Citrus Sinensis ID: 029862

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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------
Protein Sequence
MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
Secondary Structure (PSIPRED)
cccccccccEEEEEcccccEEEEEEEcccccccEEEEEccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccEEEEEEccccEEEEEEcccHHHccEEEEEccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHccccccEcccccccccccccccccccccccHHccccc
Coil and Loop (DISEMBL)
msldlaseRVCYVHCNYCNTILAVSVpcsslfnivtvrcGHCANLLNVNMVSAlqavplqdpqlqkqhinledsitkdcgssskcnkfssafetaehetprmppirppekrqrvpsAYNRFIKEEIQRikasnpdishREAFSTAAknwahfphihfglkldgnkqaKLDKAAAYaegtqksngfy
Flexible Loop (DISEMBL)
MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAfetaehetprmppirppekrqrvPSAYNRFIKEEIqrikasnpdiSHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAyaegtqksngfy
Low Complexity Region (SEG)
MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
Disordered region (IsUnstruct)
*******ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPL*********************************************************************************AFSTAAKNWAHFPHIHFGLKLDG***********************
Disordered Region (DISOPRED)
****LASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMV********************************************************************RFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP******************************GFY
Disordered Region (DISEMBL)
MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSA**********MPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
Disordered Region (DISPRO)
******SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAV*********************************************PPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKSNGFY
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	186	2.2.26 [Sep-21-2011]
Q9XFB0	184	Putative axial regulator	yes	no	0.962	0.972	0.664	7e-64
Q8GW46	164	Axial regulator YABBY 5 O	no	no	0.844	0.957	0.632	5e-52
Q10FZ7	186	Protein YABBY 2 OS=Oryza	yes	no	0.946	0.946	0.565	2e-50
Q7XIM7	169	Protein YABBY 1 OS=Oryza	no	no	0.854	0.940	0.559	1e-45
Q2QM17	207	Protein YABBY 6 OS=Oryza	no	no	0.978	0.879	0.5	2e-45
O22152	229	Axial regulator YABBY 1 O	no	no	0.951	0.772	0.527	9e-45
Q0JBF0	266	Protein YABBY 5 OS=Oryza	no	no	0.962	0.672	0.454	1e-43
Q01JG2	266	Protein YABBY 5 OS=Oryza	N/A	no	0.962	0.672	0.454	1e-43
Q6H668	256	Protein YABBY 4 OS=Oryza	no	no	0.838	0.609	0.515	4e-43
A2X7Q3	256	Protein YABBY 4 OS=Oryza	N/A	no	0.838	0.609	0.515	4e-43

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

 Score =  243 bits (619), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 127/191 (66%), Positives = 146/191 (76%), Gaps = 12/191 (6%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQ---AV 57
           MS+D +SERVCYVHC++C TILAVSVP +SLF +VTVRCGHC NLL++N+  +L    A 
Sbjct: 1   MSVDFSSERVCYVHCSFCTTILAVSVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAP 60

Query: 58  PL-QDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPS 116
           P+ QD Q  +QH        KDC SSS+     S  E  + E PRMPPIRPPEKRQRVPS
Sbjct: 61  PIHQDLQPHRQHTT-SLVTRKDCASSSRSTNNLS--ENIDREAPRMPPIRPPEKRQRVPS 117

Query: 117 AYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAK-LDKAAAY 175
           AYNRFIKEEIQRIKA NP+ISHREAFSTAAKNWAHFPHIHFGLKLDGNK+ K LD++ A 
Sbjct: 118 AYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLDQSVA- 176

Query: 176 AEGTQKSNGFY 186
               QKSNG+Y
Sbjct: 177 ---GQKSNGYY 184

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

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

 Score =  203 bits (517), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 105/166 (63%), Positives = 126/166 (75%), Gaps = 9/166 (5%)

Query: 5   LASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQL 64
           +A+E++CY+ CN+CN ILAV+VPCSSLF+IVTVRCGHC NL +VNM +ALQ+  L  P  
Sbjct: 6   MATEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQS--LSRPNF 63

Query: 65  QKQHINLEDSITKDCGSSSKCN-KFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIK 123
           Q  +  + +      GSSS+ + K  S   T      R+   RPPEKRQRVPSAYN+FIK
Sbjct: 64  QATNYAVPEY-----GSSSRSHTKIPSRISTRTITEQRIVN-RPPEKRQRVPSAYNQFIK 117

Query: 124 EEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKL 169
           EEIQRIKA+NPDISHREAFSTAAKNWAHFPHIHFGL L+ NKQAK+
Sbjct: 118 EEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNKQAKI 163

Arabidopsis thaliana (taxid: 3702)

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

 Score =  198 bits (503), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 104/184 (56%), Positives = 132/184 (71%), Gaps = 8/184 (4%)

Query: 6   ASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQD---P 62
           A E VCYVHCN+CNTI AVSVP +S+ NIVTVRCGHC +LL+VN+   +QA+P +D    
Sbjct: 8   APEHVCYVHCNFCNTIFAVSVPSNSMLNIVTVRCGHCTSLLSVNLRGLVQALPAEDHLQD 67

Query: 63  QLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFI 122
            L+  +++  ++ + + GSSS+  +    F  ++++T  M  +RPPEKRQRVPSAYNRFI
Sbjct: 68  NLKMHNMSFRENYS-EYGSSSRYGRVPMMF--SKNDTEHMLHVRPPEKRQRVPSAYNRFI 124

Query: 123 KEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQKS 182
           KEEI+RIKA+NPDISHREAFSTAAKNWAHFP+IHFGL        KLD+A   A   QK 
Sbjct: 125 KEEIRRIKANNPDISHREAFSTAAKNWAHFPNIHFGLG-SHESSKKLDEAIG-APSPQKV 182

Query: 183 NGFY 186
              Y
Sbjct: 183 QRLY 186

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  182 bits (462), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 90/161 (55%), Positives = 114/161 (70%), Gaps = 2/161 (1%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
           MS+   SE VCYV+CNYCNTIL V+VP +  +NIVTVRCGHC  +L++++    QA  +Q
Sbjct: 1   MSVQFTSEHVCYVNCNYCNTILVVNVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQ 60

Query: 61  DPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNR 120
           D Q+Q +     +  + D  S ++  + S+A         ++ PIRPPEKRQRVPSAYNR
Sbjct: 61  DHQVQNRGFQGNNFGSYDIASRNQ--RTSTAMYPMPTSQQQVSPIRPPEKRQRVPSAYNR 118

Query: 121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKL 161
           FIKEEIQRIK SNP+ISHREAFS AAKNWAH P +HFGL +
Sbjct: 119 FIKEEIQRIKTSNPEISHREAFSAAAKNWAHLPRLHFGLSV 159

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  181 bits (460), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 105/210 (50%), Positives = 128/210 (60%), Gaps = 28/210 (13%)

Query: 1   MSLDLA-SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVP- 58
           MS  +A +E+VCYVHCN+CNTILAVSVP +S+ NIVTVRCGHC NLL+VN+   + + P 
Sbjct: 1   MSAQIAPAEQVCYVHCNFCNTILAVSVPGNSMLNIVTVRCGHCTNLLSVNLRGLMHSAPA 60

Query: 59  LQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPI------------- 105
           LQD      H +L++S    C               +     R+PP              
Sbjct: 61  LQD----HHHHHLQESGLSGCFRDQSGYPEFGFSAASSSSKLRLPPAAAAMVSYSQQNQQ 116

Query: 106 -------RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFG 158
                  RPPEKRQRVPSAYNRFIKEEI+RIKA+NPDISHREAFSTAAKNWAH+P+IHFG
Sbjct: 117 LEQALHARPPEKRQRVPSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHYPNIHFG 176

Query: 159 LKL--DGNKQAKLDKAAAYAEGTQKSNGFY 186
           L    +G K+         A  ++K  GFY
Sbjct: 177 LSPGHEGGKKLVDVDPIPTAPSSKKIQGFY 206

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  179 bits (454), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 105/199 (52%), Positives = 124/199 (62%), Gaps = 22/199 (11%)

Query: 7   SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQK 66
           S+ +CYV CN+C TILAV+VP +SLF  VTVRCG C NLL+VNM S +  +P  + QLQ 
Sbjct: 22  SDHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYV--LPASN-QLQL 78

Query: 67  Q-----HINLEDSI--TKDCGSSS---------KCNKFSSAFET-AEHETPRMPPI-RPP 108
           Q     + N +D +   +D  S+            N   S  +   +HE P+ PP+ RPP
Sbjct: 79  QLGPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAPPVNRPP 138

Query: 109 EKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAK 168
           EKRQRVPSAYNRFIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL  D     K
Sbjct: 139 EKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDNQPVKK 198

Query: 169 LDKAAAYAEGTQ-KSNGFY 186
            +      E       GFY
Sbjct: 199 TNMPQQEGEDNMVMKEGFY 217

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  175 bits (444), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 99/218 (45%), Positives = 120/218 (55%), Gaps = 39/218 (17%)

