Citrus Sinensis ID: 028980

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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-
Protein Sequence
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRVLVNNFPTVLMHEKKKKKDLHR
Secondary Structure (PSIPRED)
ccccccccccccEEEEEcccccEEEEEcccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccccccccccccccccccccccccHHHccccccHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEEccccEEEEEEcccHHHHcEEEEEccccccEEEEccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccccEcccccccccccccccccHHEcccccccEEEEHHHccccccc
Coil and Loop (DISEMBL)
msscgidvapeqlcyipcnfcnIVLAVSvpcsslldivtvrcghcsnLWSVNMAAAFQslswqdvhhhqapsyaspecridlgssskcnnkisamrtptnkateervvnrppekrqrvpsAYNQFIKEEIQRIkannpdishREAFSTAAknwahfphiHFGLmleannqpklddvstrvlvnnfptvlmHEKKKKKDLHR
Flexible Loop (DISEMBL)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDlgssskcnnkisamrtptnkateervvnrppekrqrvpsaYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRVLVnnfptvlmhekkkkkdlhr
Low Complexity Region (SEG)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRVLVNNFPTVLMHEKKKKKDLHR
Disordered region (IsUnstruct)
****GIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHH********************************************************FI****************REAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRVLVNNFPTV*************
Disordered Region (DISOPRED)
***********QLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAF*******************************************************************FIKEEIQRIK*N*PDISHREAFSTAAKNWAHFP********************************************
Disordered Region (DISEMBL)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQ***********SPECRIDLGSSSKCNNKISAM***********************PSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRVLVNNFPTVLMH**********
Disordered Region (DISPRO)
*********PEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL*********************************************RVVNRP***RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRVLVNNFPTVLMHEKKK******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRVLVNNFPTVLMHEKKKKKDLHR
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	201	2.2.26 [Sep-21-2011]
Q8GW46	164	Axial regulator YABBY 5 O	yes	no	0.786	0.963	0.759	1e-66
Q9XFB0	184	Putative axial regulator	no	no	0.840	0.918	0.537	2e-45
Q10FZ7	186	Protein YABBY 2 OS=Oryza	yes	no	0.830	0.897	0.559	8e-45
Q2QM17	207	Protein YABBY 6 OS=Oryza	no	no	0.845	0.821	0.534	9e-43
Q0JBF0	266	Protein YABBY 5 OS=Oryza	no	no	0.766	0.578	0.534	2e-42
Q01JG2	266	Protein YABBY 5 OS=Oryza	N/A	no	0.766	0.578	0.534	2e-42
Q6H668	256	Protein YABBY 4 OS=Oryza	no	no	0.766	0.601	0.481	1e-41
A2X7Q3	256	Protein YABBY 4 OS=Oryza	N/A	no	0.766	0.601	0.481	1e-41
O22152	229	Axial regulator YABBY 1 O	no	no	0.791	0.694	0.525	2e-39
Q7XIM7	169	Protein YABBY 1 OS=Oryza	no	no	0.771	0.917	0.481	1e-36

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

 Score =  252 bits (643), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 126/166 (75%), Positives = 139/166 (83%), Gaps = 8/166 (4%)

Query: 8   VAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHH 67
           +A EQLCYIPCNFCNI+LAV+VPCSSL DIVTVRCGHC+NLWSVNMAAA QSLS  +   
Sbjct: 6   MATEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQSLSRPNF-- 63

Query: 68  HQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQFIK 127
            QA +YA PE     GSSS+ + KI + R  T   TE+R+VNRPPEKRQRVPSAYNQFIK
Sbjct: 64  -QATNYAVPE----YGSSSRSHTKIPS-RISTRTITEQRIVNRPPEKRQRVPSAYNQFIK 117

Query: 128 EEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 173
           EEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+N Q K+
Sbjct: 118 EEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNKQAKI 163

Arabidopsis thaliana (taxid: 3702)

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

 Score =  182 bits (461), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 94/175 (53%), Positives = 116/175 (66%), Gaps = 6/175 (3%)

Query: 6   IDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDV 65
           +D + E++CY+ C+FC  +LAVSVP +SL  +VTVRCGHC+NL S+N+  +    S   +
Sbjct: 3   VDFSSERVCYVHCSFCTTILAVSVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAPPI 62

Query: 66  HHHQAPS---YASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAY 122
           H    P      S   R D  SSS+  N +S      ++        RPPEKRQRVPSAY
Sbjct: 63  HQDLQPHRQHTTSLVTRKDCASSSRSTNNLSEN---IDREAPRMPPIRPPEKRQRVPSAY 119

Query: 123 NQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVS 177
           N+FIKEEIQRIKA NP+ISHREAFSTAAKNWAHFPHIHFGL L+ N + K  D S
Sbjct: 120 NRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLDQS 174

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 =  179 bits (455), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 99/177 (55%), Positives = 126/177 (71%), Gaps = 10/177 (5%)

Query: 3   SCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSW 62
           S  I  APE +CY+ CNFCN + AVSVP +S+L+IVTVRCGHC++L SVN+    Q+L  
Sbjct: 2   SAQIVPAPEHVCYVHCNFCNTIFAVSVPSNSMLNIVTVRCGHCTSLLSVNLRGLVQALPA 61

Query: 63  QDVHHHQ----APSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRV 118
           +D  H Q      + +  E   + GSSS+   ++  M +  +  TE  +  RPPEKRQRV
Sbjct: 62  ED--HLQDNLKMHNMSFRENYSEYGSSSRYG-RVPMMFSKND--TEHMLHVRPPEKRQRV 116

Query: 119 PSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDD 175
           PSAYN+FIKEEI+RIKANNPDISHREAFSTAAKNWAHFP+IHFGL    +++ KLD+
Sbjct: 117 PSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHFPNIHFGLGSHESSK-KLDE 172

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  172 bits (437), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 100/187 (53%), Positives = 120/187 (64%), Gaps = 17/187 (9%)

Query: 7   DVAP-EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL-SWQD 64
            +AP EQ+CY+ CNFCN +LAVSVP +S+L+IVTVRCGHC+NL SVN+     S  + QD
Sbjct: 4   QIAPAEQVCYVHCNFCNTILAVSVPGNSMLNIVTVRCGHCTNLLSVNLRGLMHSAPALQD 63

Query: 65  VHHHQAPSYASPECRIDLGSSSKCN----NKISAMRTP-----------TNKATEERVVN 109
            HHH         C  D     +      +  S +R P            N+  E+ +  
Sbjct: 64  HHHHHLQESGLSGCFRDQSGYPEFGFSAASSSSKLRLPPAAAAMVSYSQQNQQLEQALHA 123

Query: 110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANN 169
           RPPEKRQRVPSAYN+FIKEEI+RIKANNPDISHREAFSTAAKNWAH+P+IHFGL      
Sbjct: 124 RPPEKRQRVPSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHYPNIHFGLSPGHEG 183

Query: 170 QPKLDDV 176
             KL DV
Sbjct: 184 GKKLVDV 190

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 102/191 (53%), Positives = 117/191 (61%), Gaps = 37/191 (19%)

Query: 11  EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNM------AAA-------- 56
           EQLCY+ CNFC+ +LAV VPCSSL   VTVRCGHC+NL SVN+      AAA        
Sbjct: 29  EQLCYVHCNFCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPF 88

Query: 57  FQSLS--------WQDVHHHQAPS-----YASPECRIDLGSSSKCNNKISA--MRTPTNK 101
            Q+L           +V   QAP+      ASP       S+S C N   A  M +  NK
Sbjct: 89  GQALLSPTSPHGLLDEVPSFQAPASLMTEQASPNVSSITSSNSSCANNAPATSMASAANK 148

Query: 102 ATEER--------VVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
           AT+            NR  EKRQRVPSAYN+FIK+EIQRIKA+NPDI+HREAFS AAKNW
Sbjct: 149 ATQREPQQPKNAPSANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNW 208

Query: 154 AHFPHIHFGLM 164
           AHFPHIHFGLM
Sbjct: 209 AHFPHIHFGLM 219

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 =  171 bits (434), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 102/191 (53%), Positives = 117/191 (61%), Gaps = 37/191 (19%)

Query: 11  EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNM------AAA-------- 56
           EQLCY+ CNFC+ +LAV VPCSSL   VTVRCGHC+NL SVN+      AAA        
Sbjct: 29  EQLCYVHCNFCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPF 88

Query: 57  FQSLS--------WQDVHHHQAPS-----YASPECRIDLGSSSKCNNKISA--MRTPTNK 101
            Q+L           +V   QAP+      ASP       S+S C N   A  M +  NK
Sbjct: 89  GQALLSPTSPHGLLDEVPSFQAPASLMTEQASPNVSSITSSNSSCANNAPATSMASAANK 148

