Psyllid ID: psy3264

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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------
Protein Sequence
MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPVNEEADEEDDE
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHcccccccHHHccHHccccccccHHHHHHHHHHHHHcccHHHccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccc
Coil and Loop (DISEMBL)
mpkekdvkprgrmTAYAFFVQVCREehkkkhpeenVVFAEFSKKCAERWKTMSEKEKKRFHEMADKdkkrydtemqsytppagekrgkikqdnpeygvgDIAKELgkkwadvdpsvKTKYEQMAEKDKARYEKEMTAyknrsvapvneeadeedde
Flexible Loop (DISEMBL)
mpkekdvkprgrmtaYAFFVQVCREEhkkkhpeenvvfaefSKKCAERWKTMsekekkrfhemadkdkkrydtemqsytppagekrgkikqdnpEYGVGDIAKelgkkwadvdpsvkTKYEQMAEKDKARYEKemtayknrsvapvneeadeedde
Low Complexity Region (SEG)
MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPVNEEADEEDDE
Disordered region (IsUnstruct)
************MTAYAFFVQVCRE**********VVFAEFSKKC***************************************************************************************************************
Disordered Region (DISOPRED)
******V***GRMTAYAFFVQVCRE***************F************************KDKKRYDTEMQSYTPPA****************GDIAKELGKKW*********KYEQMAEKDKARYEKEM*********************
Disordered Region (DISEMBL)
*********RGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR***************
Disordered Region (DISPRO)
***********RMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR***************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYxxxxxxxxxxxxxxxxxxxxxSVAPVNEEADEEDDE
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	156	2.2.26 [Sep-21-2011]
Q24537	393	High mobility group prote	yes	N/A	0.858	0.340	0.628	3e-54
P07746	204	High mobility group-T pro	N/A	N/A	0.897	0.686	0.475	1e-36
P26584	207	High mobility group prote	yes	N/A	0.865	0.652	0.496	3e-36
P17741	210	High mobility group prote	yes	N/A	0.846	0.628	0.5	6e-35
P26583	209	High mobility group prote	yes	N/A	0.846	0.631	0.5	7e-35
P40673	209	High mobility group prote	yes	N/A	0.846	0.631	0.5	7e-35
P52925	210	High mobility group prote	yes	N/A	0.916	0.680	0.467	8e-35
P30681	210	High mobility group prote	yes	N/A	0.846	0.628	0.493	2e-34
P63159	215	High mobility group prote	no	N/A	0.865	0.627	0.477	6e-33
A9RA84	215	High mobility group prote	N/A	N/A	0.865	0.627	0.477	6e-33

>sp|Q24537|HMG2_DROME High mobility group protein DSP1 OS=Drosophila melanogaster GN=Dsp1 PE=2 SV=1

 Score =  210 bits (535), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 103/164 (62%), Positives = 120/164 (73%), Gaps = 30/164 (18%)

Query: 6   DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMAD 65
           D KPRGRMTAYA+FVQ CREEHKKKHP+E V+FAEFS+KCAERWKTM +KEKKRFHEMA+
Sbjct: 176 DAKPRGRMTAYAYFVQTCREEHKKKHPDETVIFAEFSRKCAERWKTMVDKEKKRFHEMAE 235

Query: 66  KDKKRYDTEMQSYTPPAG------------------------------EKRGKIKQDNPE 95
           KDK+RY+ EMQ+Y PP G                              ++R K+K  NPE
Sbjct: 236 KDKQRYEAEMQNYVPPKGAVVGRGKKRKQIKDPNAPKRSLSAFFWFCNDERNKVKALNPE 295

Query: 96  YGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           +GVGDIAKELG+KW+DVDP VK KYE MAE+DKARYE+EMT YK
Sbjct: 296 FGVGDIAKELGRKWSDVDPEVKQKYESMAERDKARYEREMTEYK 339

Binds preferentially single-stranded DNA and unwinds double stranded DNA.
Drosophila melanogaster (taxid: 7227)

>sp|P07746|HMGT_ONCMY High mobility group-T protein OS=Oncorhynchus mykiss PE=2 SV=2

 Score =  151 bits (382), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 78/164 (47%), Positives = 107/164 (65%), Gaps = 24/164 (14%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YA+FVQ  REEHKKKHPE +V F+EFSKKC+ERWKTMS KEK +F ++A  D
Sbjct: 7   KPRGKMSSYAYFVQTRREEHKKKHPEASVNFSEFSKKCSERWKTMSAKEKGKFEDLAKLD 66

Query: 68  KKRYDTEMQSYTPPAGEK------------------------RGKIKQDNPEYGVGDIAK 103
           K RY+ EM+SY PP GEK                        R ++K + P   +GD+AK
Sbjct: 67  KVRYEREMRSYIPPKGEKKKRFKDPNAPKRPSSAFFIFCADFRPQVKGETPGLSIGDVAK 126

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPVN 147
           +LG+KW ++    K  YE+ A + K +YEK++TAY+N+   PV+
Sbjct: 127 KLGEKWNNLTAEDKVPYEKKASRLKEKYEKDITAYRNKGKVPVS 170

Binds preferentially single-stranded DNA and unwinds double stranded DNA.

Oncorhynchus mykiss (taxid: 8022)

>sp|P26584|HMGB2_CHICK High mobility group protein B2 OS=Gallus gallus GN=HMGB2 PE=2 SV=2

 Score =  150 bits (379), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 79/159 (49%), Positives = 101/159 (63%), Gaps = 24/159 (15%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YA+FVQ CREEHKKKHP+ +V FAEFS+KC+ERWKTMS KEK +F EMA  D
Sbjct: 8   KPRGKMSSYAYFVQTCREEHKKKHPDSSVNFAEFSRKCSERWKTMSSKEKGKFEEMAKGD 67

Query: 68  KKRYDTEMQSYTPP------------------------AGEKRGKIKQDNPEYGVGDIAK 103
           K RYD EM++Y PP                          E R KIK D+P   +GD AK
Sbjct: 68  KARYDREMKNYVPPKGEKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKNDHPGLSIGDTAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           +LG+ W++     K  YEQ A K K +YEK++ AY+ +S
Sbjct: 128 KLGEMWSEQLAKDKQPYEQKAAKLKEKYEKDIAAYRAKS 166

Binds preferentially single-stranded DNA and unwinds double stranded DNA.

Gallus gallus (taxid: 9031)

>sp|P17741|HMGB2_PIG High mobility group protein B2 OS=Sus scrofa GN=HMGB2 PE=1 SV=2

 Score =  146 bits (368), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 78/156 (50%), Positives = 100/156 (64%), Gaps = 24/156 (15%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 8   KPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSD 67

Query: 68  KKRYDTEMQSYT------------------PPAG------EKRGKIKQDNPEYGVGDIAK 103
           K RYD EM++Y                   PP+       E R KIK ++P   +GD AK
Sbjct: 68  KARYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           +LG+ W++     K  YEQ A K K +YEK++ AY+
Sbjct: 128 KLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYR 163

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS).

Sus scrofa (taxid: 9823)

>sp|P26583|HMGB2_HUMAN High mobility group protein B2 OS=Homo sapiens GN=HMGB2 PE=1 SV=2

 Score =  145 bits (367), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 78/156 (50%), Positives = 100/156 (64%), Gaps = 24/156 (15%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 8   KPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSD 67

Query: 68  KKRYDTEMQSYT------------------PPAG------EKRGKIKQDNPEYGVGDIAK 103
           K RYD EM++Y                   PP+       E R KIK ++P   +GD AK
Sbjct: 68  KARYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           +LG+ W++     K  YEQ A K K +YEK++ AY+
Sbjct: 128 KLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYR 163

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS).

Homo sapiens (taxid: 9606)

>sp|P40673|HMGB2_BOVIN High mobility group protein B2 OS=Bos taurus GN=HMGB2 PE=1 SV=3

 Score =  145 bits (367), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 78/156 (50%), Positives = 100/156 (64%), Gaps = 24/156 (15%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 8   KPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSD 67

Query: 68  KKRYDTEMQSYT------------------PPAG------EKRGKIKQDNPEYGVGDIAK 103
           K RYD EM++Y                   PP+       E R KIK ++P   +GD AK
Sbjct: 68  KARYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           +LG+ W++     K  YEQ A K K +YEK++ AY+
Sbjct: 128 KLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYR 163

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS).

Bos taurus (taxid: 9913)

>sp|P52925|HMGB2_RAT High mobility group protein B2 OS=Rattus norvegicus GN=Hmgb2 PE=2 SV=2

 Score =  145 bits (367), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 78/167 (46%), Positives = 105/167 (62%), Gaps = 24/167 (14%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F ++A  D
Sbjct: 8   KPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDLAKSD 67

Query: 68  KKRYDTEMQSYT------------------PPAG------EKRGKIKQDNPEYGVGDIAK 103
           K RYD EM++Y                   PP+       E R KIK ++P   +GD AK
Sbjct: 68  KARYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPVNEEA 150
           +LG+ W++     K  YEQ A K K +YEK++ AY+ +  + V ++ 
Sbjct: 128 KLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYRAKGKSEVGKKG 174

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS).

Rattus norvegicus (taxid: 10116)

>sp|P30681|HMGB2_MOUSE High mobility group protein B2 OS=Mus musculus GN=Hmgb2 PE=1 SV=3

 Score =  144 bits (364), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 77/156 (49%), Positives = 100/156 (64%), Gaps = 24/156 (15%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F ++A  D
Sbjct: 8   KPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDLAKSD 67

Query: 68  KKRYDTEMQSYT------------------PPAG------EKRGKIKQDNPEYGVGDIAK 103
           K RYD EM++Y                   PP+       E R KIK ++P   +GD AK
Sbjct: 68  KARYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSENRPKIKIEHPGLSIGDTAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           +LG+ W++     K  YEQ A K K +YEK++ AY+
Sbjct: 128 KLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYR 163

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS).

Mus musculus (taxid: 10090)

>sp|P63159|HMGB1_RAT High mobility group protein B1 OS=Rattus norvegicus GN=Hmgb1 PE=1 SV=2

 Score =  139 bits (351), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 76/159 (47%), Positives = 101/159 (63%), Gaps = 24/159 (15%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 8   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 67

Query: 68  KKRYDTEMQSYTPPAGEK------------------------RGKIKQDNPEYGVGDIAK 103
           K RY+ EM++Y PP GE                         R KIK ++P   +GD+AK
Sbjct: 68  KARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           +LG+ W +     K  YE+ A K K +YEK++ AY+ + 
Sbjct: 128 KLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 166

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes in developing cells.

Rattus norvegicus (taxid: 10116)

>sp|A9RA84|HMGB1_PAPAN High mobility group protein B1 OS=Papio anubis GN=HMGB1 PE=3 SV=1

 Score =  139 bits (351), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 76/159 (47%), Positives = 101/159 (63%), Gaps = 24/159 (15%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 8   KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 67

Query: 68  KKRYDTEMQSYTPPAGEK------------------------RGKIKQDNPEYGVGDIAK 103
           K RY+ EM++Y PP GE                         R KIK ++P   +GD+AK
Sbjct: 68  KARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAK 127

Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           +LG+ W +     K  YE+ A K K +YEK++ AY+ + 
Sbjct: 128 KLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 166

DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes in developing cells.

Papio anubis (taxid: 9555)

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	156
332375054	306	unknown [Dendroctonus ponderosae]	0.891	0.454	0.690	2e-59
193664382	410	PREDICTED: hypothetical protein LOC10016	0.910	0.346	0.682	4e-58
307192728	445	High mobility group protein DSP1 [Harpeg	1.0	0.350	0.615	2e-57
332025497	305	High mobility group protein DSP1 [Acromy	0.891	0.455	0.674	4e-57
350402647	456	PREDICTED: high mobility group protein D	1.0	0.342	0.613	6e-57
380025638	420	PREDICTED: high mobility group protein D	1.0	0.371	0.613	6e-57
322797840	203	hypothetical protein SINV_09636 [Solenop	0.903	0.694	0.666	1e-56
307191141	305	High mobility group protein DSP1 [Campon	1.0	0.511	0.599	2e-56
156552179	433	PREDICTED: high mobility group protein D	0.865	0.311	0.674	5e-56
189236107	505	PREDICTED: similar to High mobility grou	0.916	0.283	0.641	7e-56

>gi|332375054|gb|AEE62668.1| unknown [Dendroctonus ponderosae]

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 116/168 (69%), Positives = 127/168 (75%), Gaps = 29/168 (17%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           MPK+ D KPRGRMTAYAFFVQ CREEHKKKHPEENVVFAEFSKKCAERWKTM +KEKKRF
Sbjct: 111 MPKKGDSKPRGRMTAYAFFVQTCREEHKKKHPEENVVFAEFSKKCAERWKTMLDKEKKRF 170

Query: 61  HEMADKDKKRYDTEMQSYTPPAGEK-----------------------------RGKIKQ 91
           HEMA+ DKKRYDTEMQSYTPP GEK                             RGK+K 
Sbjct: 171 HEMAETDKKRYDTEMQSYTPPKGEKQRGKKRKQIKDPNAPKRSLSAFFWFSNDERGKVKA 230