Query: 8   ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNM----------------- 50
           E++CYVHCN+C+TILAV VPCSSLF  VTVRCGHCANLL+VN+                 
Sbjct: 29  EQLCYVHCNFCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPF 88

Query: 51  ----------------VSALQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFET 94
                           V + QA      +    +++   S    C +++     +SA   
Sbjct: 89  GQALLSPTSPHGLLDEVPSFQAPASLMTEQASPNVSSITSSNSSCANNAPATSMASAANK 148

Query: 95  AEHETPRMPPIRPP-----EKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
           A    P+ P   P      EKRQRVPSAYNRFIK+EIQRIKASNPDI+HREAFS AAKNW
Sbjct: 149 ATQREPQQPKNAPSANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNW 208

Query: 150 AHFPHIHFGLKLD-GNKQAKLDKAAAYAEGTQKSNGFY 186
           AHFPHIHFGL  D G K+  +       E     +G Y
Sbjct: 209 AHFPHIHFGLMPDQGLKKTGIQSQDGAGECMLFKDGLY 246

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  175 bits (444), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 99/218 (45%), Positives = 120/218 (55%), Gaps = 39/218 (17%)

Query: 8   ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNM----------------- 50
           E++CYVHCN+C+TILAV VPCSSLF  VTVRCGHCANLL+VN+                 
Sbjct: 29  EQLCYVHCNFCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAAASTANQLPF 88

Query: 51  ----------------VSALQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFET 94
                           V + QA      +    +++   S    C +++     +SA   
Sbjct: 89  GQALLSPTSPHGLLDEVPSFQAPASLMTEQASPNVSSITSSNSSCANNAPATSMASAANK 148

Query: 95  AEHETPRMPPIRPP-----EKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
           A    P+ P   P      EKRQRVPSAYNRFIK+EIQRIKASNPDI+HREAFS AAKNW
Sbjct: 149 ATQREPQQPKNAPSANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNW 208

Query: 150 AHFPHIHFGLKLD-GNKQAKLDKAAAYAEGTQKSNGFY 186
           AHFPHIHFGL  D G K+  +       E     +G Y
Sbjct: 209 AHFPHIHFGLMPDQGLKKTGIQSQDGAGECMLFKDGLY 246

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 =  174 bits (440), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 100/194 (51%), Positives = 112/194 (57%), Gaps = 38/194 (19%)

Query: 7   SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSA------------- 53
           +E++CYVHCN C+TILAV VPCSSLF  VTVRCGHCANLL+VN+                
Sbjct: 22  TEQLCYVHCNCCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQL 81

Query: 54  ---------------LQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETA--- 95
                          L  V  Q P L  +        +    SSS C   + A +     
Sbjct: 82  HFGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAK 141

Query: 96  ----EHETPRMPPI---RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKN 148
               E E P+  P    RPPEKRQRVPSAYNRFIK+EIQRIKA NPDISHREAFS AAKN
Sbjct: 142 PVQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN 201

Query: 149 WAHFPHIHFGLKLD 162
           WAHFPHIHFGL  D
Sbjct: 202 WAHFPHIHFGLMPD 215

Seems to be associated with phloem cell differentiation.

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  174 bits (440), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 100/194 (51%), Positives = 112/194 (57%), Gaps = 38/194 (19%)

Query: 7   SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSA------------- 53
           +E++CYVHCN C+TILAV VPCSSLF  VTVRCGHCANLL+VN+                
Sbjct: 22  TEQLCYVHCNCCDTILAVGVPCSSLFKTVTVRCGHCANLLSVNLRGLLLPAPAPAPANQL 81

Query: 54  ---------------LQAVPLQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETA--- 95
                          L  V  Q P L  +        +    SSS C   + A +     
Sbjct: 82  HFGPSLLSPTSPHGLLDEVAFQTPSLLMEQAASASLSSITGRSSSSCASNAPAMQMPPAK 141

Query: 96  ----EHETPRMPPI---RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKN 148
               E E P+  P    RPPEKRQRVPSAYNRFIK+EIQRIKA NPDISHREAFS AAKN
Sbjct: 142 PVQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN 201

Query: 149 WAHFPHIHFGLKLD 162
           WAHFPHIHFGL  D
Sbjct: 202 WAHFPHIHFGLMPD 215

Oryza sativa subsp. indica (taxid: 39946)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	186
427199347	181	YABBY2-like transcription factor YAB2 [M	0.956	0.983	0.830	2e-83
225436100	183	PREDICTED: putative axial regulator YABB	0.983	1.0	0.806	4e-82
118487174	191	unknown [Populus trichocarpa]	0.994	0.968	0.763	2e-77
224058941	185	predicted protein [Populus trichocarpa]	0.994	1.0	0.763	2e-77
351727853	183	uncharacterized protein LOC100500091 [Gl	0.962	0.978	0.731	3e-73
255549657	190	Axial regulator YABBY2, putative [Ricinu	0.989	0.968	0.790	6e-73
41745658	186	YABBY2-like transcription factor YAB2 [A	0.967	0.967	0.729	9e-71
255638173	181	unknown [Glycine max]	0.956	0.983	0.724	1e-70
356550042	181	PREDICTED: putative axial regulator YABB	0.956	0.983	0.719	4e-70
356543672	179	PREDICTED: putative axial regulator YABB	0.951	0.988	0.718	2e-69

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

 Score =  313 bits (802), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 157/189 (83%), Positives = 167/189 (88%), Gaps = 11/189 (5%)

Query: 1   MSLDL--ASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVP 58
           MSLD+  ASERVCYVHCN+CNTILAVSVPCSSLF IVTVRCGHCANLL+VNM ++LQAVP
Sbjct: 1   MSLDMMMASERVCYVHCNFCNTILAVSVPCSSLFTIVTVRCGHCANLLSVNMGASLQAVP 60

Query: 59  LQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAY 118
            QD Q  KQH+     I++DCGSSSKCNKFS AFET EHE PRMPPIRPPEKRQRVPSAY
Sbjct: 61  PQDSQ--KQHV-----ISEDCGSSSKCNKFS-AFETVEHEQPRMPPIRPPEKRQRVPSAY 112

Query: 119 NRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKA-AAYAE 177
           NRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLD+  A   +
Sbjct: 113 NRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDQTLAGSDQ 172

Query: 178 GTQKSNGFY 186
           GTQ SNGFY
Sbjct: 173 GTQNSNGFY 181

Source: Morella rubra

Species: Morella rubra

Genus: Morella

Family: Myricaceae

Order: Fagales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  309 bits (791), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 150/186 (80%), Positives = 164/186 (88%), Gaps = 3/186 (1%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
           MSLD+  ERVCYVHCN+CNTILAVSVPC+SLF IVTVRCGHCANLL+VNM + LQ VP Q
Sbjct: 1   MSLDITPERVCYVHCNFCNTILAVSVPCTSLFTIVTVRCGHCANLLSVNMGALLQTVPTQ 60

Query: 61  DPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNR 120
           D Q QKQ ++  D  ++DCGSSSKCNKFS AFE+AEHE PRMPPIRPPEKRQRVPSAYNR
Sbjct: 61  DLQSQKQQLSCGDP-SEDCGSSSKCNKFS-AFESAEHEQPRMPPIRPPEKRQRVPSAYNR 118

Query: 121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQ 180
           FIKEEIQRIKASNPDI+HREAFSTAAKNWAHFPHIHFGLKLDGNKQ KLD+A A  EG  
Sbjct: 119 FIKEEIQRIKASNPDITHREAFSTAAKNWAHFPHIHFGLKLDGNKQGKLDQAFA-GEGPH 177

Query: 181 KSNGFY 186
           K++GFY
Sbjct: 178 KAHGFY 183

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 142/186 (76%), Positives = 156/186 (83%), Gaps = 1/186 (0%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
           MSL+L SE VCYVHCN CNTILAVSVP SSLFNIVTVRCGHC NLL+VNM ++LQ +PLQ
Sbjct: 1   MSLELVSEPVCYVHCNLCNTILAVSVPSSSLFNIVTVRCGHCGNLLSVNMGASLQTLPLQ 60

Query: 61  DPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNR 120
           DPQ QK  +   + + K+ GSSSKCNK + A E+ EHE PRMP IRPPEKRQRVPSAYNR
Sbjct: 61  DPQSQKLLLINSEDLNKNFGSSSKCNKVT-ASESTEHEPPRMPAIRPPEKRQRVPSAYNR 119

Query: 121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQ 180
           FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD NK AKLD  +   EGTQ
Sbjct: 120 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDSNKHAKLDHQSFAGEGTQ 179

