Citrus Sinensis ID: 029214

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------
Protein Sequence
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDASGNRLMSRTALRNK
Secondary Structure (PSIPRED)
ccccccccccccEEEEEcccccEEEEEcccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHcccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEEccccEEEEEEcccHHHccEEEEEccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccEcHcccccc
Coil and Loop (DISEMBL)
msscgidvapeqlcyipcnfcnIVLAVSvpcsslldivtvrcghcsnLWSVNMAAAFQslswqdvhhhqapsyaspecridlgssskcnnkisamrtptnkateervvnrresphsttpekrqrvpsAYNQFIKEEIQRIkannpdishREAFSTAAknwahfphiHFGLmleannqpklddasgnrlMSRTALRNK
Flexible Loop (DISEMBL)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDlgssskcnnkisamrtptnkateervvnrresphsttpekrqrvpsaYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPklddasgnrlmsrtalrnk
Low Complexity Region (SEG)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDASGNRLMSRTALRNK
Disordered region (IsUnstruct)
****GIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHH****************************************************************I*****************EAFSTAAKNWAHFPHIHFGLMLE************************
Disordered Region (DISOPRED)
***********QLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAF*************************************************************************QFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP*********************************
Disordered Region (DISEMBL)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQ***********SPECRIDLGSSSKCNNKISAM*****************************VPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDASGNRLMSRTALRNK
Disordered Region (DISPRO)
*********PEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL*****************************************************PHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE***************MS*T*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSiihhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDDASGNRLMSRTALRNK
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	197	2.2.26 [Sep-21-2011]
Q8GW46	164	Axial regulator YABBY 5 O	yes	no	0.802	0.963	0.722	1e-63
Q9XFB0	184	Putative axial regulator	no	no	0.842	0.902	0.518	8e-44
Q10FZ7	186	Protein YABBY 2 OS=Oryza	yes	no	0.862	0.913	0.534	1e-43
Q0JBF0	266	Protein YABBY 5 OS=Oryza	no	no	0.817	0.605	0.534	5e-43
Q01JG2	266	Protein YABBY 5 OS=Oryza	N/A	no	0.817	0.605	0.534	5e-43
Q2QM17	207	Protein YABBY 6 OS=Oryza	no	no	0.893	0.850	0.521	6e-41
Q6H668	256	Protein YABBY 4 OS=Oryza	no	no	0.817	0.628	0.476	1e-40
A2X7Q3	256	Protein YABBY 4 OS=Oryza	N/A	no	0.817	0.628	0.476	1e-40
O22152	229	Axial regulator YABBY 1 O	no	no	0.842	0.724	0.508	3e-37
Q9XFB1	240	Axial regulator YABBY 3 O	no	no	0.827	0.679	0.494	6e-37

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

 Score =  242 bits (618), Expect = 1e-63,   Method: Compositional matrix adjust.
 Identities = 125/173 (72%), Positives = 138/173 (79%), Gaps = 15/173 (8%)

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

Query: 68  HQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPS 127
            QA +YA PE     GSSS+ + KI + R  T   TE+R+VNR        PEKRQRVPS
Sbjct: 64  -QATNYAVPE----YGSSSRSHTKIPS-RISTRTITEQRIVNR-------PPEKRQRVPS 110

Query: 128 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 180
           AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+N Q K+
Sbjct: 111 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNKQAKI 163

Arabidopsis thaliana (taxid: 3702)

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

 Score =  176 bits (447), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 96/185 (51%), Positives = 118/185 (63%), Gaps = 19/185 (10%)

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

Query: 66  HHHQAPS---YASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHS---TTP 119
           H    P      S   R D  SSS+  N +S           E +   RE+P       P
Sbjct: 63  HQDLQPHRQHTTSLVTRKDCASSSRSTNNLS-----------ENI--DREAPRMPPIRPP 109

Query: 120 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPK 179
           EKRQRVPSAYN+FIKEEIQRIKA NP+ISHREAFSTAAKNWAHFPHIHFGL L+ N + K
Sbjct: 110 EKRQRVPSAYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLDGNKKGK 169

Query: 180 LDDAS 184
             D S
Sbjct: 170 QLDQS 174

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  175 bits (444), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 100/187 (53%), Positives = 127/187 (67%), Gaps = 17/187 (9%)

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

Query: 63  QDVHHHQ----APSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTT 118
           +D  H Q      + +  E   + GSSS+   ++  M +  +  TE  +       H   
Sbjct: 62  ED--HLQDNLKMHNMSFRENYSEYGSSSRYG-RVPMMFSKND--TEHML-------HVRP 109

Query: 119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQP 178
           PEKRQRVPSAYN+FIKEEI+RIKANNPDISHREAFSTAAKNWAHFP+IHFGL    +++ 
Sbjct: 110 PEKRQRVPSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHFPNIHFGLGSHESSK- 168

Query: 179 KLDDASG 185
           KLD+A G
Sbjct: 169 KLDEAIG 175

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  173 bits (439), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 102/191 (53%), Positives = 120/191 (62%), Gaps = 30/191 (15%)

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

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

Query: 102 ATEERVVNRRESPHST-TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 160
           AT+      + +P +  T EKRQRVPSAYN+FIK+EIQRIKA+NPDI+HREAFS AAKNW
Sbjct: 149 ATQREPQQPKNAPSANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNW 208

Query: 161 AHFPHIHFGLM 171
           AHFPHIHFGLM
Sbjct: 209 AHFPHIHFGLM 219

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

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  173 bits (439), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 102/191 (53%), Positives = 120/191 (62%), Gaps = 30/191 (15%)

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

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

Query: 102 ATEERVVNRRESPHST-TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 160
           AT+      + +P +  T EKRQRVPSAYN+FIK+EIQRIKA+NPDI+HREAFS AAKNW
Sbjct: 149 ATQREPQQPKNAPSANRTSEKRQRVPSAYNRFIKDEIQRIKASNPDITHREAFSAAAKNW 208

Query: 161 AHFPHIHFGLM 171
           AHFPHIHFGLM
Sbjct: 209 AHFPHIHFGLM 219

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

Oryza sativa subsp. indica (taxid: 39946)

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

 Score =  167 bits (422), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 97/186 (52%), Positives = 119/186 (63%), Gaps = 10/186 (5%)

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

Query: 65  VHHHQAPSYASPECRIDLGSSSKCN----NKISAMRTPTNKAT----EERVVNRRESPHS 116
            HHH         C  D     +      +  S +R P   A      ++     ++ H+
Sbjct: 64  HHHHHLQESGLSGCFRDQSGYPEFGFSAASSSSKLRLPPAAAAMVSYSQQNQQLEQALHA 123

Query: 117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANN 176
             PEKRQRVPSAYN+FIKEEI+RIKANNPDISHREAFSTAAKNWAH+P+IHFGL      
Sbjct: 124 RPPEKRQRVPSAYNRFIKEEIRRIKANNPDISHREAFSTAAKNWAHYPNIHFGLSPGHEG 183

Query: 177 QPKLDD 182
             KL D
Sbjct: 184 GKKLVD 189

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  166 bits (419), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 91/191 (47%), Positives = 111/191 (58%), Gaps = 30/191 (15%)

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

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

Query: 103 TEERVVNRRESPHSTT--PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 160
            ++     + +P S    PEKRQRVPSAYN+FIK+EIQRIKA NPDISHREAFS AAKNW
Sbjct: 143 VQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 202

Query: 161 AHFPHIHFGLM 171
           AHFPHIHFGLM
Sbjct: 203 AHFPHIHFGLM 213

Seems to be associated with phloem cell differentiation.