Query: 92  DNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
            NPEYGVGDIAKELG++WAD DP V++K+E +A+KDK RYEKEMTAYK
Sbjct: 231 QNPEYGVGDIAKELGRRWADADPEVRSKFEALADKDKIRYEKEMTAYK 278

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193664382|ref|XP_001944154.1| PREDICTED: hypothetical protein LOC100167132 [Acyrthosiphon pisum]

 Score =  229 bits (583), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 118/173 (68%), Positives = 128/173 (73%), Gaps = 31/173 (17%)

Query: 1   MPKEK--DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKK 58
           MP+ K  D KPRGRMTAYAFFVQ CREEHKKKHP+ENV+FAEFSKKCAERWKTM+EKEKK
Sbjct: 186 MPRGKGTDAKPRGRMTAYAFFVQTCREEHKKKHPDENVIFAEFSKKCAERWKTMNEKEKK 245

Query: 59  RFHEMADKDKKRYDTEMQSYTPPAGEK-----------------------------RGKI 89
           RFHEMADKDK RYDTEMQSY PP GEK                             RGK+
Sbjct: 246 RFHEMADKDKLRYDTEMQSYIPPKGEKVRGKKRKQIKDPNAPKRSLSAFFWFCNDERGKV 305

Query: 90  KQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           K  NPEYGVGD+AKELGKKW+D D +VK KYE MAEKDKARYE+EMT YKN+ 
Sbjct: 306 KAVNPEYGVGDVAKELGKKWSDADITVKQKYEAMAEKDKARYEREMTEYKNKG 358

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307192728|gb|EFN75836.1| High mobility group protein DSP1 [Harpegnathos saltator]

 Score =  226 bits (577), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 123/200 (61%), Positives = 135/200 (67%), Gaps = 44/200 (22%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           MP+ KD KPRGRMTAYAFFVQ CR+EHKKKHPEE +VF EFSKKCA RWKTMS+KEKKRF
Sbjct: 246 MPRGKDSKPRGRMTAYAFFVQTCRQEHKKKHPEEKIVFREFSKKCAMRWKTMSDKEKKRF 305

Query: 61  HEMADKDKKRYDTEMQSYTPPAGEK------------------------------RGKIK 90
           HEMA+KDKKRYD EMQ+YTPP GE                               RGK+K
Sbjct: 306 HEMAEKDKKRYDAEMQNYTPPKGENKGRGKKRKHIKDHNAPKRSLSAFFWFCNDERGKVK 365

Query: 91  QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR--------S 142
             NPEYGVGDIAKELGKKW+D DP  K+KYE MAEKDKARYE+EMTAYK +         
Sbjct: 366 MLNPEYGVGDIAKELGKKWSDADPETKSKYEAMAEKDKARYEREMTAYKKKMQDGAPVVG 425

Query: 143 VAPVN------EEADEEDDE 156
            AP N      EE  +EDDE
Sbjct: 426 GAPANTVKSDSEEEWKEDDE 445

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332025497|gb|EGI65660.1| High mobility group protein DSP1 [Acromyrmex echinatior]

 Score =  225 bits (574), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 114/169 (67%), Positives = 124/169 (73%), Gaps = 30/169 (17%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           MP+ KD KPRGRMTAYAFFVQ CR+EHKKKHPEE +VF EFSKKCA RWKTMS+ EKKRF
Sbjct: 103 MPRGKDSKPRGRMTAYAFFVQTCRQEHKKKHPEEKIVFREFSKKCAMRWKTMSDIEKKRF 162

Query: 61  HEMADKDKKRYDTEMQSYTPPAGEK------------------------------RGKIK 90
           HEMA+KDKKRYDTEMQ+YTPP GE                               RGK+K
Sbjct: 163 HEMAEKDKKRYDTEMQNYTPPKGENKGRGKKRKHIKDHNAPKRSLSAFFWFCNDERGKVK 222

Query: 91  QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
             NPEYGVGDIAKELGKKW+D DP  K+KYE MAEKDKARYE+EMTAYK
Sbjct: 223 MLNPEYGVGDIAKELGKKWSDADPETKSKYEAMAEKDKARYEREMTAYK 271

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350402647|ref|XP_003486555.1| PREDICTED: high mobility group protein DSP1-like [Bombus impatiens]

 Score =  225 bits (573), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 122/199 (61%), Positives = 136/199 (68%), Gaps = 43/199 (21%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           MP+ KD KPRGRMTAYAFFVQ CR+EHKKKHPEE +VF EFSKKCA RWKTMS+KEKKRF
Sbjct: 258 MPRGKDSKPRGRMTAYAFFVQTCRQEHKKKHPEEKIVFREFSKKCAMRWKTMSDKEKKRF 317

Query: 61  HEMADKDKKRYDTEMQSYTPPAGEK------------------------------RGKIK 90
           HEMA+KDKKRYD EMQ+YTPP GE                               RGK+K
Sbjct: 318 HEMAEKDKKRYDAEMQNYTPPKGESKGRGKKRKHIKDHNAPKRSLSAFFWFCNDERGKVK 377

Query: 91  QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN--RSVAPV-- 146
             NPE+GVGDIAKELGKKW+D DP  K+KYE MAEKDKARYE+EMTAYK   +  APV  
Sbjct: 378 MLNPEFGVGDIAKELGKKWSDADPETKSKYEAMAEKDKARYEREMTAYKKKMKDGAPVVG 437

Query: 147 ---------NEEADEEDDE 156
                    +EE  +EDDE
Sbjct: 438 VPANTVKSDSEEEYKEDDE 456

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025638|ref|XP_003696576.1| PREDICTED: high mobility group protein DSP1-like [Apis florea]

 Score =  224 bits (572), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 122/199 (61%), Positives = 136/199 (68%), Gaps = 43/199 (21%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           MP+ KD KPRGRMTAYAFFVQ CR+EHKKKHPEE +VF EFSKKCA RWKTMS+KEKKRF
Sbjct: 222 MPRGKDSKPRGRMTAYAFFVQTCRQEHKKKHPEEKIVFREFSKKCAMRWKTMSDKEKKRF 281

Query: 61  HEMADKDKKRYDTEMQSYTPPAGEK------------------------------RGKIK 90
           HEMA+KDKKRYD EMQ+YTPP GE                               RGK+K
Sbjct: 282 HEMAEKDKKRYDAEMQNYTPPKGESKGRGKKRKHIKDHNAPKRSLSAFFWFCNDERGKVK 341

Query: 91  QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN--RSVAPV-- 146
             NPE+GVGDIAKELGKKW+D DP  K+KYE MAEKDKARYE+EMTAYK   +  APV  
Sbjct: 342 MLNPEFGVGDIAKELGKKWSDADPETKSKYEAMAEKDKARYEREMTAYKKKMKDGAPVVG 401

Query: 147 ---------NEEADEEDDE 156
                    +EE  +EDDE
Sbjct: 402 VPANTVKSDSEEEYKEDDE 420

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322797840|gb|EFZ19748.1| hypothetical protein SINV_09636 [Solenopsis invicta]

 Score =  224 bits (570), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 114/171 (66%), Positives = 125/171 (73%), Gaps = 30/171 (17%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           MP+ KD KPRGRMTAYAFFVQ CR+EHKKKHPEE +VF EFSKKCA RWKTMS+ EKKRF
Sbjct: 1   MPRGKDSKPRGRMTAYAFFVQTCRQEHKKKHPEEKIVFREFSKKCAMRWKTMSDIEKKRF 60

Query: 61  HEMADKDKKRYDTEMQSYTPPAGEK------------------------------RGKIK 90
           HEMA+KDKKRYDTEMQ+YTPP GE                               RGK+K
Sbjct: 61  HEMAEKDKKRYDTEMQNYTPPKGENKGRGKKRKHIKDHNAPKRSLSAFFWFCNDERGKVK 120

Query: 91  QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
             NPEYGVGDIAKELGKKW+D DP  K+KYE MAEKDKARYE+EMTAYK +
Sbjct: 121 MLNPEYGVGDIAKELGKKWSDADPETKSKYEAMAEKDKARYEREMTAYKKK 171

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307191141|gb|EFN74839.1| High mobility group protein DSP1 [Camponotus floridanus]

 Score =  223 bits (568), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 121/202 (59%), Positives = 135/202 (66%), Gaps = 46/202 (22%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           MP+ KD KPRGRMTAYAFFVQ CR+EHKKKHPEE +VF EFSKKCA RWKTMS+ EKKRF
Sbjct: 104 MPRGKDSKPRGRMTAYAFFVQTCRQEHKKKHPEEKIVFREFSKKCAMRWKTMSDIEKKRF 163

Query: 61  HEMADKDKKRYDTEMQSYTPPAGEK------------------------------RGKIK 90
           HEMA+KDKKRYD EMQ+YTPP GE                               RGK+K
Sbjct: 164 HEMAEKDKKRYDAEMQNYTPPKGENKGRGKKRKHIKDHNAPKRSLSAFFWFCNDERGKVK 223

Query: 91  QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK----------- 139
             NPEYGVGDIAKELGKKW+D DP  K+KYE MAEKDKARYE+EMTAYK           
Sbjct: 224 MLNPEYGVGDIAKELGKKWSDADPETKSKYEAMAEKDKARYEREMTAYKKKIQNDGAPMM 283

Query: 140 -----NRSVAPVNEEADEEDDE 156
                N++V   +EE  +EDDE
Sbjct: 284 GGAPANQTVKSDSEEEWKEDDE 305

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156552179|ref|XP_001605958.1| PREDICTED: high mobility group protein DSP1 [Nasonia vitripennis]

 Score =  222 bits (565), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 112/166 (67%), Positives = 121/166 (72%), Gaps = 31/166 (18%)

Query: 5   KDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMA 64
           K  KPRGRMTAYAFFVQ CR+EHKKKHP+EN+VF EFSKKCA RWKTMS+KEKKRFHEMA
Sbjct: 236 KSTKPRGRMTAYAFFVQTCRQEHKKKHPDENIVFQEFSKKCALRWKTMSDKEKKRFHEMA 295

Query: 65  DKDKKRYDTEMQSYTPPAGEK-------------------------------RGKIKQDN 93
           +KDKKRYDTEMQSY PP GEK                               RGK+K  N
Sbjct: 296 EKDKKRYDTEMQSYIPPKGEKVTGRGKKRKHIKDPNAPKRSLSAFFWFCNDERGKVKMLN 355

Query: 94  PEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           PEYGVGDIAKELGKKW+D  P +K KYE MAEKDKARYE+EMTAYK
Sbjct: 356 PEYGVGDIAKELGKKWSDAGPELKGKYEAMAEKDKARYEREMTAYK 401

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189236107|ref|XP_973934.2| PREDICTED: similar to High mobility group protein DSP1 (Protein dorsal switch 1) [Tribolium castaneum]

 Score =  221 bits (563), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 111/173 (64%), Positives = 129/173 (74%), Gaps = 30/173 (17%)

Query: 1   MPKEK-DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKR 59
           MP+ K D +PRGRMTAYAFFVQ CREEHKKKHPEENVVFAEFSKKCAERWKTM +KEKKR
Sbjct: 298 MPRAKADSRPRGRMTAYAFFVQTCREEHKKKHPEENVVFAEFSKKCAERWKTMLDKEKKR 357

Query: 60  FHEMADKDKKRYDTEMQSYTPPAGEK-----------------------------RGKIK 90
           FHEMA+ DKKRYD EM++YTPP GEK                             R K+K
Sbjct: 358 FHEMAENDKKRYDDEMKNYTPPKGEKQRGKKRKQVKDPNAPKRSLSAFFWFSNDERAKVK 417

Query: 91  QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV 143
             NPE+GVGDIAKELG++WAD +P +K+KYE +A+KDKARYEKEMTAYK +++
Sbjct: 418 SQNPEFGVGDIAKELGRRWADAEPEMKSKYEALADKDKARYEKEMTAYKKKNM 470

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

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	156
UNIPROTKB|F1N927	214	HMGB1 "High mobility group pro	0.596	0.434	0.623	3.6e-40
UNIPROTKB|Q9YH06	215	HMG1 "High mobility group 1 pr	0.596	0.432	0.623	3.6e-40
ZFIN|ZDB-GENE-030131-8480	165	hmgb1b "high-mobility group bo	0.903	0.854	0.523	2.9e-39
UNIPROTKB|P17741	210	HMGB2 "High mobility group pro	0.891	0.661	0.496	3.2e-39
UNIPROTKB|D4A2L7	135	D4A2L7 "Uncharacterized protei	0.865	1.0	0.510	9.2e-36
ZFIN|ZDB-GENE-050417-290	198	hmgb3b "high-mobility group bo	0.576	0.454	0.576	6.3e-35
UNIPROTKB|F1NPU8	207	HMGB2 "High mobility group pro	0.596	0.449	0.655	9e-34
FB|FBgn0011764	393	Dsp1 "Dorsal switch protein 1"	0.564	0.223	0.712	9.5e-34
UNIPROTKB|E2QY30	210	HMGB2 "Uncharacterized protein	0.596	0.442	0.655	3e-33
RGD|1563668	211	RGD1563668 "similar to High mo	0.891	0.658	0.472	4.1e-33

UNIPROTKB|F1N927 HMGB1 "High mobility group protein B1" [Gallus gallus (taxid:9031)]

