNEDEDVSRVYQVVNK 130

Query:   135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSDQ 192
             PPEKRQR PSAYN FIK+EI+R+KA NP ++H+EAFS AAKNWAHFP  H     SDQ
Sbjct:   131 PPEKRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPAHNKRAASDQ 188

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

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

 Score = 310 (114.2 bits), Expect = 1.0e-27, P = 1.0e-27
 Identities = 76/156 (48%), Positives = 91/156 (58%)

Query:    39 IFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNV 98
             I  V+VP    +  VTVRCGHCT +LS++    L P        H   T Q+   + R  
Sbjct:    21 ILVVNVPNNCSYNIVTVRCGHCTMVLSMD----LAPF-------HQARTVQDHQVQNRGF 69

Query:    99 PANMLM---INPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQ 155
               N      I   N    + M       Q++  SP+  RPPEKRQRVPSAYNRFIK+EIQ
Sbjct:    70 QGNNFGSYDIASRNQRTSTAMYPMPTSQQQV--SPI--RPPEKRQRVPSAYNRFIKEEIQ 125

Query:   156 RIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMPSD 191
             RIK  NP+ISHREAFSAAAKNWAH P +HFGL  +D
Sbjct:   126 RIKTSNPEISHREAFSAAAKNWAHLPRLHFGLSVAD 161

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 221 (82.9 bits), Expect = 1.1e-27, Sum P(2) = 1.1e-27
 Identities = 40/59 (67%), Positives = 48/59 (81%)

Query:   122 DHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 180
             D    P  P V +PPEK+QR+PSAYNRF++DEIQRIK+ NP+I HREAFSAAAKNWA +
Sbjct:    98 DQPPSPSPPFVVKPPEKKQRLPSAYNRFMRDEIQRIKSANPEIPHREAFSAAAKNWAKY 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 = 270 (100.1 bits), Expect = 1.8e-23, P = 1.8e-23
 Identities = 62/140 (44%), Positives = 81/140 (57%)

Query:    39 IFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQNLLEEIRNV 98
             + +V VPC  L  TVTV+CGHC NL  ++ R  ++   +     HP    Q    + R  
Sbjct:    21 VLAVGVPCKRLMDTVTVKCGHCNNLSFLSPRPPMVQPLSPTD--HPLGPFQGPCTDCRR- 77

Query:    99 PANMLMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIK 158
                    N P P    V P     ++  P++P V +PPEK+ R+PSAYNRF+++EIQRIK
Sbjct:    78 -------NQPLPL---VSPT---SNEGSPRAPFVVKPPEKKHRLPSAYNRFMREEIQRIK 124

Query:   159 AGNPDISHREAFSAAAKNWA 178
             A  PDI HREAFS AAKNWA
Sbjct:   125 AAKPDIPHREAFSMAAKNWA 144

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)
O22152	YAB1_ARATH	No assigned EC number	0.6696	0.9336	0.9213	yes	no
Q0JBF0	YAB5_ORYSJ	No assigned EC number	0.5054	0.9601	0.8157	yes	no
Q01JG2	YAB5_ORYSI	No assigned EC number	0.5054	0.9601	0.8157	N/A	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

Your Input: GSVIVG00026383001 SubName- Full=Chromosome chr15 scaffold_37, whole genome shotgun sequence; (210 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	226
pfam04690	170	pfam04690, YABBY, YABBY protein	2e-77
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	2e-04
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	4e-04

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

 Score =  230 bits (587), Expect = 2e-77
 Identities = 103/179 (57%), Positives = 116/179 (64%), Gaps = 11/179 (6%)

Query: 11  PDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRG 70
                SSE +CYVHC FC T+LAV        SVP TSLF  VTVRCGHCTNLLSVN+  
Sbjct: 1   MSVFFSSEHVCYVHCNFCTTILAV--------SVPYTSLFNIVTVRCGHCTNLLSVNLMM 52

Query: 71  LLLPAANQLHLGHPFFTP--QNLLEEIRNVPANMLMINPPNPADQSVMPVRVVDHQEIPK 128
                    HL         QNL    +N  +NM+  +  +    S   +     +E+P+
Sbjct: 53  RSHLLPALSHLDETGKPELLQNLGVHGQNFNSNMMKSHSAS-TSVSSYMMSDNQDEEMPR 111

Query: 129 SPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 187
            P VNRPPEKRQRVPSAYNRFIK+EIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL
Sbjct: 112 VPPVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 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 = 38.0 bits (89), Expect = 2e-04
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           R  SAY  F +++  ++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 = 37.2 bits (87), Expect = 4e-04
 Identities = 12/37 (32%), Positives = 17/37 (45%)

Query: 141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           R  SAY  F ++    +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	226
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	100.0
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.13
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	97.68
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	97.6
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	97.59
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.58
smart00398	70	HMG high mobility group.	97.44
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	97.38
PTZ00199	94	high mobility group protein; Provisional	97.26
KOG0381	96	consensus HMG box-containing protein [General func	96.02
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	95.95
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	93.87
KOG3223	221	consensus Uncharacterized conserved protein [Funct	92.79
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	85.4
PF14599	61	zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.	80.41