Oryza sativa subsp. japonica (taxid: 39947)

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

 Score =  166 bits (419), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 91/191 (47%), Positives = 111/191 (58%), Gaps = 30/191 (15%)

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

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

Query: 103 TEERVVNRRESPHSTT--PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 160
            ++     + +P S    PEKRQRVPSAYN+FIK+EIQRIKA NPDISHREAFS AAKNW
Sbjct: 143 VQQEPELPKNAPASANRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNW 202

Query: 161 AHFPHIHFGLM 171
           AHFPHIHFGLM
Sbjct: 203 AHFPHIHFGLM 213

Oryza sativa subsp. indica (taxid: 39946)

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

 Score =  154 bits (390), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 89/175 (50%), Positives = 110/175 (62%), Gaps = 9/175 (5%)

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

Query: 71  PSYASPECRID-LGSSSKCNNKISAMRTPTNKATEERVVNRRE------SPHSTTPEKRQ 123
            SY +P+  ++ L  +    N +   + PT       +   ++       P +  PEKRQ
Sbjct: 83  HSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAPPVNRPPEKRQ 142

Query: 124 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQP 178
           RVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL+   +NQP
Sbjct: 143 RVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV--PDNQP 195

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  153 bits (387), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 90/182 (49%), Positives = 108/182 (59%), Gaps = 19/182 (10%)

Query: 11  EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSV-------------NMAAAF 57
           +QLCY+ C+FC+ VLAVSVP SSL   VTVRCGHCSNL SV             N+  +F
Sbjct: 23  DQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVSMRALLLPSVSNLGHSF 82

Query: 58  QSLSWQDVHHHQAPSYASPECRIDLG------SSSKCNNKISAMRTPTNKATEERVVNRR 111
                     +      S    I++       +S+   N+   M T   ++ +      R
Sbjct: 83  LPPPPPPPPPNLLEEMRSGGQNINMNMMMSHHASAHHPNEHLVMATRNGRSVDHLQEMPR 142

Query: 112 ESPHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLM 171
             P +  PEKRQRVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGLM
Sbjct: 143 PPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLM 202

Query: 172 LE 173
            +
Sbjct: 203 AD 204

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

Arabidopsis thaliana (taxid: 3702)

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	197
225445565	185	PREDICTED: axial regulator YABBY 5 [Viti	0.939	1.0	0.812	7e-85
351724725	186	uncharacterized protein LOC100499942 [Gl	0.944	1.0	0.802	6e-84
356548475	186	PREDICTED: axial regulator YABBY 5-like	0.944	1.0	0.796	2e-83
255638088	186	unknown [Glycine max]	0.944	1.0	0.791	8e-83
224087122	188	predicted protein [Populus trichocarpa]	0.939	0.984	0.803	1e-80
357478135	191	YABBY protein [Medicago truncatula] gi|3	0.949	0.979	0.761	1e-79
217073506	191	unknown [Medicago truncatula] gi|3884906	0.949	0.979	0.761	2e-79
255572533	185	Axial regulator YABBY5, putative [Ricinu	0.934	0.994	0.782	1e-77
302399149	188	YABBY domain class transcription factor	0.944	0.989	0.771	2e-75
449464626	193	PREDICTED: axial regulator YABBY 5-like	0.944	0.963	0.730	8e-75

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

 Score =  318 bits (815), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 160/197 (81%), Positives = 169/197 (85%), Gaps = 12/197 (6%)

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

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPE 120
           SWQDV   QAP+Y SP+ RIDLGSSSKCN K+ AMR P +  +EER+VNR        PE
Sbjct: 60  SWQDV---QAPNYTSPDYRIDLGSSSKCNTKM-AMRAPASNISEERIVNR-------PPE 108

Query: 121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 180
           KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE NNQPKL
Sbjct: 109 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLETNNQPKL 168

Query: 181 DDASGNRLMSRTALRNK 197
           D+ S   LMS+ ALRNK
Sbjct: 169 DEGSEKHLMSKAALRNK 185

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  315 bits (807), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 158/197 (80%), Positives = 165/197 (83%), Gaps = 11/197 (5%)

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

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPE 120
           SWQDV   Q P   +PE RID GS+SKCNN+I AMR PT   TEERVVNR        PE
Sbjct: 61  SWQDV---QGPGQCNPEYRIDTGSTSKCNNRI-AMRAPTTHVTEERVVNR-------PPE 109

Query: 121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 180
           KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ K+
Sbjct: 110 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQAKM 169

Query: 181 DDASGNRLMSRTALRNK 197
           D+ S   LM R AL NK
Sbjct: 170 DNVSEKHLMPRAALLNK 186

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 157/197 (79%), Positives = 166/197 (84%), Gaps = 11/197 (5%)

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

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPE 120
           SWQDV   Q   + +PE RID GS+SKCNN+I AMR PT   TEERVVNR        PE
Sbjct: 61  SWQDV---QGSGHCNPEYRIDTGSTSKCNNRI-AMRAPTTHVTEERVVNR-------PPE 109

Query: 121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 180
           KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ K+
Sbjct: 110 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQVKM 169

Query: 181 DDASGNRLMSRTALRNK 197
           ++ S   LMSR AL NK
Sbjct: 170 ENVSEKHLMSRAALLNK 186

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  311 bits (797), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 156/197 (79%), Positives = 165/197 (83%), Gaps = 11/197 (5%)

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

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPE 120
           SWQDV   Q   + +PE RID GS+SKCNN+I AMR PT   TEERVVNR        PE
Sbjct: 61  SWQDV---QGSGHCNPEYRIDTGSTSKCNNRI-AMRAPTTHVTEERVVNR-------PPE 109

Query: 121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 180
           KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NNQ K+
Sbjct: 110 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNNQVKM 169

Query: 181 DDASGNRLMSRTALRNK 197
           ++     LMSR AL NK
Sbjct: 170 ENVFEKHLMSRAALLNK 186

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  304 bits (778), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 159/198 (80%), Positives = 167/198 (84%), Gaps = 13/198 (6%)

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

Query: 60  LSWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPT-NKATEERVVNRRESPHSTT 118
           LSWQD    QA +Y S + RIDLGSSSKCNNKIS MRTP  N  T+ERVVNR        
Sbjct: 60  LSWQD--QVQASNYNSHDYRIDLGSSSKCNNKIS-MRTPAANIVTQERVVNR-------P 109

Query: 119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQP 178
           PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE NNQ 
Sbjct: 110 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLETNNQT 169

Query: 179 KLDDASGNRLMSRTALRN 196
           K+DD S  RLMSR+AL+N
Sbjct: 170 KVDDGSEKRLMSRSALQN 187

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 153/201 (76%), Positives = 166/201 (82%), Gaps = 14/201 (6%)

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

Query: 58  QSLSWQDVHHHQAPSY-ASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHS 116
           QSLSWQDV   QAPS+  +PE RI   S+ KCN++I+    PT   TEERVVNR      
Sbjct: 61  QSLSWQDV---QAPSHCMNPEYRIRTSSTPKCNDRIAMRSAPTTHVTEERVVNR------ 111

Query: 117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANN 176
             PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NN
Sbjct: 112 -PPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNN 170

Query: 177 QPKLDDASGNRLMSRTALRNK 197
           Q ++++ S  RLMSR+AL NK
Sbjct: 171 QAQIENVSEKRLMSRSALMNK 191

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  300 bits (769), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 153/201 (76%), Positives = 165/201 (82%), Gaps = 14/201 (6%)

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

Query: 58  QSLSWQDVHHHQAPSY-ASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHS 116
           QSLSWQDV   QAPS+  +PE RI   S+ KCN++I+    PT   TEERVVNR      
Sbjct: 61  QSLSWQDV---QAPSHCMNPEYRIRTSSTPKCNDRIAMRSAPTTHVTEERVVNR------ 111

Query: 117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANN 176
             PEKRQRVPSAYNQFIKEEIQRIK NNPDISHREAFSTAAKNWAHFPHIHFGLMLE+NN
Sbjct: 112 -PPEKRQRVPSAYNQFIKEEIQRIKVNNPDISHREAFSTAAKNWAHFPHIHFGLMLESNN 170

Query: 177 QPKLDDASGNRLMSRTALRNK 197
           Q K+++ S  RLMSR+AL NK
Sbjct: 171 QAKIENVSEKRLMSRSALMNK 191

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 155/198 (78%), Positives = 165/198 (83%), Gaps = 14/198 (7%)