Query: 102 ATEER--------VVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
           AT+            NR  EKRQRVPSAYN+FIK+EIQRIKA+NPDI+HREAFS AAKNW
Sbjct: 149 ATQREPQQPKNAPSANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNW 208

Query: 154 AHFPHIHFGLM 164
           AHFPHIHFGLM
Sbjct: 209 AHFPHIHFGLM 219

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 =  169 bits (427), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 92/191 (48%), Positives = 110/191 (57%), Gaps = 37/191 (19%)

Query: 11  EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHH--H 68
           EQLCY+ CN C+ +LAV VPCSSL   VTVRCGHC+NL SVN+             +  H
Sbjct: 23  EQLCYVHCNCCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQLH 82

Query: 69  QAPS---------------YASPECRIDLGSSSK-----------CNNKISAMRTPTNKA 102
             PS               + +P   ++  +S+            C +   AM+ P  K 
Sbjct: 83  FGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAKP 142

Query: 103 TEER---------VVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
            ++            NRPPEKRQRVPSAYN+FIK+EIQRIKA NPDISHREAFS AAKNW
Sbjct: 143 VQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 202

Query: 154 AHFPHIHFGLM 164
           AHFPHIHFGLM
Sbjct: 203 AHFPHIHFGLM 213

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 =  169 bits (427), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 92/191 (48%), Positives = 110/191 (57%), Gaps = 37/191 (19%)

Query: 11  EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHH--H 68
           EQLCY+ CN C+ +LAV VPCSSL   VTVRCGHC+NL SVN+             +  H
Sbjct: 23  EQLCYVHCNCCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQLH 82

Query: 69  QAPS---------------YASPECRIDLGSSSK-----------CNNKISAMRTPTNKA 102
             PS               + +P   ++  +S+            C +   AM+ P  K 
Sbjct: 83  FGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAKP 142

Query: 103 TEER---------VVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
            ++            NRPPEKRQRVPSAYN+FIK+EIQRIKA NPDISHREAFS AAKNW
Sbjct: 143 VQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 202

Query: 154 AHFPHIHFGLM 164
           AHFPHIHFGLM
Sbjct: 203 AHFPHIHFGLM 213

Oryza sativa subsp. indica (taxid: 39946)

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

 Score =  162 bits (409), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 92/175 (52%), Positives = 112/175 (64%), Gaps = 16/175 (9%)

Query: 11  EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQA 70
           + LCY+ CNFC  +LAV+VP +SL   VTVRCG C+NL SVNM +     S Q       
Sbjct: 23  DHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYVLPASNQLQLQLGP 82

Query: 71  PSYASPECRID-LGSSSKCNNKISAMRTPT-------------NKATEERVVNRPPEKRQ 116
            SY +P+  ++ L  +    N +   + PT             ++  +   VNRPPEKRQ
Sbjct: 83  HSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAPPVNRPPEKRQ 142

Query: 117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQP 171
           RVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL+   +NQP
Sbjct: 143 RVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV--PDNQP 195

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

 Score =  152 bits (384), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 76/158 (48%), Positives = 101/158 (63%), Gaps = 3/158 (1%)

Query: 6   IDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDV 65
           +    E +CY+ CN+CN +L V+VP +   +IVTVRCGHC+ + S+++A   Q+ + QD 
Sbjct: 3   VQFTSEHVCYVNCNYCNTILVVNVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQD- 61

Query: 66  HHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQF 125
             HQ  +             +  N + S    P   + ++    RPPEKRQRVPSAYN+F
Sbjct: 62  --HQVQNRGFQGNNFGSYDIASRNQRTSTAMYPMPTSQQQVSPIRPPEKRQRVPSAYNRF 119

Query: 126 IKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL 163
           IKEEIQRIK +NP+ISHREAFS AAKNWAH P +HFGL
Sbjct: 120 IKEEIQRIKTSNPEISHREAFSAAAKNWAHLPRLHFGL 157

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

Oryza sativa subsp. japonica (taxid: 39947)

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	201
351724725	186	uncharacterized protein LOC100499942 [Gl	0.885	0.956	0.846	3e-84
225445565	185	PREDICTED: axial regulator YABBY 5 [Viti	0.885	0.962	0.841	2e-83
356548475	186	PREDICTED: axial regulator YABBY 5-like	0.885	0.956	0.835	2e-83
255638088	186	unknown [Glycine max]	0.885	0.956	0.829	1e-82
224087122	188	predicted protein [Populus trichocarpa]	0.885	0.946	0.831	5e-79
357478135	191	YABBY protein [Medicago truncatula] gi|3	0.895	0.942	0.786	2e-78
217073506	191	unknown [Medicago truncatula] gi|3884906	0.895	0.942	0.786	2e-78
224142611	176	predicted protein [Populus trichocarpa]	0.870	0.994	0.826	1e-77
255572533	185	Axial regulator YABBY5, putative [Ricinu	0.875	0.951	0.808	2e-76
449464626	193	PREDICTED: axial regulator YABBY 5-like	0.885	0.922	0.760	2e-75

>gi|351724725|ref|NP_001238347.1| uncharacterized protein LOC100499942 [Glycine max] gi|255627893|gb|ACU14291.1| unknown [Glycine max]

 Score =  317 bits (811), Expect = 3e-84,   Method: Compositional matrix adjust.
 Identities = 154/182 (84%), Positives = 163/182 (89%), Gaps = 4/182 (2%)

Query: 1   MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60
           MSSC IDVAPEQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAFQSL
Sbjct: 1   MSSCSIDVAPEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSL 60

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPS 120
           SWQDV   Q P   +PE RID GS+SKCNN+I AMR PT   TEERVVNRPPEKRQRVPS
Sbjct: 61  SWQDV---QGPGQCNPEYRIDTGSTSKCNNRI-AMRAPTTHVTEERVVNRPPEKRQRVPS 116

Query: 121 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRV 180
           AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ K+D+VS + 
Sbjct: 117 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQAKMDNVSEKH 176

Query: 181 LV 182
           L+
Sbjct: 177 LM 178

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225445565|ref|XP_002285328.1| PREDICTED: axial regulator YABBY 5 [Vitis vinifera] gi|297738980|emb|CBI28225.3| unnamed protein product [Vitis vinifera]

 Score =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 154/183 (84%), Positives = 165/183 (90%), Gaps = 5/183 (2%)

Query: 1   MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60
           MSSC IDVA EQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAFQSL
Sbjct: 1   MSSC-IDVASEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSL 59

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPS 120
           SWQDV   QAP+Y SP+ RIDLGSSSKCN K+ AMR P +  +EER+VNRPPEKRQRVPS
Sbjct: 60  SWQDV---QAPNYTSPDYRIDLGSSSKCNTKM-AMRAPASNISEERIVNRPPEKRQRVPS 115

Query: 121 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRV 180
           AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE NNQPKLD+ S + 
Sbjct: 116 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLETNNQPKLDEGSEKH 175

Query: 181 LVN 183
           L++
Sbjct: 176 LMS 178

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548475|ref|XP_003542627.1| PREDICTED: axial regulator YABBY 5-like [Glycine max]

 Score =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 152/182 (83%), Positives = 163/182 (89%), Gaps = 4/182 (2%)

Query: 1   MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60
           MSSC IDVAPEQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAFQSL
Sbjct: 1   MSSCSIDVAPEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSL 60

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPS 120
           SWQDV   Q   + +PE RID GS+SKCNN+I AMR PT   TEERVVNRPPEKRQRVPS
Sbjct: 61  SWQDV---QGSGHCNPEYRIDTGSTSKCNNRI-AMRAPTTHVTEERVVNRPPEKRQRVPS 116

Query: 121 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRV 180
           AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ K+++VS + 
Sbjct: 117 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQVKMENVSEKH 176

Query: 181 LV 182
           L+
Sbjct: 177 LM 178

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255638088|gb|ACU19358.1| unknown [Glycine max]

 Score =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 151/182 (82%), Positives = 162/182 (89%), Gaps = 4/182 (2%)

Query: 1   MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60
           MSSC IDVAPEQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAFQSL
Sbjct: 1   MSSCSIDVAPEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSL 60

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPS 120
           SWQDV   Q   + +PE RID GS+SKCNN+I AMR PT   TEERVVNRPPEKRQRVPS
Sbjct: 61  SWQDV---QGSGHCNPEYRIDTGSTSKCNNRI-AMRAPTTHVTEERVVNRPPEKRQRVPS 116