>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=4.7e-82  Score=532.33  Aligned_cols=167  Identities=66%  Similarity=1.100  Sum_probs=130.9

Q ss_pred             CCCCCCCCceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcccccccccCCccccccccCCCCCCCch
Q 027215           11 PDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQN   90 (226)
Q Consensus        11 ~d~l~~~EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSVNmr~ll~p~~~q~~~~~~~~~~~~   90 (226)
                      ||++.++||||||||||||||||        |||||+|||+|||||||||+|||||||++++++.+.|+++++.++.+..
T Consensus         1 ~~~~~~sE~lCYVhCnFC~TiLa--------VsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~   72 (170)
T PF04690_consen    1 MDLFSPSEQLCYVHCNFCNTILA--------VSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQS   72 (170)
T ss_pred             CCccCCCCcEEEEEcCCcCeEEE--------EecchhhhhhhhceeccCccceeeeeccccccCCCcccchhcccccccc
Confidence            57778899999999999999999        9999999999999999999999999999999888888776666543321


Q ss_pred             hHHhhhcCccc--c-ccCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHH
Q 027215           91 LLEEIRNVPAN--M-LMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHR  167 (226)
Q Consensus        91 ~~~e~~~~~~~--~-~~~~~s~~~~ss~~~~~~~~~~~~p~~p~v~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~Hk  167 (226)
                        ++.......  . ..+..+..+..+.......++++.|+.++|+||||||||+|||||+||||||||||++||||+||
T Consensus        73 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishk  150 (170)
T PF04690_consen   73 --QELQFQPENFGSNSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHK  150 (170)
T ss_pred             --ccccccccccccccccCCCccccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHH
Confidence              111111011  0 01111101111011112233568899988999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhccCCcccccc
Q 027215          168 EAFSAAAKNWAHFPHIHFGL  187 (226)
Q Consensus       168 EaFs~aAknWa~~PhIhfGL  187 (226)
                      |||++|||||||+|||||||
T Consensus       151 eaFs~aAknW~h~phihfgl  170 (170)
T PF04690_consen  151 EAFSAAAKNWAHFPHIHFGL  170 (170)
T ss_pred             HHHHHHHHhhhhCcccccCC
Confidence            99999999999999999998

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

Probab=98.13  E-value=3.7e-06  Score=60.39  Aligned_cols=46  Identities=33%  Similarity=0.611  Sum_probs=38.2

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhc-CCCCCHHHHHHHHHHhhccCC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAG-NPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~-nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |.|-.|.+|||+.||++.+.++|+. .+.++.+|++..++..|+..+
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            5566899999999999999999999 888999999999999999753

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=97.68  E-value=8.3e-05  Score=50.81  Aligned_cols=41  Identities=29%  Similarity=0.470  Sum_probs=38.4

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |-+|||..|+++....+++++|+++..|....++..|+..+
T Consensus         3 rp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls   43 (66)
T cd01390           3 RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS   43 (66)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            56899999999999999999999999999999999999754

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=97.60  E-value=0.00012  Score=52.55  Aligned_cols=41  Identities=17%  Similarity=0.263  Sum_probs=38.3

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |-++||..|+++.-.++++++|+++..|.-+.++..|+..+
T Consensus         4 rP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls   44 (72)
T cd01388           4 RPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALS   44 (72)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            56899999999999999999999999999999999998754

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=97.59  E-value=0.00011  Score=50.71  Aligned_cols=41  Identities=32%  Similarity=0.619  Sum_probs=36.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      .|-++||..|+++....||+++|+++..|.-+.+++.|+..
T Consensus         2 krP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l   42 (69)
T PF00505_consen    2 KRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNL   42 (69)
T ss_dssp             SSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCS
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcC
Confidence            36789999999999999999999999999999999999974

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=97.58  E-value=0.00015  Score=48.99  Aligned_cols=41  Identities=29%  Similarity=0.410  Sum_probs=38.5

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |-++||..|++++...+++++|+++..|....+++.|+..+
T Consensus         3 rp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~   43 (66)
T cd00084           3 RPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLS   43 (66)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            56899999999999999999999999999999999999754

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=97.44  E-value=0.00031  Score=47.91  Aligned_cols=42  Identities=31%  Similarity=0.501  Sum_probs=38.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      .|-+|+|..|+++....+++++|+++..|.-+.++..|+..+
T Consensus         3 krp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~   44 (70)
T smart00398        3 KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLS   44 (70)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCC
Confidence            457899999999999999999999999999999999999754

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

Probab=97.38  E-value=0.00037  Score=50.39  Aligned_cols=42  Identities=19%  Similarity=0.371  Sum_probs=39.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      .|-++||-.|+++....|+++||++++.|.-+.++..|+..+
T Consensus         3 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls   44 (77)
T cd01389           3 PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSES   44 (77)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            477899999999999999999999999999999999999754

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=97.26  E-value=0.00068  Score=51.73  Aligned_cols=48  Identities=25%  Similarity=0.438  Sum_probs=41.3