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

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPT-NKATEERVVNRRESPHSTTP 119
           SWQD    QAPS+ SP+ RI+LGSSSKCNN+IS MR P  +   EERVVNR        P
Sbjct: 60  SWQDF---QAPSHNSPDYRIELGSSSKCNNRIS-MRAPAPHNIAEERVVNR-------PP 108

Query: 120 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPK 179
           EKRQRVPSAYNQFIKEEIQRIKANNP+ISHREAFSTAAKNWAH+PHIHFGL L  N+Q K
Sbjct: 109 EKRQRVPSAYNQFIKEEIQRIKANNPEISHREAFSTAAKNWAHYPHIHFGLTLN-NHQTK 167

Query: 180 LDDASGNRLMSRTALRNK 197
           LDDAS   LMSR AL NK
Sbjct: 168 LDDASEKHLMSRAALYNK 185

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302399149|gb|ADL36869.1| YABBY domain class transcription factor [Malus x domestica]

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 152/197 (77%), Positives = 160/197 (81%), Gaps = 11/197 (5%)

Query: 1   MSSCGIDVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60
           M+SC +DVA EQLCYIPCNFC+IVLAVSVPCSSL DIVTVRCGHC+NLWSVNMAAAFQS 
Sbjct: 1   MTSC-VDVATEQLCYIPCNFCSIVLAVSVPCSSLFDIVTVRCGHCTNLWSVNMAAAFQSP 59

Query: 61  SWQDVHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPT-NKATEERVVNRRESPHSTTP 119
           SWQDV   Q  +Y S   RIDLGSSSKCN K +A R PT +  TEER VNR        P
Sbjct: 60  SWQDVQA-QNYNYNSQNYRIDLGSSSKCNKK-NATRDPTSDHVTEERGVNR-------PP 110

Query: 120 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPK 179
           EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQ K
Sbjct: 111 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQAK 170

Query: 180 LDDASGNRLMSRTALRN 196
           LD+     LMSR AL N
Sbjct: 171 LDNDPEKHLMSRAALLN 187

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  285 bits (728), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 149/204 (73%), Positives = 159/204 (77%), Gaps = 18/204 (8%)

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

Query: 61  SWQDVHHHQAPSYASPEC-----RIDLGSSSKCNNKISAM--RTPTNKATEERVVNRRES 113
           SWQDV   Q PSY    C     + D GSSSKCNN ++ M  R PT    EERVVNR   
Sbjct: 61  SWQDV---QVPSYNLYGCNGADFQGDFGSSSKCNNNVNKMEIRVPTTIPAEERVVNR--- 114

Query: 114 PHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE 173
                PEKRQRVPSAYNQFIKEEIQRIKA+NP+ISHREAFSTAAKNWAHFP IHFGLMLE
Sbjct: 115 ----PPEKRQRVPSAYNQFIKEEIQRIKASNPEISHREAFSTAAKNWAHFPRIHFGLMLE 170

Query: 174 ANNQPKLDDASGNRLMSRTALRNK 197
            NNQ KLDD S  RLM R AL NK
Sbjct: 171 TNNQVKLDDGS-ERLMPRAALLNK 193

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	197
TAIR|locus:2066311	164	YAB5 "YABBY5" [Arabidopsis tha	0.802	0.963	0.728	6.4e-60
TAIR|locus:2826731	184	YAB2 "YABBY2" [Arabidopsis tha	0.857	0.918	0.521	5.2e-42
TAIR|locus:2126931	240	YAB3 "YABBY3" [Arabidopsis tha	0.426	0.35	0.654	1.7e-40
TAIR|locus:2005492	229	AFO "AT2G45190" [Arabidopsis t	0.873	0.751	0.508	7e-38
UNIPROTKB|Q7XIM7	169	YAB1 "Protein YABBY 1" [Oryza	0.781	0.911	0.481	9.5e-34
TAIR|locus:2028020	231	INO "INNER NO OUTER" [Arabidop	0.786	0.670	0.457	1e-29
UNIPROTKB|Q76EJ0	194	DL "Protein DROOPING LEAF" [Or	0.690	0.701	0.465	3.5e-27
TAIR|locus:2026418	181	CRC "AT1G69180" [Arabidopsis t	0.700	0.762	0.424	7.6e-25

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

 Score = 614 (221.2 bits), Expect = 6.4e-60, P = 6.4e-60
 Identities = 126/173 (72%), Positives = 139/173 (80%)

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

Query:    68 HQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPS 127
              QA +YA PE     GSSS+ + KI + R  T   TE+R+VNR   P    PEKRQRVPS
Sbjct:    64 -QATNYAVPE----YGSSSRSHTKIPS-RISTRTITEQRIVNR---P----PEKRQRVPS 110

Query:   128 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKL 180
             AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE+N Q K+
Sbjct:   111 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLESNKQAKI 163

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0006417 "regulation of translation" evidence=RCA

GO:0009657 "plastid organization" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

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

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

 Score = 445 (161.7 bits), Expect = 5.2e-42, P = 5.2e-42
 Identities = 95/182 (52%), Positives = 116/182 (63%)

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

Query:    66 HHHQAPSY---ASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKR 122
             H    P      S   R D  SSS+  N +S           +R   R   P    PEKR
Sbjct:    63 HQDLQPHRQHTTSLVTRKDCASSSRSTNNLSE--------NIDREAPRM--PPIRPPEKR 112

Query:   123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLEANNQPKLDD 182
             QRVPSAYN+FIKEEIQRIKA NP+ISHREAFSTAAKNWAHFPHIHFGL L+ N + K  D
Sbjct:   113 QRVPSAYNRFIKEEIQRIKACNPEISHREAFSTAAKNWAHFPHIHFGLKLDGNKKGKQLD 172

Query:   183 AS 184
              S
Sbjct:   173 QS 174

GO:0005634 "nucleus" evidence=ISM

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

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

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

 Score = 284 (105.0 bits), Expect = 1.7e-40, Sum P(2) = 1.7e-40
 Identities = 55/84 (65%), Positives = 62/84 (73%)

Query:    90 NKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISH 149
             N+   M T   ++ +      R  P +  PEKRQRVPSAYN+FIKEEIQRIKA NPDISH
Sbjct:   121 NEHLVMATRNGRSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISH 180

Query:   150 REAFSTAAKNWAHFPHIHFGLMLE 173
             REAFS AAKNWAHFPHIHFGLM +
Sbjct:   181 REAFSAAAKNWAHFPHIHFGLMAD 204

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

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

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

 Score = 406 (148.0 bits), Expect = 7.0e-38, P = 7.0e-38
 Identities = 94/185 (50%), Positives = 117/185 (63%)

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

Query:    62 WQDVHHHQAP-SYASPECRIDLGSSSKCNNKISAMRT-PT-NKATEERVVNRRES----- 113
              Q +     P SY +P+  ++    +  N  +  M   PT N       ++++       
Sbjct:    74 NQ-LQLQLGPHSYFNPQDILEELRDAPSNMNMMMMNQHPTMNDIPSFMDLHQQHEIPKAP 132

Query:   114 PHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLMLE 173
             P +  PEKRQRVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL+  
Sbjct:   133 PVNRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGLV-- 190

Query:   174 ANNQP 178
              +NQP
Sbjct:   191 PDNQP 195

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

GO:0005634 "nucleus" evidence=ISM;TAS

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0010154 "fruit development" evidence=IMP

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

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

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

GO:0010450 "inflorescence meristem growth" evidence=IMP

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

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

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

GO:0009845 "seed germination" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

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

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

GO:0048481 "ovule development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=IMP

GO:0045165 "cell fate commitment" evidence=IMP

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

 Score = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 80/166 (48%), Positives = 104/166 (62%)