Query: 121 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTRV 180
           AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ K+++V  + 
Sbjct: 117 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQVKMENVFEKH 176

Query: 181 LV 182
           L+
Sbjct: 177 LM 178

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224087122|ref|XP_002308074.1| predicted protein [Populus trichocarpa] gi|222854050|gb|EEE91597.1| predicted protein [Populus trichocarpa]

 Score =  299 bits (765), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 153/184 (83%), Positives = 161/184 (87%), Gaps = 6/184 (3%)

Query: 1   MSSCGIDVAP-EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQS 59
           MSSC ID  P EQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+N+WSVNMAAAFQS
Sbjct: 1   MSSC-IDAVPNEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNIWSVNMAAAFQS 59

Query: 60  LSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPT-NKATEERVVNRPPEKRQRV 118
           LSWQD    QA +Y S + RIDLGSSSKCNNKIS MRTP  N  T+ERVVNRPPEKRQRV
Sbjct: 60  LSWQD--QVQASNYNSHDYRIDLGSSSKCNNKIS-MRTPAANIVTQERVVNRPPEKRQRV 116

Query: 119 PSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVST 178
           PSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE NNQ K+DD S 
Sbjct: 117 PSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLETNNQTKVDDGSE 176

Query: 179 RVLV 182
           + L+
Sbjct: 177 KRLM 180

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357478135|ref|XP_003609353.1| YABBY protein [Medicago truncatula] gi|355510408|gb|AES91550.1| YABBY protein [Medicago truncatula]

 Score =  297 bits (761), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 147/187 (78%), Positives = 162/187 (86%), Gaps = 7/187 (3%)

Query: 1   MSSCGIDVAP---EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAF 57
           MSSC IDVAP   EQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAF
Sbjct: 1   MSSCSIDVAPAAAEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAF 60

Query: 58  QSLSWQDVHHHQAPSYA-SPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQ 116
           QSLSWQDV   QAPS+  +PE RI   S+ KCN++I+    PT   TEERVVNRPPEKRQ
Sbjct: 61  QSLSWQDV---QAPSHCMNPEYRIRTSSTPKCNDRIAMRSAPTTHVTEERVVNRPPEKRQ 117

Query: 117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDV 176
           RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ ++++V
Sbjct: 118 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQAQIENV 177

Query: 177 STRVLVN 183
           S + L++
Sbjct: 178 SEKRLMS 184

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217073506|gb|ACJ85113.1| unknown [Medicago truncatula] gi|388490620|gb|AFK33376.1| unknown [Medicago truncatula]

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 147/187 (78%), Positives = 161/187 (86%), Gaps = 7/187 (3%)

Query: 1   MSSCGIDVAP---EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAF 57
           MSSC IDVAP   EQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAF
Sbjct: 1   MSSCSIDVAPAAAEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAF 60

Query: 58  QSLSWQDVHHHQAPSYA-SPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQ 116
           QSLSWQDV   QAPS+  +PE RI   S+ KCN++I+    PT   TEERVVNRPPEKRQ
Sbjct: 61  QSLSWQDV---QAPSHCMNPEYRIRTSSTPKCNDRIAMRSAPTTHVTEERVVNRPPEKRQ 117

Query: 117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDV 176
           RVPSAYNQFIKEEIQRIK NNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ K+++V
Sbjct: 118 RVPSAYNQFIKEEIQRIKVNNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQAKIENV 177

Query: 177 STRVLVN 183
           S + L++
Sbjct: 178 SEKRLMS 184

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224142611|ref|XP_002324648.1| predicted protein [Populus trichocarpa] gi|222866082|gb|EEF03213.1| predicted protein [Populus trichocarpa]

 Score =  295 bits (754), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 148/179 (82%), Positives = 157/179 (87%), Gaps = 4/179 (2%)

Query: 1   MSSCGIDVAP-EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQS 59
           MSSC +DV P EQLCYIPCNFCNIVLAVSVPCS+L DIVTVRCGHC+NLWSVNMAAAFQS
Sbjct: 1   MSSC-VDVVPHEQLCYIPCNFCNIVLAVSVPCSNLFDIVTVRCGHCTNLWSVNMAAAFQS 59

Query: 60  LSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVP 119
           LSWQD  H QA ++ S + RID+GSSSK NNKIS     TN  T+ERVVNRPPEKRQRVP
Sbjct: 60  LSWQD--HVQASNHISHDYRIDMGSSSKFNNKISTRTPATNIVTQERVVNRPPEKRQRVP 117

Query: 120 SAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVST 178
           SAYNQFIKEEIQRIKANNP+ISHREAFSTAAKNWAHFPHI FGLMLE NNQ KLDDVST
Sbjct: 118 SAYNQFIKEEIQRIKANNPEISHREAFSTAAKNWAHFPHIQFGLMLETNNQAKLDDVST 176

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255572533|ref|XP_002527201.1| Axial regulator YABBY5, putative [Ricinus communis] gi|223533466|gb|EEF35214.1| Axial regulator YABBY5, putative [Ricinus communis]

 Score =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 148/183 (80%), Positives = 160/183 (87%), Gaps = 7/183 (3%)

Query: 1   MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60
           MSSC +DV PEQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAFQSL
Sbjct: 1   MSSC-VDVVPEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSL 59

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPT-NKATEERVVNRPPEKRQRVP 119
           SWQD    QAPS+ SP+ RI+LGSSSKCNN+IS MR P  +   EERVVNRPPEKRQRVP
Sbjct: 60  SWQDF---QAPSHNSPDYRIELGSSSKCNNRIS-MRAPAPHNIAEERVVNRPPEKRQRVP 115

Query: 120 SAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVSTR 179
           SAYNQFIKEEIQRIKANNP+ISHREAFSTAAKNWAH+PHIHFGL L  N+Q KLDD S +
Sbjct: 116 SAYNQFIKEEIQRIKANNPEISHREAFSTAAKNWAHYPHIHFGLTLN-NHQTKLDDASEK 174

Query: 180 VLV 182
            L+
Sbjct: 175 HLM 177

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464626|ref|XP_004150030.1| PREDICTED: axial regulator YABBY 5-like [Cucumis sativus]

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 143/188 (76%), Positives = 155/188 (82%), Gaps = 10/188 (5%)

Query: 1   MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60
           M++  +D+APEQLCYIPCNFCNIVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAF SL
Sbjct: 1   MATTCLDIAPEQLCYIPCNFCNIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFHSL 60

Query: 61  SWQDVHHHQAPSYASPEC-----RIDLGSSSKCNNKISAM--RTPTNKATEERVVNRPPE 113
           SWQDV   Q PSY    C     + D GSSSKCNN ++ M  R PT    EERVVNRPPE
Sbjct: 61  SWQDV---QVPSYNLYGCNGADFQGDFGSSSKCNNNVNKMEIRVPTTIPAEERVVNRPPE 117

Query: 114 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 173
           KRQRVPSAYNQFIKEEIQRIKA+NP+ISHREAFSTAAKNWAHFP IHFGLMLE NNQ KL
Sbjct: 118 KRQRVPSAYNQFIKEEIQRIKASNPEISHREAFSTAAKNWAHFPRIHFGLMLETNNQVKL 177

Query: 174 DDVSTRVL 181
           DD S R++
Sbjct: 178 DDGSERLM 185

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	201
TAIR|locus:2066311	164	YAB5 "YABBY5" [Arabidopsis tha	0.786	0.963	0.759	6.9e-63
TAIR|locus:2826731	184	YAB2 "YABBY2" [Arabidopsis tha	0.840	0.918	0.542	6.4e-44
TAIR|locus:2005492	229	AFO "AT2G45190" [Arabidopsis t	0.820	0.720	0.518	9.9e-39
UNIPROTKB|Q7XIM7	169	YAB1 "Protein YABBY 1" [Oryza	0.766	0.911	0.490	4.4e-36
TAIR|locus:2028020	231	INO "INNER NO OUTER" [Arabidop	0.751	0.653	0.472	1.6e-31
UNIPROTKB|Q76EJ0	194	DL "Protein DROOPING LEAF" [Or	0.671	0.695	0.490	1.3e-29
TAIR|locus:2026418	181	CRC "AT1G69180" [Arabidopsis t	0.686	0.762	0.438	2.8e-27
TAIR|locus:2126931	240	YAB3 "YABBY3" [Arabidopsis tha	0.761	0.637	0.425	3.2e-26

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

 Score = 642 (231.1 bits), Expect = 6.9e-63, P = 6.9e-63
 Identities = 126/166 (75%), Positives = 139/166 (83%)