Query: 181 KSNGFY 186
           K++G Y
Sbjct: 180 KTSGLY 185

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  293 bits (750), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 142/186 (76%), Positives = 156/186 (83%), Gaps = 1/186 (0%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
           MSL+L SE VCYVHCN CNTILAVSVP SSLFNIVTVRCGHC NLL+VNM ++LQ +PLQ
Sbjct: 1   MSLELVSEPVCYVHCNLCNTILAVSVPSSSLFNIVTVRCGHCGNLLSVNMGASLQTLPLQ 60

Query: 61  DPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNR 120
           DPQ QK  +   + + K+ GSSSKCNK + A E+ EHE PRMP IRPPEKRQRVPSAYNR
Sbjct: 61  DPQSQKLLLINSEDLNKNFGSSSKCNKVT-ASESTEHEPPRMPAIRPPEKRQRVPSAYNR 119

Query: 121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQ 180
           FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLD NK AKLD  +   EGTQ
Sbjct: 120 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDSNKHAKLDHQSFAGEGTQ 179

Query: 181 KSNGFY 186
           K++G Y
Sbjct: 180 KTSGLY 185

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 139/190 (73%), Positives = 159/190 (83%), Gaps = 11/190 (5%)

Query: 1   MSLDL-ASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPL 59
           MS+++ A+ERVCYVHCN+CNTILAVSVP SSL  IVTVRCGHCANLL+VNM ++LQA P 
Sbjct: 1   MSMEMMATERVCYVHCNFCNTILAVSVPYSSLLTIVTVRCGHCANLLSVNMGASLQAFPP 60

Query: 60  QDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYN 119
           QDPQ  KQH++ ++  +K+ GSSSKC+K +  FE  EHE PR+PPIRP EKR RVPSAYN
Sbjct: 61  QDPQ--KQHLSFQEPSSKELGSSSKCSKIA-PFEAVEHELPRIPPIRPTEKRHRVPSAYN 117

Query: 120 RFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFG---LKLDGNKQAKLDKAAAYA 176
           RFIKEEIQRIKASNPDISHREAFS+AAKNWAHFPHIHFG   LKLDGNKQ KLD+     
Sbjct: 118 RFIKEEIQRIKASNPDISHREAFSSAAKNWAHFPHIHFGLKNLKLDGNKQEKLDQ----G 173

Query: 177 EGTQKSNGFY 186
           EG +KSNGFY
Sbjct: 174 EGAEKSNGFY 183

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 147/186 (79%), Positives = 159/186 (85%), Gaps = 2/186 (1%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
           MSL+L SERVCYVHCN+CNTILAVSVP S+L  IVTVRCGH ANLL+VNM  +LQ  PLQ
Sbjct: 1   MSLELVSERVCYVHCNFCNTILAVSVPSSNLLTIVTVRCGHGANLLSVNMGGSLQTFPLQ 60

Query: 61  DPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNR 120
           DPQ QK  +N ED + KD GSSSKCNK +S FE+A++E PRMPPIRPPEKRQRVPSAYNR
Sbjct: 61  DPQSQKVQLNSED-LNKDTGSSSKCNKVTS-FESADNEPPRMPPIRPPEKRQRVPSAYNR 118

Query: 121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEGTQ 180
           FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNK AK+D     AE TQ
Sbjct: 119 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKHAKIDHQTFGAESTQ 178

Query: 181 KSNGFY 186
           KSNG Y
Sbjct: 179 KSNGLY 184

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  271 bits (693), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 140/192 (72%), Positives = 155/192 (80%), Gaps = 12/192 (6%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
           MSLD+ SE VCYVHCN+CNTILAVSVPCS++F IVTVRCGHCANLL+VNM + LQ+V LQ
Sbjct: 1   MSLDMTSECVCYVHCNFCNTILAVSVPCSNMFTIVTVRCGHCANLLSVNMGALLQSVHLQ 60

Query: 61  DPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNR 120
           D Q Q QH    ++  KD GSSSK N+++     AEHE P+MPPIRPPEKRQRVPSAYNR
Sbjct: 61  DFQKQ-QH---AEAAAKDNGSSSKSNRYAPL--QAEHEQPKMPPIRPPEKRQRVPSAYNR 114

Query: 121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKL-DKAAAYAEGT 179
           FIKEEIQRIKA NP+ISHREAFSTAAKNWAHFPHIHFGLKLD NKQAKL D + A   GT
Sbjct: 115 FIKEEIQRIKAGNPEISHREAFSTAAKNWAHFPHIHFGLKLDSNKQAKLQDHSVAGGSGT 174

Query: 180 -----QKSNGFY 186
                QKS GFY
Sbjct: 175 TMARAQKSLGFY 186

Source: Antirrhinum majus

Species: Antirrhinum majus

Genus: Antirrhinum

Family: Plantaginaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 137/189 (72%), Positives = 156/189 (82%), Gaps = 11/189 (5%)

Query: 1   MSLDL-ASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPL 59
           MS+D+ A+ERVCYVHCN+CNT LAVSVPCSSL  IVTVRCGHCANLL VNM ++LQ  P 
Sbjct: 1   MSMDMMATERVCYVHCNFCNTTLAVSVPCSSLLTIVTVRCGHCANLLTVNMGASLQTFPS 60

Query: 60  QDP-QLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPP-EKRQRVPSA 117
           QD  QLQ+QH++++++ +K+ GSSSKC     +FET +HE     P   P EKRQRVPSA
Sbjct: 61  QDTTQLQRQHLSVQEACSKELGSSSKCK----SFETVDHEQQPRIPPIRPPEKRQRVPSA 116

Query: 118 YNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAE 177
           YNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLD+     +
Sbjct: 117 YNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDQ----GD 172

Query: 178 GTQKSNGFY 186
           GTQKSNGFY
Sbjct: 173 GTQKSNGFY 181

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356550042|ref|XP_003543399.1| PREDICTED: putative axial regulator YABBY 2-like isoform 1 [Glycine max]

 Score =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 136/189 (71%), Positives = 155/189 (82%), Gaps = 11/189 (5%)

Query: 1   MSLDL-ASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPL 59
           MS+D+ A+ERVCYVHCN+CNT LAVSVPCSSL  IVTVRCGHCANLL VNM ++LQ  P 
Sbjct: 1   MSMDMMATERVCYVHCNFCNTTLAVSVPCSSLLTIVTVRCGHCANLLTVNMGASLQTFPS 60

Query: 60  QDP-QLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPP-EKRQRVPSA 117
           QD  QLQ+QH++++++ +K+ GSSSKC      FET +H+     P   P EKRQRVPSA
Sbjct: 61  QDTTQLQRQHLSVQEACSKELGSSSKCK----TFETVDHDQQPRIPPIRPPEKRQRVPSA 116

Query: 118 YNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAE 177
           YNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLD+     +
Sbjct: 117 YNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDQ----GD 172

Query: 178 GTQKSNGFY 186
           GTQKSNGFY
Sbjct: 173 GTQKSNGFY 181

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 135/188 (71%), Positives = 154/188 (81%), Gaps = 11/188 (5%)

Query: 1   MSLDL-ASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPL 59
           MS+D+ A+ERVCYVHCN+CNT LAVSVPCSSL  IVTVRCGHCANLL VNM ++LQ  P 
Sbjct: 1   MSMDMMATERVCYVHCNFCNTTLAVSVPCSSLLTIVTVRCGHCANLLTVNMGASLQTFPS 60

Query: 60  QDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPP-EKRQRVPSAY 118
           QD   Q+QH++++++ +K+ GSSSKC     +FET +HE     P   P EKRQRVPSAY
Sbjct: 61  QDT-TQRQHLSVQEACSKELGSSSKCK----SFETVDHEQQPRIPPIRPPEKRQRVPSAY 115

Query: 119 NRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAEG 178
           NRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLD+     +G
Sbjct: 116 NRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDQ----GDG 171

Query: 179 TQKSNGFY 186
           TQKSNGFY
Sbjct: 172 TQKSNGFY 179

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	186
TAIR|locus:2826731	184	YAB2 "YABBY2" [Arabidopsis tha	0.956	0.967	0.682	4.3e-61
TAIR|locus:2066311	164	YAB5 "YABBY5" [Arabidopsis tha	0.844	0.957	0.632	7.4e-50
UNIPROTKB|Q7XIM7	169	YAB1 "Protein YABBY 1" [Oryza	0.865	0.952	0.560	6.4e-44
TAIR|locus:2005492	229	AFO "AT2G45190" [Arabidopsis t	0.962	0.781	0.527	2.2e-43
UNIPROTKB|Q76EJ0	194	DL "Protein DROOPING LEAF" [Or	0.763	0.731	0.486	2.6e-31
TAIR|locus:2028020	231	INO "INNER NO OUTER" [Arabidop	0.811	0.653	0.437	2.6e-31
TAIR|locus:2026418	181	CRC "AT1G69180" [Arabidopsis t	0.725	0.745	0.493	2.1e-29
TAIR|locus:2126931	240	YAB3 "YABBY3" [Arabidopsis tha	0.919	0.712	0.441	5.6e-29