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

Query:    66 HHHQAPSYASPEC-RIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQR 124
             H  Q   +        D+ S    N + S    P    T ++ V    SP    PEKRQR
Sbjct:    62 HQVQNRGFQGNNFGSYDIASR---NQRTSTAMYPM--PTSQQQV----SP-IRPPEKRQR 111

Query:   125 VPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL 170
             VPSAYN+FIKEEIQRIK +NP+ISHREAFS AAKNWAH P +HFGL
Sbjct:   112 VPSAYNRFIKEEIQRIKTSNPEISHREAFSAAAKNWAHLPRLHFGL 157

GO:0005634 "nucleus" evidence=IDA

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

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

 Score = 329 (120.9 bits), Expect = 1.0e-29, P = 1.0e-29
 Identities = 76/166 (45%), Positives = 100/166 (60%)

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

Query:    63 QD-VHHHQAPSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEK 121
              D     +  +    E      +  K N+  + + +  N   E+  V+R     +  PEK
Sbjct:    78 LDETGKEEVAATDGVEEEAWKVNQEKENSPTTLVSSSDN---EDEDVSRVYQVVNKPPEK 134

Query:   122 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIH 167
             RQR PSAYN FIKEEI+R+KA NP ++H+EAFS AAKNWAHFP  H
Sbjct:   135 RQRAPSAYNCFIKEEIRRLKAQNPSMAHKEAFSLAAKNWAHFPPAH 180

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0048481 "ovule development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

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

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

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 74/159 (46%), Positives = 94/159 (59%)

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

Query:    66 HHHQAPSYASP--ECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTP-EKR 122
              H   P +  P  +CR          N+   + +PT+     R      +P    P EK+
Sbjct:    63 -HPLGP-FQGPCTDCR---------RNQPLPLVSPTSNEGSPR------APFVVKPPEKK 105

Query:   123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWA 161
              R+PSAYN+F++EEIQRIKA  PDI HREAFS AAKNWA
Sbjct:   106 HRLPSAYNRFMREEIQRIKAAKPDIPHREAFSMAAKNWA 144

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

GO:0048366 "leaf development" evidence=IMP

GO:0048440 "carpel development" evidence=IMP

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

 Score = 283 (104.7 bits), Expect = 7.6e-25, P = 7.6e-25
 Identities = 65/153 (42%), Positives = 91/153 (59%)

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

Query:    71 PSYASPECRIDLGSSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPSAYN 130
              S+   + +   GSSS  ++  S+ + P+   +   VV     P    PEK+QR+PSAYN
Sbjct:    76 QSFGGSDYK--KGSSSSSSSSTSSDQPPS--PSPPFVVK----P----PEKKQRLPSAYN 123

Query:   131 QFIKEEIQRIKANNPDISHREAFSTAAKNWAHF 163
             +F+++EIQRIK+ NP+I HREAFS AAKNWA +
Sbjct:   124 RFMRDEIQRIKSANPEIPHREAFSAAAKNWAKY 156


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.128   0.399    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      197       197   0.00082  111 3  11 22  0.46    32
                                                     31  0.44    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  8
  No. of states in DFA:  614 (65 KB)
  Total size of DFA:  193 KB (2109 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  22.06u 0.14s 22.20t   Elapsed:  00:00:01
  Total cpu time:  22.06u 0.14s 22.20t   Elapsed:  00:00:01
  Start:  Mon May 20 21:18:30 2013   End:  Mon May 20 21:18:31 2013

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8GW46	YAB5_ARATH	No assigned EC number	0.7225	0.8020	0.9634	yes	no
Q10FZ7	YAB2_ORYSJ	No assigned EC number	0.5347	0.8629	0.9139	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	197
pfam04690	170	pfam04690, YABBY, YABBY protein	2e-61
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	5e-04
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	0.001

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

 Score =  188 bits (479), Expect = 2e-61
 Identities = 84/169 (49%), Positives = 100/169 (59%), Gaps = 5/169 (2%)

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

Query: 66  HHHQAPSYASPECRIDLGSSSKCN----NKISAMRTPTNKATEERVVNRRESPHSTTPEK 121
                            G +   N    +  S   +    +  +     R  P +  PEK
Sbjct: 63  LDETGKPELLQNLG-VHGQNFNSNMMKSHSASTSVSSYMMSDNQDEEMPRVPPVNRPPEK 121

Query: 122 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGL 170
           RQRVPSAYN+FIKEEIQRIKA NPDISHREAFS AAKNWAHFPHIHFGL
Sbjct: 122 RQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 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 = 5e-04
 Identities = 13/37 (35%), Positives = 18/37 (48%)

Query: 124 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 160
           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 = 36.1 bits (84), Expect = 0.001
 Identities = 13/37 (35%), Positives = 17/37 (45%)

Query: 124 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 160
           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	197
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	100.0
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.34
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	97.9
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.84
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	97.83
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	97.79
smart00398	70	HMG high mobility group.	97.78
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	97.72
PTZ00199	94	high mobility group protein; Provisional	97.72
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	96.96
KOG0381	96	consensus HMG box-containing protein [General func	96.8
KOG3223	221	consensus Uncharacterized conserved protein [Funct	94.66
PF11331	46	DUF3133: Protein of unknown function (DUF3133); In	93.02
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	80.27

>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=5.2e-78  Score=499.90  Aligned_cols=157  Identities=61%  Similarity=0.948  Sum_probs=116.9

Q ss_pred             CCCCCceeeecCCCcceeeeccccCCCccceeeeecCCCCCccccccchhccCCCcchhcc--ccCC---CC--CCCccc
Q 029214            7 DVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVHH--HQAP---SY--ASPECR   79 (197)
Q Consensus         7 ~~~~E~lCYV~CnfC~TILaVsVPcssL~~tVTVRCGHCtnLlSVNmr~llqsl~~~~~~~--~~~~---~~--~~~~~~   79 (197)
                      +.++|||||||||||||||||||||+|||+|||||||||+|||||||++++++++.+++..  +..+   ..  ..+...
T Consensus         4 ~~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   83 (170)
T PF04690_consen    4 FSPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPENFG   83 (170)
T ss_pred             cCCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhccccccccccccccccccc
Confidence            4468999999999999999999999999999999999999999999999998887665411  0000   00  001111


Q ss_pred             ccCCCC-Cccccccc-ccCCCCCccccccc-cccCCCCCCCCCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 029214           80 IDLGSS-SKCNNKIS-AMRTPTNKATEERV-VNRRESPHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTA  156 (197)
Q Consensus        80 ~~~~ss-s~~~~~~~-~~~~~~~~~~~~~~-~~k~~~~~~kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~a  156 (197)
                      ....++ +.++.... .+....+++.|+.+ ++|       |||||||+|||||+||||||||||++||||+|||||++|
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~k-------PPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~a  156 (170)
T PF04690_consen   84 SNSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNK-------PPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAA  156 (170)
T ss_pred             cccccCCCccccccccccCccccccccccccccC-------CccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence            111111 11111100 11112233455443 345       999999999999999999999999999999999999999


Q ss_pred             HHhhccCCCccccc
Q 029214          157 AKNWAHFPHIHFGL  170 (197)
Q Consensus       157 AknW~~~Phihfgl  170 (197)
                      ||||||+|||||||
T Consensus       157 AknW~h~phihfgl  170 (170)
T PF04690_consen  157 AKNWAHFPHIHFGL  170 (170)
T ss_pred             HHhhhhCcccccCC
Confidence            99999999999997

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

Probab=98.34  E-value=8e-07  Score=62.88  Aligned_cols=46  Identities=35%  Similarity=0.634  Sum_probs=38.6

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhccCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKAN-NPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~-~P~i~hkEaFs~aAknW~~~P  164 (197)
                      |.|..|.+|||+.||++.+.++++. .+.++++|++..++..|+..+
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls   47 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLS   47 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcC
Confidence            6677899999999999999999999 888999999999999999754

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

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

Probab=97.90  E-value=2.8e-05  Score=52.39  Aligned_cols=42  Identities=31%  Similarity=0.498  Sum_probs=39.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|-+|||..|+++....+++.+|+++..|....++..|+..+
T Consensus         2 krp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls   43 (66)
T cd01390           2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS   43 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            467899999999999999999999999999999999999754

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.