 Score = 322 (118.4 bits), Expect = 3.6e-40, Sum P(2) = 3.6e-40
 Identities = 58/93 (62%), Positives = 71/93 (76%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F
Sbjct:     1 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSSKEKGKF 60

Query:    61 HEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDN 93
              +MA  DK RY+ EM++Y PP GE + K K  N
Sbjct:    61 EDMAKADKLRYEKEMKNYVPPKGETKKKFKDPN 93

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

GO:0002437 "inflammatory response to antigenic stimulus" evidence=IEA

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006288 "base-excision repair, DNA ligation" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0010858 "calcium-dependent protein kinase regulator activity" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0017055 "negative regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0030295 "protein kinase activator activity" evidence=IEA

GO:0030324 "lung development" evidence=IEA

GO:0033151 "V(D)J recombination" evidence=IEA

GO:0043005 "neuron projection" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0045639 "positive regulation of myeloid cell differentiation" evidence=IEA

GO:0045819 "positive regulation of glycogen catabolic process" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0051384 "response to glucocorticoid stimulus" evidence=IEA

GO:0070491 "repressing transcription factor binding" evidence=IEA

GO:2000426 "negative regulation of apoptotic cell clearance" evidence=IEA

UNIPROTKB|Q9YH06 HMG1 "High mobility group 1 protein" [Gallus gallus (taxid:9031)]

 Score = 322 (118.4 bits), Expect = 3.6e-40, Sum P(2) = 3.6e-40
 Identities = 58/93 (62%), Positives = 71/93 (76%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F
Sbjct:     1 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSSKEKGKF 60

Query:    61 HEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDN 93
              +MA  DK RY+ EM++Y PP GE + K K  N
Sbjct:    61 EDMAKADKLRYEKEMKNYVPPKGETKKKFKDPN 93

GO:0003677 "DNA binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001654 "eye development" evidence=IEA

GO:0002437 "inflammatory response to antigenic stimulus" evidence=IEA

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

GO:0005125 "cytokine activity" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006288 "base-excision repair, DNA ligation" evidence=IEA

GO:0009986 "cell surface" evidence=IEA

GO:0010858 "calcium-dependent protein kinase regulator activity" evidence=IEA

GO:0017053 "transcriptional repressor complex" evidence=IEA

GO:0017055 "negative regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0030295 "protein kinase activator activity" evidence=IEA

GO:0030324 "lung development" evidence=IEA

GO:0033151 "V(D)J recombination" evidence=IEA

GO:0043005 "neuron projection" evidence=IEA

GO:0043065 "positive regulation of apoptotic process" evidence=IEA

GO:0043280 "positive regulation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0045639 "positive regulation of myeloid cell differentiation" evidence=IEA

GO:0045819 "positive regulation of glycogen catabolic process" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0051384 "response to glucocorticoid stimulus" evidence=IEA

GO:0070491 "repressing transcription factor binding" evidence=IEA

GO:2000426 "negative regulation of apoptotic cell clearance" evidence=IEA

ZFIN|ZDB-GENE-030131-8480 hmgb1b "high-mobility group box 1b" [Danio rerio (taxid:7955)]

 Score = 419 (152.6 bits), Expect = 2.9e-39, P = 2.9e-39
 Identities = 78/149 (52%), Positives = 105/149 (70%)

Query:     8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
             KPRG+M++YA+FVQ CREEHKKKHPE +V F+EFSKKC+ERWKTMS KEK +F +MA +D
Sbjct:     7 KPRGKMSSYAYFVQTCREEHKKKHPEASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKQD 66

Query:    68 KKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKD 127
             K RY+ EM++Y PP GE        NP   +GDIAK+LG+ W      VK  YE+ A K 
Sbjct:    67 KVRYEREMKNYIPPKGE--------NPGLSIGDIAKKLGEMWNSSSAEVKQPYEKKAAKL 118

Query:   128 KARYEKEMTAYKNRSVAPVNEEADEEDDE 156
             K +Y+K++  Y+ + +A  +++   EDDE
Sbjct:   119 KEKYDKDIALYRTKGIAGFSKKEGGEDDE 147

GO:0005634 "nucleus" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P17741 HMGB2 "High mobility group protein B2" [Sus scrofa (taxid:9823)]

 Score = 398 (145.2 bits), Expect = 3.2e-39, Sum P(2) = 3.2e-39
 Identities = 81/163 (49%), Positives = 104/163 (63%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    KPRG+M++YAFFVQ CREEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F
Sbjct:     1 MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKF 60

Query:    61 HEMADKDKKRYDTEMQSYTPPAGEKRGK------------------------IKQDNPEY 96
              +MA  DK RYD EM++Y PP G+K+GK                        IK ++P  
Sbjct:    61 EDMAKSDKARYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGL 120

Query:    97 GVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
              +GD AK+LG+ W++     K  YEQ A K K +YEK++ AY+
Sbjct:   121 SIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYR 163

GO:0006265 "DNA topological change" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0008301 "DNA binding, bending" evidence=ISS;IDA

GO:0051103 "DNA ligation involved in DNA repair" evidence=IDA

GO:0048471 "perinuclear region of cytoplasm" evidence=ISS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0000793 "condensed chromosome" evidence=ISS

GO:0006288 "base-excision repair, DNA ligation" evidence=ISS

UNIPROTKB|D4A2L7 D4A2L7 "Uncharacterized protein" [Rattus norvegicus (taxid:10116)]

 Score = 386 (140.9 bits), Expect = 9.2e-36, P = 9.2e-36
 Identities = 73/143 (51%), Positives = 98/143 (68%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F
Sbjct:     1 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF 60

Query:    61 HEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKY 120
              +MA  DK RY+ EM++Y PP GE        +P   +GD+ K+LG+ W +     K  Y
Sbjct:    61 EDMAKADKARYEREMKTYIPPKGE--------HPGLSIGDVVKKLGEMWNNTAADDKQPY 112

Query:   121 EQMAEKDKARYEKEMTAYKNRSV 143
             E+ A K K +YEK++ AY+ + +
Sbjct:   113 EKKAAKLKEKYEKDIAAYRAKGM 135

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

ZFIN|ZDB-GENE-050417-290 hmgb3b "high-mobility group box 3b" [Danio rerio (taxid:7955)]

 Score = 278 (102.9 bits), Expect = 6.3e-35, Sum P(2) = 6.3e-35
 Identities = 53/92 (57%), Positives = 67/92 (72%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    KP+G+M+AYA+FV+ CREEH KK+P   V F+EFSKKC+ERWKTMS KEK +F
Sbjct:     1 MAKGDPGKPKGKMSAYAYFVKTCREEHNKKNPGVTVNFSEFSKKCSERWKTMSPKEKTKF 60

Query:    61 HEMADKDKKRYDTEMQSYTPPAGEKRGKIKQD 92
              ++A +DK RYD EM  Y P  G+K  K K+D
Sbjct:    61 EDLAKQDKARYDQEMMHYNP--GKKGRKQKKD 90

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

UNIPROTKB|F1NPU8 HMGB2 "High mobility group protein B2" [Gallus gallus (taxid:9031)]

 Score = 337 (123.7 bits), Expect = 9.0e-34, Sum P(2) = 9.0e-34
 Identities = 61/93 (65%), Positives = 73/93 (78%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    KPRG+M++YA+FVQ CREEHKKKHP+ +V FAEFS+KC+ERWKTMS KEK +F
Sbjct:     1 MGKGDPNKPRGKMSSYAYFVQTCREEHKKKHPDSSVNFAEFSRKCSERWKTMSSKEKGKF 60

Query:    61 HEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDN 93
              EMA  DK RYD EM++Y PP GEK+GK K  N
Sbjct:    61 EEMAKGDKARYDREMKNYVPPKGEKKGKKKDPN 93

GO:0005634 "nucleus" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0001938 "positive regulation of endothelial cell proliferation" evidence=IEA

GO:0003684 "damaged DNA binding" evidence=IEA

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

GO:0005615 "extracellular space" evidence=IEA

GO:0006288 "base-excision repair, DNA ligation" evidence=IEA

GO:0007289 "spermatid nucleus differentiation" evidence=IEA

GO:0008301 "DNA binding, bending" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0032075 "positive regulation of nuclease activity" evidence=IEA

GO:0042056 "chemoattractant activity" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0045648 "positive regulation of erythrocyte differentiation" evidence=IEA

GO:0045654 "positive regulation of megakaryocyte differentiation" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0048545 "response to steroid hormone stimulus" evidence=IEA

GO:0050786 "RAGE receptor binding" evidence=IEA

GO:0060326 "cell chemotaxis" evidence=IEA

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

FB|FBgn0011764 Dsp1 "Dorsal switch protein 1" [Drosophila melanogaster (taxid:7227)]

 Score = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 67/94 (71%), Positives = 78/94 (82%)

Query:     6 DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMAD 65
             D KPRGRMTAYA+FVQ CREEHKKKHP+E V+FAEFS+KCAERWKTM +KEKKRFHEMA+
Sbjct:   176 DAKPRGRMTAYAYFVQTCREEHKKKHPDETVIFAEFSRKCAERWKTMVDKEKKRFHEMAE 235

Query:    66 KDKKRYDTEMQSYTPPAG------EKRGKIKQDN 93
             KDK+RY+ EMQ+Y PP G      +KR +IK  N
Sbjct:   236 KDKQRYEAEMQNYVPPKGAVVGRGKKRKQIKDPN 269

GO:0005634 "nucleus" evidence=IC;IDA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IMP;IDA

GO:0043388 "positive regulation of DNA binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0017025 "TBP-class protein binding" evidence=IPI

GO:0017055 "negative regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=IDA

GO:0032502 "developmental process" evidence=IMP

GO:0008134 "transcription factor binding" evidence=IPI

GO:0006338 "chromatin remodeling" evidence=IMP

GO:0007379 "segment specification" evidence=IMP

GO:0008301 "DNA binding, bending" evidence=IDA

GO:0035218 "leg disc development" evidence=IMP

GO:0008348 "negative regulation of antimicrobial humoral response" evidence=IGI;IMP

GO:0005700 "polytene chromosome" evidence=IDA

UNIPROTKB|E2QY30 HMGB2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 340 (124.7 bits), Expect = 3.0e-33, Sum P(2) = 3.0e-33
 Identities = 61/93 (65%), Positives = 73/93 (78%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    KPRG+M++YAFFVQ CREEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F
Sbjct:     1 MGKGDPNKPRGKMSSYAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKF 60

Query:    61 HEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDN 93
              +MA  DK RYD EM++Y PP G+K+GK K  N
Sbjct:    61 EDMAKSDKARYDREMKNYVPPKGDKKGKKKDPN 93

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

GO:0060326 "cell chemotaxis" evidence=IEA

GO:0050786 "RAGE receptor binding" evidence=IEA

GO:0048545 "response to steroid hormone stimulus" evidence=IEA

GO:0048471 "perinuclear region of cytoplasm" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0045654 "positive regulation of megakaryocyte differentiation" evidence=IEA

GO:0045648 "positive regulation of erythrocyte differentiation" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0042056 "chemoattractant activity" evidence=IEA

GO:0032075 "positive regulation of nuclease activity" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0008301 "DNA binding, bending" evidence=IEA

GO:0007289 "spermatid nucleus differentiation" evidence=IEA

GO:0006288 "base-excision repair, DNA ligation" evidence=IEA

GO:0005615 "extracellular space" evidence=IEA

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

GO:0003684 "damaged DNA binding" evidence=IEA

GO:0001938 "positive regulation of endothelial cell proliferation" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

RGD|1563668 RGD1563668 "similar to High mobility group protein 1 (HMG-1)" [Rattus norvegicus (taxid:10116)]

 Score = 361 (132.1 bits), Expect = 4.1e-33, P = 4.1e-33
 Identities = 77/163 (47%), Positives = 102/163 (62%)

Query:     1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
             M K    K RG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F
Sbjct:     1 MGKGDPKKLRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF 60

Query:    61 HEMADKDKKRYDTEMQSY------------------TPPAG------EKRGKIKQDNPEY 96
              +MA  DK RY+ EM++Y                  TPP+       E R KIK ++P  
Sbjct:    61 EDMAKADKARYEREMKTYISPKGETKKKFKDPNAPKTPPSAFFLFCSEYRPKIKGEHPGL 120

Query:    97 GVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
              +GD+ K+LG+ W +     K  YE+MA K K +YEK++ AY+
Sbjct:   121 SIGDVVKKLGEMWTNTAADDKQPYEKMAAKLKEKYEKDIAAYR 163

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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)
P17741	HMGB2_PIG	No assigned EC number	0.5	0.8461	0.6285	yes	N/A
P30681	HMGB2_MOUSE	No assigned EC number	0.4935	0.8461	0.6285	yes	N/A
P52925	HMGB2_RAT	No assigned EC number	0.4670	0.9166	0.6809	yes	N/A
P40644	HMGH_STRPU	No assigned EC number	0.4567	0.8653	0.675	yes	N/A
P40673	HMGB2_BOVIN	No assigned EC number	0.5	0.8461	0.6315	yes	N/A
P26583	HMGB2_HUMAN	No assigned EC number	0.5	0.8461	0.6315	yes	N/A
P26584	HMGB2_CHICK	No assigned EC number	0.4968	0.8653	0.6521	yes	N/A
Q24537	HMG2_DROME	No assigned EC number	0.6280	0.8589	0.3409	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	156
pfam09011	69	pfam09011, DUF1898, Domain of unknown function (DU	2e-14
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	1e-13
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	3e-12
smart00398	70	smart00398, HMG, high mobility group	1e-10
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	3e-10
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	1e-09
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	2e-09
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	4e-09
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	1e-08
smart00398	70	smart00398, HMG, high mobility group	1e-07
cd01389	77	cd01389, MATA_HMG-box, MATA_HMG-box, class I membe	5e-05
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	1e-04
COG5648	211	COG5648, NHP6B, Chromatin-associated proteins cont	2e-04
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	7e-04
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	8e-04
cd01388	72	cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I	0.003