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCC--HHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDIS--HREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~--HkEaFs~aAknWa~~P  181 (226)
                      +.|.+-.|-+|||..|+++.-..|+++||+++  -.|.-+.++..|+..+
T Consensus        18 kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls   67 (94)
T PTZ00199         18 KDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLS   67 (94)
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCC
Confidence            45556668899999999999999999999986  5788889999999865

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

Probab=96.02  E-value=0.014  Score=43.05  Aligned_cols=43  Identities=30%  Similarity=0.442  Sum_probs=38.9

Q ss_pred             cCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          138 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       138 KRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      .-+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|...
T Consensus        22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l   64 (96)
T KOG0381|consen   22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNL   64 (96)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC
Confidence            4467788999999999999999999999999999999999864

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

Probab=95.95  E-value=0.011  Score=48.60  Aligned_cols=50  Identities=26%  Similarity=0.531  Sum_probs=44.8

Q ss_pred             CCCCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCCc
Q 027215          131 VVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPH  182 (226)
Q Consensus       131 ~v~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~Ph  182 (226)
                      .+-|.||||-+  -||..|--.+|.+||++||++.+-+-=-..=|.|..+|.
T Consensus        67 ~~drHPErR~K--AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   67 PIDRHPERRMK--AAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPE  116 (122)
T ss_pred             CCCCCcchhHH--HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCC
Confidence            35689999865  699999999999999999999999988888999999884

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

Probab=93.87  E-value=0.057  Score=37.98  Aligned_cols=39  Identities=38%  Similarity=0.835  Sum_probs=29.3

Q ss_pred             eeeCCchhhhhcCCCcccceeeecCCCCcc--eeeeecCCcCCccccccc
Q 027215           22 YVHCTFCDTVLAVPYHFIFSVSVPCTSLFK--TVTVRCGHCTNLLSVNMR   69 (226)
Q Consensus        22 YV~CnFCnTILa~~~~~~~~VsVPcssL~~--~VTVRCGHCtnLlSVNmr   69 (226)
                      ||-|.-|..+|=+|-.+         .+.+  .-.+|||.|..++++.++
T Consensus         6 Fv~C~~C~~lLqlP~~~---------~~~~k~~~klrCGaCs~vl~~s~~   46 (46)
T PF11331_consen    6 FVVCSSCFELLQLPAKF---------SLSKKNQQKLRCGACSEVLSFSLP   46 (46)
T ss_pred             EeECccHHHHHcCCCcc---------CCCccceeEEeCCCCceeEEEecC
Confidence            78999999998854432         1222  578999999999998753

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.79  E-value=0.063  Score=48.09  Aligned_cols=49  Identities=31%  Similarity=0.550  Sum_probs=43.3

Q ss_pred             CCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCCcc
Q 027215          133 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHI  183 (226)
Q Consensus       133 ~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~PhI  183 (226)
                      -|-||||-|.  ||--|=..++-|||.++|+++|-+-=-..-|.|...|-=
T Consensus       161 drHPEkRmrA--A~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDN  209 (221)
T KOG3223|consen  161 DRHPEKRMRA--AFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDN  209 (221)
T ss_pred             ccChHHHHHH--HHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCC
Confidence            4899999775  999999999999999999999998777788899988753

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=85.40  E-value=0.33  Score=31.80  Aligned_cols=34  Identities=32%  Similarity=0.670  Sum_probs=25.4

Q ss_pred             eeCCchhhhhcCCCcccceeeecCCCC-cceeeeecCCcCCcccc
Q 027215           23 VHCTFCDTVLAVPYHFIFSVSVPCTSL-FKTVTVRCGHCTNLLSV   66 (226)
Q Consensus        23 V~CnFCnTILa~~~~~~~~VsVPcssL-~~~VTVRCGHCtnLlSV   66 (226)
                      ++|.-|.|..-          ||-+.| -....|||++|.+.+.|
T Consensus         3 i~CP~C~~~f~----------v~~~~l~~~~~~vrC~~C~~~f~v   37 (37)
T PF13719_consen    3 ITCPNCQTRFR----------VPDDKLPAGGRKVRCPKCGHVFRV   37 (37)
T ss_pred             EECCCCCceEE----------cCHHHcccCCcEEECCCCCcEeeC
Confidence            68899988877          455544 34679999999987654

>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A

Probab=80.41  E-value=0.66  Score=34.14  Aligned_cols=31  Identities=29%  Similarity=0.862  Sum_probs=18.1

Q ss_pred             CceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCC
Q 027215           18 EQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTN   62 (226)
Q Consensus        18 EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtn   62 (226)
                      ...+.+.||=|..-=-|+|||+.              .+|+||.+
T Consensus        26 ~~~v~IlCNDC~~~s~v~fH~lg--------------~KC~~C~S   56 (61)
T PF14599_consen   26 NKKVWILCNDCNAKSEVPFHFLG--------------HKCSHCGS   56 (61)
T ss_dssp             --EEEEEESSS--EEEEE--TT------------------TTTS-
T ss_pred             CCEEEEECCCCCCccceeeeHhh--------------hcCCCCCC
Confidence            46799999999998888899865              58999975