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

 Score = 625 (225.1 bits), Expect = 4.3e-61, P = 4.3e-61
 Identities = 131/192 (68%), Positives = 150/192 (78%)

Query:     1 MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNM-VSALQ--AV 57
             MS+D +SERVCYVHC++C TILAVSVP +SLF +VTVRCGHC NLL++N+ VS  Q  A 
Sbjct:     1 MSVDFSSERVCYVHCSFCTTILAVSVPYASLFTLVTVRCGHCTNLLSLNIGVSLHQTSAP 60

Query:    58 PL-QDPQLQKQHINLEDSIT-KDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVP 115
             P+ QD Q  +QH      +T KDC SSS+     S  E  + E PRMPPIRPPEKRQRVP
Sbjct:    61 PIHQDLQPHRQHTT--SLVTRKDCASSSRSTNNLS--ENIDREAPRMPPIRPPEKRQRVP 116

Query:   116 SAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAK-LDKAAA 174
             SAYNRFIKEEIQRIKA NP+ISHREAFSTAAKNWAHFPHIHFGLKLDGNK+ K LD++ A
Sbjct:   117 SAYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLDQSVA 176

Query:   175 YAEGTQKSNGFY 186
                G QKSNG+Y
Sbjct:   177 ---G-QKSNGYY 184

GO:0005634 "nucleus" evidence=ISM

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

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

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

 Score = 519 (187.8 bits), Expect = 7.4e-50, P = 7.4e-50
 Identities = 105/166 (63%), Positives = 126/166 (75%)

Query:     5 LASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQL 64
             +A+E++CY+ CN+CN ILAV+VPCSSLF+IVTVRCGHC NL +VNM +ALQ+  L  P  
Sbjct:     6 MATEQLCYIPCNFCNIILAVNVPCSSLFDIVTVRCGHCTNLWSVNMAAALQS--LSRPNF 63

Query:    65 QKQHINLEDSITKDCGSSSKCN-KFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIK 123
             Q  +  + +      GSSS+ + K  S   T      R+   RPPEKRQRVPSAYN+FIK
Sbjct:    64 QATNYAVPEY-----GSSSRSHTKIPSRISTRTITEQRIVN-RPPEKRQRVPSAYNQFIK 117

Query:   124 EEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKL 169
             EEIQRIKA+NPDISHREAFSTAAKNWAHFPHIHFGL L+ NKQAK+
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

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

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 92/164 (56%), Positives = 116/164 (70%)

Query:     1 MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
             MS+   SE VCYV+CNYCNTIL V+VP +  +NIVTVRCGHC  +L++++    QA  +Q
Sbjct:     1 MSVQFTSEHVCYVNCNYCNTILVVNVPNNCSYNIVTVRCGHCTMVLSMDLAPFHQARTVQ 60

Query:    61 DPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNR 120
             D Q+Q +     +  + D  S ++  + S+A         ++ PIRPPEKRQRVPSAYNR
Sbjct:    61 DHQVQNRGFQGNNFGSYDIASRNQ--RTSTAMYPMPTSQQQVSPIRPPEKRQRVPSAYNR 118

Query:   121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKL-DG 163
             FIKEEIQRIK SNP+ISHREAFS AAKNWAH P +HFGL + DG
Sbjct:   119 FIKEEIQRIKTSNPEISHREAFSAAAKNWAHLPRLHFGLSVADG 162

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 458 (166.3 bits), Expect = 2.2e-43, P = 2.2e-43
 Identities = 104/197 (52%), Positives = 121/197 (61%)

Query:     7 SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQ- 65
             S+ +CYV CN+C TILAV+VP +SLF  VTVRCG C NLL+VNM S +     Q  QLQ 
Sbjct:    22 SDHLCYVQCNFCQTILAVNVPYTSLFKTVTVRCGCCTNLLSVNMRSYVLPASNQ-LQLQL 80

Query:    66 --KQHINLEDSIT--KDCGSSSKC---------NKFSSAFET-AEHETPRMPPI-RPPEK 110
                 + N +D +   +D  S+            N   S  +   +HE P+ PP+ RPPEK
Sbjct:    81 GPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAPPVNRPPEK 140

Query:   111 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLD 170
             RQRVPSAYNRFIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL  D     K +
Sbjct:   141 RQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLVPDNQPVKKTN 200

Query:   171 KAAAYAEGTQ-KSNGFY 186
                   E       GFY
Sbjct:   201 MPQQEGEDNMVMKEGFY 217

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

GO:0005634 "nucleus" evidence=ISM;TAS

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

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

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

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

GO:0010450 "inflorescence meristem growth" evidence=IMP

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

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

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

GO:0009845 "seed germination" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

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

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

GO:0048481 "ovule development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=IMP

GO:0045165 "cell fate commitment" evidence=IMP

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

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 74/152 (48%), Positives = 92/152 (60%)

Query:     1 MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQ 60
             M L   SE +CYV C YCNT+LAV VPC  L + VTV+CGHC NL   + +S     P+ 
Sbjct:     1 MDLVSPSEHLCYVRCTYCNTVLAVGVPCKRLMDTVTVKCGHCNNL---SFLSPRP--PMV 55

Query:    61 DPQLQKQH-INLEDSITKDCGSSSKCNKFSSAFETAEHETPRMP-PIRPPEKRQRVPSAY 118
              P     H +        DC  +      S    T+   +PR P  ++PPEK+ R+PSAY
Sbjct:    56 QPLSPTDHPLGPFQGPCTDCRRNQPLPLVSP---TSNEGSPRAPFVVKPPEKKHRLPSAY 112

Query:   119 NRFIKEEIQRIKASNPDISHREAFSTAAKNWA 150
             NRF++EEIQRIKA+ PDI HREAFS AAKNWA
Sbjct:   113 NRFMREEIQRIKAAKPDIPHREAFSMAAKNWA 144

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

GO:0048366 "leaf development" evidence=IMP

GO:0048440 "carpel development" evidence=IMP

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

 Score = 344 (126.2 bits), Expect = 2.6e-31, P = 2.6e-31
 Identities = 73/167 (43%), Positives = 105/167 (62%)

Query:     4 DLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQD-- 61
             DL  + +C+V C +C TIL VSVP +SL  +VTVRCGHC +LL+VN++ A   +PL    
Sbjct:    16 DLPGQ-ICHVQCGFCTTILLVSVPFTSLSMVVTVRCGHCTSLLSVNLMKA-SFIPLHLLA 73

Query:    62 -----PQLQKQHINLEDSITKDCG--SSSKCNKFSSAFETAEHETPRMPPI-----RPPE 109
                   +  K+ +   D + ++    +  K N  ++   ++++E   +  +     +PPE
Sbjct:    74 SLSHLDETGKEEVAATDGVEEEAWKVNQEKENSPTTLVSSSDNEDEDVSRVYQVVNKPPE 133

Query:   110 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIH 156
             KRQR PSAYN FIKEEI+R+KA NP ++H+EAFS AAKNWAHFP  H
Sbjct:   134 KRQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPAH 180

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0048481 "ovule development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

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

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

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 74/150 (49%), Positives = 96/150 (64%)

Query:     7 SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQA-VPLQDPQLQ 65
             +E + YV C+ CNTILAV +P   + + VTV+CGHC NL  +     LQ  V L    LQ
Sbjct:    18 AEHLYYVRCSICNTILAVGIPLKRMLDTVTVKCGHCGNLSFLTTTPPLQGHVSLT---LQ 74

Query:    66 KQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPR-MPP--IRPPEKRQRVPSAYNRFI 122
              Q     D   K  GSSS     SS+  T+  + P   PP  ++PPEK+QR+PSAYNRF+
Sbjct:    75 MQSFGGSD-YKK--GSSS-----SSSSSTSSDQPPSPSPPFVVKPPEKKQRLPSAYNRFM 126

Query:   123 KEEIQRIKASNPDISHREAFSTAAKNWAHF 152
             ++EIQRIK++NP+I HREAFS AAKNWA +
Sbjct:   127 RDEIQRIKSANPEIPHREAFSAAAKNWAKY 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 = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 80/181 (44%), Positives = 99/181 (54%)

Query:    13 VHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQHINLE 72
             V C +C+ +L+V+V   +L        GH  + L          + L++ +   Q+IN+ 
Sbjct:    52 VRCGHCSNLLSVTVSMRALLLPSVSNLGH--SFLPPPPPPPPPNL-LEEMRSGGQNINMN 108

Query:    73 DSITKDCGSSSKCNKFSSAFE---TAEH--ETPRMPPI-RPPEKRQRVPSAYNRFIKEEI 126
               ++    +         A     + +H  E PR PP  RPPEKRQRVPSAYNRFIKEEI
Sbjct:   109 MMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEI 168