>gnl|CDD|204115 pfam09011, DUF1898, Domain of unknown function (DUF1898)

 Score = 63.6 bits (155), Expect = 2e-14
 Identities = 36/68 (52%), Positives = 48/68 (70%), Gaps = 1/68 (1%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KP+ +  AY FFVQ  R E K++ P+     AEFSK C+E+WK MSE+EK+++ E A +D
Sbjct: 3  KPKAKRNAYFFFVQTMRPELKREGPQVPG-VAEFSKLCSEKWKAMSEEEKEKYEEKARED 61

Query: 68 KKRYDTEM 75
          KKRYD EM
Sbjct: 62 KKRYDREM 69

This domain is predominantly found in Maelstrom homolog proteins. It has no known function. Length = 69

>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 = 61.5 bits (150), Expect = 1e-13
 Identities = 29/68 (42%), Positives = 47/68 (69%), Gaps = 2/68 (2%)

Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
          P+  ++AY  F Q  R + KK++P+ +V   E +K   E+WK +SE+EKK++ E A+KDK
Sbjct: 1  PKRPLSAYFLFSQEQRPKLKKENPDASV--TEVTKILGEKWKELSEEEKKKYEEKAEKDK 58

Query: 69 KRYDTEMQ 76
          +RY+ EM+
Sbjct: 59 ERYEKEMK 66

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 = 58.0 bits (141), Expect = 3e-12
 Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 2/67 (2%)

Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
          P+  ++AY  F Q  R E K ++P  +    E SK   E WK++SE+EKK++ E A+KDK
Sbjct: 1  PKRPLSAYFLFSQEHRAEVKAENPGLS--VGEISKILGEMWKSLSEEEKKKYEEKAEKDK 58

Query: 69 KRYDTEM 75
          +RY+ EM
Sbjct: 59 ERYEKEM 65

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

>gnl|CDD|197700 smart00398, HMG, high mobility group

 Score = 54.2 bits (131), Expect = 1e-10
 Identities = 32/71 (45%), Positives = 45/71 (63%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KP+  M+A+  F Q  R + K ++P  ++  AE SKK  ERWK +SE+EK  + E A KD
Sbjct: 1  KPKRPMSAFMLFSQENRAKIKAENP--DLSNAEISKKLGERWKLLSEEEKAPYEEKAKKD 58

Query: 68 KKRYDTEMQSY 78
          K+RY+ EM  Y
Sbjct: 59 KERYEEEMPEY 69

Length = 70

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

 Score = 52.6 bits (127), Expect = 3e-10
 Identities = 27/52 (51%), Positives = 35/52 (67%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEM 135
           E R ++K +NP   VG+I+K LG+ W  +    K KYE+ AEKDK RYEKEM
Sbjct: 14  EHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM 65

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

>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 = 51.1 bits (123), Expect = 1e-09
 Identities = 27/52 (51%), Positives = 38/52 (73%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEM 135
           E+R K+K++NP+  V ++ K LG+KW ++    K KYE+ AEKDK RYEKEM
Sbjct: 14  EQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM 65

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|189580 pfam00505, HMG_box, HMG (high mobility group) box

 Score = 50.7 bits (122), Expect = 2e-09
 Identities = 27/56 (48%), Positives = 37/56 (66%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           E+R K+K +NP     +I+K LG+KW ++    K  YE+ AEK+KARYEK   AYK
Sbjct: 14  EQRAKLKAENPGLKNAEISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69

Length = 69

>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 2/66 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
          ++A+  F Q  R + K ++P      AE SK   E+WK +SE+EKK + E A+K+K RY+
Sbjct: 5  LSAFFLFSQEQRAKLKAENPGLKN--AEISKILGEKWKNLSEEEKKPYEEKAEKEKARYE 62

Query: 73 TEMQSY 78
              +Y
Sbjct: 63 KAYPAY 68

Length = 69

>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 35/140 (25%), Positives = 70/140 (50%), Gaps = 15/140 (10%)

Query: 9   PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
           P+  ++AY  +    R+E +K++P+  + F E  K  +E+WK ++++EK+ +++ A+ D+
Sbjct: 71  PKRPLSAYFLYSAENRDEIRKENPK--LTFGEVGKLLSEKWKELTDEEKEPYYKEANSDR 128

Query: 69  KRYDTEMQSYTP--PAGEKRGKIKQDNPE-----------YGVGDIAKELGKKWADVDPS 115
           +RY  E + Y    P     G   ++ P+             + +  K + K W+++D S
Sbjct: 129 ERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDES 188

Query: 116 VKTKYEQMAEKDKARYEKEM 135
            K KY    +K K  Y+   
Sbjct: 189 KKKKYIDKYKKLKEEYDSFY 208

Length = 211

>gnl|CDD|197700 smart00398, HMG, high mobility group

 Score = 46.2 bits (110), Expect = 1e-07
 Identities = 26/56 (46%), Positives = 37/56 (66%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           E R KIK +NP+    +I+K+LG++W  +    K  YE+ A+KDK RYE+EM  YK
Sbjct: 15  ENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

Length = 70

>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 39.2 bits (92), Expect = 5e-05
 Identities = 18/56 (32%), Positives = 34/56 (60%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           +K  ++K +NP     +I++ +G+ W    P VK  Y+++AE++K R+ +E   YK
Sbjct: 15  DKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYK 70

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. Length = 77

>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 2/90 (2%)

Query: 53  SEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWA 110
             K   R ++   KD       + +Y   A EKR +I  +NPE    V  + K +G+ W 
Sbjct: 5   QGKVLVRKNKRKKKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWN 64

Query: 111 DVDPSVKTKYEQMAEKDKARYEKEMTAYKN 140
            +    K  YE+ A++DK RYEKE   Y  
Sbjct: 65  KLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Length = 94

>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 25/102 (24%), Positives = 45/102 (44%)

Query: 38  FAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYG 97
             E  K   +      +K K +      KD       + +Y   + E R +I+++NP+  
Sbjct: 38  LVELEKPLQQLLTKPRKKTKSKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLT 97

Query: 98  VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
            G++ K L +KW ++    K  Y + A  D+ RY++E   Y 
Sbjct: 98  FGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYN 139

Length = 211

>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional

 Score = 36.8 bits (85), Expect = 7e-04
 Identities = 24/70 (34%), Positives = 36/70 (51%)

Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
          P+  ++AY FF +  R E   ++PE     A   K   E W  +SE+EK  + + A +DK
Sbjct: 23 PKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDK 82

Query: 69 KRYDTEMQSY 78
           RY+ E   Y
Sbjct: 83 VRYEKEKAEY 92

Length = 94

>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 35.7 bits (83), Expect = 8e-04
 Identities = 18/58 (31%), Positives = 26/58 (44%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
             R K+ Q+ P      I+K LG +W  +    K  Y + A+K K  + K    YK R
Sbjct: 15  RHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKWR 72

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. Length = 72

>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins

 Score = 34.2 bits (79), Expect = 0.003
 Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 4/60 (6%)

Query: 13 MTAYAFFVQVCREEHKKKHPE-ENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRY 71
          M A+  F +  R +  +++P  EN      SK   +RWK +S +EK+ ++E A K K+ +
Sbjct: 6  MNAFMLFSKRHRRKVLQEYPLKEN---RAISKILGDRWKALSNEEKQPYYEEAKKLKELH 62

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. Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	156
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.93
PTZ00199	94	high mobility group protein; Provisional	99.89
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.82
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.8
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.8
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.8
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.79
smart00398	70	HMG high mobility group.	99.78
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.73
KOG0381|consensus	96		99.66
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	99.54
KOG0527|consensus	331		99.53
KOG0526|consensus	615		99.52
PTZ00199	94	high mobility group protein; Provisional	99.5
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	99.48
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	99.42
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	99.37
KOG0527|consensus	331		99.35
smart00398	70	HMG high mobility group.	99.34
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	99.27
KOG0381|consensus	96		99.22
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	99.16
KOG3248|consensus	421		99.13
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.11
KOG4715|consensus	410		99.1
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.83
KOG0526|consensus	615		98.79
KOG0528|consensus	511		98.61
KOG0528|consensus	511		98.34
KOG4715|consensus	410		98.29
KOG2746|consensus	683		98.29
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.13
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	97.94
KOG3248|consensus	421		97.89
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	97.39
KOG2746|consensus	683		96.77
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	96.57
PF11304	107	DUF3106: Protein of unknown function (DUF3106); In	94.55
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	94.5
PF06244	122	DUF1014: Protein of unknown function (DUF1014); In	93.07
PF04769	201	MAT_Alpha1: Mating-type protein MAT alpha 1; Inter	93.02
PF08073	55	CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958	92.12
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	92.04
PRK15117	211	ABC transporter periplasmic binding protein MlaC;	88.89
PF05494	170	Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro:	80.48
PF04690	170	YABBY: YABBY protein; InterPro: IPR006780 YABBY pr	80.46

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=99.93  E-value=4.8e-26  Score=166.21  Aligned_cols=132  Identities=27%  Similarity=0.495  Sum_probs=121.7

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPA   82 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~   82 (156)
                      +++||.||||+|||++|+.++|..+...+|++++  ++|++.+|+.|++||+++|++|...|..++.+|.+++..|+...
T Consensus        65 k~dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~--~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~  142 (211)
T COG5648          65 KKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTF--GEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKL  142 (211)
T ss_pred             hcCCCCCCCchhHHHHHHHHHHHHHHHhCCCCCh--HHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhccc
Confidence            5899999999999999999999999999999965  99999999999999999999999999999999999999997533


Q ss_pred             cc-------------ccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          83 GE-------------KRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMT  136 (156)
Q Consensus        83 ~~-------------~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~  136 (156)
                      ..             .++.+.+.+|..+..+.++.++..|.+|+++-|.+|++.+.+++..|...++
T Consensus       143 ~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         143 PNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             CCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            22             2778888899999999999999999999999999999999999999987654

>PTZ00199 high mobility group protein; Provisional

Probab=99.89  E-value=3.1e-23  Score=137.02  Aligned_cols=77  Identities=32%  Similarity=0.542  Sum_probs=73.0

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      ++||+.||||+|||+|||.++|..|..+||+++.++++|+++||++|++||+++|.+|.++|..++.+|..++.+|.
T Consensus        17 ~kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~   93 (94)
T PTZ00199         17 KKDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA   93 (94)
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            57999999999999999999999999999998755699999999999999999999999999999999999998884

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

Probab=99.82  E-value=4.9e-20  Score=117.51  Aligned_cols=71  Identities=23%  Similarity=0.346  Sum_probs=67.8

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      +||||+|||+||+++.|..|+.+||+++.  .+|+++||.+|+.||+++|++|.++|..++.+|..++..|.-
T Consensus         1 ~~kRP~naf~lf~~~~r~~~~~~~p~~~~--~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky   71 (77)
T cd01389           1 KIPRPRNAFILYRQDKHAQLKTENPGLTN--NEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKY   71 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcc
Confidence            48999999999999999999999999875  899999999999999999999999999999999999999864

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.

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

Probab=99.80  E-value=1.8e-19  Score=113.47  Aligned_cols=69  Identities=26%  Similarity=0.363  Sum_probs=66.0

Q ss_pred             CCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         9 PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      .|||+|||++||+++|..++.+||++++  .+|+++||.+|+.||+++|++|.++|..++.+|.+++..|.
T Consensus         2 iKrP~naf~~F~~~~r~~~~~~~p~~~~--~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388           2 IKRPMNAFMLFSKRHRRKVLQEYPLKEN--RAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            5899999999999999999999999876  89999999999999999999999999999999999998874

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.

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

Probab=99.80  E-value=1.6e-19  Score=111.50  Aligned_cols=65  Identities=45%  Similarity=0.791  Sum_probs=62.4

Q ss_pred             CCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhcccc
Q psy3264           9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEM   75 (156)
Q Consensus         9 PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~   75 (156)
                      ||+|+|||++|++++|..+...||+++.  .+|++.||..|++||+++|++|.+.|..++.+|..+|
T Consensus         1 Pkrp~saf~~f~~~~r~~~~~~~p~~~~--~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           1 PKRPLSAYFLFSQEQRPKLKKENPDASV--TEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999999999865  8999999999999999999999999999999999876

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.