Query:     8 VAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHH 67
             +A EQLCYIPCNFCNI+LAV+VPCSSL DIVTVRCGHC+NLWSVNMAAA QSLS  +   
Sbjct:     6 MATEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQSLSRPNF-- 63

Query:    68 HQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQFIK 127
              QA +YA PE     GSSS+ + KI + R  T   TE+R+VNRPPEKRQRVPSAYNQFIK
Sbjct:    64 -QATNYAVPE----YGSSSRSHTKIPS-RISTRTITEQRIVNRPPEKRQRVPSAYNQFIK 117

Query:   128 EEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 173
             EEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+N Q K+
Sbjct:   118 EEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNKQAKI 163

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0006417 "regulation of translation" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

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

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

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 95/175 (54%), Positives = 117/175 (66%)

Query:     6 IDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDV 65
             +D + E++CY+ C+FC  +LAVSVP +SL  +VTVRCGHC+NL S+N+  +    S   +
Sbjct:     3 VDFSSERVCYVHCSFCTTILAVSVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAPPI 62

Query:    66 HHHQAPSY---ASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAY 122
             H    P      S   R D  SSS+  N +S       +A     + RPPEKRQRVPSAY
Sbjct:    63 HQDLQPHRQHTTSLVTRKDCASSSRSTNNLS--ENIDREAPRMPPI-RPPEKRQRVPSAY 119

Query:   123 NQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDVS 177
             N+FIKEEIQRIKA NP+ISHREAFSTAAKNWAHFPHIHFGL L+ N + K  D S
Sbjct:   120 NRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLDQS 174

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

 Score = 414 (150.8 bits), Expect = 9.9e-39, P = 9.9e-39
 Identities = 96/185 (51%), Positives = 117/185 (63%)

Query:     4 CGID-VAP-EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLS 61
             C  D  +P + LCY+ CNFC  +LAV+VP +SL   VTVRCG C+NL SVNM +     S
Sbjct:    14 CSPDHFSPSDHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYVLPAS 73

Query:    62 WQDVHHHQAP-SYASPECRIDLGSSSKCNNKISAMRT-PT-------------NKATEER 106
              Q +     P SY +P+  ++    +  N  +  M   PT             ++  +  
Sbjct:    74 NQ-LQLQLGPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAP 132

Query:   107 VVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE 166
              VNRPPEKRQRVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL+  
Sbjct:   133 PVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV-- 190

Query:   167 ANNQP 171
              +NQP
Sbjct:   191 PDNQP 195

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

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

 Score = 389 (142.0 bits), Expect = 4.4e-36, P = 4.4e-36
 Identities = 78/159 (49%), Positives = 103/159 (64%)

Query:     6 IDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDV 65
             +    E +CY+ CN+CN +L V+VP +   +IVTVRCGHC+ + S+++A   Q+ + QD 
Sbjct:     3 VQFTSEHVCYVNCNYCNTILVVNVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQD- 61

Query:    66 HHHQAPSYASPEC-RIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQ 124
             H  Q   +        D+ S    N + S    P   + ++    RPPEKRQRVPSAYN+
Sbjct:    62 HQVQNRGFQGNNFGSYDIASR---NQRTSTAMYPMPTSQQQVSPIRPPEKRQRVPSAYNR 118

Query:   125 FIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL 163
             FIKEEIQRIK +NP+ISHREAFS AAKNWAH P +HFGL
Sbjct:   119 FIKEEIQRIKTSNPEISHREAFSAAAKNWAHLPRLHFGL 157

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 77/163 (47%), Positives = 102/163 (62%)

Query:    10 PEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVN-MAAAF------QSLSW 62
             P Q+C++ C FC  +L VSVP +SL  +VTVRCGHC++L SVN M A+F       SLS 
Sbjct:    18 PGQICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCTSLLSVNLMKASFIPLHLLASLSH 77

Query:    63 QD-VHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEE----RVVNRPPEKRQR 117
              D     +  +    E      +  K N+  + + +  N+  +     +VVN+PPEKRQR
Sbjct:    78 LDETGKEEVAATDGVEEEAWKVNQEKENSPTTLVSSSDNEDEDVSRVYQVVNKPPEKRQR 137

Query:   118 VPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIH 160
              PSAYN FIKEEI+R+KA NP ++H+EAFS AAKNWAHFP  H
Sbjct:   138 APSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPAH 180

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0048481 "ovule development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

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

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

 Score = 328 (120.5 bits), Expect = 1.3e-29, P = 1.3e-29
 Identities = 75/153 (49%), Positives = 95/153 (62%)

Query:     8 VAP-EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAF-QSLSWQDV 65
             V+P E LCY+ C +CN VLAV VPC  L+D VTV+CGHC+NL  ++      Q LS  D 
Sbjct:     4 VSPSEHLCYVRCTYCNTVLAVGVPCKRLMDTVTVKCGHCNNLSFLSPRPPMVQPLSPTD- 62

Query:    66 HHHQAPSYASP--ECRIDLGSSSKCNNKISAMRTPTNKATEERV--VNRPPEKRQRVPSA 121
              H   P +  P  +CR          N+   + +PT+     R   V +PPEK+ R+PSA
Sbjct:    63 -HPLGP-FQGPCTDCR---------RNQPLPLVSPTSNEGSPRAPFVVKPPEKKHRLPSA 111

Query:   122 YNQFIKEEIQRIKANNPDISHREAFSTAAKNWA 154
             YN+F++EEIQRIKA  PDI HREAFS AAKNWA
Sbjct:   112 YNRFMREEIQRIKAAKPDIPHREAFSMAAKNWA 144

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

GO:0048366 "leaf development" evidence=IMP

GO:0048440 "carpel development" evidence=IMP

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

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 64/146 (43%), Positives = 90/146 (61%)

Query:    11 EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQA 70
             E L Y+ C+ CN +LAV +P   +LD VTV+CGHC NL  +      Q      +   Q 
Sbjct:    19 EHLYYVRCSICNTILAVGIPLKRMLDTVTVKCGHCGNLSFLTTTPPLQGHVSLTL---QM 75

Query:    71 PSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEI 130
              S+   + +   GSSS  ++  S+ + P+        V +PPEK+QR+PSAYN+F+++EI
Sbjct:    76 QSFGGSDYK--KGSSSSSSSSTSSDQPPSPSPP---FVVKPPEKKQRLPSAYNRFMRDEI 130

Query:   131 QRIKANNPDISHREAFSTAAKNWAHF 156
             QRIK+ NP+I HREAFS AAKNWA +
Sbjct:   131 QRIKSANPEIPHREAFSAAAKNWAKY 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

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

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 74/174 (42%), Positives = 95/174 (54%)

Query:     6 IDVAPEQL---CYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHC----------SNLWSVN 52
             + V P  L     + C  C+ +L+V+V   +LL       GH            NL    
Sbjct:    39 VSVPPSSLFKTVTVRCGHCSNLLSVTVSMRALLLPSVSNLGHSFLPPPPPPPPPNLLE-E 97

Query:    53 MAAAFQSLSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRPP 112
             M +  Q+++   +  H A ++   E  +    + +  + +  M  P          NRPP
Sbjct:    98 MRSGGQNINMNMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPP-------ANRPP 150

Query:   113 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE 166
             EKRQRVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGLM +
Sbjct:   151 EKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMAD 204

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

---

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)
Q8GW46	YAB5_ARATH	No assigned EC number	0.7590	0.7860	0.9634	yes	no
Q10FZ7	YAB2_ORYSJ	No assigned EC number	0.5593	0.8308	0.8978	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	201
pfam04690	170	pfam04690, YABBY, YABBY protein	1e-63
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	0.001
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	0.002

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

 Score =  194 bits (494), Expect = 1e-63
 Identities = 88/172 (51%), Positives = 107/172 (62%), Gaps = 18/172 (10%)

Query: 6   IDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDV 65
           +  + E +CY+ CNFC  +LAVSVP +SL +IVTVRCGHC+NL SVN+      L     
Sbjct: 3   VFFSSEHVCYVHCNFCTTILAVSVPYTSLFNIVTVRCGHCTNLLSVNLMMRSHLLPALSH 62

Query: 66  HHHQAPSYASPECRIDLGSS--------SKCNNKISAMRTPTNKATEERV------VNRP 111
                     PE   +LG           K ++  +++ +      ++        VNRP
Sbjct: 63  LDETG----KPELLQNLGVHGQNFNSNMMKSHSASTSVSSYMMSDNQDEEMPRVPPVNRP 118

Query: 112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL 163
           PEKRQRVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL
Sbjct: 119 PEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 170

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

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

 Score = 36.1 bits (84), Expect = 0.001
 Identities = 13/37 (35%), Positives = 18/37 (48%)