Query:   127 QRIKASNPDISHREAFSTAAKNWAHFPHIHFGLKLDGNKQAKLDKAAAYAE-GTQKSNGF 185
             QRIKA NPDISHREAFS AAKNWAHFPHIHFGL  D     K +      E G     GF
Sbjct:   169 QRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLMADHPPTKKANVRQQEGEDGMMGREGF 228

Query:   186 Y 186
             Y
Sbjct:   229 Y 229

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9XFB0	YAB2_ARATH	No assigned EC number	0.6649	0.9623	0.9728	yes	no
Q10FZ7	YAB2_ORYSJ	No assigned EC number	0.5652	0.9462	0.9462	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	186
pfam04690	170	pfam04690, YABBY, YABBY protein	4e-77
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	4e-04
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	6e-04

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

 Score =  227 bits (581), Expect = 4e-77
 Identities = 103/173 (59%), Positives = 119/173 (68%), Gaps = 17/173 (9%)

Query: 1   MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVP-- 58
           MS+  +SE VCYVHCN+C TILAVSVP +SLFNIVTVRCGHC NLL+VN++     +P  
Sbjct: 1   MSVFFSSEHVCYVHCNFCTTILAVSVPYTSLFNIVTVRCGHCTNLLSVNLMMRSHLLPAL 60

Query: 59  -----------LQDPQLQKQHINLEDSITKDCGSSSKCNKFSSAFETAEHETPRMPP-IR 106
                      LQ+  +  Q+ N    +     S+S  +   S  +    E PR+PP  R
Sbjct: 61  SHLDETGKPELLQNLGVHGQNFNSNM-MKSHSASTSVSSYMMSDNQD--EEMPRVPPVNR 117

Query: 107 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL 159
           PPEKRQRVPSAYNRFIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL
Sbjct: 118 PPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 170

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

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

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

Query: 113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
           R  SAY  F +E+  ++K  NPD S  E      + W
Sbjct: 3   RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKW 39

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

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

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

Query: 113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
           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	186
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	100.0
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.23
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	97.77
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	97.7
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.7
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	97.69
smart00398	70	HMG high mobility group.	97.59
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	97.54
PTZ00199	94	high mobility group protein; Provisional	97.46
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	96.72
KOG0381	96	consensus HMG box-containing protein [General func	96.34
KOG3223	221	consensus Uncharacterized conserved protein [Funct	95.22
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	94.33
KOG4684	275	consensus Uncharacterized conserved protein, conta	84.45
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	82.51
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	80.75

>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=2.1e-81  Score=516.44  Aligned_cols=159  Identities=64%  Similarity=1.002  Sum_probs=123.2

Q ss_pred             CCcccCCCceeEEeCCCcceeeEecccCCCccceeeeecccCCCcccccccccccCCCCCCchhhhhc-------CCCcc
Q 029862            1 MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQH-------INLED   73 (186)
Q Consensus         1 ms~~~~~E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~llqs~~~q~~~~~~~~-------~~~~~   73 (186)
                      |+.+.++|||||||||||||||||||||+|||+|||||||||+|||||||++++++++.|++..+...       ....+
T Consensus         1 ~~~~~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~   80 (170)
T PF04690_consen    1 MDLFSPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPE   80 (170)
T ss_pred             CCccCCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhcccccccccccccccc
Confidence            66777899999999999999999999999999999999999999999999999999887665211110       00011


Q ss_pred             cccccCC---CCCcCCCCCCccccCCCCCCCCC-CCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhh
Q 029862           74 SITKDCG---SSSKCNKFSSAFETAEHETPRMP-PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW  149 (186)
Q Consensus        74 ~~~~~~~---sss~~~~~~~~~~~~~~e~p~~~-~~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW  149 (186)
                      .......   +++.+.....+....+++.|+++ ++||||||||+|||||+||||||||||++||||+|||||++|||||
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW  160 (170)
T PF04690_consen   81 NFGSNSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNW  160 (170)
T ss_pred             ccccccccCCCccccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Confidence            1111111   11111110011233445566654 6899999999999999999999999999999999999999999999


Q ss_pred             ccCCcccccc
Q 029862          150 AHFPHIHFGL  159 (186)
Q Consensus       150 ~~~P~ihfGl  159 (186)
                      ||+|||||||
T Consensus       161 ~h~phihfgl  170 (170)
T PF04690_consen  161 AHFPHIHFGL  170 (170)
T ss_pred             hhCcccccCC
Confidence            9999999997

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

Probab=98.23  E-value=2e-06  Score=60.37  Aligned_cols=46  Identities=35%  Similarity=0.624  Sum_probs=38.5

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhccCC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKAS-NPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~-~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |.|-.|.+|||+.||++.+.+++.. .+.++++|++..++..|+..+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls   47 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLS   47 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcC
Confidence            5677899999999999999999999 889999999999999999753

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=97.77  E-value=5.7e-05  Score=50.49  Aligned_cols=42  Identities=31%  Similarity=0.487  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|-+|||..|+++....+++.+|+++..|....++..|+..+
T Consensus         2 krp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls   43 (66)
T cd01390           2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS   43 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            367899999999999999999999999999999999999754

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=97.70  E-value=7.6e-05  Score=52.26  Aligned_cols=42  Identities=17%  Similarity=0.284  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|-|+||..|+++.-.+|++++|+++..|.-+.++..|+..+
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            467899999999999999999999999999999999999754

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=97.70  E-value=8.9e-05  Score=48.98  Aligned_cols=43  Identities=30%  Similarity=0.422  Sum_probs=39.6

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      .|-+|+|..|++++...+++.+|+++..|....+++.|+..+.
T Consensus         2 krp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~   44 (66)
T cd00084           2 KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE   44 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence            4678999999999999999999999999999999999997654

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=97.69  E-value=7.1e-05  Score=50.58  Aligned_cols=41  Identities=34%  Similarity=0.636  Sum_probs=36.9

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF  152 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~  152 (186)
                      .|-++||..|+++....||+++|+++..|.-+.+++.|+..
T Consensus         2 krP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l   42 (69)
T PF00505_consen    2 KRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNL   42 (69)
T ss_dssp             SSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCS
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcC
Confidence            47899999999999999999999999999999999999974

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=97.59  E-value=0.00016  Score=48.27  Aligned_cols=43  Identities=33%  Similarity=0.511  Sum_probs=39.5

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      .|-+|+|..|+++....+++.+|+++..|....++..|+..+.
T Consensus         3 krp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~   45 (70)
T smart00398        3 KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSE   45 (70)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCH
Confidence            4678999999999999999999999999999999999997543

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

Probab=97.54  E-value=0.00018  Score=50.77  Aligned_cols=43  Identities=16%  Similarity=0.348  Sum_probs=40.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      .|-++||-.|+++....|+++||++++.|.-+.++..|+..+.
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            5789999999999999999999999999999999999997654

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=97.46  E-value=0.0003  Score=52.36  Aligned_cols=49  Identities=27%  Similarity=0.445  Sum_probs=42.5

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCc
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDIS--HREAFSTAAKNWAHFPH  154 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~--hkEaF~~aAknW~~~P~  154 (186)
                      +.|.+-.|-+|||..|+++.-..|+++||+++  -.|.-+.++..|+..+.
T Consensus        18 kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~   68 (94)
T PTZ00199         18 KDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSE   68 (94)
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCH
Confidence            55667778999999999999999999999986  57888889999998653

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

Probab=96.72  E-value=0.0027  Score=50.78  Aligned_cols=54  Identities=28%  Similarity=0.510  Sum_probs=48.3

Q ss_pred             CCCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCccccc
Q 029862          103 PPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFG  158 (186)
Q Consensus       103 ~~~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ihfG  158 (186)
                      .+-|.||||-+  -||..|--.+|.+||++||++.+-+-=-..=|.|..+|...|-
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            45589999874  6999999999999999999999999888999999999998763

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

Probab=96.34  E-value=0.0087  Score=43.19  Aligned_cols=45  Identities=29%  Similarity=0.429  Sum_probs=40.4

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          110 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       110 KRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      .-+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|.....
T Consensus        22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~   66 (96)
T KOG0381|consen   22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAE   66 (96)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCH
Confidence            457788899999999999999999999999999999999987544

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=95.22  E-value=0.0097  Score=51.76  Aligned_cols=53  Identities=30%  Similarity=0.508  Sum_probs=47.6

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccccc
Q 029862          105 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL  159 (186)
Q Consensus       105 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ihfGl  159 (186)
                      -|-||||-|.  ||--|=..+|-|||.+||+++|-+-=-..-|.|...|...|.-
T Consensus       161 drHPEkRmrA--A~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~Nq  213 (221)
T KOG3223|consen  161 DRHPEKRMRA--AFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFNQ  213 (221)
T ss_pred             ccChHHHHHH--HHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhhH
Confidence            3899999875  8999999999999999999999988788889999999988753

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

Probab=94.33  E-value=0.022  Score=38.88  Aligned_cols=38  Identities=26%  Similarity=0.725  Sum_probs=29.6