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

Probab=99.80  E-value=1.1e-19  Score=114.84  Aligned_cols=71  Identities=38%  Similarity=0.701  Sum_probs=61.7

Q ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHh-CCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           6 DVKPRGRMTAYAFFVQVCREEHKKK-HPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         6 p~~PkrP~say~lF~~e~r~~~~~~-~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      |++||+|+|||+|||.+++..++.. ++...  +.++++.||..|++||++||.+|.++|+.++.+|..++..|
T Consensus         1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~--~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~   72 (73)
T PF09011_consen    1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQS--FREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEW   72 (73)
T ss_dssp             SSS--SSSSHHHHHHHHHHHHHHHHT-T-SS--HHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCHHHHHHHHHHHHHHHhcccCCC--HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            7899999999999999999999988 55443  58999999999999999999999999999999999998876

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 ....

>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=99.79  E-value=1.4e-19  Score=112.78  Aligned_cols=68  Identities=35%  Similarity=0.635  Sum_probs=63.5

Q ss_pred             CCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         9 PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      |+||+|||+|||.+++..++..||+++.  .+|+++||.+|++||+++|.+|.+.|..++..|..++..|
T Consensus         1 PkrP~~af~lf~~~~~~~~k~~~p~~~~--~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y   68 (69)
T PF00505_consen    1 PKRPPNAFMLFCKEKRAKLKEENPDLSN--KEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEY   68 (69)
T ss_dssp             SSSS--HHHHHHHHHHHHHHHHSTTSTH--HHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCHHHHHHHHHHHHHHHHhccccc--ccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            8999999999999999999999999985  9999999999999999999999999999999999988776

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=99.78  E-value=5.7e-19  Score=109.96  Aligned_cols=69  Identities=46%  Similarity=0.745  Sum_probs=66.1

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      +|++|+|||++|++++|..+..+||+++.  .+|++.||.+|+.||+++|+.|.+.|..++..|.+.+..|
T Consensus         1 ~pkrp~~~y~~f~~~~r~~~~~~~~~~~~--~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y   69 (70)
T smart00398        1 KPKRPMSAFMLFSQENRAKIKAENPDLSN--AEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEY   69 (70)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHHCcCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            69999999999999999999999999875  8999999999999999999999999999999999998877

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

Probab=99.73  E-value=1.5e-17  Score=102.35  Aligned_cols=65  Identities=46%  Similarity=0.753  Sum_probs=61.5

Q ss_pred             CCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhcccc
Q psy3264           9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEM   75 (156)
Q Consensus         9 PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~   75 (156)
                      |+||+|||++|+++.+..++..+|+++.  .+|++.||.+|+.||+++|..|.+.|...+..|.+.+
T Consensus         1 pkrp~~af~~f~~~~~~~~~~~~~~~~~--~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           1 PKRPLSAYFLFSQEHRAEVKAENPGLSV--GEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCcCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            8999999999999999999999999765  8999999999999999999999999999999998764

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

>KOG0381|consensus

Probab=99.66  E-value=3.4e-16  Score=103.63  Aligned_cols=72  Identities=31%  Similarity=0.567  Sum_probs=67.7

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccc-cCCC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQ-SYTP   80 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~-~~~~   80 (156)
                      +.|+||+|||++|+.+.+..++..||++++  .+|++++|.+|++|++++|.+|...|..++.+|..+|. .|..
T Consensus        21 ~~pkrp~sa~~~f~~~~~~~~k~~~p~~~~--~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~   93 (96)
T KOG0381|consen   21 QAPKRPLSAFFLFSSEQRSKIKAENPGLSV--GEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKA   93 (96)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            489999999999999999999999999776  89999999999999999999999999999999999998 6643

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

Probab=99.54  E-value=1.7e-15  Score=95.28  Aligned_cols=69  Identities=26%  Similarity=0.304  Sum_probs=64.9

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN  140 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~  140 (156)
                      .+.+++|+.+..+.++.++.+||++++++|++.||+.|+.||+++|++|.++|+.++++|.++++.|+-
T Consensus         3 KrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~y   71 (72)
T cd01388           3 KRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYKW   71 (72)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            467888888889999999999999999999999999999999999999999999999999999999863

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.

>KOG0527|consensus

Probab=99.53  E-value=1.5e-14  Score=114.29  Aligned_cols=76  Identities=26%  Similarity=0.407  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      ++...+.|||+||||+|.+..|.+|..++|++-+  .||+|.||.+|+.|+++||.+|++.|+..|..+.++...|.-
T Consensus        57 k~~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHN--SEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKY  132 (331)
T KOG0527|consen   57 KTSTDRIKRPMNAFMVWSQGQRRKLAKQNPKMHN--SEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKY  132 (331)
T ss_pred             CCCccccCCCcchhhhhhHHHHHHHHHhCcchhh--HHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCccc
Confidence            4566789999999999999999999999999976  999999999999999999999999999999999999999864

>KOG0526|consensus

Probab=99.52  E-value=7.8e-15  Score=119.84  Aligned_cols=71  Identities=34%  Similarity=0.637  Sum_probs=67.5

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      +|+||.||||+||||+|++..|..|+..  ++++  ++|.+.+|++|++||.  |++|.+.|+.++.+|+.+|..|.
T Consensus       530 ~kdpnapkra~sa~m~w~~~~r~~ik~d--gi~~--~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk  600 (615)
T KOG0526|consen  530 KKDPNAPKRATSAYMLWLNASRESIKED--GISV--GDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYK  600 (615)
T ss_pred             CCCCCCCccchhHHHHHHHhhhhhHhhc--CchH--HHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhc
Confidence            6899999999999999999999999987  6655  8999999999999999  99999999999999999999996

>PTZ00199 high mobility group protein; Provisional

Probab=99.50  E-value=1.3e-14  Score=95.87  Aligned_cols=73  Identities=36%  Similarity=0.590  Sum_probs=65.2

Q ss_pred             hhhhhccccccCCCCCccccccccccCCCCC--chhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          67 DKKRYDTEMQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        67 ~k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~--~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      +-..-.+.+.+|+.|..+.|..+..+||+++  +.+|+++||+.|+.||+++|.+|.++|+.++.+|..+|..|+
T Consensus        19 dp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~   93 (94)
T PTZ00199         19 DPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA   93 (94)
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3344556778888888888999999999986  799999999999999999999999999999999999999995

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

Probab=99.48  E-value=8.4e-15  Score=93.26  Aligned_cols=71  Identities=25%  Similarity=0.517  Sum_probs=65.9

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      .+.+++|+.+....+..++.+||++++++|+++||..|+.||+++|++|.++|+.++++|..+++.|+..-
T Consensus         3 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p   73 (77)
T cd01389           3 PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYTP   73 (77)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcccC
Confidence            45678888888888999999999999999999999999999999999999999999999999999998753

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.

>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=99.42  E-value=7e-14  Score=86.84  Aligned_cols=67  Identities=36%  Similarity=0.625  Sum_probs=59.7

Q ss_pred             cccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          73 TEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        73 ~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      +.++.|..+....++.++..||+++..+|++.||..|++||+++|++|.+.|+.++.+|..+++.|+
T Consensus         3 rP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    3 RPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             SS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3455666666777888999999999999999999999999999999999999999999999999995

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 ....

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

Probab=99.37  E-value=2.8e-13  Score=83.34  Aligned_cols=63  Identities=44%  Similarity=0.742  Sum_probs=58.1

Q ss_pred             cccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHH
Q psy3264          73 TEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEM  135 (156)
Q Consensus        73 ~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~  135 (156)
                      +.+..|..+..+.+..+...||++++.+|++.||..|+.||+++|.+|.+.|+.++.+|..+|
T Consensus         3 rp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390           3 RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            456677777778899999999999999999999999999999999999999999999999987

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.

>KOG0527|consensus

Probab=99.35  E-value=2.3e-13  Score=107.55  Aligned_cols=77  Identities=26%  Similarity=0.407  Sum_probs=72.4

Q ss_pred             hhhhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy3264          67 DKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV  143 (156)
Q Consensus        67 ~k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~  143 (156)
                      ...+.++.|++|..+....|.+|..+||.+.+.||+|.||..||.|+++||.||+++|++++..|.+|+.+|+.+-.
T Consensus        59 ~~~hIKRPMNAFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYKYRPR  135 (331)
T KOG0527|consen   59 STDRIKRPMNAFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYKYRPR  135 (331)
T ss_pred             CccccCCCcchhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcccccc
Confidence            45688899999999999999999999999999999999999999999999999999999999999999999987644

>smart00398 HMG high mobility group

Probab=99.34  E-value=5.7e-13  Score=82.62  Aligned_cols=67  Identities=40%  Similarity=0.703  Sum_probs=60.7

Q ss_pred             cccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          73 TEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        73 ~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      +.+..|+.+....++.+...||++++++|++.||..|+.||+++|.+|.++|+.++++|..++..|+
T Consensus         4 rp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        4 RPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4556666777777888999999999999999999999999999999999999999999999999884

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

Probab=99.27  E-value=1.8e-12  Score=81.63  Aligned_cols=66  Identities=27%  Similarity=0.543  Sum_probs=53.2

Q ss_pred             ccccCCCCCcccccccccc-CCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          74 EMQSYTPPAGEKRGKIKQD-NPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        74 ~~~~~~~~~~~~r~~~~~~-~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      ...+|..+....+..++.. .+..+..++++.|+..|++||++||.+|.+.|+.++.+|+.+|..|.
T Consensus         7 ~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen    7 PPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             SSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            3445555555666677666 66788999999999999999999999999999999999999999984

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 ....

>KOG0381|consensus

Probab=99.22  E-value=9.2e-12  Score=82.25  Aligned_cols=73  Identities=36%  Similarity=0.602  Sum_probs=65.1

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHH-HHHhcC
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMT-AYKNRS  142 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~-~~~~~~  142 (156)
                      ...+.+.+|..++...+..++..||++++.++++.+|++|++|++++|.+|...|..++++|..+|. .|+...
T Consensus        22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~~   95 (96)
T KOG0381|consen   22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKASL   95 (96)
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            4555666777777777899999999999999999999999999999999999999999999999999 887654

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

Probab=99.16  E-value=1.7e-11  Score=75.08  Aligned_cols=63  Identities=44%  Similarity=0.735  Sum_probs=57.2

Q ss_pred             cccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHH
Q psy3264          73 TEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEM  135 (156)
Q Consensus        73 ~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~  135 (156)
                      +.+..|+.+..+.+..+...+|+++..+|++.||..|+.||+++|.+|.++|+.++.+|..++
T Consensus         3 rp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           3 RPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            456667777777888899999999999999999999999999999999999999999999875

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

>KOG3248|consensus

Probab=99.13  E-value=9.3e-11  Score=91.51  Aligned_cols=70  Identities=14%  Similarity=0.313  Sum_probs=62.5

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      ..|+|+|||+||++++|+.|.+++. ++. -.+|-++||..|+.||-+|..+|.++|+++++.+...+..|.
T Consensus       191 hiKKPLNAFmlyMKEmRa~vvaEct-lKe-SAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WS  260 (421)
T KOG3248|consen  191 HIKKPLNAFMLYMKEMRAKVVAECT-LKE-SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS  260 (421)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHhh-hhh-HHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcc
Confidence            3599999999999999999999986 333 289999999999999999999999999999998888877774

>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]

Probab=99.11  E-value=4.1e-11  Score=88.12  Aligned_cols=83  Identities=24%  Similarity=0.472  Sum_probs=74.6

Q ss_pred             hhhhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy3264          67 DKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPV  146 (156)
Q Consensus        67 ~k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~~  146 (156)
                      +...-++.+.+|..++...|..+...+|.++++++++.+|+.|++|+++||.+|...|..++++|+.++..|..+.+...
T Consensus        67 dpN~PKRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~  146 (211)
T COG5648          67 DPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKA  146 (211)
T ss_pred             CCCCCCCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCC
Confidence            55666778888888888889999999999999999999999999999999999999999999999999999999887765


Q ss_pred             CCc
Q psy3264         147 NEE  149 (156)
Q Consensus       147 ~~~  149 (156)
                      -.+
T Consensus       147 ~~~  149 (211)
T COG5648         147 PIG  149 (211)
T ss_pred             CCc
Confidence            433

>KOG4715|consensus

Probab=99.10  E-value=9.2e-11  Score=90.83  Aligned_cols=74  Identities=19%  Similarity=0.398  Sum_probs=69.9

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           4 EKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         4 ~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      +.|.+|-+|+-+|+.|.+..+..|++.||++.+  =+|.++||.+|..|+++||+.|.+.+...+..|.+.|.+|.
T Consensus        60 kpPkppekpl~pymrySrkvWd~VkA~nPe~kL--WeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh  133 (410)
T KOG4715|consen   60 KPPKPPEKPLMPYMRYSRKVWDQVKASNPELKL--WEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYH  133 (410)
T ss_pred             CCCCCCCcccchhhHHhhhhhhhhhccCcchHH--HHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            467888899999999999999999999999976  89999999999999999999999999999999999999884

>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A

Probab=98.83  E-value=1.3e-08  Score=63.36  Aligned_cols=73  Identities=23%  Similarity=0.360  Sum_probs=60.5

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCCc
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAG   83 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~~   83 (156)
                      .|..|.+|-.||.+.....+++.+++.+.   -..+.+...|++|++.+|-.|+..|.+++.+|+++|.+|..+..
T Consensus         3 lPE~PKt~qe~Wqq~vi~dYla~~~~dr~---K~~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~   75 (85)
T PF14887_consen    3 LPETPKTAQEIWQQSVIGDYLAKFRNDRK---KALKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPA   75 (85)
T ss_dssp             -S----THHHHHHHHHHHHHHHHTTSTHH---HHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhhHhHH---HHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            47778899999999999999999998764   44679999999999999999999999999999999999975443