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

Probab=97.84  E-value=4.3e-05  Score=50.84  Aligned_cols=43  Identities=30%  Similarity=0.432  Sum_probs=39.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      .|-+|+|..|++++...+++.+|+++..|....+++.|+..+.
T Consensus         2 krp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~   44 (66)
T cd00084           2 KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE   44 (66)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence            4678999999999999999999999999999999999997653

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

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

Probab=97.83  E-value=3.6e-05  Score=54.27  Aligned_cols=42  Identities=17%  Similarity=0.294  Sum_probs=39.3

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|-|+||..|+++.-.+|+++||+++..|.-+.++..|+..+
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            478999999999999999999999999999999999999754

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

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

Probab=97.79  E-value=3.9e-05  Score=52.23  Aligned_cols=42  Identities=33%  Similarity=0.635  Sum_probs=37.5

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|-++||..|+++....|++.+|+++..|.-..+++.|+..+
T Consensus         2 krP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~   43 (69)
T PF00505_consen    2 KRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLS   43 (69)
T ss_dssp             SSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSH
T ss_pred             cCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCC
Confidence            578999999999999999999999999999999999999753

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=97.78  E-value=6e-05  Score=50.67  Aligned_cols=43  Identities=33%  Similarity=0.511  Sum_probs=39.9

Q ss_pred             cCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          122 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       122 RQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      ..|-+|+|..|+++....+++.+|+++..|....++..|+..+
T Consensus         2 pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~   44 (70)
T smart00398        2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLS   44 (70)
T ss_pred             cCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCC
Confidence            4578999999999999999999999999999999999999754

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

Probab=97.72  E-value=7.9e-05  Score=53.03  Aligned_cols=43  Identities=16%  Similarity=0.358  Sum_probs=40.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      .|-|+||-.|+++....|+++||++++.|.-..++..|+..+.
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            5889999999999999999999999999999999999998654

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=97.72  E-value=8.6e-05  Score=55.70  Aligned_cols=49  Identities=27%  Similarity=0.441  Sum_probs=43.2

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCC
Q 029214          117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDIS--HREAFSTAAKNWAHFPH  165 (197)
Q Consensus       117 kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~--hkEaFs~aAknW~~~Ph  165 (197)
                      +.|.+..|-+|||..|+++.-..|+++||+++  ..|....++..|+..+.
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            36777889999999999999999999999986  67888999999998653

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

Probab=96.96  E-value=0.0011  Score=53.41  Aligned_cols=51  Identities=25%  Similarity=0.513  Sum_probs=46.5

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCcccc
Q 029214          117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFG  169 (197)
Q Consensus       117 kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Phihfg  169 (197)
                      +.||||-+  -||..|--.+|.+||++||++.+-+---..=|.|..+|..+|-
T Consensus        70 rHPErR~K--AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeNP~N  120 (122)
T PF06244_consen   70 RHPERRMK--AAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPENPFN  120 (122)
T ss_pred             CCcchhHH--HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCCCcc
Confidence            38999875  5999999999999999999999999888999999999998874

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

Probab=96.80  E-value=0.0031  Score=45.87  Aligned_cols=46  Identities=28%  Similarity=0.441  Sum_probs=41.4

Q ss_pred             cccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          120 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       120 EKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      ...+|-+|||..|+.+.-.+||++||+++..|.-+.+..+|.....
T Consensus        21 ~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~   66 (96)
T KOG0381|consen   21 QAPKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAE   66 (96)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCH
Confidence            3567889999999999999999999999999999999999987543

>KOG3223 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.66  E-value=0.022  Score=49.98  Aligned_cols=55  Identities=27%  Similarity=0.496  Sum_probs=48.8

Q ss_pred             CCCCCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCCcccccc
Q 029214          115 HSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFGLM  171 (197)
Q Consensus       115 ~~kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Phihfgl~  171 (197)
                      +.+-||||-|+  ||--|=..++-|||.+||+++|-+-=-..-|.|...|..+|.-+
T Consensus       160 ddrHPEkRmrA--A~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~Nq~  214 (221)
T KOG3223|consen  160 DDRHPEKRMRA--AFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFNQA  214 (221)
T ss_pred             cccChHHHHHH--HHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhhHH
Confidence            33689999885  89999999999999999999999888888899999999998643

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

Probab=93.02  E-value=0.057  Score=37.23  Aligned_cols=38  Identities=29%  Similarity=0.697  Sum_probs=29.3

Q ss_pred             eecCCCcceeeeccccCCCccc---eeeeecCCCCCccccccc
Q 029214           15 YIPCNFCNIVLAVSVPCSSLLD---IVTVRCGHCSNLWSVNMA   54 (197)
Q Consensus        15 YV~CnfC~TILaVsVPcssL~~---tVTVRCGHCtnLlSVNmr   54 (197)
                      ||-|..|..+|-  +|-+.+..   .-.+|||.|+.++++.++
T Consensus         6 Fv~C~~C~~lLq--lP~~~~~~~k~~~klrCGaCs~vl~~s~~   46 (46)
T PF11331_consen    6 FVVCSSCFELLQ--LPAKFSLSKKNQQKLRCGACSEVLSFSLP   46 (46)
T ss_pred             EeECccHHHHHc--CCCccCCCccceeEEeCCCCceeEEEecC
Confidence            788999977665  47765443   568999999999988653

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=80.27  E-value=1.5  Score=27.40  Aligned_cols=34  Identities=35%  Similarity=0.721  Sum_probs=24.0

Q ss_pred             ecCCCcceeeeccccCCCcc-ceeeeecCCCCCcccc
Q 029214           16 IPCNFCNIVLAVSVPCSSLL-DIVTVRCGHCSNLWSV   51 (197)
Q Consensus        16 V~CnfC~TILaVsVPcssL~-~tVTVRCGHCtnLlSV   51 (197)
                      +.|..|.+..-|..  +.+- +...|+|++|.+.+.+
T Consensus         3 ~~CP~C~~~~~v~~--~~~~~~~~~v~C~~C~~~~~~   37 (38)
T TIGR02098         3 IQCPNCKTSFRVVD--SQLGANGGKVRCGKCGHVWYA   37 (38)
T ss_pred             EECCCCCCEEEeCH--HHcCCCCCEEECCCCCCEEEe
Confidence            67999999876653  2221 3347999999987764

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.

---

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	197
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	3e-05
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	5e-05
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-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 = 42.1 bits (98), Expect = 3e-05
 Identities = 20/81 (24%), Positives = 30/81 (37%), Gaps = 6/81 (7%)

Query: 84  SSSKCNNKISAMRTPTNKATEERVVNRRESPHSTTPEKRQRVPSAYNQFIKEEIQRIKAN 143
            SS    + S M + T      R  +             ++  S+Y +F KE++   KA 
Sbjct: 10  HSSGLVPRGSHMASMTGGQQMGRGSSSVL------ASCPKKPVSSYLRFSKEQLPIFKAQ 63

Query: 144 NPDISHREAFSTAAKNWAHFP 164
           NPD    E     A+ W   P
Sbjct: 64  NPDAKTTELIRRIAQRWRELP 84

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

 Score = 41.7 bits (97), Expect = 5e-05
 Identities = 15/49 (30%), Positives = 22/49 (44%)

Query: 116 STTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 164
           S      ++  S+Y +F KE++   KA NPD    E     A+ W   P
Sbjct: 4   SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP 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 = 39.6 bits (92), Expect = 2e-04
 Identities = 12/52 (23%), Positives = 19/52 (36%)

Query: 109 NRRESPHSTTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNW 160
                     P   +R PSA+  F  E   +IK  +P +S  +      + W
Sbjct: 89  KGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMW 140