Query: 117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
           R  SAY  F +E+  ++K  NPD S  E      + W
Sbjct: 3   RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKW 39

These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

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

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 13/37 (35%), Positives = 17/37 (45%)

Query: 117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
           R  SAY  F +E    +KA NP +S  E      + W
Sbjct: 3   RPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMW 39

HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. Length = 66

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	201
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	100.0
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.14
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	97.62
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	97.54
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.51
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	97.5
smart00398	70	HMG high mobility group.	97.4
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	97.3
PTZ00199	94	high mobility group protein; Provisional	97.28
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	96.47
KOG0381	96	consensus HMG box-containing protein [General func	96.05
KOG3223	221	consensus Uncharacterized conserved protein [Funct	94.31
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	93.6

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

Probab=100.00  E-value=9.2e-80  Score=511.28  Aligned_cols=156  Identities=62%  Similarity=0.997  Sum_probs=118.5

Q ss_pred             CCCCceeeecCCCcceeeeccccCCCccceeeeecCCCCCcccccccccccCCChhhhccc--CCC---CC--CCCcccc
Q 028980            8 VAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHH--QAP---SY--ASPECRI   80 (201)
Q Consensus         8 ~~~E~lCYV~CnfC~TILaVsVPcssL~~tVTVRCGHCtnLlsVNmr~ll~s~~~q~~~~~--~~~---~~--~~~~~~~   80 (201)
                      .++|||||||||||||||||||||+|||+|||||||||+|||||||++++++++.+++..+  ..+   ..  .......
T Consensus         5 ~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   84 (170)
T PF04690_consen    5 SPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPENFGS   84 (170)
T ss_pred             CCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhcccccccccccccccccccc
Confidence            3689999999999999999999999999999999999999999999999988876654111  000   00  0111111


Q ss_pred             cCCC-CCccccccc-ccCCCCCCccccC-CCCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980           81 DLGS-SSKCNNKIS-AMRTPTNKATEER-VVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus        81 ~~~s-ss~~~~~~~-~~~~~~~~e~p~~-~v~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      ...+ ++.++.... .+....+++.|++ +++||||||||+|||||+||||||||||++||||+|||||++|||||||+|
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen   85 NSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             ccccCCCccccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence            1111 111111100 1112334456654 579999999999999999999999999999999999999999999999999


Q ss_pred             cccccc
Q 028980          158 HIHFGL  163 (201)
Q Consensus       158 hihfGl  163 (201)
                      ||||||
T Consensus       165 hihfgl  170 (170)
T PF04690_consen  165 HIHFGL  170 (170)
T ss_pred             ccccCC
Confidence            999997

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

Probab=98.14  E-value=3.7e-06  Score=59.53  Aligned_cols=46  Identities=35%  Similarity=0.634  Sum_probs=38.7

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhccCC
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKAN-NPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~-~P~i~HkEaFs~aAknWa~~P  157 (201)
                      |.|-.|.+|||+.||++.+.+++.. .+.++.+|++..++..|+..+
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            6677899999999999999999999 888999999999999999754

It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....

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

Probab=97.62  E-value=0.00012  Score=49.25  Aligned_cols=41  Identities=32%  Similarity=0.498  Sum_probs=38.8

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       117 RvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      |-+|||..|+++....+++.+|+++..|....++..|+..+
T Consensus         3 rp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls   43 (66)
T cd01390           3 RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS   43 (66)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            56899999999999999999999999999999999999765

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

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

Probab=97.54  E-value=0.00017  Score=50.88  Aligned_cols=42  Identities=17%  Similarity=0.294  Sum_probs=39.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      -|-++||..|+++.-.++++++|+++..|.-+.++..|+..+
T Consensus         3 KrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls   44 (72)
T cd01388           3 KRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALS   44 (72)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            367899999999999999999999999999999999999754

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

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

Probab=97.51  E-value=0.00023  Score=47.32  Aligned_cols=43  Identities=30%  Similarity=0.432  Sum_probs=39.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .|-++||..|++++...+++.+|+++..|....+++.|+..+.
T Consensus         2 krp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~   44 (66)
T cd00084           2 KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE   44 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence            3568999999999999999999999999999999999997653

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

>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=97.50  E-value=0.00017  Score=49.07  Aligned_cols=42  Identities=33%  Similarity=0.635  Sum_probs=37.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .|-++||..|+++....|++++|+++..|.-+.+++.|+..+
T Consensus         2 krP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~   43 (69)
T PF00505_consen    2 KRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLS   43 (69)
T ss_dssp             SSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCC
Confidence            467899999999999999999999999999999999999754

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 ....

>smart00398 HMG high mobility group

Probab=97.40  E-value=0.00044  Score=46.48  Aligned_cols=43  Identities=33%  Similarity=0.521  Sum_probs=39.5

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .|-+|+|..|+++....+++.+|+++..|....++..|+..+.
T Consensus         3 krp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~   45 (70)
T smart00398        3 KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSE   45 (70)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCH
Confidence            4678999999999999999999999999999999999998653

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

Probab=97.30  E-value=0.00061  Score=48.53  Aligned_cols=43  Identities=16%  Similarity=0.358  Sum_probs=40.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .|-++||-.|+++....|+++||++++.|.-+.++..|+..+.
T Consensus         3 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~   45 (77)
T cd01389           3 PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESP   45 (77)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCH
Confidence            4789999999999999999999999999999999999998654

These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.

>PTZ00199 high mobility group protein; Provisional

Probab=97.28  E-value=0.00073  Score=50.80  Aligned_cols=50  Identities=26%  Similarity=0.450  Sum_probs=42.9

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCc
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDIS--HREAFSTAAKNWAHFPH  158 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~--HkEaFs~aAknWa~~Ph  158 (201)
                      .+.|.+-.|-+|||..|+.+.-..|+++||+++  -.|.-+.++..|+..+.
T Consensus        17 ~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~   68 (94)
T PTZ00199         17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSE   68 (94)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCH
Confidence            456667778999999999999999999999986  56778889999998763

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

Probab=96.47  E-value=0.0046  Score=49.99  Aligned_cols=54  Identities=26%  Similarity=0.531  Sum_probs=48.6

Q ss_pred             CCCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCccccc
Q 028980          107 VVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFG  162 (201)
Q Consensus       107 ~v~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~PhihfG  162 (201)
                      .+-|.||||-+  -||..|--.+|.+||++||++.+-+-=-..=|.|...|...|-
T Consensus        67 ~~drHPErR~K--AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeNP~N  120 (122)
T PF06244_consen   67 PIDRHPERRMK--AAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPENPFN  120 (122)
T ss_pred             CCCCCcchhHH--HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCCCcc
Confidence            56789999864  6999999999999999999999999888899999999988763

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

Probab=96.05  E-value=0.015  Score=42.34  Aligned_cols=46  Identities=28%  Similarity=0.441  Sum_probs=40.8

Q ss_pred             CCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          113 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       113 EKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      ..-+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|.....
T Consensus        21 ~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~   66 (96)
T KOG0381|consen   21 QAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAE   66 (96)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCH
Confidence            3557778899999999999999999999999999999999987643

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.31  E-value=0.02  Score=50.48  Aligned_cols=54  Identities=30%  Similarity=0.531  Sum_probs=48.1

Q ss_pred             CCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccccc
Q 028980          108 VNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL  163 (201)
Q Consensus       108 v~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~PhihfGl  163 (201)
                      .-|-||||-|  -||--|=..+|.|||.+||+++|-+-=-..-|.|...|...|.-
T Consensus       160 ddrHPEkRmr--AA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~Nq  213 (221)
T KOG3223|consen  160 DDRHPEKRMR--AAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFNQ  213 (221)
T ss_pred             cccChHHHHH--HHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhhH
Confidence            3489999877  49999999999999999999999998888889999999988853

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

Probab=93.60  E-value=0.041  Score=38.07  Aligned_cols=38  Identities=29%  Similarity=0.697  Sum_probs=29.4

Q ss_pred             eecCCCcceeeeccccCCCccc---eeeeecCCCCCccccccc
Q 028980           15 YIPCNFCNIVLAVSVPCSSLLD---IVTVRCGHCSNLWSVNMA   54 (201)
Q Consensus        15 YV~CnfC~TILaVsVPcssL~~---tVTVRCGHCtnLlsVNmr   54 (201)
                      ||-|+.|..+|-  +|-+.+..   .-.+|||.|+.++++.++
T Consensus         6 Fv~C~~C~~lLq--lP~~~~~~~k~~~klrCGaCs~vl~~s~~   46 (46)
T PF11331_consen    6 FVVCSSCFELLQ--LPAKFSLSKKNQQKLRCGACSEVLSFSLP   46 (46)
T ss_pred             EeECccHHHHHc--CCCccCCCccceeEEeCCCCceeEEEecC
Confidence            788999977665  47765443   568999999999988653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	201
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	4e-06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	8e-05
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	3e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	3e-04
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	8e-04