>KOG0526|consensus

Probab=98.79  E-value=2.5e-09  Score=88.00  Aligned_cols=64  Identities=39%  Similarity=0.645  Sum_probs=55.7

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      ++++.+|..+....|..++.+  |+++++++|.+|++|++||.  |.+|.+.|+.++++|+.||.+|+
T Consensus       537 kra~sa~m~w~~~~r~~ik~d--gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk  600 (615)
T KOG0526|consen  537 KRATSAYMLWLNASRESIKED--GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYK  600 (615)
T ss_pred             ccchhHHHHHHHhhhhhHhhc--CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhc
Confidence            345555555555558888887  99999999999999999999  99999999999999999999999

>KOG0528|consensus

Probab=98.61  E-value=1.6e-08  Score=82.42  Aligned_cols=71  Identities=23%  Similarity=0.314  Sum_probs=61.0

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      .-|||+||||+|.++.|..|...+|++-.  ..|+++||..|+.||-.||++|.+.-...-..+-+....|..
T Consensus       325 HIKRPMNAFMVWAkDERRKILqA~PDMHN--SnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrY  395 (511)
T KOG0528|consen  325 HIKRPMNAFMVWAKDERRKILQAFPDMHN--SNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRY  395 (511)
T ss_pred             cccCCcchhhcccchhhhhhhhcCccccc--cchhHHhcccccccccccccchHHHHHHHHHhhhccCccccc
Confidence            46999999999999999999999999986  899999999999999999999987655555566666666654

>KOG0528|consensus

Probab=98.34  E-value=1.3e-07  Score=77.22  Aligned_cols=78  Identities=19%  Similarity=0.287  Sum_probs=69.2

Q ss_pred             hhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy3264          69 KRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPV  146 (156)
Q Consensus        69 ~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~~  146 (156)
                      -..++.|++|..+....|..+.+.+|++....|+|+||..|+.||..||+||.++-+++-..|....+.|+.+-.++.
T Consensus       324 PHIKRPMNAFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkPRPKR  401 (511)
T KOG0528|consen  324 PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKPRPKR  401 (511)
T ss_pred             ccccCCcchhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCCCCCc
Confidence            355678888887777667778888999999999999999999999999999999999999999999999999877653

>KOG4715|consensus

Probab=98.29  E-value=8.6e-07  Score=69.10  Aligned_cols=56  Identities=32%  Similarity=0.544  Sum_probs=52.9

Q ss_pred             ccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3264          85 KRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN  140 (156)
Q Consensus        85 ~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~  140 (156)
                      ..+.++..||++...+|.|+||.+|..|+++||+.|+..++..+..|.+.|..|..
T Consensus        79 vWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~  134 (410)
T KOG4715|consen   79 VWDQVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHN  134 (410)
T ss_pred             hhhhhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            36779999999999999999999999999999999999999999999999999853

>KOG2746|consensus

Probab=98.29  E-value=5.4e-07  Score=76.22  Aligned_cols=66  Identities=26%  Similarity=0.415  Sum_probs=60.2

Q ss_pred             CCCCCCCcHHHHHHHHHH--HHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccc
Q psy3264           7 VKPRGRMTAYAFFVQVCR--EEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTE   74 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r--~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~   74 (156)
                      ..-+||+|+|++|++.+|  ..+...||+..+  +-|+++||+.|-.|.+.||+.|.++|.+.+..+-++
T Consensus       180 ~HirrPMnaf~ifskrhr~~g~vhq~~pn~DN--rtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  180 DHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDN--RTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             hhhhhhhHHHHHHHhhcCCccchhccCccccc--hhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            346899999999999999  899999999876  899999999999999999999999999988776654

>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A

Probab=98.13  E-value=4.9e-06  Score=51.92  Aligned_cols=54  Identities=19%  Similarity=0.358  Sum_probs=44.2

Q ss_pred             ccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264          91 QDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus        91 ~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      ..++.....+ .+.+...|++|++.+|-+|+..|.++..+|+.+|-+|+.-....
T Consensus        24 a~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~~   77 (85)
T PF14887_consen   24 AKFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPADA   77 (85)
T ss_dssp             HHTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCTT
T ss_pred             HHhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence            3455554444 45899999999999999999999999999999999999876654

>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=97.94  E-value=2.2e-05  Score=56.75  Aligned_cols=48  Identities=19%  Similarity=0.257  Sum_probs=42.3

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCC
Q psy3264           4 EKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMS   53 (156)
Q Consensus         4 ~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls   53 (156)
                      |-|++-.|-+|||..|+++....|+..+|+++.  .|+++.++..|...+
T Consensus       117 kPPEKRqR~psaYn~f~k~ei~rik~~~p~ish--keaFs~aAknW~h~p  164 (170)
T PF04690_consen  117 KPPEKRQRVPSAYNRFMKEEIQRIKAENPDISH--KEAFSAAAKNWAHFP  164 (170)
T ss_pred             CCccccCCCchhHHHHHHHHHHHHHhcCCCCCH--HHHHHHHHHhhhhCc
Confidence            445555677899999999999999999999998  899999999998764

>KOG3248|consensus

Probab=97.89  E-value=1.7e-06  Score=68.07  Aligned_cols=79  Identities=16%  Similarity=0.274  Sum_probs=68.3

Q ss_pred             hhhhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264          67 DKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus        67 ~k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      .+...++.+++|..+-.+.|..+..+-...-..+|.++||.+|..||-+|.++|.++|+++++.|..-+..|-++.+..
T Consensus       188 KkphiKKPLNAFmlyMKEmRa~vvaEctlKeSAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYg  266 (421)
T KOG3248|consen  188 KKPHIKKPLNAFMLYMKEMRAKVVAECTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG  266 (421)
T ss_pred             cCccccccHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhh
Confidence            3456678889998888898999888766555678999999999999999999999999999999999999998776654

>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta

Probab=97.39  E-value=0.00045  Score=49.98  Aligned_cols=47  Identities=32%  Similarity=0.511  Sum_probs=40.8

Q ss_pred             CcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhh
Q psy3264          13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMAD   65 (156)
Q Consensus        13 ~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~   65 (156)
                      -+||+-|+.+.+.    .|.++..  .|++...+..|..||+.+|..|..++-
T Consensus        83 nnaYLNFLReFRr----kh~~L~p--~dlI~~AAraW~rLSe~eK~rYrr~~~  129 (183)
T PF06382_consen   83 NNAYLNFLREFRR----KHCGLSP--QDLIQRAARAWCRLSEAEKNRYRRMAP  129 (183)
T ss_pred             chHHHHHHHHHHH----HccCCCH--HHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence            4699999999876    5667765  899999999999999999999998654

The function of this family is unknown.

>KOG2746|consensus

Probab=96.77  E-value=0.0011  Score=56.80  Aligned_cols=68  Identities=28%  Similarity=0.429  Sum_probs=58.3

Q ss_pred             hhhhhccccccCCCCCcccc--ccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHH
Q psy3264          67 DKKRYDTEMQSYTPPAGEKR--GKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE  134 (156)
Q Consensus        67 ~k~~y~~~~~~~~~~~~~~r--~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e  134 (156)
                      ++....+.|++|..+....|  +.+.+.||+..+..|+++||+.|-.|-+.||+.|.++|-+.++.|-+.
T Consensus       178 ~k~HirrPMnaf~ifskrhr~~g~vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  178 DKDHIRRPMNAFHIFSKRHRGEGRVHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             cchhhhhhhHHHHHHHhhcCCccchhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            33445567777777666666  778899999999999999999999999999999999999999998876

>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases []

Probab=96.57  E-value=0.0034  Score=36.92  Aligned_cols=40  Identities=23%  Similarity=0.434  Sum_probs=35.9

Q ss_pred             CcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCH
Q psy3264          13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSE   54 (156)
Q Consensus        13 ~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~   54 (156)
                      +|.|-+|.+..|+.|...||++.+  +.+..+++.+|+..++
T Consensus        13 lt~yK~Fsq~vRP~l~~~NPk~~~--sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   13 LTNYKAFSQHVRPLLAKANPKAPM--SKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCcH--HHHHHHHHHHHHHHHh
Confidence            567889999999999999999976  8999999999997654

; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed

Probab=94.55  E-value=0.071  Score=35.81  Aligned_cols=81  Identities=15%  Similarity=0.433  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHhccCCHHHHHHHHHhhhh-------hhhhhccccccCCCCCccccccccccC---CCCCchhHHHHHHHH
Q psy3264          39 AEFSKKCAERWKTMSEKEKKRFHEMADK-------DKKRYDTEMQSYTPPAGEKRGKIKQDN---PEYGVGDIAKELGKK  108 (156)
Q Consensus        39 ~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~-------~k~~y~~~~~~~~~~~~~~r~~~~~~~---p~~~~~e~~k~~~~~  108 (156)
                      .++..-++..|+.|++..+..|...|..       .+.++...|..|..-.++.|..+...+   ..++..+.. .|...
T Consensus        10 q~~L~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~rm~~W~~LspeqR~~~R~~~~~~~~Lpp~qR~-~lr~~   88 (107)
T PF11304_consen   10 QQALAPLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRERMRRWAALSPEQRQQARENYQRFKQLPPEQRQ-ALRAR   88 (107)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHcCCHHHHH-HHHHH
Confidence            5677888899999999999988887755       566677777777665555555544433   344444333 46666


Q ss_pred             h---ccCChHHHHHH
Q psy3264         109 W---ADVDPSVKTKY  120 (156)
Q Consensus       109 W---k~ls~~eK~~y  120 (156)
                      |   ..||+++|...
T Consensus        89 w~~yq~l~~eeR~~l  103 (107)
T PF11304_consen   89 WEAYQQLPPEERQAL  103 (107)
T ss_pred             HHHHHcCCHHHHHHH
Confidence            6   78888888654

Currently no function is known.

>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta

Probab=94.50  E-value=0.038  Score=40.16  Aligned_cols=38  Identities=16%  Similarity=0.437  Sum_probs=34.1

Q ss_pred             cccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHH
Q psy3264          88 KIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAE  125 (156)
Q Consensus        88 ~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~  125 (156)
                      .+...|.+++..|+....+..|..||+.+|..|...+-
T Consensus        92 eFRrkh~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~  129 (183)
T PF06382_consen   92 EFRRKHCGLSPQDLIQRAARAWCRLSEAEKNRYRRMAP  129 (183)
T ss_pred             HHHHHccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence            36678899999999999999999999999999998654

The function of this family is unknown.

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

Probab=93.07  E-value=0.18  Score=34.66  Aligned_cols=48  Identities=23%  Similarity=0.383  Sum_probs=40.0

Q ss_pred             CCCCC-CCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCH
Q psy3264           5 KDVKP-RGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSE   54 (156)
Q Consensus         5 ~p~~P-krP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~   54 (156)
                      ...+| +|-.-||.-|...+.+.++.++|++..  +++..+|-..|..-++
T Consensus        68 ~drHPErR~KAAy~afeE~~Lp~lK~E~PgLrl--sQ~kq~l~K~w~KSPe  116 (122)
T PF06244_consen   68 IDRHPERRMKAAYKAFEERRLPELKEENPGLRL--SQYKQMLWKEWQKSPE  116 (122)
T ss_pred             CCCCcchhHHHHHHHHHHHHhHHHHhhCCCchH--HHHHHHHHHHHhcCCC
Confidence            34445 455579999999999999999999987  8999999999987654

>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT)

Probab=93.02  E-value=0.27  Score=36.81  Aligned_cols=55  Identities=16%  Similarity=0.220  Sum_probs=40.8

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhh
Q psy3264           4 EKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADK   66 (156)
Q Consensus         4 ~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~   66 (156)
                      ..+..++||+|+|++|..-.-    ...|+...  .+++.+|+..|..=+-  |..|.-+|..
T Consensus        39 ~~~~~~kr~lN~Fm~FRsyy~----~~~~~~~Q--k~~S~~l~~lW~~dp~--k~~W~l~ak~   93 (201)
T PF04769_consen   39 RSPEKAKRPLNGFMAFRSYYS----PIFPPLPQ--KELSGILTKLWEKDPF--KNKWSLMAKA   93 (201)
T ss_pred             ccccccccchhHHHHHHHHHH----hhcCCcCH--HHHHHHHHHHHhCCcc--HhHHHHHhhh
Confidence            345678999999999977654    44566654  8999999999997443  5666666654

MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus

>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases []

Probab=92.12  E-value=0.054  Score=31.88  Aligned_cols=33  Identities=18%  Similarity=0.357  Sum_probs=28.3

Q ss_pred             CccccccccccCCCCCchhHHHHHHHHhccCCh
Q psy3264          82 AGEKRGKIKQDNPEYGVGDIAKELGKKWADVDP  114 (156)
Q Consensus        82 ~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~  114 (156)
                      ..--||.+...||++....+..+++.+|+..+.
T Consensus        20 sq~vRP~l~~~NPk~~~sKl~~l~~AKwrEF~~   52 (55)
T PF08073_consen   20 SQHVRPLLAKANPKAPMSKLMMLLQAKWREFQE   52 (55)
T ss_pred             HHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHh
Confidence            334489999999999999999999999997654

; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=92.04  E-value=0.38  Score=35.83  Aligned_cols=47  Identities=17%  Similarity=0.523  Sum_probs=40.9

Q ss_pred             CCCchhHHH-HHHHHhccCChHHHHHHHHHHHH-HHHHHHHHHHHHHhc
Q psy3264          95 EYGVGDIAK-ELGKKWADVDPSVKTKYEQMAEK-DKARYEKEMTAYKNR  141 (156)
Q Consensus        95 ~~~~~e~~k-~~~~~Wk~ls~~eK~~y~~~a~~-~k~~y~~e~~~~~~~  141 (156)
                      .+++..+++ .||..|+.+|+++++.|.+.... ....|-..+..|...
T Consensus        63 ~~Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~  111 (198)
T TIGR03481        63 AFDLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGE  111 (198)
T ss_pred             hCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence            456788875 78999999999999999999998 888999999999654

The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.