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	197
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	98.11
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	98.07
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	98.01
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	97.98
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	97.94
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	97.93
1wgf_A	90	Upstream binding factor 1; transcription factor, D	97.9
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	97.9
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	97.9
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	97.88
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	97.87
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	97.81
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	97.8
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	97.8
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	97.79
1ckt_A	71	High mobility group 1 protein; high-mobility group	97.78
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	97.78
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	97.73
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	97.72
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	97.64
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	97.58
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.57
2lhj_A	97	High mobility group protein homolog NHP1; structur	97.56
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	97.56
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	97.52
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	97.5
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	97.5
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	97.39
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	97.16
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	97.11
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	96.93
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	96.86
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	96.76
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	96.32
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	96.29
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	96.04
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	95.32
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	95.29
2cto_A	93	Novel protein; high mobility group box domain, hel	93.41

>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=98.11  E-value=4.3e-06  Score=58.87  Aligned_cols=49  Identities=22%  Similarity=0.341  Sum_probs=45.3

Q ss_pred             CCCCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          116 STTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       116 ~kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      ..+|.+..|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus         2 ~~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   50 (82)
T 1wz6_A            2 SSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLD   50 (82)
T ss_dssp             CSSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            3478888999999999999999999999999999999999999999765

>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=98.07  E-value=6.2e-06  Score=57.16  Aligned_cols=47  Identities=26%  Similarity=0.446  Sum_probs=43.7

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      -|.+..|-+|||..|+++.-..|++++|+++..|.-..++..|+..+
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            57777899999999999999999999999999999999999999754

>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=98.01  E-value=8.6e-06  Score=56.31  Aligned_cols=44  Identities=27%  Similarity=0.430  Sum_probs=41.0

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +..|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+
T Consensus         3 ~PKrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   46 (73)
T 3nm9_A            3 KPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK   46 (73)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCS
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            45788999999999999999999999999999999999999864

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

Probab=97.98  E-value=1.5e-05  Score=57.55  Aligned_cols=48  Identities=17%  Similarity=0.430  Sum_probs=44.7

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       117 kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +-|.+..|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+
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            467788899999999999999999999999999999999999999765

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

Probab=97.94  E-value=1.9e-05  Score=57.04  Aligned_cols=48  Identities=17%  Similarity=0.251  Sum_probs=43.7

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      .|.+..|-+|||..|+++.-..|+++||+++..|.-+.++..|+..+.
T Consensus         4 ~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~   51 (92)
T 2cs1_A            4 GSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSE   51 (92)
T ss_dssp             CCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCH
Confidence            566677899999999999999999999999999999999999997653

>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=97.93  E-value=1.2e-05  Score=55.64  Aligned_cols=46  Identities=13%  Similarity=0.355  Sum_probs=41.9

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      |.+..|-+|||..|+++.-+.|++++|+++..|.-+.++..|+..+
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            5566789999999999999999999999999999999999999754

>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=97.90  E-value=1.4e-05  Score=57.59  Aligned_cols=47  Identities=26%  Similarity=0.406  Sum_probs=43.7

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|.+..|-+|||..|+++.-..|+++||++++.|.-..++..|+..+
T Consensus        17 dp~~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   63 (90)
T 1wgf_A           17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLS   63 (90)
T ss_dssp             CCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            67777889999999999999999999999999999999999999754

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

Probab=97.90  E-value=1.8e-05  Score=54.66  Aligned_cols=45  Identities=20%  Similarity=0.422  Sum_probs=41.6

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHF  163 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~  163 (197)
                      |.+..|-+|||..|+++.-..|+++||+++..|.-+.++..|+..
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            455678899999999999999999999999999999999999975

>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=97.90  E-value=1.6e-05  Score=56.94  Aligned_cols=47  Identities=19%  Similarity=0.285  Sum_probs=43.6

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      -|.+..|-++||..|+++.-+.|++++|++++.|.-+.++..|+..+
T Consensus        14 dp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   60 (87)
T 2e6o_A           14 SPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMK   60 (87)
T ss_dssp             CCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence            56777889999999999999999999999999999999999999754

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

Probab=97.88  E-value=2e-05  Score=58.14  Aligned_cols=47  Identities=28%  Similarity=0.476  Sum_probs=43.6

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|.+..|-++||..|+++.-..|+++||+++..|.-..++..|+..+
T Consensus        14 dp~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls   60 (102)
T 2co9_A           14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLG   60 (102)
T ss_dssp             CCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCC
Confidence            56777889999999999999999999999999999999999999765

>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=97.87  E-value=2.3e-05  Score=55.70  Aligned_cols=47  Identities=13%  Similarity=0.350  Sum_probs=42.7

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      |.+..|-+|||..|+++.-..|++++|++++.|.-+.++..|+..+.
T Consensus         2 p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~   48 (85)
T 1j46_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTE   48 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCH
T ss_pred             cCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCH
Confidence            45667889999999999999999999999999999999999997653

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

Probab=97.81  E-value=2.7e-05  Score=57.41  Aligned_cols=48  Identities=17%  Similarity=0.366  Sum_probs=44.3

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       117 kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +.|.+..|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
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            367778899999999999999999999999999999999999999754

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

Probab=97.80  E-value=3.3e-05  Score=57.58  Aligned_cols=47  Identities=15%  Similarity=0.270  Sum_probs=42.6

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|.+..|-++||..|+++.-..|++++|++++.|.-+.++..|+..+
T Consensus        26 ~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls   72 (106)
T 4euw_A           26 NKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLN   72 (106)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCC
T ss_pred             CCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence            67778899999999999999999999999999999999999998765

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

Probab=97.80  E-value=3.4e-05  Score=54.91  Aligned_cols=47  Identities=23%  Similarity=0.419  Sum_probs=42.0

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISH--REAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~h--kEaFs~aAknW~~~P  164 (197)
                      -|.+..|-+|||..|+++.-..|+++||+++.  .|.-..++..|+..+
T Consensus        12 dp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   60 (86)
T 2eqz_A           12 DPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMS   60 (86)
T ss_dssp             CSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSC
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCC
Confidence            46666788999999999999999999999974  999999999999754

>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=97.79  E-value=2.9e-05  Score=54.45  Aligned_cols=46  Identities=24%  Similarity=0.459  Sum_probs=40.6

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +.|-.|-++||..|+++.-..|++++|++++.|.-..++..|+..+
T Consensus         4 ~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   49 (83)
T 3f27_D            4 TSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   49 (83)
T ss_dssp             ---CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            4566789999999999999999999999999999999999998754

>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=97.78  E-value=3.6e-05  Score=52.37  Aligned_cols=44  Identities=23%  Similarity=0.354  Sum_probs=39.6

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISH--REAFSTAAKNWAHFP  164 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~h--kEaFs~aAknW~~~P  164 (197)
                      |..|-+|||..|+++.-+.|++.||+++.  .|.-+.++..|+..+
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls   46 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS   46 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCC
Confidence            45688999999999999999999999976  999999999998643

>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=97.78  E-value=4.3e-05  Score=53.58  Aligned_cols=44  Identities=18%  Similarity=0.336  Sum_probs=40.8

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +..|-++||..|+++.-+.|++++|++++.|.-+.++..|+..+
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            45678999999999999999999999999999999999999764

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

Probab=97.73  E-value=4e-05  Score=51.87  Aligned_cols=44  Identities=25%  Similarity=0.458  Sum_probs=38.9

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      |-.|-+|||..|+++.-..|++.+|++++.|.-+.++..|+..+
T Consensus         2 k~krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (71)
T 4a3n_A            2 SIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALT   45 (71)
T ss_dssp             ---CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCC
Confidence            34678999999999999999999999999999999999998754

>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=97.72  E-value=5.4e-05  Score=52.85  Aligned_cols=44  Identities=14%  Similarity=0.354  Sum_probs=40.7

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +..|-+|||..|+++.-..|++++|+++..|.-+.++..|+..+
T Consensus         2 ~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (80)
T 1gt0_D            2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            45678999999999999999999999999999999999999754