---

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	226
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	3e-06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	6e-06
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	7e-05
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-04
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	1e-04
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	6e-04
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	7e-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 = 46.0 bits (108), Expect = 3e-06
 Identities = 14/48 (29%), Positives = 21/48 (43%)

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181
                 ++  S+Y RF K+++   KA NPD    E     A+ W   P
Sbjct: 37  VLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 84

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

 Score = 44.7 bits (105), Expect = 6e-06
 Identities = 14/48 (29%), Positives = 21/48 (43%)

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181
                 ++  S+Y RF K+++   KA NPD    E     A+ W   P
Sbjct: 5   VLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 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 = 41.1 bits (96), Expect = 7e-05
 Identities = 11/62 (17%), Positives = 22/62 (35%)

Query: 116 MPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAK 175
                       ++    + P   +R PSA+  F  +   +IK  +P +S  +      +
Sbjct: 79  EREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGE 138

Query: 176 NW 177
            W
Sbjct: 139 MW 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 = 39.6 bits (92), Expect = 2e-04
 Identities = 11/56 (19%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 128 KSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPD--ISHREAFSAAAKNWAHFP 181
            S +    P+K +   S+Y  F++   +  K  +PD  ++  E     ++ W    
Sbjct: 5   SSGMGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 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 = 38.9 bits (91), Expect = 1e-04
 Identities = 7/45 (15%), Positives = 22/45 (48%)

Query: 133 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
            + P+  ++  + Y RF  ++  +    +P++S+ +     +K +
Sbjct: 5   KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKY 49

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

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 14/44 (31%), Positives = 20/44 (45%)

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           + P + Q+  SAY  F +D    IK  NP+ +  E     A  W
Sbjct: 13  KDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMW 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 = 36.9 bits (86), Expect = 6e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           + P   +R  SAY  F  +    +++ NPDI+  +      + W
Sbjct: 16  KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

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

 Score = 36.5 bits (85), Expect = 7e-04
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           + P   +R PSA+  F  +   +IK  +P +S  +      + W
Sbjct: 2   KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 45

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	226
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	97.78
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	97.71
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	97.61
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	97.6
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	97.6
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	97.59
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	97.57
1wgf_A	90	Upstream binding factor 1; transcription factor, D	97.57
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	97.54
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	97.51
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	97.51
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	97.47
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	97.42
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	97.42
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	97.41
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	97.41
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	97.39
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	97.33
1ckt_A	71	High mobility group 1 protein; high-mobility group	97.31
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	97.29
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.25
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	97.16
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	97.15
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.15
2lhj_A	97	High mobility group protein homolog NHP1; structur	97.13
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	97.09
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	96.98
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	96.94
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	96.6
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	96.55
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	96.37
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	96.01
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	95.85
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	94.64
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	94.56
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	93.61
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	93.58
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	92.67
2cto_A	93	Novel protein; high mobility group box domain, hel	87.51

>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=97.78  E-value=3.5e-05  Score=54.14  Aligned_cols=46  Identities=24%  Similarity=0.421  Sum_probs=41.7

Q ss_pred             CCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      -|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..
T Consensus         3 dp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   48 (77)
T 1hme_A            3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNT   48 (77)
T ss_dssp             CSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            4555667899999999999999999999999999999999999964

>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=97.71  E-value=4.4e-05  Score=54.52  Aligned_cols=46  Identities=22%  Similarity=0.314  Sum_probs=42.0

Q ss_pred             CCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      +|.+-.|-+|||..|+++.-++|++++|+++..|.-+.++..|+..
T Consensus         4 ~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   49 (82)
T 1wz6_A            4 GSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVL   49 (82)
T ss_dssp             SCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhC
Confidence            5566667899999999999999999999999999999999999964

>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=97.61  E-value=8.2e-05  Score=52.15  Aligned_cols=42  Identities=26%  Similarity=0.413  Sum_probs=39.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      .|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus         5 KrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   46 (73)
T 3nm9_A            5 KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK   46 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            567899999999999999999999999999999999999764

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

Probab=97.60  E-value=0.0001  Score=54.06  Aligned_cols=45  Identities=20%  Similarity=0.266  Sum_probs=40.3

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      |.+-.|-+|||..|+++.-++||++||+++..|.-+.++..|+..
T Consensus         5 p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   49 (92)
T 2cs1_A            5 SSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTL   49 (92)
T ss_dssp             CSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcC
Confidence            444456799999999999999999999999999999999999964

>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=97.60  E-value=8e-05  Score=54.08  Aligned_cols=48  Identities=19%  Similarity=0.250  Sum_probs=43.2

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      +-|.+-.|-++||..|+++.-++|++++|+++..|.-+.++..|+..+
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            456666788999999999999999999999999999999999999743

>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=97.59  E-value=6.6e-05  Score=52.62  Aligned_cols=45  Identities=16%  Similarity=0.359  Sum_probs=40.3