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

 Score = 44.8 bits (105), Expect = 4e-06
 Identities = 16/74 (21%), Positives = 25/74 (33%)

Query: 84  SSSKCNNKISAMRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHR 143
           SS               +       +      ++  S+Y +F KE++   KA NPD    
Sbjct: 11  SSGLVPRGSHMASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTT 70

Query: 144 EAFSTAAKNWAHFP 157
           E     A+ W   P
Sbjct: 71  ELIRRIAQRWRELP 84

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

 Score = 40.9 bits (95), Expect = 8e-05
 Identities = 14/48 (29%), Positives = 21/48 (43%)

Query: 110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 157
                 ++  S+Y +F KE++   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 = 38.8 bits (90), Expect = 3e-04
 Identities = 15/59 (25%), Positives = 25/59 (42%)

Query: 95  MRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
           M+T      E +   + P   +R PSA+  F  E   +IK  +P +S  +      + W
Sbjct: 82  MKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 140

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

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 15/59 (25%), Positives = 23/59 (38%)

Query: 95  MRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
           M TP           + P   +R  SAY  F  E    +++ NPDI+  +      + W
Sbjct: 1   MVTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

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

 Score = 36.6 bits (85), Expect = 8e-04
 Identities = 7/45 (15%), Positives = 22/45 (48%)

Query: 109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
            + P+  ++  + Y +F  E+  +    +P++S+ +     +K +
Sbjct: 5   KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKY 49

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	201
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	97.76
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	97.69
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	97.59
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	97.57
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	97.56
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	97.54
1wgf_A	90	Upstream binding factor 1; transcription factor, D	97.53
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	97.52
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	97.51
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	97.5
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	97.49
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	97.41
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	97.39
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	97.38
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	97.38
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	97.34
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	97.3
1ckt_A	71	High mobility group 1 protein; high-mobility group	97.28
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	97.26
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.22
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	97.19
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.12
2lhj_A	97	High mobility group protein homolog NHP1; structur	97.12
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	97.11
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	97.04
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	96.98
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	96.94
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	96.9
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	96.5
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	96.42
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	96.24
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	95.78
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	95.68
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	94.28
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	94.27
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	94.2
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	93.33
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	93.32
2cto_A	93	Novel protein; high mobility group box domain, hel	86.47

>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=97.76  E-value=4.8e-05  Score=52.66  Aligned_cols=47  Identities=26%  Similarity=0.441  Sum_probs=42.9

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          111 PPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       111 PPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      -|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         3 dp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   49 (77)
T 1hme_A            3 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA   49 (77)
T ss_dssp             CSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            46666788999999999999999999999999999999999999754

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

Probab=97.69  E-value=6.2e-05  Score=52.94  Aligned_cols=48  Identities=21%  Similarity=0.317  Sum_probs=43.9

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       110 KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .+|.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         3 ~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (82)
T 1wz6_A            3 SGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLD   50 (82)
T ss_dssp             SSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            466777788999999999999999999999999999999999999764

>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=97.59  E-value=0.00011  Score=50.76  Aligned_cols=43  Identities=26%  Similarity=0.415  Sum_probs=40.1

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          115 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       115 RQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      -.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         4 PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   46 (73)
T 3nm9_A            4 PKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK   46 (73)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            4578999999999999999999999999999999999999765

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

Probab=97.57  E-value=0.00014  Score=52.41  Aligned_cols=48  Identities=17%  Similarity=0.248  Sum_probs=42.7

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          111 PPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       111 PPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+.
T Consensus         4 ~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~   51 (92)
T 2cs1_A            4 GSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSE   51 (92)
T ss_dssp             CCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCH
Confidence            355556789999999999999999999999999999999999997653

>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=97.56  E-value=0.0001  Score=50.94  Aligned_cols=46  Identities=13%  Similarity=0.355  Sum_probs=41.6

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      |.+-.|-+|||..|+++.-+.|++++|+++..|.-+.++..|+..+
T Consensus         2 p~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   47 (76)
T 1hry_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (76)
T ss_dssp             -CCCCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCC
Confidence            4566788999999999999999999999999999999999999764

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

Probab=97.54  E-value=0.00017  Score=51.99  Aligned_cols=48  Identities=17%  Similarity=0.414  Sum_probs=43.5

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       110 KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      +-|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         3 kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (92)
T 2crj_A            3 SGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQ   50 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            446666788999999999999999999999999999999999999764

>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=97.53  E-value=0.00012  Score=52.78  Aligned_cols=49  Identities=24%  Similarity=0.385  Sum_probs=44.1

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .+.|.+-.|-+|||..|+++.-..|+++||++++.|.-+.++..|+..+
T Consensus        15 ~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   63 (90)
T 1wgf_A           15 KGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLS   63 (90)
T ss_dssp             SSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            3456666788999999999999999999999999999999999999754

>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=97.52  E-value=0.00014  Score=52.06  Aligned_cols=49  Identities=18%  Similarity=0.262  Sum_probs=44.2

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .+-|.+-.|-++||..|+++.-+.|++++|+++..|.-+.++..|+..+
T Consensus        12 ~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   60 (87)
T 2e6o_A           12 ATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMK   60 (87)
T ss_dssp             CCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            4456677788999999999999999999999999999999999999754

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

Probab=97.51  E-value=0.00016  Score=53.26  Aligned_cols=50  Identities=26%  Similarity=0.469  Sum_probs=44.4

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .+.|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+.
T Consensus        12 ~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~   61 (102)
T 2co9_A           12 KKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGE   61 (102)
T ss_dssp             CCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCH
Confidence            34566667889999999999999999999999999999999999997653

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

Probab=97.50  E-value=0.00018  Score=49.65  Aligned_cols=45  Identities=20%  Similarity=0.422  Sum_probs=41.1

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHF  156 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~  156 (201)
                      |.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l   45 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL   45 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh
Confidence            445567899999999999999999999999999999999999975

>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=97.49  E-value=0.0002  Score=50.92  Aligned_cols=46  Identities=13%  Similarity=0.355  Sum_probs=41.8

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      |.+-.|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+
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            4555678999999999999999999999999999999999999764

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

Probab=97.41  E-value=0.0002  Score=52.79  Aligned_cols=48  Identities=17%  Similarity=0.379  Sum_probs=43.3

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       110 KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      +.|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+
T Consensus         6 kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls   53 (99)
T 1k99_A            6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP   53 (99)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            456666788999999999999999999999999999999999999754

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

Probab=97.39  E-value=0.00028  Score=52.58  Aligned_cols=49  Identities=14%  Similarity=0.274  Sum_probs=42.2

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .+.|.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus        24 ~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   72 (106)
T 4euw_A           24 SKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLN   72 (106)
T ss_dssp             ----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             cCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            4567777889999999999999999999999999999999999998765

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

Probab=97.38  E-value=0.00029  Score=50.14  Aligned_cols=47  Identities=23%  Similarity=0.414  Sum_probs=41.0

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 028980          111 PPEKRQRVPSAYNQFIKEEIQRIKANNPDISH--REAFSTAAKNWAHFP  157 (201)
Q Consensus       111 PPEKRQRvpSaYN~fmK~ei~riK~~~P~i~H--kEaFs~aAknWa~~P  157 (201)
                      -|.+-.|-+|||..|+++.-+.|++++|+++.  .|.-+.++..|+..+
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            35555678899999999999999999999974  999999999998754

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

Probab=97.38  E-value=0.00024  Score=49.79  Aligned_cols=46  Identities=24%  Similarity=0.459  Sum_probs=40.0

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      +.|-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         4 ~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   49 (83)
T 3f27_D            4 TSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   49 (83)
T ss_dssp             ---CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            3445678999999999999999999999999999999999998754

>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=97.34  E-value=0.00038  Score=48.76  Aligned_cols=44  Identities=18%  Similarity=0.336  Sum_probs=40.1

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          114 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       114 KRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      +-.|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+
T Consensus         4 ~pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   47 (81)
T 1i11_A            4 HIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMT   47 (81)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCC
Confidence            34577999999999999999999999999999999999999754

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

Probab=97.30  E-value=0.00031  Score=47.45  Aligned_cols=43  Identities=26%  Similarity=0.468  Sum_probs=38.6

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          115 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       115 RQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      -.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         3 ~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (71)
T 4a3n_A            3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   45 (71)
T ss_dssp             --CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            3577899999999999999999999999999999999998754