>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=97.64  E-value=7.5e-05  Score=57.95  Aligned_cols=47  Identities=26%  Similarity=0.446  Sum_probs=43.2

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      -|.+..|-+|||..|+++.-..|+++||+++..|.-..++..|+..+
T Consensus        85 dp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls  131 (159)
T 2gzk_A           85 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA  131 (159)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSC
T ss_pred             ccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            56667889999999999999999999999999999999999999754

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

Probab=97.58  E-value=4.1e-05  Score=53.92  Aligned_cols=47  Identities=23%  Similarity=0.416  Sum_probs=42.3

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCH--HHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISH--REAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~h--kEaFs~aAknW~~~P  164 (197)
                      -|.+..|-+|||..|+++.-..|+++||+++.  .|.-+.++..|+..+
T Consensus         4 dp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls   52 (83)
T 1aab_A            4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMS   52 (83)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCC
Confidence            56777889999999999999999999999975  999999999998754

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

Probab=97.57  E-value=0.0001  Score=58.20  Aligned_cols=47  Identities=26%  Similarity=0.446  Sum_probs=43.3

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      -|.+..|-+|||..|+++....|++++|+++..|.-..++..|+..+
T Consensus        98 dp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls  144 (173)
T 2yrq_A           98 DPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA  144 (173)
T ss_dssp             CSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSC
T ss_pred             CCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            46677888999999999999999999999999999999999999754

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

Probab=97.56  E-value=3.4e-05  Score=56.16  Aligned_cols=47  Identities=28%  Similarity=0.413  Sum_probs=43.7

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDIS--HREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~--hkEaFs~aAknW~~~P  164 (197)
                      .|.+..|-+|||..|+++.-..|+++||+++  ..|.-..++..|+..+
T Consensus        19 dp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls   67 (97)
T 2lhj_A           19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALS   67 (97)
T ss_dssp             CCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCC
Confidence            6777889999999999999999999999999  9999999999999753

>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=97.56  E-value=0.00011  Score=50.97  Aligned_cols=43  Identities=21%  Similarity=0.356  Sum_probs=39.8

Q ss_pred             cCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          122 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       122 RQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      -.|-++||..|+++.-..|++++|++++.|.-..++..|+..+
T Consensus         3 iKRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls   45 (79)
T 3u2b_C            3 IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLK   45 (79)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence            3578999999999999999999999999999999999998754

>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=97.52  E-value=0.00015  Score=51.41  Aligned_cols=44  Identities=11%  Similarity=0.191  Sum_probs=40.5

Q ss_pred             cCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          122 RQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       122 RQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      -.|-+|||..|+++.-..|++++|++++.|.-..++..|+..+.
T Consensus         3 pKRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~   46 (86)
T 2lef_A            3 IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSR   46 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCH
Confidence            45789999999999999999999999999999999999997653

>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=97.50  E-value=0.00019  Score=51.69  Aligned_cols=46  Identities=15%  Similarity=0.338  Sum_probs=41.3

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCC-HHHHHHHHHHhhccCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDIS-HREAFSTAAKNWAHFP  164 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~-hkEaFs~aAknW~~~P  164 (197)
                      |.+..|-+|||..|+++.-..|+++||+++ ..|.-+.++..|+..+
T Consensus         3 ~~~PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls   49 (81)
T 2d7l_A            3 SGSSGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLS   49 (81)
T ss_dssp             CCCSSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCC
Confidence            344567899999999999999999999998 9999999999999754

>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=97.50  E-value=2.3e-05  Score=56.82  Aligned_cols=47  Identities=26%  Similarity=0.482  Sum_probs=43.4

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|.+..|-+|||..|+++.-..|+++||+++..|.-..++..|+..+
T Consensus        17 dp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls   63 (93)
T 1cg7_A           17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALT   63 (93)
T ss_dssp             CSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCC
Confidence            67777889999999999999999999999999999999999999753

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

Probab=97.39  E-value=0.00025  Score=55.95  Aligned_cols=48  Identities=21%  Similarity=0.411  Sum_probs=43.4

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPD--ISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~--i~hkEaFs~aAknW~~~Ph  165 (197)
                      -|.+..|-+|||..|+++....|++.||+  ++..|....++..|+..+.
T Consensus        12 dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~   61 (173)
T 2yrq_A           12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSA   61 (173)
T ss_dssp             CSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCH
Confidence            56777889999999999999999999999  6899999999999987654

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

Probab=97.16  E-value=0.00035  Score=57.77  Aligned_cols=47  Identities=30%  Similarity=0.510  Sum_probs=43.1

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|.+..|-+|||..|+++....|+++||+++..|....++..|+..+
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   52 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   52 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccC
Confidence            45666789999999999999999999999999999999999999765

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

Probab=97.11  E-value=0.0004  Score=58.24  Aligned_cols=47  Identities=30%  Similarity=0.510  Sum_probs=43.4

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      -|.+..|-+|||..|+++....|+++||+++..|....++..|+..+
T Consensus        38 ~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls   84 (238)
T 3tmm_A           38 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELP   84 (238)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCC
Confidence            46777889999999999999999999999999999999999999754

>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=96.93  E-value=0.0012  Score=49.43  Aligned_cols=43  Identities=12%  Similarity=0.135  Sum_probs=39.0

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      |..|-+|||+.|+++....+++.+|+ +..|.-+.++..|+...
T Consensus         4 kPKrP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~ls   46 (91)
T 1l8y_A            4 LPESPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNME   46 (91)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCC
Confidence            45678999999999999999999999 99999999999998753

>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=96.86  E-value=0.0015  Score=50.56  Aligned_cols=47  Identities=13%  Similarity=0.350  Sum_probs=43.0

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      |++..|-++||-.|++++-.+|++.||+++..|....++..|+..+.
T Consensus         2 ~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~~eisk~lg~~Wk~ls~   48 (159)
T 2gzk_A            2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTE   48 (159)
T ss_dssp             TTCCCCCCCHHHHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHSCH
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhH
Confidence            56777889999999999999999999999999999999999997654

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

Probab=96.76  E-value=0.00097  Score=45.06  Aligned_cols=40  Identities=35%  Similarity=0.679  Sum_probs=35.2

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      |..|-+|||..|+++.-..++..+|    .|..+.++..|+..+
T Consensus         2 ~PKrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls   41 (67)
T 3fgh_A            2 KPKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLS   41 (67)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCC
Confidence            3467889999999999999999887    599999999999754

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

Probab=96.32  E-value=0.00086  Score=49.91  Aligned_cols=44  Identities=16%  Similarity=0.192  Sum_probs=35.7

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      |-+..|.||||-.|+.++-.+||++||+++  +.|..+++.|+..+
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            334467899999999999999999999984  44666679998754

>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=96.29  E-value=0.0066  Score=44.83  Aligned_cols=44  Identities=11%  Similarity=0.328  Sum_probs=34.3

Q ss_pred             cccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          120 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       120 EKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      .+..|-+|||..|+++.+.  +..+++++..|..+.++..|+..+.
T Consensus         7 ~~PKrP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~   50 (101)
T 1v63_A            7 GPKKPPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQ   50 (101)
T ss_dssp             SSCCCCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCCCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCH
Confidence            3445679999999999964  3345567889999999999997543

>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=96.04  E-value=0.0063  Score=45.53  Aligned_cols=44  Identities=16%  Similarity=0.423  Sum_probs=37.9

Q ss_pred             CCccc-CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          118 TPEKR-QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       118 PPEKR-QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      -|.+. .|-+|||..|+++.-..|+    +++..|..+.++..|+..+.
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            44555 6789999999999999888    89999999999999998653

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

Probab=95.32  E-value=0.0038  Score=52.25  Aligned_cols=42  Identities=33%  Similarity=0.617  Sum_probs=37.2

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      |.+..|-+|||+.|+++...+|+.++|+    |..+.++..|+..+
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            5667889999999999999999988876    89999999999764

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

Probab=95.29  E-value=0.0039  Score=51.42  Aligned_cols=43  Identities=33%  Similarity=0.593  Sum_probs=37.6