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      |.+-.|-+|||..|+++.-++|++++|+++..|.-+.++..|+..
T Consensus         2 p~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   46 (76)
T 1hry_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKML   46 (76)
T ss_dssp             -CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhC
Confidence            344567799999999999999999999999999999999999974

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

Probab=97.57  E-value=0.00012  Score=53.62  Aligned_cols=47  Identities=17%  Similarity=0.431  Sum_probs=42.0

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      |-|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..
T Consensus         3 kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   49 (92)
T 2crj_A            3 SGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKL   49 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcC
Confidence            34555567899999999999999999999999999999999999974

>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=97.57  E-value=8.9e-05  Score=54.26  Aligned_cols=47  Identities=23%  Similarity=0.372  Sum_probs=42.7

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      +.|.+-.|-+|||..|+++.-++|++++|+++..|.-+.++..|+..
T Consensus        16 kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~l   62 (90)
T 1wgf_A           16 GGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDL   62 (90)
T ss_dssp             SCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            45666678899999999999999999999999999999999999974

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

Probab=97.54  E-value=0.00012  Score=54.84  Aligned_cols=48  Identities=29%  Similarity=0.477  Sum_probs=43.0

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      +.|.+-.|-++||..|+++.-.+|++++|+++..|.-+.++..|+..+
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            456666778999999999999999999999999999999999999753

>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=97.51  E-value=0.00014  Score=52.38  Aligned_cols=46  Identities=15%  Similarity=0.352  Sum_probs=40.8

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |.+-.|-+|||..|+++.-+.|++++|+++..|.-+.++..|+..+
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            3444567899999999999999999999999999999999999743

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

Probab=97.51  E-value=0.00014  Score=50.94  Aligned_cols=44  Identities=23%  Similarity=0.422  Sum_probs=40.0

Q ss_pred             ccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          137 EKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       137 EKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      .+-.|-+|||..|+++.-.+|+++||+++..|.-+.++..|+..
T Consensus         2 ~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   45 (73)
T 1wxl_A            2 HMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL   45 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh
Confidence            34456789999999999999999999999999999999999974

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

Probab=97.47  E-value=0.00015  Score=54.31  Aligned_cols=47  Identities=15%  Similarity=0.338  Sum_probs=42.2

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      +.|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..
T Consensus         6 kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~l   52 (99)
T 1k99_A            6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKEL   52 (99)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            44555667899999999999999999999999999999999999963

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

Probab=97.42  E-value=0.00019  Score=54.23  Aligned_cols=48  Identities=13%  Similarity=0.243  Sum_probs=41.7

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      +.|.+-.|-++||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus        25 k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   72 (106)
T 4euw_A           25 KNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLN   72 (106)
T ss_dssp             ---CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             CCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            566667788999999999999999999999999999999999998754

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

Probab=97.42  E-value=0.00021  Score=51.67  Aligned_cols=47  Identities=23%  Similarity=0.393  Sum_probs=40.4

Q ss_pred             CCccCCCCchhhhHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhccCC
Q 027215          135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISH--REAFSAAAKNWAHFP  181 (226)
Q Consensus       135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~H--kEaFs~aAknWa~~P  181 (226)
                      -|.+-.|-+|||..|+++.-++|++++|+++.  .|.-+.++..|+..+
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            34444667899999999999999999999974  999999999998643

>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=97.41  E-value=0.00018  Score=51.16  Aligned_cols=44  Identities=27%  Similarity=0.475  Sum_probs=39.4

Q ss_pred             cCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          138 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       138 KRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         6 ~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   49 (83)
T 3f27_D            6 RIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   49 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            34577899999999999999999999999999999999998743

>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=97.41  E-value=0.00027  Score=50.25  Aligned_cols=41  Identities=22%  Similarity=0.391  Sum_probs=38.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      .|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..
T Consensus         6 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   46 (81)
T 1i11_A            6 KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAM   46 (81)
T ss_dssp             CCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhC
Confidence            46789999999999999999999999999999999999964

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

Probab=97.39  E-value=0.00021  Score=49.04  Aligned_cols=41  Identities=29%  Similarity=0.507  Sum_probs=38.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      .|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..
T Consensus         4 krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   44 (71)
T 4a3n_A            4 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKAL   44 (71)
T ss_dssp             -CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcC
Confidence            46789999999999999999999999999999999999864

>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=97.33  E-value=0.00035  Score=49.47  Aligned_cols=41  Identities=15%  Similarity=0.357  Sum_probs=38.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      .|-+|||..|+++.-..|++++|+++..|.-+.++..|+..
T Consensus         4 krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   44 (80)
T 1gt0_D            4 KRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLL   44 (80)
T ss_dssp             CCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            46789999999999999999999999999999999999864

>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=97.31  E-value=0.0003  Score=48.51  Aligned_cols=41  Identities=22%  Similarity=0.334  Sum_probs=37.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISH--REAFSAAAKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~H--kEaFs~aAknWa~~  180 (226)
                      .|-+|||..|+++.-+.||++||+++.  .|.-+.++..|+..
T Consensus         3 KrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~l   45 (71)
T 1ckt_A            3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTM   45 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhC
Confidence            467899999999999999999999976  99999999999863