>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional

Probab=88.89  E-value=1.3  Score=33.39  Aligned_cols=49  Identities=20%  Similarity=0.328  Sum_probs=41.5

Q ss_pred             CCCCCchhHHH-HHHHHhccCChHHHHHHHHHHHH-HHHHHHHHHHHHHhc
Q psy3264          93 NPEYGVGDIAK-ELGKKWADVDPSVKTKYEQMAEK-DKARYEKEMTAYKNR  141 (156)
Q Consensus        93 ~p~~~~~e~~k-~~~~~Wk~ls~~eK~~y~~~a~~-~k~~y~~e~~~~~~~  141 (156)
                      .|.+.+..+++ .||.-|+.+|+++++.|.+.... +...|-..+..|...
T Consensus        65 ~p~~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q  115 (211)
T PRK15117         65 LPYVQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQ  115 (211)
T ss_pred             cccCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence            46778888874 78999999999999999999887 556899999999754

>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []

Probab=80.48  E-value=2.8  Score=30.11  Aligned_cols=47  Identities=19%  Similarity=0.525  Sum_probs=34.4

Q ss_pred             CCCCchhHH-HHHHHHhccCChHHHHHHHHHHHHH-HHHHHHHHHHHHh
Q psy3264          94 PEYGVGDIA-KELGKKWADVDPSVKTKYEQMAEKD-KARYEKEMTAYKN  140 (156)
Q Consensus        94 p~~~~~e~~-k~~~~~Wk~ls~~eK~~y~~~a~~~-k~~y~~e~~~~~~  140 (156)
                      |.+.+..++ ..||.-|+.+|+++++.|.+..... ...|-..+..|..
T Consensus        36 ~~~D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~   84 (170)
T PF05494_consen   36 PYFDFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG   84 (170)
T ss_dssp             GGB-HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred             HhCCHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            556677777 5677899999999999999998774 5567777777764

Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.

>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=80.46  E-value=0.54  Score=34.19  Aligned_cols=45  Identities=20%  Similarity=0.338  Sum_probs=37.5

Q ss_pred             hhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCC
Q psy3264          69 KRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVD  113 (156)
Q Consensus        69 ~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls  113 (156)
                      ++.++.-.+|+.+..+.-++++..+|+++-.|+++..+..|...+
T Consensus       120 EKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~p  164 (170)
T PF04690_consen  120 EKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHFP  164 (170)
T ss_pred             cccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhCc
Confidence            445566677777777778889999999999999999999998765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	156
2yrq_A	173	Solution Structure Of The Tandem Hmg Box Domain Fro		6e-34
2ly4_A	83	Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-Bo		2e-27
1aab_A	83	Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83		3e-26
1ckt_A	71	Crystal Structure Of Hmg1 Domain A Bound To A Cispl		2e-24
1j3x_A	77	Solution Structure Of The N-Terminal Domain Of The		6e-24
2eqz_A	86	Solution Structure Of The First Hmg-Box Domain From		4e-22
1cg7_A	93	Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len		1e-06
1cg7_A	93	Hmg Protein Nhp6a From Saccharomyces Cerevisiae Len		3e-06
1j5n_A	93	Solution Structure Of The Non-Sequence-Specific Hmg		1e-06
1j5n_A	93	Solution Structure Of The Non-Sequence-Specific Hmg		3e-06
2yqi_A	81	Solution Structure Of The Second Hmg-Box Domain Fro		1e-06
1j3d_A	78	Solution Structure Of The C-Terminal Domain Of The		1e-06
1j3c_A	79	Solution Structure Of The C-Terminal Domain Of The		2e-06
2gzk_A	159	Structure Of A Complex Of Tandem Hmg Boxes And Dna		5e-06
1wxl_A	73	Solution Structure Of The Hmg-Box Domain In The Ssr		2e-05
2lhj_A	97	Nmr Structure Of The High Mobility Group Protein-Li		2e-05
2crj_A	92	Solution Structure Of The Hmg Domain Of Mouse Hmg D		5e-05
2crj_A	92	Solution Structure Of The Hmg Domain Of Mouse Hmg D		1e-04
1hme_A	77	Structure Of The Hmg Box Motif In The B-Domain Of H		4e-04
1hsm_A	79	The Structure Of The Hmg Box And Its Interaction Wi		4e-04
1nhm_A	81	The Structure Of The Hmg Box And Its Interaction Wi		4e-04

>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human High Mobility Group Protein B1 Length = 173

Iteration: 1
 Score =  139 bits (350), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 76/159 (47%), Positives = 101/159 (63%), Gaps = 24/159 (15%)
Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 15  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 74
Query: 68  KKRYDTEMQSYTPPAGEK------------------------RGKIKQDNPEYGVGDIAK 103
           K RY+ EM++Y PP GE                         R KIK ++P   +GD+AK
Sbjct: 75  KARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAK 134
Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           +LG+ W +     K  YE+ A K K +YEK++ AY+ + 
Sbjct: 135 KLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 173

>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53 Transactivation Domain Interaction And Is Regulated By The Acidic Tail Length = 83

Iteration: 1
 Score =  117 bits (294), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 53/77 (68%), Positives = 65/77 (84%)
Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 7  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 66
Query: 68 KKRYDTEMQSYTPPAGE 84
          K RY+ EM++Y PP GE
Sbjct: 67 KARYEREMKTYIPPKGE 83

>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment Length = 83

Iteration: 1
 Score =  114 bits (284), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 52/77 (67%), Positives = 64/77 (83%)
Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KPRG+M++YAFFVQ  REEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 7  KPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 66
Query: 68 KKRYDTEMQSYTPPAGE 84
          K RY+ EM++Y PP GE
Sbjct: 67 KARYEREMKTYIPPKGE 83

>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A Cisplatin-modified Dna Duplex Length = 71

Iteration: 1
 Score =  108 bits (269), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 49/71 (69%), Positives = 61/71 (85%)
Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 1  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60
Query: 68 KKRYDTEMQSY 78
          K RY+ EM++Y
Sbjct: 61 KARYEREMKTY 71

>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2 Length = 77

Iteration: 1
 Score =  106 bits (264), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 49/70 (70%), Positives = 59/70 (84%)
Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KPRG+M++YAFFVQ  REEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 8  KPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSD 67
Query: 68 KKRYDTEMQS 77
          K RYD EM++
Sbjct: 68 KARYDREMKN 77

>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High Mobility Group Protein B3 Length = 86

Iteration: 1
 Score =  100 bits (249), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 49/66 (74%), Positives = 54/66 (81%)
Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
          M+AYAFFVQ CREEHKKK+PE  V FAEFSKKC+ERWKTMS KEK +F EMA  DK RYD
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD 79
Query: 73 TEMQSY 78
           EM+ Y
Sbjct: 80 REMKDY 85

>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
          P+  ++AY FF    R+  + ++P+  + F +  KK  E+WK ++ +EK+ +   A  DK
Sbjct: 21 PKRALSAYMFFANENRDIVRSENPD--ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADK 78
Query: 69 KRYDTEMQSYT 79
          KRY++E + Y 
Sbjct: 79 KRYESEKELYN 89

>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae Length = 93

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 75  MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
           + +Y   A E R  ++ +NP+   G + K+LG+KW  + P  K  YE  A+ DK RYE E
Sbjct: 25  LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
Query: 135 MTAYKNRSVA 144
              Y N ++A
Sbjct: 85  KELY-NATLA 93

>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna Length = 93

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
          P+  ++AY FF    R+  + ++P+  + F +  KK  E+WK ++ +EK+ +   A  DK
Sbjct: 21 PKRALSAYMFFANENRDIVRSENPD--ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADK 78
Query: 69 KRYDTEMQSYT 79
          KRY++E + Y 
Sbjct: 79 KRYESEKELYN 89

>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna Length = 93

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 75  MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
           + +Y   A E R  ++ +NP+   G + K+LG+KW  + P  K  YE  A+ DK RYE E
Sbjct: 25  LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
Query: 135 MTAYKNRSVA 144
              Y N ++A
Sbjct: 85  KELY-NATLA 93

>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High Mobility Group Protein B3 Length = 81

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 6/69 (8%)
Query: 80  PPAG------EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEK 133
           PP+G      E R KIK  NP   +GD+AK+LG+ W +++ S K  Y   A K K +YEK
Sbjct: 13  PPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEK 72
Query: 134 EMTAYKNRS 142
           ++  YK++ 
Sbjct: 73  DVADYKSKG 81

>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 78

Iteration: 1
 Score = 48.9 bits (115), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 37/60 (61%)
Query: 82  AGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
             E R KIK ++P   +GD AK+LG+ W++     K  YEQ A K K +YEK++ AY+ +
Sbjct: 19  CSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYRAK 78

>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2 Length = 79

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 37/60 (61%)
Query: 82  AGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
             E R KIK ++P   +GD AK+LG+ W++     K  YEQ A K K +YEK++ AY+ +
Sbjct: 20  CSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYRAK 79

>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna Length = 159

Iteration: 1
 Score = 47.0 bits (110), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 43/146 (29%), Positives = 69/146 (47%), Gaps = 25/146 (17%)
Query: 19  FVQVCREEHKKKHPEE-NVVFAEFSKKCAERWKTMSEKEKKRFHEMADK----------- 66
           F+   R++ +K   E   +  +E SK+   +WK ++E EK  F + A K           
Sbjct: 12  FIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPN 71
Query: 67  -------DKKRYDTEMQSYTPPAG------EKRGKIKQDNPEYGVGDIAKELGKKWADVD 113
                   KK++        PP+       E R KIK ++P   +GD+AK+LG+ W +  
Sbjct: 72  YKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 131
Query: 114 PSVKTKYEQMAEKDKARYEKEMTAYK 139
              K  YE+ A K K +YEK++ AY+
Sbjct: 132 ADDKQPYEKKAAKLKEKYEKDIAAYR 157

>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1 Subunit Of Fact Length = 73

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
          P+   TA+  ++   RE  K+++P   +   E +KK  E WK +  K+K ++ + A KDK
Sbjct: 4  PKRATTAFMLWLNDTRESIKRENP--GIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDK 59
Query: 69 KRYDTEMQSYTPPA 82
          +RY  EM++Y P A
Sbjct: 60 QRYHDEMRNYKPEA 73

>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A) Length = 97

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 75  MQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYE 132
           + SY   A EKR +I  +NPE    V  I K +G  W  +    K  YE+M+++D+ RYE
Sbjct: 27  LSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYE 86
Query: 133 KEMTAYKNRSV 143
           +E   Y  R V
Sbjct: 87  REKAEYAQRKV 97

>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain Protein Hmgx2 Length = 92

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
          P+  +T Y  F+   RE+ + +HP  ++ F E +K     W  +   EK+R+ + A+K+K
Sbjct: 8  PKAPVTGYVRFLNERREQIRTRHP--DLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEK 65
Query: 69 KRYDTEMQSY 78
          ++Y  E+ +Y
Sbjct: 66 QQYLKELWAY 75

>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain Protein Hmgx2 Length = 92

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 36/57 (63%)
Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN 140
           E+R +I+  +P+    +I K LG +W+ + P+ K +Y   AEK+K +Y KE+ AY+ 
Sbjct: 21  ERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQ 77

>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1 Length = 77

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           E R KIK ++P   +GD+AK+LG+ W +     K  YE+ A K K +YEK++ AY+
Sbjct: 20  EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR 75

>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 79

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           E R KIK ++P   +GD+AK+LG+ W +     K  YE+ A K K +YEK++ AY+ + 
Sbjct: 16  EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 74

>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna Length = 81

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           E R KIK ++P   +GD+AK+LG+ W +     K  YE+ A K K +YEK++ AY+ + 
Sbjct: 18  EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 76