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      -|.+..|-+|||..|+++....|+..+|+    |..+.++..|+..+
T Consensus       111 dp~~PKrP~say~lF~~e~r~~~k~~~p~----ei~k~lg~~Wk~ls  153 (214)
T 3tq6_A          111 LLGKPKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLS  153 (214)
T ss_dssp             HTTCCCCCCCHHHHHHHHHTTTSSCSSHH----HHHHHHHHHHHTCC
T ss_pred             cccCcccccchhhhhHHHHHHhhccCCHH----HHHHHHHHHHHcCC
Confidence            35666889999999999999999988876    89999999999865

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

Probab=93.41  E-value=0.048  Score=40.36  Aligned_cols=44  Identities=18%  Similarity=0.402  Sum_probs=36.9

Q ss_pred             CcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHH---HHhhccCC
Q 029214          119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTA---AKNWAHFP  164 (197)
Q Consensus       119 PEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~a---AknW~~~P  164 (197)
                      +.+..|-+|||..|+++.-.+||.+  +++..|.=+.+   +..|+...
T Consensus         8 ~~~PKRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~ls   54 (93)
T 2cto_A            8 MPNRKASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWALLR   54 (93)
T ss_dssp             CCCCCSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHHSC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHcCC
Confidence            4455688999999999999999998  78888887777   99998753

---

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	197
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	6e-04
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	0.002

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

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

 Score = 35.3 bits (81), Expect = 6e-04
 Identities = 8/46 (17%), Positives = 22/46 (47%)

Query: 119 PEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 164
           P+  ++  + Y +F  E+  +    +P++S+ +     +K +   P
Sbjct: 8   PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELP 53

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

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

 Score = 33.7 bits (77), Expect = 0.002
 Identities = 11/41 (26%), Positives = 18/41 (43%)

Query: 124 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 164
           R PSA+  F  E   +IK  +P +S  +      + W +  
Sbjct: 5   RPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	197
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.18
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.11
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	98.01
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	97.94
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.91
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	97.85
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	97.67
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	97.66
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	97.36
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	97.29
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	96.87
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	96.66

>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=98.18  E-value=9.4e-07  Score=61.84  Aligned_cols=48  Identities=25%  Similarity=0.401  Sum_probs=43.2

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      .|.+..|-+|||.+|+++..++|++.+|++++.|.-..++..|+..+.
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            455666889999999999999999999999999999999999998653

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

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

Probab=98.11  E-value=1.7e-06  Score=60.58  Aligned_cols=48  Identities=17%  Similarity=0.366  Sum_probs=44.9

Q ss_pred             CCCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          117 TTPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       117 kPPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +.|++..|-+|+|..|+++....|++.+|+++..|.-..++..|+..+
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            478888999999999999999999999999999999999999999754

>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=98.01  E-value=4e-06  Score=59.38  Aligned_cols=48  Identities=25%  Similarity=0.465  Sum_probs=44.5

Q ss_pred             CCcccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          118 TPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       118 PPEKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      .|.+..|-+|||..|+++....||+.+|++++.|.-..++..|+..+.
T Consensus        17 ~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~   64 (93)
T d1lwma_          17 DPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTP   64 (93)
T ss_dssp             CSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCH
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCH
Confidence            677778999999999999999999999999999999999999998653

>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=97.94  E-value=4e-06  Score=57.38  Aligned_cols=42  Identities=26%  Similarity=0.442  Sum_probs=39.4

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      .|-+|||..|+++....|++.||++++.|....++..|+..+
T Consensus         4 KrP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls   45 (79)
T d1hsma_           4 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA   45 (79)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSC
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCC
Confidence            467899999999999999999999999999999999999865

>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=97.91  E-value=7.4e-06  Score=55.50  Aligned_cols=40  Identities=28%  Similarity=0.429  Sum_probs=38.2

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhcc
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAH  162 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~  162 (197)
                      .|-+|||..|+++.-+.|+++||++++.|.-..++..|+.
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            5779999999999999999999999999999999999984

>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=97.85  E-value=1.3e-05  Score=53.58  Aligned_cols=45  Identities=20%  Similarity=0.373  Sum_probs=39.5

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhhccCCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPD--ISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~--i~hkEaFs~aAknW~~~Ph  165 (197)
                      |..|-+|||..|+++.-+.|++.||+  +++.|.-..++..|+..+.
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~   47 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSA   47 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCT
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCH
Confidence            34578999999999999999999996  6678999999999998653

>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=97.67  E-value=3.2e-05  Score=53.74  Aligned_cols=45  Identities=13%  Similarity=0.367  Sum_probs=41.6

Q ss_pred             cccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029214          120 EKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP  164 (197)
Q Consensus       120 EKRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~P  164 (197)
                      +|-.|-+|||-.|+++.-++|++++|++++.|.=..++..|+..+
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~   45 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLS   45 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCC
Confidence            355688999999999999999999999999999999999999865

>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=97.66  E-value=3.5e-05  Score=53.65  Aligned_cols=45  Identities=13%  Similarity=0.347  Sum_probs=41.3

Q ss_pred             ccCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          121 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       121 KRQR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      |-.|-+|||..|+++.-..|+++||++++.|.=..++..|+..+.
T Consensus         4 ~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~   48 (85)
T d1j46a_           4 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTE   48 (85)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCH
Confidence            346889999999999999999999999999999999999998654

>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=97.36  E-value=0.00016  Score=48.46  Aligned_cols=42  Identities=19%  Similarity=0.363  Sum_probs=39.1

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          124 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       124 R~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      |-+|||-.|+++.-++|++++|++++.|.=..++..|+..+.
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            668999999999999999999999999999999999997643

>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=97.29  E-value=0.00018  Score=50.02  Aligned_cols=42  Identities=12%  Similarity=0.207  Sum_probs=38.9

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          124 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       124 R~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      |-++||-.|+++.-++|+++||+++..|.=..++..|+..+.
T Consensus         5 RP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~   46 (86)
T d2lefa_           5 KPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSR   46 (86)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCH
T ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCH
Confidence            567999999999999999999999999999999999997653

>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=96.87  E-value=0.00056  Score=48.97  Aligned_cols=39  Identities=18%  Similarity=0.451  Sum_probs=32.8

Q ss_pred             CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          123 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       123 QR~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      .|-++||..|+++..+    ..|+++.+|.+..+++.|+..+.
T Consensus        19 K~P~~ay~lF~~~~r~----~~~~~~~~e~~k~ig~~W~~Ls~   57 (108)
T d1v64a_          19 KPPPNSYSLYCAELMA----NMKDVPSTERMVLCSQQWKLLSQ   57 (108)
T ss_dssp             CCCSSHHHHHHHHHHH----HCTTSCHHHHHHHHHHHHHHSCH
T ss_pred             CCCCcHHHHHHHHHHH----HccCCCHHHHHHHHHHHHccCCH
Confidence            3457999999998665    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=96.66  E-value=0.001  Score=46.60  Aligned_cols=40  Identities=15%  Similarity=0.312  Sum_probs=34.6

Q ss_pred             CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCC
Q 029214          124 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH  165 (197)
Q Consensus       124 R~PSaYN~FmK~ei~riK~~~P~i~hkEaFs~aAknW~~~Ph  165 (197)
                      |-++||.+|+++.++.|+..+|  +.+|.-+.++..|+..+.
T Consensus        11 rP~~ay~~F~~e~r~~~~~~~~--~~~ei~k~~g~~Wk~ls~   50 (101)
T d1v63a_          11 PPMNGYQKFSQELLSNGELNHL--PLKERMVEIGSRWQRISQ   50 (101)
T ss_dssp             CCSSSHHHHHHHHHHHCTTTTS--CHHHHHHHHHHHHTTSCH
T ss_pred             CCCCHHHHHHHHHHHHHHhcCC--CHHHHHHHHHHHHhhCCH
Confidence            4679999999999999987665  679999999999998654