>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=97.29  E-value=0.00031  Score=49.37  Aligned_cols=42  Identities=21%  Similarity=0.354  Sum_probs=38.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      .|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
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            467899999999999999999999999999999999998643

>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=97.25  E-value=0.00041  Score=54.59  Aligned_cols=48  Identities=23%  Similarity=0.425  Sum_probs=42.4

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      +-|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..+
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            345555678999999999999999999999999999999999999743

>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=97.16  E-value=0.00013  Score=53.71  Aligned_cols=47  Identities=23%  Similarity=0.470  Sum_probs=42.6

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      +.|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..
T Consensus        16 kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~l   62 (93)
T 1cg7_A           16 KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKAL   62 (93)
T ss_dssp             CCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTT
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            45666678899999999999999999999999999999999999974

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

Probab=97.15  E-value=0.00028  Score=50.36  Aligned_cols=46  Identities=24%  Similarity=0.396  Sum_probs=40.0

Q ss_pred             CCccCCCCchhhhHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhccC
Q 027215          135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISH--REAFSAAAKNWAHF  180 (226)
Q Consensus       135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~H--kEaFs~aAknWa~~  180 (226)
                      -|.+-.|-+|||..|+++.-..|++++|+++.  .|.-+.++..|+..
T Consensus         4 dp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~l   51 (83)
T 1aab_A            4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTM   51 (83)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhC
Confidence            34555678899999999999999999999875  99999999999863

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

Probab=97.15  E-value=0.00053  Score=54.89  Aligned_cols=47  Identities=23%  Similarity=0.415  Sum_probs=42.0

Q ss_pred             CCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      -|.+-.|-+|||..|+++...+|++++|+++..|.-+.++..|+..+
T Consensus        98 dp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls  144 (173)
T 2yrq_A           98 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA  144 (173)
T ss_dssp             CSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             CCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            45555677899999999999999999999999999999999999743

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

Probab=97.13  E-value=0.0002  Score=52.93  Aligned_cols=48  Identities=25%  Similarity=0.395  Sum_probs=43.6

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCC--HHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDIS--HREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~--HkEaFs~aAknWa~~P  181 (226)
                      +.|.+-.|-+|||..|+++.-.+|++++|+++  ..|.-+.++..|+..+
T Consensus        18 kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   67 (97)
T 2lhj_A           18 KDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALS   67 (97)
T ss_dssp             SCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCC
Confidence            56677778899999999999999999999999  9999999999999743

>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=97.09  E-value=0.00067  Score=48.82  Aligned_cols=42  Identities=10%  Similarity=0.188  Sum_probs=38.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      -|-+|||..|+++.-+.|++++|+++..|.-+.++..|+..+
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            467899999999999999999999999999999999999643

>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=96.98  E-value=0.0012  Score=48.22  Aligned_cols=41  Identities=15%  Similarity=0.350  Sum_probs=38.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCC-HHHHHHHHHHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDIS-HREAFSAAAKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~-HkEaFs~aAknWa~~  180 (226)
                      .|-+|||..|+++.-.+||++||+++ ..|.-+.++..|+..
T Consensus         7 KRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~l   48 (81)
T 2d7l_A            7 GRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVL   48 (81)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcC
Confidence            45699999999999999999999998 999999999999864

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

Probab=96.94  E-value=0.0011  Score=53.00  Aligned_cols=48  Identities=21%  Similarity=0.385  Sum_probs=42.1

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCC--CCHHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPD--ISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~--i~HkEaFs~aAknWa~~P  181 (226)
                      +-|.+-.|-+|||..|+++.-..|+++||+  ++-.|..+.++..|+..+
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            445566788999999999999999999999  689999999999998753

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

Probab=96.60  E-value=0.0016  Score=54.70  Aligned_cols=46  Identities=30%  Similarity=0.532  Sum_probs=40.8

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |.+-.|-+|||..|+++....|+++||+++..|..+.++..|+..+
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            3344567899999999999999999999999999999999999754

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

Probab=96.55  E-value=0.0017  Score=55.29  Aligned_cols=47  Identities=30%  Similarity=0.504  Sum_probs=42.3

Q ss_pred             CCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      -|.+-.|-+|||..|+++....||++||+++..|..+.++..|+..+
T Consensus        38 ~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   84 (238)
T 3tmm_A           38 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   84 (238)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            45666788999999999999999999999999999999999998743

>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=96.37  E-value=0.0044  Score=48.66  Aligned_cols=46  Identities=15%  Similarity=0.352  Sum_probs=41.4

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |++..|-++||-.|++++-.+|++++|+++..|.-+.++..|+..+
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            4556677899999999999999999999999999999999998654

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

Probab=96.01  E-value=0.0055  Score=41.97  Aligned_cols=38  Identities=29%  Similarity=0.647  Sum_probs=33.7

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      .|-+|||..|+++.-..+|..+|    .|..+.++..|+..+
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            46779999999999999999987    599999999999754