>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=97.28  E-value=0.00043  Score=47.03  Aligned_cols=43  Identities=21%  Similarity=0.337  Sum_probs=38.7

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 028980          115 RQRVPSAYNQFIKEEIQRIKANNPDISH--REAFSTAAKNWAHFP  157 (201)
Q Consensus       115 RQRvpSaYN~fmK~ei~riK~~~P~i~H--kEaFs~aAknWa~~P  157 (201)
                      -.|-+|||..|+++.-+.|+++||+++.  .|.-+.++..|+..+
T Consensus         2 PKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls   46 (71)
T 1ckt_A            2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   46 (71)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCC
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCC
Confidence            3578999999999999999999999976  999999999998643

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

Probab=97.26  E-value=0.00052  Score=47.81  Aligned_cols=44  Identities=14%  Similarity=0.354  Sum_probs=40.0

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          114 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       114 KRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      +-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         2 ~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (80)
T 1gt0_D            2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            34577999999999999999999999999999999999999754

>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=97.22  E-value=0.00053  Score=53.16  Aligned_cols=48  Identities=25%  Similarity=0.450  Sum_probs=43.0

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       110 KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      +-|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
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            345566788999999999999999999999999999999999999754

>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=97.19  E-value=0.00045  Score=47.79  Aligned_cols=42  Identities=21%  Similarity=0.383  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
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            477899999999999999999999999999999999998754

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

Probab=97.12  E-value=0.00069  Score=53.44  Aligned_cols=47  Identities=26%  Similarity=0.441  Sum_probs=42.7

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          111 PPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       111 PPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      -|.+-.|-+|||..|+++...+|++++|+++..|.-+.++..|+..+
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            45566788999999999999999999999999999999999999764

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

Probab=97.12  E-value=0.00025  Score=51.62  Aligned_cols=49  Identities=27%  Similarity=0.415  Sum_probs=44.5

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCC
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDIS--HREAFSTAAKNWAHFP  157 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~--HkEaFs~aAknWa~~P  157 (201)
                      .+.|.+-.|-+|||..|+++.-..|+++||+++  ..|.-+.++..|+..+
T Consensus        17 ~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   67 (97)
T 2lhj_A           17 KKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALS   67 (97)
T ss_dssp             TSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCC
Confidence            456777788999999999999999999999999  9999999999999754

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

Probab=97.11  E-value=0.0004  Score=48.87  Aligned_cols=47  Identities=23%  Similarity=0.411  Sum_probs=41.2

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 028980          111 PPEKRQRVPSAYNQFIKEEIQRIKANNPDISH--REAFSTAAKNWAHFP  157 (201)
Q Consensus       111 PPEKRQRvpSaYN~fmK~ei~riK~~~P~i~H--kEaFs~aAknWa~~P  157 (201)
                      -|.+-.|-+|||..|+++.-..|++++|+++.  .|.-+.++..|+..+
T Consensus         4 dp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls   52 (83)
T 1aab_A            4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMS   52 (83)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCC
Confidence            45566788999999999999999999999875  899999999998754

>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=97.04  E-value=0.00017  Score=52.28  Aligned_cols=49  Identities=24%  Similarity=0.482  Sum_probs=43.8

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .+.|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+
T Consensus        15 ~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   63 (93)
T 1cg7_A           15 KKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALT   63 (93)
T ss_dssp             CCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            3456666788999999999999999999999999999999999999754

>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=96.98  E-value=0.0013  Score=46.54  Aligned_cols=43  Identities=12%  Similarity=0.214  Sum_probs=39.5

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      -|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+.
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~   46 (86)
T 2lef_A            4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSR   46 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCH
Confidence            4679999999999999999999999999999999999997543

>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=96.94  E-value=0.0017  Score=46.75  Aligned_cols=44  Identities=16%  Similarity=0.356  Sum_probs=39.6

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCC-HHHHHHHHHHhhccCC
Q 028980          114 KRQRVPSAYNQFIKEEIQRIKANNPDIS-HREAFSTAAKNWAHFP  157 (201)
Q Consensus       114 KRQRvpSaYN~fmK~ei~riK~~~P~i~-HkEaFs~aAknWa~~P  157 (201)
                      +-.|-+|||..|+++.-..|+++||+++ ..|.-+..+..|+..+
T Consensus         5 ~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls   49 (81)
T 2d7l_A            5 SSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLS   49 (81)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCC
Confidence            3456799999999999999999999998 9999999999998754

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

Probab=96.90  E-value=0.0015  Score=51.54  Aligned_cols=49  Identities=20%  Similarity=0.391  Sum_probs=43.1

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCCc
Q 028980          110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPD--ISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       110 KPPEKRQRvpSaYN~fmK~ei~riK~~~P~--i~HkEaFs~aAknWa~~Ph  158 (201)
                      +-|.+-.|-+|||..|+++.-..|+++||+  ++-.|..+.++..|+..+.
T Consensus        11 ~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~   61 (173)
T 2yrq_A           11 GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSA   61 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCH
Confidence            446666788999999999999999999999  6899999999999987654

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

Probab=96.50  E-value=0.002  Score=53.25  Aligned_cols=46  Identities=30%  Similarity=0.530  Sum_probs=41.2

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      |.+-.|-+|||..|+++....|+++||+++..|..+.++..|+..+
T Consensus         7 p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   52 (214)
T 3tq6_A            7 ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   52 (214)
T ss_dssp             HHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccC
Confidence            3444578999999999999999999999999999999999999765

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

Probab=96.42  E-value=0.0023  Score=53.67  Aligned_cols=48  Identities=29%  Similarity=0.479  Sum_probs=43.0

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       110 KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      +-|.+-.|-+|||..|+++....|+++||+++..|..+.++..|+..+
T Consensus        37 ~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   84 (238)
T 3tmm_A           37 VLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   84 (238)
T ss_dssp             HHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            345666788999999999999999999999999999999999999754

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

Probab=96.24  E-value=0.0066  Score=46.94  Aligned_cols=47  Identities=13%  Similarity=0.350  Sum_probs=42.7

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |++.-|-++||-.|++++-.+|+..||+++..|.-+.++..|+..+.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls~   48 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTE   48 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSCH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhH
Confidence            56677889999999999999999999999999999999999997653

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

Probab=95.78  E-value=0.0079  Score=40.55  Aligned_cols=39  Identities=33%  Similarity=0.669  Sum_probs=34.5

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          115 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       115 RQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      -.|-+|||..|+++.-..++..+|    .|..+.++..|+..+
T Consensus         3 PKrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls   41 (67)
T 3fgh_A            3 PKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLS   41 (67)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCC
T ss_pred             CCCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCC
Confidence            357789999999999999999988    599999999999764

>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=95.68  E-value=0.016  Score=43.33  Aligned_cols=42  Identities=12%  Similarity=0.155  Sum_probs=37.6

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          115 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       115 RQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .-|-+|||+.|+.+....+++++|+ ...|.-+.+...|+...
T Consensus         5 PKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~ls   46 (91)
T 1l8y_A            5 PESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNME   46 (91)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTG
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCC
Confidence            3467999999999999999999999 88998899999998753

>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=94.28  E-value=0.052  Score=40.56  Aligned_cols=39  Identities=18%  Similarity=0.493  Sum_probs=35.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .|-+|||..|+++.-+.|+    +++..|.-+.++..|+..+.
T Consensus        19 KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~   57 (108)
T 1v64_A           19 KPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQ   57 (108)
T ss_dssp             CCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCH
Confidence            5679999999999999988    89999999999999998653

>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=94.27  E-value=0.07  Score=39.35  Aligned_cols=40  Identities=13%  Similarity=0.337  Sum_probs=31.7

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       117 RvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |-+|||..|+++.++  +..+|+++..|.-+.++..|+..+.
T Consensus        11 rP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~   50 (101)
T 1v63_A           11 PPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQ   50 (101)
T ss_dssp             CCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCH
Confidence            358999999999964  3344557788999999999997543

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

Probab=94.20  E-value=0.016  Score=43.09  Aligned_cols=40  Identities=18%  Similarity=0.241  Sum_probs=33.3

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .|-||||-.|+.++-.+||++||+++  +.|..+|+.|+..+
T Consensus        24 KRp~sAf~lf~~e~R~kik~enP~~s--~~~~eIse~Wk~ls   63 (90)
T 2yuk_A           24 EMATVAPVLYTNINFPNLKEEFPDWT--TRVKQIAKLWRKAS   63 (90)
T ss_dssp             GGCSSSHHHHHHHHCTTHHHHCCSHH--HHHHHHHHHHHHSC
T ss_pred             CCCccHHHHHHHHhHHHHHHHCcCcc--chHHHHHHHHHcCC
Confidence            57899999999999999999999975  33566669998754