Q ss_pred             EEeCCCcceeeEecccCCCccc---eeeeecccCCCccccccc
Q 029862           12 YVHCNYCNTILAVSVPCSSLFN---IVTVRCGHCANLLNVNMV   51 (186)
Q Consensus        12 YV~CnfCnTiLaVsVPcssL~~---~VTVRCGHCtnLlSVNm~   51 (186)
                      ||-|+-|..+|-  +|-+.++.   .-.+|||.|+.++++.++
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            788999977765  47775443   568999999999988653

>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]

Probab=84.45  E-value=1  Score=40.38  Aligned_cols=17  Identities=35%  Similarity=0.778  Sum_probs=12.6

Q ss_pred             ceeeeecccCCCccccc
Q 029862           33 NIVTVRCGHCANLLNVN   49 (186)
Q Consensus        33 ~~VTVRCGHCtnLlSVN   49 (186)
                      ..+-|+||||++..--|
T Consensus       167 ~gcRV~CgHC~~tFLfn  183 (275)
T KOG4684|consen  167 TGCRVKCGHCNETFLFN  183 (275)
T ss_pred             cceEEEecCccceeehh
Confidence            34889999999875433

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=82.51  E-value=1.5  Score=27.30  Aligned_cols=35  Identities=34%  Similarity=0.598  Sum_probs=24.6

Q ss_pred             EEeCCCcceeeEecccCCCcc-ceeeeecccCCCcccc
Q 029862           12 YVHCNYCNTILAVSVPCSSLF-NIVTVRCGHCANLLNV   48 (186)
Q Consensus        12 YV~CnfCnTiLaVsVPcssL~-~~VTVRCGHCtnLlSV   48 (186)
                      .+.|..|.+..-|..  +.+. +...|+|++|.+.+.+
T Consensus         2 ~~~CP~C~~~~~v~~--~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         2 RIQCPNCKTSFRVVD--SQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             EEECCCCCCEEEeCH--HHcCCCCCEEECCCCCCEEEe
Confidence            378999999877653  2221 3347999999987754

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=80.75  E-value=1.3  Score=28.15  Aligned_cols=34  Identities=32%  Similarity=0.678  Sum_probs=25.5

Q ss_pred             EeCCCcceeeEecccCCCc-cceeeeecccCCCcccc
Q 029862           13 VHCNYCNTILAVSVPCSSL-FNIVTVRCGHCANLLNV   48 (186)
Q Consensus        13 V~CnfCnTiLaVsVPcssL-~~~VTVRCGHCtnLlSV   48 (186)
                      ++|--|.|.+.|  |-+.| -....|||++|.+.+.|
T Consensus         3 i~CP~C~~~f~v--~~~~l~~~~~~vrC~~C~~~f~v   37 (37)
T PF13719_consen    3 ITCPNCQTRFRV--PDDKLPAGGRKVRCPKCGHVFRV   37 (37)
T ss_pred             EECCCCCceEEc--CHHHcccCCcEEECCCCCcEeeC
Confidence            789999998865  44443 34679999999987654

---

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	186
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	9e-06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-05
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-05
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	4e-04
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	3e-04
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	7e-04
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	7e-04

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

 Score = 43.7 bits (102), Expect = 9e-06
 Identities = 16/54 (29%), Positives = 22/54 (40%)

Query: 100 PRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153
            R          ++  S+Y RF KE++   KA NPD    E     A+ W   P
Sbjct: 31  GRGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 84

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

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 16/52 (30%), Positives = 22/52 (42%)

Query: 102 MPPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153
           M         ++  S+Y RF KE++   KA NPD    E     A+ W   P
Sbjct: 1   MGSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 52

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

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 15/78 (19%), Positives = 26/78 (33%)

Query: 72  EDSITKDCGSSSKCNKFSSAFETAEHETPRMPPIRPPEKRQRVPSAYNRFIKEEIQRIKA 131
           E    +D   + K             +       + P   +R PSA+  F  E   +IK 
Sbjct: 63  EKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKG 122

Query: 132 SNPDISHREAFSTAAKNW 149
            +P +S  +      + W
Sbjct: 123 EHPGLSIGDVAKKLGEMW 140

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

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPD--ISHREAFSTAAKNWAHFP 153
             P+K +   S+Y  F++   +  K  +PD  ++  E     ++ W    
Sbjct: 11  GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 60

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

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

Query: 106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
           + P+  ++  + Y RF  E+  +    +P++S+ +     +K +
Sbjct: 6   KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKY 49

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

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 13/46 (28%), Positives = 20/46 (43%)

Query: 104 PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
             + P + Q+  SAY  F ++    IK  NP+ +  E     A  W
Sbjct: 11  KKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMW 56

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

 Score = 36.1 bits (84), Expect = 7e-04
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 11/59 (18%)

Query: 102 MPPIRPPEKRQ-----------RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
           M   R P+KR            R  SAY  F  E    +++ NPDI+  +      + W
Sbjct: 1   MVTPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	186
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	97.92
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	97.85
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	97.77
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	97.75
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	97.74
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	97.73
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	97.73
1wgf_A	90	Upstream binding factor 1; transcription factor, D	97.71
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	97.69
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	97.68
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	97.68
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	97.62
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	97.6
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	97.59
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	97.58
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	97.57
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	97.53
1ckt_A	71	High mobility group 1 protein; high-mobility group	97.51
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	97.48
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.41
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	97.4
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	97.37
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.36
2lhj_A	97	High mobility group protein homolog NHP1; structur	97.34
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	97.29
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	97.26
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	97.22
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.15
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	96.86
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	96.8
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	96.65
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	96.32
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	96.25
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	95.24
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	95.19
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	94.29
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	94.15
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	93.43
2cto_A	93	Novel protein; high mobility group box domain, hel	90.36

>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=97.92  E-value=1.7e-05  Score=54.50  Aligned_cols=47  Identities=26%  Similarity=0.432  Sum_probs=42.7

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          107 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       107 PPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      -|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
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            46666788999999999999999999999999999999999999654

>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=97.85  E-value=2.4e-05  Score=54.64  Aligned_cols=48  Identities=21%  Similarity=0.308  Sum_probs=43.5

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .+|.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
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            356677788999999999999999999999999999999999999654

>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=97.77  E-value=4.4e-05  Score=52.36  Aligned_cols=43  Identities=26%  Similarity=0.405  Sum_probs=40.1

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          111 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       111 RQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      -.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         4 PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   46 (73)
T 3nm9_A            4 PKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK   46 (73)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            3578999999999999999999999999999999999999865

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

Probab=97.75  E-value=5.9e-05  Score=54.03  Aligned_cols=48  Identities=19%  Similarity=0.433  Sum_probs=43.3

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +-|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         3 kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (92)
T 2crj_A            3 SGSSGPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQ   50 (92)
T ss_dssp             CCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            446666788999999999999999999999999999999999999754

>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=97.74  E-value=3.2e-05  Score=53.01  Aligned_cols=46  Identities=13%  Similarity=0.346  Sum_probs=41.3

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |.+-.|-+|||..|+++.-+.|++++|+++..|.-+.++..|+..+
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            4556788999999999999999999999999999999999999753

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

Probab=97.73  E-value=5.4e-05  Score=54.22  Aligned_cols=47  Identities=17%  Similarity=0.241  Sum_probs=42.0

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          107 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       107 PPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|.+-.|-+|||..|+++.-.+|+++||+++..|.-+.++..|+..+
T Consensus         4 ~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (92)
T 2cs1_A            4 GSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLS   50 (92)
T ss_dssp             CCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            34555678999999999999999999999999999999999999754

>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=97.73  E-value=4e-05  Score=54.39  Aligned_cols=48  Identities=19%  Similarity=0.271  Sum_probs=43.9

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +-|.+-.|-++||..|+++.-++|++++|++++.|.-+.++..|+..+
T Consensus        13 kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   60 (87)
T 2e6o_A           13 TSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMK   60 (87)
T ss_dssp             CCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            556777889999999999999999999999999999999999999654

>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=97.71  E-value=4.6e-05  Score=54.52  Aligned_cols=48  Identities=25%  Similarity=0.379  Sum_probs=43.6

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +.|.+-.|-+|||..|+++.-..|+++||++++.|.-+.++..|+..+
T Consensus        16 kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   63 (90)
T 1wgf_A           16 GGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLS   63 (90)
T ss_dssp             SCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            456667788999999999999999999999999999999999999743

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

Probab=97.69  E-value=6.6e-05  Score=51.43  Aligned_cols=45  Identities=20%  Similarity=0.412  Sum_probs=41.1

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF  152 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~  152 (186)
                      |.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..
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=97.68  E-value=6.7e-05  Score=52.92  Aligned_cols=46  Identities=13%  Similarity=0.346  Sum_probs=41.6

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         2 p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   47 (85)
T 1j46_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSC
T ss_pred             cCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCC
Confidence            4455678999999999999999999999999999999999999754