>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=95.85  E-value=0.011  Score=44.98  Aligned_cols=40  Identities=15%  Similarity=0.177  Sum_probs=36.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      -|-+|||+.|+.+...++++++|+ ...|.=+.+...|+..
T Consensus         6 KrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~l   45 (91)
T 1l8y_A            6 ESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNM   45 (91)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcC
Confidence            457999999999999999999999 9999999999999873

>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=94.64  E-value=0.048  Score=40.83  Aligned_cols=37  Identities=11%  Similarity=0.346  Sum_probs=30.6

Q ss_pred             CchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          142 VPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       142 vPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      -+|||..|+++.++  +.++++++..|.-+.++..|+..
T Consensus        12 P~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~l   48 (101)
T 1v63_A           12 PMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRI   48 (101)
T ss_dssp             CSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhC
Confidence            58999999999964  44556688899999999999964

>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=94.56  E-value=0.039  Score=41.91  Aligned_cols=38  Identities=16%  Similarity=0.483  Sum_probs=34.3

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      .|-+|||..|+++.-++||    +++..|.-+.++..|+..+
T Consensus        19 KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls   56 (108)
T 1v64_A           19 KPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLS   56 (108)
T ss_dssp             CCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCC
Confidence            4568999999999999998    8999999999999999754

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

Probab=93.61  E-value=0.019  Score=48.76  Aligned_cols=42  Identities=29%  Similarity=0.574  Sum_probs=36.3

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |.+-.|-+|||+.|+++...+||.++|+    |..+.++..|+..+
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            4455678999999999999999998886    89999999999753

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

Probab=93.58  E-value=0.02  Score=47.93  Aligned_cols=42  Identities=29%  Similarity=0.574  Sum_probs=36.0

Q ss_pred             CccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          136 PEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       136 PEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |.+-.|-+|||+.|+++...+||.++|+    |..+.++..|+..+
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            4444678999999999999999998886    89999999999754

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

Probab=92.67  E-value=0.017  Score=43.69  Aligned_cols=41  Identities=17%  Similarity=0.178  Sum_probs=33.6

Q ss_pred             cCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          138 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       138 KRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      +-.|-||||-.|+.++-.+||++||+++  +.|..+|+.|+..
T Consensus        22 aPKRp~sAf~lf~~e~R~kik~enP~~s--~~~~eIse~Wk~l   62 (90)
T 2yuk_A           22 LGEMATVAPVLYTNINFPNLKEEFPDWT--TRVKQIAKLWRKA   62 (90)
T ss_dssp             HGGGCSSSHHHHHHHHCTTHHHHCCSHH--HHHHHHHHHHHHS
T ss_pred             CCCCCccHHHHHHHHhHHHHHHHCcCcc--chHHHHHHHHHcC
Confidence            3467899999999999999999999985  3355566999864

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

Probab=87.51  E-value=0.23  Score=37.33  Aligned_cols=39  Identities=18%  Similarity=0.430  Sum_probs=33.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHH---HHhhccC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAA---AKNWAHF  180 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~a---AknWa~~  180 (226)
                      .|-+|||..|+++.-.+||.+  +++-.|.=+..   ...|+..
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            467899999999999999998  78888877777   9999873

---

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	226
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-05
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	4e-04
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	7e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	0.001
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	0.003

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

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

 Score = 38.8 bits (90), Expect = 5e-05
 Identities = 8/48 (16%), Positives = 23/48 (47%)

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181
           + P+  ++  + Y RF  ++  +    +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 = 36.0 bits (83), Expect = 4e-04
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 133 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181
           N P    +R PSA+  F  +   +IK  +P +S  +      + W +  
Sbjct: 1   NAP----KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 45

>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 = 34.8 bits (80), Expect = 7e-04
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 4/45 (8%)

Query: 133 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           ++P     R  SAY  ++    + IK  NP I   E      + W
Sbjct: 2   DKPK----RPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELW 42

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

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

 Score = 34.9 bits (80), Expect = 0.001
 Identities = 12/51 (23%), Positives = 23/51 (45%)

Query: 127 PKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           P         EK +R  SA   F +++ ++++   P++S  E     A+ W
Sbjct: 9   PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMW 59

>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 = 33.7 bits (77), Expect = 0.003
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 177
           + P   +R  SAY  F  +    +++ NPDI+  +      + W
Sbjct: 16  KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	226
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	97.92
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	97.88
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	97.72
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	97.65
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.5
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	97.44
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.22
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.2
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	96.99
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	96.88
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	96.25
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	95.31

>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=97.92  E-value=7.8e-06  Score=57.92  Aligned_cols=47  Identities=23%  Similarity=0.381  Sum_probs=41.5

Q ss_pred             CCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      .|.|..|-+|||..|+++..++|++++|++++.|.-..++..|+..+
T Consensus        17 ~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls   63 (90)
T d1wgfa_          17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLS   63 (90)
T ss_dssp             CCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            34444577899999999999999999999999999999999999753