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

Probab=93.33  E-value=0.022  Score=47.01  Aligned_cols=43  Identities=33%  Similarity=0.606  Sum_probs=37.1

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |.+-.|-+|||+.|+++...+|+.++|+    |..+.++..|+..+.
T Consensus       112 p~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls~  154 (214)
T 3tq6_A          112 LGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSD  154 (214)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSSCSSHH----HHHHHHHHHHHTCCH
T ss_pred             ccCcccccchhhhhHHHHHHhhccCCHH----HHHHHHHHHHHcCCH
Confidence            4555778999999999999999998886    899999999998653

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

Probab=93.32  E-value=0.022  Score=47.70  Aligned_cols=42  Identities=33%  Similarity=0.617  Sum_probs=37.1

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          112 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       112 PEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      |.+-.|-+|||+.|+++...+|+.++|+    |..+.++..|+..+
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            5566788999999999999999988886    89999999999854

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

Probab=86.47  E-value=0.35  Score=35.77  Aligned_cols=39  Identities=18%  Similarity=0.439  Sum_probs=33.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHH---HHhhccC
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTA---AKNWAHF  156 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~a---AknWa~~  156 (201)
                      .|-+|||..|+++.-.+||.+  +++-.|.=+..   ...|+..
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            567999999999999999998  77777776666   8889874

---

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	201
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	4e-04
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-04
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	0.002

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

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

 Score = 36.0 bits (83), Expect = 4e-04
 Identities = 15/59 (25%), Positives = 23/59 (38%)

Query: 95  MRTPTNKATEERVVNRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 153
           M TP           + P   +R  SAY  F  E    +++ NPDI+  +      + W
Sbjct: 1   MVTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

>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 = 35.7 bits (82), Expect = 5e-04
 Identities = 8/48 (16%), Positives = 23/48 (47%)

Query: 110 RPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 157
           + P+  ++  + Y +F  E+  +    +P++S+ +     +K +   P
Sbjct: 6   KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP 53

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

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

 Score = 33.7 bits (77), Expect = 0.002
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 4/49 (8%)

Query: 109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 157
           N P    +R PSA+  F  E   +IK  +P +S  +      + W +  
Sbjct: 1   NAP----KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	201
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	97.91
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	97.84
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	97.72
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	97.64
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.48
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	97.44
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.17
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.13
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	96.88
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	96.81
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	96.14
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	95.09

>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=97.91  E-value=1.3e-05  Score=55.85  Aligned_cols=48  Identities=25%  Similarity=0.397  Sum_probs=42.5

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          111 PPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       111 PPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .|.+..|-+|||..|+++..++|++++|++++.|.-..++..|+..+.
T Consensus        17 ~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~   64 (90)
T d1wgfa_          17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSE   64 (90)
T ss_dssp             CCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCH
Confidence            344445788999999999999999999999999999999999998654

>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=97.84  E-value=1.1e-05  Score=56.31  Aligned_cols=49  Identities=16%  Similarity=0.377  Sum_probs=44.7

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      .+.|++-.|-+|||..|+++....|++.+|+++..|.-+.++..|+..+
T Consensus         5 kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls   53 (91)
T d1k99a_           5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP   53 (91)
T ss_dssp             CSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCC
Confidence            4567777889999999999999999999999999999999999999754

>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=2.5e-05  Score=55.15  Aligned_cols=50  Identities=24%  Similarity=0.465  Sum_probs=45.3

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          109 NRPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       109 ~KPPEKRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      .+.|.+..|-+|||..|+++....||+++|++++.|.-..++..|+..+.
T Consensus        15 ~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~   64 (93)
T d1lwma_          15 KKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTP   64 (93)
T ss_dssp             CCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCH
T ss_pred             CCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCH
Confidence            45667777889999999999999999999999999999999999998654

>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=97.64  E-value=2.1e-05  Score=53.70  Aligned_cols=41  Identities=27%  Similarity=0.440  Sum_probs=38.7

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 028980          117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  157 (201)
Q Consensus       117 RvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~P  157 (201)
                      |-+|||..|+++....|++++|++++.|.-+.++..|+..+
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            56899999999999999999999999999999999999865

>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=97.48  E-value=8.3e-05  Score=50.18  Aligned_cols=40  Identities=28%  Similarity=0.429  Sum_probs=37.7

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhcc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAH  155 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~  155 (201)
                      .|-+|||..|+++.-+.|+++||++++.|.-+.++..|+.
T Consensus         5 KrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~   44 (73)
T d1qrva_           5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRA   44 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcC
Confidence            4669999999999999999999999999999999999984

>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=0.00012  Score=48.85  Aligned_cols=43  Identities=19%  Similarity=0.373  Sum_probs=38.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCCc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPD--ISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~--i~HkEaFs~aAknWa~~Ph  158 (201)
                      .|-+|||..|+++.-+.|+++||+  +.+.|.-+.++..|+..+.
T Consensus         3 KrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~   47 (71)
T d1ckta_           3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSA   47 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCH
Confidence            477899999999999999999997  6678999999999998653

>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=97.17  E-value=0.0003  Score=48.77  Aligned_cols=43  Identities=14%  Similarity=0.358  Sum_probs=40.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          116 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       116 QRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      -|-+|||..|+++.-..|+++||++++.|.=+.++..|+..+.
T Consensus         6 KRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~   48 (85)
T d1j46a_           6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTE   48 (85)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCH
Confidence            5778999999999999999999999999999999999998654

>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=97.13  E-value=0.00037  Score=48.21  Aligned_cols=45  Identities=13%  Similarity=0.350  Sum_probs=41.0

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          114 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       114 KRQRvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |--|-+|||-.|+++.-++|++++|++++.|.=+.++..|+..+.
T Consensus         2 kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~   46 (80)
T d1gt0d_           2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSE   46 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCH
Confidence            445788999999999999999999999999999999999998653

>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=96.88  E-value=0.00075  Score=45.15  Aligned_cols=42  Identities=19%  Similarity=0.363  Sum_probs=38.8

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       117 RvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |-+|||-.|+++.-++|++++|++++.|.=+.++..|+..+.
T Consensus         5 RP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~   46 (70)
T d1i11a_           5 RPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTN   46 (70)
T ss_dssp             CSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCS
T ss_pred             CCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCH
Confidence            568999999999999999999999999999999999998643

>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=96.81  E-value=0.00088  Score=46.41  Aligned_cols=42  Identities=12%  Similarity=0.207  Sum_probs=38.4

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       117 RvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |-+|||-.|+++.-++|+++||+++..|.=..++..|+..+.
T Consensus         5 RP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~   46 (86)
T d2lefa_           5 KPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSR   46 (86)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCH
Confidence            456999999999999999999999999999999999997553

>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=96.14  E-value=0.003  Score=45.05  Aligned_cols=38  Identities=18%  Similarity=0.449  Sum_probs=32.2

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       117 RvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |-++||..|+++..+    ..|+++.+|.+..++..|+..+.
T Consensus        20 ~P~~ay~lF~~~~r~----~~~~~~~~e~~k~ig~~W~~Ls~   57 (108)
T d1v64a_          20 PPPNSYSLYCAELMA----NMKDVPSTERMVLCSQQWKLLSQ   57 (108)
T ss_dssp             CCSSHHHHHHHHHHH----HCTTSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCcHHHHHHHHHHH----HccCCCHHHHHHHHHHHHccCCH
Confidence            457999999998665    45889999999999999998654

>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=95.09  E-value=0.011  Score=41.12  Aligned_cols=40  Identities=15%  Similarity=0.312  Sum_probs=34.2

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 028980          117 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  158 (201)
Q Consensus       117 RvpSaYN~fmK~ei~riK~~~P~i~HkEaFs~aAknWa~~Ph  158 (201)
                      |=++||..|+++.++.|+..+|  +.+|.-+.++..|+..+.
T Consensus        11 rP~~ay~~F~~e~r~~~~~~~~--~~~ei~k~~g~~Wk~ls~   50 (101)
T d1v63a_          11 PPMNGYQKFSQELLSNGELNHL--PLKERMVEIGSRWQRISQ   50 (101)
T ss_dssp             CCSSSHHHHHHHHHHHCTTTTS--CHHHHHHHHHHHHTTSCH
T ss_pred             CCCCHHHHHHHHHHHHHHhcCC--CHHHHHHHHHHHHhhCCH
Confidence            3479999999999999987664  688999999999998654