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

Probab=97.68  E-value=6.5e-05  Score=54.95  Aligned_cols=48  Identities=27%  Similarity=0.472  Sum_probs=43.8

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +.|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+
T Consensus        13 kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls   60 (102)
T 2co9_A           13 KDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLG   60 (102)
T ss_dssp             CCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCC
Confidence            556667788999999999999999999999999999999999999754

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

Probab=97.62  E-value=7.5e-05  Score=54.59  Aligned_cols=48  Identities=19%  Similarity=0.407  Sum_probs=43.4

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +.|.+-.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
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            456666788999999999999999999999999999999999999643

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

Probab=97.60  E-value=9.8e-05  Score=54.56  Aligned_cols=49  Identities=14%  Similarity=0.249  Sum_probs=42.3

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          105 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       105 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|.|.+-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus        24 ~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   72 (106)
T 4euw_A           24 SKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLN   72 (106)
T ss_dssp             ----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             cCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            3667777889999999999999999999999999999999999998754

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

Probab=97.59  E-value=0.0001  Score=52.11  Aligned_cols=48  Identities=23%  Similarity=0.389  Sum_probs=41.6

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISH--REAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~h--kEaF~~aAknW~~~P  153 (186)
                      +-|.+-.|-+|||..|+++.-..|++++|+++.  .|.-+.++..|+..+
T Consensus        11 kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   60 (86)
T 2eqz_A           11 GDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMS   60 (86)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCC
Confidence            345555778999999999999999999999974  999999999999644

>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=97.58  E-value=0.00013  Score=50.72  Aligned_cols=44  Identities=18%  Similarity=0.342  Sum_probs=40.1

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          110 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       110 KRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +-.|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+
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            34577999999999999999999999999999999999999654

>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=97.57  E-value=9.3e-05  Score=51.44  Aligned_cols=45  Identities=24%  Similarity=0.461  Sum_probs=39.8

Q ss_pred             CCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          109 EKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       109 EKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|-.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         5 ~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   49 (83)
T 3f27_D            5 SRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   49 (83)
T ss_dssp             --CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            444688999999999999999999999999999999999998644

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

Probab=97.53  E-value=0.00011  Score=49.24  Aligned_cols=43  Identities=26%  Similarity=0.460  Sum_probs=38.5

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          111 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       111 RQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      -.|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
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            3578899999999999999999999999999999999998643

>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=97.51  E-value=0.00016  Score=48.83  Aligned_cols=42  Identities=21%  Similarity=0.332  Sum_probs=38.3

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccC
Q 029862          111 RQRVPSAYNRFIKEEIQRIKASNPDISH--REAFSTAAKNWAHF  152 (186)
Q Consensus       111 RQR~psayN~fmK~ei~riK~~~P~i~h--kEaF~~aAknW~~~  152 (186)
                      -.|-+|||..|+++.-+.|+++||+++.  .|.-+.++..|+..
T Consensus         2 PKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~l   45 (71)
T 1ckt_A            2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTM   45 (71)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTC
T ss_pred             cCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhC
Confidence            3578999999999999999999999976  99999999999864

>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=97.48  E-value=0.00017  Score=49.89  Aligned_cols=43  Identities=14%  Similarity=0.332  Sum_probs=39.6

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          111 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       111 RQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      -.|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         3 pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (80)
T 1gt0_D            3 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            3577999999999999999999999999999999999999644

>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=97.41  E-value=0.00024  Score=54.69  Aligned_cols=48  Identities=25%  Similarity=0.441  Sum_probs=42.9

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +-|.+-.|-+|||..|+++.-.+|++++|+++..|.-+.++..|+..+
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            445566788999999999999999999999999999999999999654

>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=97.40  E-value=0.00019  Score=49.26  Aligned_cols=42  Identities=21%  Similarity=0.375  Sum_probs=39.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
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            578999999999999999999999999999999999998644

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

Probab=97.37  E-value=0.00014  Score=50.77  Aligned_cols=46  Identities=24%  Similarity=0.408  Sum_probs=40.7

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccC
Q 029862          107 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISH--REAFSTAAKNWAHF  152 (186)
Q Consensus       107 PPEKRQR~psayN~fmK~ei~riK~~~P~i~h--kEaF~~aAknW~~~  152 (186)
                      -|.+-.|-+|||..|+++.-..|++++|+++.  .|.-+.++..|+..
T Consensus         4 dp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~l   51 (83)
T 1aab_A            4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTM   51 (83)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTS
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhC
Confidence            45556788999999999999999999999975  99999999999864

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

Probab=97.36  E-value=0.00028  Score=55.30  Aligned_cols=48  Identities=25%  Similarity=0.441  Sum_probs=43.0

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +-|.+-.|-+|||..|+++...+|++++|+++..|.-+.++..|+..+
T Consensus        97 kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls  144 (173)
T 2yrq_A           97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA  144 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             cCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            345666788999999999999999999999999999999999999754

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

Probab=97.34  E-value=9.5e-05  Score=53.40  Aligned_cols=50  Identities=26%  Similarity=0.381  Sum_probs=44.9

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCc
Q 029862          105 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDIS--HREAFSTAAKNWAHFPH  154 (186)
Q Consensus       105 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~--hkEaF~~aAknW~~~P~  154 (186)
                      .+.|.+-.|-+|||..|+++.-.+|+++||+++  ..|.-+.++..|+..+.
T Consensus        17 ~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~   68 (97)
T 2lhj_A           17 KKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSD   68 (97)
T ss_dssp             TSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCH
Confidence            356777788999999999999999999999999  99999999999997543

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

Probab=97.29  E-value=6.1e-05  Score=54.16  Aligned_cols=48  Identities=25%  Similarity=0.477  Sum_probs=43.4

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +.|.+-.|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+
T Consensus        16 kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   63 (93)
T 1cg7_A           16 KDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALT   63 (93)
T ss_dssp             CCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            456667788999999999999999999999999999999999999653

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

Probab=97.26  E-value=0.00044  Score=48.63  Aligned_cols=42  Identities=12%  Similarity=0.204  Sum_probs=39.1

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|-+|||..|+++.-+.|++++|++++.|.-+.++..|+..+
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   45 (86)
T 2lef_A            4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALS   45 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            477999999999999999999999999999999999999654

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

Probab=97.22  E-value=0.00065  Score=48.50  Aligned_cols=44  Identities=16%  Similarity=0.338  Sum_probs=39.4

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCC-HHHHHHHHHHhhccCC
Q 029862          110 KRQRVPSAYNRFIKEEIQRIKASNPDIS-HREAFSTAAKNWAHFP  153 (186)
Q Consensus       110 KRQR~psayN~fmK~ei~riK~~~P~i~-hkEaF~~aAknW~~~P  153 (186)
                      +-.|-+|||..|+++.-..||++||+++ ..|.-+.++..|+..+
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            3356799999999999999999999998 9999999999999643

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

Probab=97.15  E-value=0.00065  Score=53.17  Aligned_cols=48  Identities=21%  Similarity=0.396  Sum_probs=42.8

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPD--ISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~--i~hkEaF~~aAknW~~~P  153 (186)
                      +-|.+-.|-+|||..|+++....|+++||+  ++-.|..+.++..|+..+
T Consensus        11 ~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   60 (173)
T 2yrq_A           11 GDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   60 (173)
T ss_dssp             CCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCC
Confidence            456666788999999999999999999999  689999999999998754

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

Probab=96.86  E-value=0.00086  Score=55.00  Aligned_cols=47  Identities=32%  Similarity=0.541  Sum_probs=41.9

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      |.+-.|-+|||..|+++....|+++||+++..|..+.++..|+..+.
T Consensus         7 p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~   53 (214)
T 3tq6_A            7 ASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPD   53 (214)
T ss_dssp             HHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccCH
Confidence            44456789999999999999999999999999999999999997553

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

Probab=96.80  E-value=0.00097  Score=55.48  Aligned_cols=48  Identities=31%  Similarity=0.497  Sum_probs=43.3

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      +-|.+-.|-+|||..|+++....|+++||+++..|..+.++..|+..+
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            346666789999999999999999999999999999999999999754

>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=96.65  E-value=0.0026  Score=48.81  Aligned_cols=46  Identities=13%  Similarity=0.346  Sum_probs=42.1

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |++..|-++||-.|++++-.+|+..+|+++..|.-+.++..|+..+
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls   47 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLT   47 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSC
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhh
Confidence            5666788999999999999999999999999999999999998654

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

Probab=96.32  E-value=0.0056  Score=45.41  Aligned_cols=41  Identities=12%  Similarity=0.155  Sum_probs=37.3

Q ss_pred             CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029862          111 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF  152 (186)
Q Consensus       111 RQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~  152 (186)
                      ..|-+|||+.|+.+...++++++|+ +..|.-+.+...|+..
T Consensus         5 PKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~l   45 (91)
T 1l8y_A            5 PESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNM   45 (91)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTT
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcC
Confidence            3467999999999999999999999 9999999999999974