>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=97.88  E-value=8.6e-06  Score=57.77  Aligned_cols=48  Identities=15%  Similarity=0.337  Sum_probs=43.8

Q ss_pred             CCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          133 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       133 ~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      .|.|++-.|-+|||..|+++....|++.+|+++..|.-+.++..|+..
T Consensus         5 kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~l   52 (91)
T d1k99a_           5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKEL   52 (91)
T ss_dssp             CSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCC
Confidence            356677778899999999999999999999999999999999999974

>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=97.72  E-value=2.4e-05  Score=56.06  Aligned_cols=48  Identities=23%  Similarity=0.461  Sum_probs=43.3

Q ss_pred             CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |.|.+-.|-+|||..|+++....||+++|++++.|.-..++..|+..+
T Consensus        16 k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls   63 (93)
T d1lwma_          16 KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALT   63 (93)
T ss_dssp             CCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSC
T ss_pred             CCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCC
Confidence            456666688899999999999999999999999999999999999854

>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=97.65  E-value=1.5e-05  Score=55.29  Aligned_cols=41  Identities=24%  Similarity=0.410  Sum_probs=38.3

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |-+|||..|+++....||+++|+++..|.-+.++..|+..+
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=97.50  E-value=6.7e-05  Score=51.41  Aligned_cols=39  Identities=28%  Similarity=0.407  Sum_probs=37.1

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcc
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAH  179 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~  179 (226)
                      |=+|||..|+++.-+.||++||++++.|.-+.++..|+.
T Consensus         6 rP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~   44 (73)
T d1qrva_           6 RPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA   44 (73)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcC
Confidence            558999999999999999999999999999999999984

>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=97.44  E-value=9.7e-05  Score=49.96  Aligned_cols=42  Identities=19%  Similarity=0.365  Sum_probs=37.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCC--CCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPD--ISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~--i~HkEaFs~aAknWa~~P  181 (226)
                      .|-+|||..|+++.-++||+++|+  +++.|.-+.++..|+..+
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            366899999999999999999996  667899999999999854

>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=97.22  E-value=0.00025  Score=49.89  Aligned_cols=44  Identities=14%  Similarity=0.342  Sum_probs=39.9

Q ss_pred             cCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          138 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       138 KRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |--|-+|||-.|+++.-++|++++|++++.|.=+.++..|+..+
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            34567899999999999999999999999999999999999754

>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=97.20  E-value=0.00024  Score=50.02  Aligned_cols=42  Identities=17%  Similarity=0.360  Sum_probs=38.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      -|-+|||..|+++.-.+|++++|++++.|.=+.++..|+..+
T Consensus         6 KRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~   47 (85)
T d1j46a_           6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (85)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCC
Confidence            466799999999999999999999999999999999999754

>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=96.99  E-value=0.00054  Score=46.57  Aligned_cols=41  Identities=22%  Similarity=0.379  Sum_probs=37.9

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |-+|||-.|+++.-++|++++|++++.|.=+.++..|+..+
T Consensus         5 RP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls   45 (70)
T d1i11a_           5 RPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMT   45 (70)
T ss_dssp             CSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCC
Confidence            45799999999999999999999999999999999999743

>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=96.88  E-value=0.00062  Score=47.96  Aligned_cols=40  Identities=10%  Similarity=0.181  Sum_probs=37.1

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF  180 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~  180 (226)
                      |-++||-.|+++.-++|+++||+++..|.=+.++..|+..
T Consensus         5 RP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~l   44 (86)
T d2lefa_           5 KPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHAL   44 (86)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTS
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhC
Confidence            3469999999999999999999999999999999999964

>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=96.25  E-value=0.0024  Score=46.32  Aligned_cols=37  Identities=14%  Similarity=0.407  Sum_probs=31.4

Q ss_pred             CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      |-++||..|+++..+.    .|+++.+|....+++.|+..+
T Consensus        20 ~P~~ay~lF~~~~r~~----~~~~~~~e~~k~ig~~W~~Ls   56 (108)
T d1v64a_          20 PPPNSYSLYCAELMAN----MKDVPSTERMVLCSQQWKLLS   56 (108)
T ss_dssp             CCSSHHHHHHHHHHHH----CTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCcHHHHHHHHHHHH----ccCCCHHHHHHHHHHHHccCC
Confidence            3479999999986654    578999999999999999854

>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=95.31  E-value=0.008  Score=42.53  Aligned_cols=38  Identities=11%  Similarity=0.344  Sum_probs=33.1

Q ss_pred             CchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215          142 VPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP  181 (226)
Q Consensus       142 vPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P  181 (226)
                      =++||..|+++.++.|+..+  ++.+|.-+.++..|+..+
T Consensus        12 P~~ay~~F~~e~r~~~~~~~--~~~~ei~k~~g~~Wk~ls   49 (101)
T d1v63a_          12 PMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRIS   49 (101)
T ss_dssp             CSSSHHHHHHHHHHHCTTTT--SCHHHHHHHHHHHHTTSC
T ss_pred             CCCHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHhhCC
Confidence            46999999999999998766  468999999999999854