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

Probab=96.25  E-value=0.0035  Score=41.97  Aligned_cols=38  Identities=34%  Similarity=0.675  Sum_probs=34.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      .|-+|||..|+++.-..+|..+|    .|..+.++..|+..+
T Consensus         4 KrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls   41 (67)
T 3fgh_A            4 KRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLS   41 (67)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCC
Confidence            57789999999999999999887    599999999999754

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

Probab=95.24  E-value=0.026  Score=41.29  Aligned_cols=40  Identities=13%  Similarity=0.341  Sum_probs=31.9

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       113 R~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      |-+|||..|+++.+.  +..+|+++..|.-+.++..|+..+.
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  3445567889999999999997543

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

Probab=95.19  E-value=0.022  Score=42.19  Aligned_cols=44  Identities=16%  Similarity=0.406  Sum_probs=37.1

Q ss_pred             CCCCC-CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          107 PPEKR-QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       107 PPEKR-QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      -|.+- .|-+|||..|+++.-..||    +++..|.-+.++..|+..+.
T Consensus        13 d~~~P~KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~   57 (108)
T 1v64_A           13 FDGRPTKPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQ   57 (108)
T ss_dssp             TTTSCCCCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCH
Confidence            34444 5679999999999999988    89999999999999997654

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

Probab=94.29  E-value=0.011  Score=49.05  Aligned_cols=42  Identities=33%  Similarity=0.600  Sum_probs=36.7

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |.+-.|-+|||+.|+++...+||.++|+    |..+.++..|+..+
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            5556788999999999999999988876    89999999999754

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

Probab=94.15  E-value=0.012  Score=48.07  Aligned_cols=42  Identities=33%  Similarity=0.600  Sum_probs=36.5

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |.+-.|-+|||..|+++...+|+.++|+    |..+.++..|+..+
T Consensus       112 p~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls  153 (214)
T 3tq6_A          112 LGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLS  153 (214)
T ss_dssp             TTCCCCCCCHHHHHHHHHTTTSSCSSHH----HHHHHHHHHHHTCC
T ss_pred             ccCcccccchhhhhHHHHHHhhccCCHH----HHHHHHHHHHHcCC
Confidence            4455678999999999999999988886    89999999999764

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

Probab=93.43  E-value=0.0092  Score=43.97  Aligned_cols=44  Identities=16%  Similarity=0.182  Sum_probs=34.8

Q ss_pred             CCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          108 PEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       108 PEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |-+-.|.||||-.|+.++-.+||++||+++  +.|..+|+.|+..+
T Consensus        20 pnaPKRp~sAf~lf~~e~R~kik~enP~~s--~~~~eIse~Wk~ls   63 (90)
T 2yuk_A           20 EALGEMATVAPVLYTNINFPNLKEEFPDWT--TRVKQIAKLWRKAS   63 (90)
T ss_dssp             HHHGGGCSSSHHHHHHHHCTTHHHHCCSHH--HHHHHHHHHHHHSC
T ss_pred             CCCCCCCccHHHHHHHHhHHHHHHHCcCcc--chHHHHHHHHHcCC
Confidence            333467899999999999999999999985  33555669998643

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

Probab=90.36  E-value=0.14  Score=37.60  Aligned_cols=39  Identities=18%  Similarity=0.429  Sum_probs=33.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHH---HHhhccC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTA---AKNWAHF  152 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~a---AknW~~~  152 (186)
                      .|-+|||..|+++.-.+||.+  +++-.|.=+..   ...|+..
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  78888877777   9999864

---

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	186
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-04
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	0.001
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	0.003

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

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

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

Query: 106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153
           + P+  ++  + Y RF  E+  +    +P++S+ +     +K +   P
Sbjct: 6   KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP 53

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

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

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

Query: 113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153
           R PSA+  F  E   +IK  +P +S  +      + W +  
Sbjct: 5   RPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 45

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

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

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

Query: 99  TPRMP------PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149
           TPR P        + P   +R  SAY  F  E    +++ NPDI+  +      + W
Sbjct: 3   TPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKW 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	186
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.05
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	97.96
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	97.88
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	97.82
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.68
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	97.64
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.41
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.4
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	97.13
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	97.08
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	96.54
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	95.82

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

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

Probab=98.05  E-value=4.8e-06  Score=57.70  Aligned_cols=48  Identities=25%  Similarity=0.389  Sum_probs=42.5

Q ss_pred             CCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          107 PPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       107 PPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      .|.+..|-+|||..|+++..++|++++|++++.|.-..++..|+..+.
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            455556788999999999999999999999999999999999997643

>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=97.96  E-value=4.9e-06  Score=57.76  Aligned_cols=48  Identities=19%  Similarity=0.407  Sum_probs=44.2

Q ss_pred             CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |.|++-.|-+|+|..|+++....|++.+|+++..|.-+.++..|+..+
T Consensus         6 k~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls   53 (91)
T d1k99a_           6 KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP   53 (91)
T ss_dssp             SSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCC
Confidence            567777888999999999999999999999999999999999999754

>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=97.88  E-value=9.8e-06  Score=56.88  Aligned_cols=50  Identities=24%  Similarity=0.437  Sum_probs=44.9

Q ss_pred             CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          105 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       105 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      .+.|.+..|-+|||..|+++....||+++|++++.|.-..++..|+..+.
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            45667777899999999999999999999999999999999999997553

>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=97.82  E-value=8e-06  Score=55.41  Aligned_cols=41  Identities=27%  Similarity=0.430  Sum_probs=38.6

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       113 R~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |-+|||..|+++....|++++|++++.|.-+.++..|+..+
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            55799999999999999999999999999999999999865

>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=97.68  E-value=3e-05  Score=52.01  Aligned_cols=40  Identities=28%  Similarity=0.419  Sum_probs=37.7

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhcc
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAH  151 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~  151 (186)
                      .|-+|||..|+++.-+.||++||++++.|.-+.++..|+.
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=97.64  E-value=4.3e-05  Score=50.58  Aligned_cols=42  Identities=19%  Similarity=0.377  Sum_probs=38.0

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCC
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPD--ISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~--i~hkEaF~~aAknW~~~P  153 (186)
                      .|-+|||..|+++.-++||++||+  +++.|.-+.++..|+..+
T Consensus         3 KrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls   46 (71)
T d1ckta_           3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   46 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCC
Confidence            467899999999999999999997  667899999999999865

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

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

Probab=97.41  E-value=0.00011  Score=50.64  Aligned_cols=43  Identities=14%  Similarity=0.349  Sum_probs=39.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      .|-+|||..|+++.-..|+++||++++.|.=+.++..|+..+.
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            5778999999999999999999999999999999999997543

>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=97.40  E-value=0.00013  Score=50.20  Aligned_cols=44  Identities=14%  Similarity=0.345  Sum_probs=40.6

Q ss_pred             CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          110 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       110 KRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |-.|-+|||-.|+++.-++|++++|++++.|.=+.++..|+..+
T Consensus         2 kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~   45 (80)
T d1gt0d_           2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCC
Confidence            44678999999999999999999999999999999999999754

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

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

Probab=97.13  E-value=0.00042  Score=46.03  Aligned_cols=42  Identities=19%  Similarity=0.370  Sum_probs=38.7

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       113 R~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      |-+|||-.|+++.-++|++++|++++.|.=+.++..|+..++
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            568999999999999999999999999999999999997543

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

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Lymphoid enhancer-binding factor, LEF1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.08  E-value=0.00038  Score=47.88  Aligned_cols=41  Identities=12%  Similarity=0.197  Sum_probs=38.0

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862          113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP  153 (186)
Q Consensus       113 R~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P  153 (186)
                      |-++||-.|+++.-++|+++||+++..|.=..++..|+..+
T Consensus         5 RP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls   45 (86)
T d2lefa_           5 KPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALS   45 (86)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSC
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            45699999999999999999999999999999999999754

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

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

Probab=96.54  E-value=0.0012  Score=46.80  Aligned_cols=38  Identities=16%  Similarity=0.419  Sum_probs=32.2

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       113 R~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      |-++||..|+++..+    ..|+++.+|.+..+++.|+..+.
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            457999999998654    46899999999999999998664

>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=95.82  E-value=0.0039  Score=43.17  Aligned_cols=40  Identities=13%  Similarity=0.341  Sum_probs=34.3

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862          113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH  154 (186)
Q Consensus       113 R~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~  154 (186)
                      |-++||..|+++-++.|+..+  ++.+|.-+.++..|+..+.
T Consensus        11 rP~~ay~~F~~e~r~~~~~~~--~~~~ei~k~~g~~Wk~ls~   50 (101)
T d1v63a_          11 PPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQ   50 (101)
T ss_dssp             CCSSSHHHHHHHHHHHCTTTT--SCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHhhCCH
Confidence            357999999999999998766  4688999999999998654