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	156
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	7e-32
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-10
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	8e-27
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	2e-24
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	1e-10
1ckt_A	71	High mobility group 1 protein; high-mobility group	1e-22
1ckt_A	71	High mobility group 1 protein; high-mobility group	4e-10
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	7e-22
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	1e-09
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	3e-16
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	3e-10
2lhj_A	97	High mobility group protein homolog NHP1; structur	9e-16
2lhj_A	97	High mobility group protein homolog NHP1; structur	7e-11
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	3e-15
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	1e-14
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	2e-13
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-14
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	6e-12
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	8e-14
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	3e-12
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	5e-13
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	2e-05
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	7e-13
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	1e-12
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	2e-12
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	3e-12
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-12
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-11
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	4e-12
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	1e-11
1wgf_A	90	Upstream binding factor 1; transcription factor, D	3e-11
1wgf_A	90	Upstream binding factor 1; transcription factor, D	1e-09
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	3e-11
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	7e-10
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	2e-08
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	3e-04
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	9e-07
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	6e-05
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	1e-06
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	2e-05
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	4e-06
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	1e-04
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	5e-06
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	6e-06
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	3e-05
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	8e-06
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	3e-05
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	8e-06
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	2e-05
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	1e-05
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	5e-05
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	1e-05
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	3e-05
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	1e-05
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	1e-05
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	2e-05
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	2e-04

>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 Length = 159

 Score =  110 bits (277), Expect = 7e-32
 Identities = 42/159 (26%), Positives = 69/159 (43%), Gaps = 24/159 (15%)

Query: 7   VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADK 66
           V+ R +    AF V    +  K       +  +E SK+   +WK ++E EK  F + A K
Sbjct: 1   VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQK 60

Query: 67  DKKRYDTEMQSYTPP------------------------AGEKRGKIKQDNPEYGVGDIA 102
            +  +  +  +Y                             E R KIK ++P   +GD+A
Sbjct: 61  LQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVA 120

Query: 103 KELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           K+LG+ W +     K  YE+ A K K +YEK++ AY+ +
Sbjct: 121 KKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 159

>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 Length = 159

 Score = 55.2 bits (133), Expect = 2e-10
 Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
              +    P+   +A+  F    R + K +HP   +   + +KK  E W   +  +K+ +
Sbjct: 81  KKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHP--GLSIGDVAKKLGEMWNNTAADDKQPY 138

Query: 61  HEMADKDKKRYDTEMQSY 78
            + A K K++Y+ ++ +Y
Sbjct: 139 EKKAAKLKEKYEKDIAAY 156

>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 = 98.1 bits (244), Expect = 8e-27
 Identities = 78/165 (47%), Positives = 103/165 (62%), Gaps = 24/165 (14%)

Query: 1   MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
           M K    KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F
Sbjct: 8   MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF 67

Query: 61  HEMADKDKKRYDTEMQSYTPPAG------------------------EKRGKIKQDNPEY 96
            +MA  DK RY+ EM++Y PP G                        E R KIK ++P  
Sbjct: 68  EDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL 127

Query: 97  GVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
            +GD+AK+LG+ W +     K  YE+ A K K +YEK++ AY+ +
Sbjct: 128 SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 172

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83

 Score = 89.3 bits (222), Expect = 2e-24
 Identities = 52/77 (67%), Positives = 64/77 (83%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KPRG+M++YAFFVQ  REEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 7  KPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 66

Query: 68 KKRYDTEMQSYTPPAGE 84
          K RY+ EM++Y PP GE
Sbjct: 67 KARYEREMKTYIPPKGE 83

>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus norvegicus} SCOP: a.21.1.1 Length = 83

 Score = 53.8 bits (130), Expect = 1e-10
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 84  EKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN 140
             R + K+ +P+  V   + +K+  ++W  +    K K+E MA+ DKARYE+EM  Y  
Sbjct: 21  TSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP 79

>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 Length = 71

 Score = 84.4 bits (209), Expect = 1e-22
 Identities = 49/71 (69%), Positives = 61/71 (85%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 1  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 68 KKRYDTEMQSY 78
          K RY+ EM++Y
Sbjct: 61 KARYEREMKTY 71

>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 Length = 71

 Score = 52.0 bits (125), Expect = 4e-10
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 84  EKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY 138
             R + K+ +P+  V   + +K+  ++W  +    K K+E MA+ DKARYE+EM  Y
Sbjct: 15  TCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86

 Score = 82.8 bits (205), Expect = 7e-22
 Identities = 54/78 (69%), Positives = 61/78 (78%)

Query: 1  MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRF 60
          M K    KP+G+M+AYAFFVQ CREEHKKK+PE  V FAEFSKKC+ERWKTMS KEK +F
Sbjct: 8  MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKF 67

Query: 61 HEMADKDKKRYDTEMQSY 78
           EMA  DK RYD EM+ Y
Sbjct: 68 DEMAKADKVRYDREMKDY 85

>2eqz_A High mobility group protein B3; HMG-box domain, mobility group protein 2A, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 86

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 84  EKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY 138
             R + K+ NPE      + +K+  ++W  +    K+K+++MA+ DK RY++EM  Y
Sbjct: 29  TCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY 85

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67

 Score = 67.7 bits (166), Expect = 3e-16
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KP+   +AY  +V    +E K   P+E        K   E WK +S+ EK+ + + A +D
Sbjct: 2  KPKRPRSAYNVYVAERFQEAKGDSPQE------KLKTVKENWKNLSDSEKELYIQHAKED 55

Query: 68 KKRYDTEMQSY 78
          + RY  EM+S+
Sbjct: 56 ETRYHNEMKSW 66

>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial transcription, activator, DNA- binding, mitochondrion, phosphoprotein; 1.35A {Homo sapiens} Length = 67

 Score = 52.3 bits (126), Expect = 3e-10
 Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 4/55 (7%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY 138
           E+  + K D+P+    +  K + + W ++  S K  Y Q A++D+ RY  EM ++
Sbjct: 16  ERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97

 Score = 67.4 bits (165), Expect = 9e-16
 Identities = 22/71 (30%), Positives = 37/71 (52%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+  +++Y FF +  R E   ++PE     A   K     W  +S++EKK +  M+D+D
Sbjct: 22 APKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDED 81

Query: 68 KKRYDTEMQSY 78
          + RY+ E   Y
Sbjct: 82 RVRYEREKAEY 92

>2lhj_A High mobility group protein homolog NHP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; NMR {Babesia bovis} Length = 97

 Score = 54.7 bits (132), Expect = 7e-11
 Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 84  EKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           EKR +I  +NPE    V  I K +G  W  +    K  YE+M+++D+ RYE+E   Y  R
Sbjct: 36  EKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR 95

Query: 142 SV 143
            V
Sbjct: 96  KV 97

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

 Score = 69.0 bits (168), Expect = 3e-15
 Identities = 29/179 (16%), Positives = 65/179 (36%), Gaps = 51/179 (28%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
            P+  +++Y  F +      K ++P+      E  ++ A+RW+ + + +KK + +    +
Sbjct: 9   CPKKPVSSYLRFSKEQLPIFKAQNPDAK--TTELIRRIAQRWRELPDSKKKIYQDAYRAE 66

Query: 68  KKRYDTEMQSYTPPAG-------------------------------------------- 83
            + Y  E+  +                                                 
Sbjct: 67  WQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYV 126

Query: 84  -EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
            E+  + K D+P     +  K + + W ++  S K  Y Q A++D+ RY  EM +++ +
Sbjct: 127 AERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQ 181

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

 Score = 63.8 bits (156), Expect = 1e-14
 Identities = 24/58 (41%), Positives = 37/58 (63%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           E R KIK ++P   +GD+AK+LG+ W +     K  YE+ A K K +YEK++ AY+ +
Sbjct: 20  EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 77

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

 Score = 61.1 bits (149), Expect = 2e-13
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+   +A+  F    R + K +HP   +   + +KK  E W   +  +K+ + + A K 
Sbjct: 6  APKRPPSAFFLFCSEYRPKIKGEHP--GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 63

Query: 68 KKRYDTEMQSY 78
          K++Y+ ++ +Y
Sbjct: 64 KEKYEKDIAAY 74

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 64.0 bits (156), Expect = 2e-14
 Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
            +  M+A A FVQ  R +   ++P+ +    + + +  E WKT+SE+EK ++ E A KD
Sbjct: 7  GIKKPMSASALFVQDHRPQFLIENPKTS--LEDATLQIEELWKTLSEEEKLKYEEKATKD 64

Query: 68 KKRYDTEMQSYTPPAGEKRGKIKQDN 93
           +RY+++M+       +   K    +
Sbjct: 65 LERYNSQMKRAIEQESQMSLKDSGPS 90

>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 92

 Score = 57.4 bits (139), Expect = 6e-12
 Identities = 15/56 (26%), Positives = 26/56 (46%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           + R +   +NP+  + D   ++ + W  +    K KYE+ A KD  RY  +M    
Sbjct: 21  DHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAI 76

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92

 Score = 62.4 bits (152), Expect = 8e-14
 Identities = 23/70 (32%), Positives = 39/70 (55%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV 143
           E+R +I+  +P+    +I K LG +W+ + P+ K +Y   AEK+K +Y KE+ AY+    
Sbjct: 21  ERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEA 80

Query: 144 APVNEEADEE 153
             V  E+   
Sbjct: 81  YKVCTESGPS 90

>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of chromatin subfamily...; structural DNA-binding protein BRAF35, DNA-bending; NMR {Mus musculus} Length = 92

 Score = 58.2 bits (141), Expect = 3e-12
 Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 2/86 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+  +T Y  F+   RE+ + +HP  ++ F E +K     W  +   EK+R+ + A+K+
Sbjct: 7  GPKAPVTGYVRFLNERREQIRTRHP--DLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKE 64

Query: 68 KKRYDTEMQSYTPPAGEKRGKIKQDN 93
          K++Y  E+ +Y      K       +
Sbjct: 65 KQQYLKELWAYQQSEAYKVCTESGPS 90

>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 = 63.3 bits (153), Expect = 5e-13
 Identities = 29/179 (16%), Positives = 65/179 (36%), Gaps = 51/179 (28%)

Query: 8   KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
            P+  +++Y  F +      K ++P+      E  ++ A+RW+ + + +KK + +    +
Sbjct: 41  CPKKPVSSYLRFSKEQLPIFKAQNPDAK--TTELIRRIAQRWRELPDSKKKIYQDAYRAE 98

Query: 68  KKRYDTEMQSYTPPAG-------------------------------------------- 83
            + Y  E+  +                                                 
Sbjct: 99  WQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYV 158

Query: 84  -EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
            E+  + K D+P     +  K + + W ++  S K  Y Q A++D+ RY  EM +++ +
Sbjct: 159 AERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQ 213

>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 = 41.7 bits (97), Expect = 2e-05
 Identities = 12/73 (16%), Positives = 33/73 (45%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV 143
           E+    K  NP+    ++ + + ++W ++  S K  Y+     +   Y++E++ +K +  
Sbjct: 55  EQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLT 114

Query: 144 APVNEEADEEDDE 156
                  ++E  +
Sbjct: 115 PSQIMSLEKEIMD 127

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73

 Score = 59.2 bits (144), Expect = 7e-13
 Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
           + R  IK++NP   V +IAK+ G+ W ++    K+K+E  A KDK RY  EM  YK  +
Sbjct: 17  DTRESIKRENPGIKVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQRYHDEMRNYKPEA 73

>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding protein; NMR {Drosophila melanogaster} Length = 73

 Score = 58.8 bits (143), Expect = 1e-12
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+   TA+  ++   RE  K+++P   +   E +KK  E WK + +K K  + + A KD
Sbjct: 3  MPKRATTAFMLWLNDTRESIKRENP--GIKVTEIAKKGGEMWKELKDKSK--WEDAAAKD 58

Query: 68 KKRYDTEMQSYTPPA 82
          K+RY  EM++Y P A
Sbjct: 59 KQRYHDEMRNYKPEA 73

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

 Score = 58.9 bits (143), Expect = 2e-12
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+  ++AY FF    R+  + ++P  ++ F +  KK  E+WK ++ +EK+ +   A  D
Sbjct: 20 APKRALSAYMFFANENRDIVRSENP--DITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77

Query: 68 KKRYDTEMQSY 78
          KKRY++E + Y
Sbjct: 78 KKRYESEKELY 88

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

 Score = 58.1 bits (141), Expect = 3e-12
 Identities = 22/57 (38%), Positives = 31/57 (54%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN 140
           E R  ++ +NP+   G + K+LG+KW  + P  K  YE  A+ DK RYE E   Y  
Sbjct: 34  ENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA 90

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

 Score = 58.6 bits (142), Expect = 3e-12
 Identities = 15/58 (25%), Positives = 27/58 (46%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           + +  IK  NP    G+++K +   W  +    K  Y++  E  K  Y K++ AY+  
Sbjct: 31  DTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRAS 88

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

 Score = 55.9 bits (135), Expect = 3e-11
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          +P+  ++AYA F +  +   K ++P  N  F E SK  A  W  + E++K+ + +  +  
Sbjct: 17 EPQKPVSAYALFFRDTQAAIKGQNP--NATFGEVSKIVASMWDGLGEEQKQVYKKKTEAA 74

Query: 68 KKRYDTEMQSY 78
          KK Y  ++ +Y
Sbjct: 75 KKEYLKQLAAY 85

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73

 Score = 57.3 bits (139), Expect = 4e-12
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
             R  IK++NP   V ++AK  G+ W  +    K+++E  A K K  Y++ +  ++
Sbjct: 17  SARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFE 70

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A 1qrv_A* Length = 73

 Score = 56.1 bits (136), Expect = 1e-11
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KP+  ++AYA ++   RE  K+++P   +   E +K+  E W+ M +K +  +   A K 
Sbjct: 3  KPKRPLSAYALWLNSARESIKRENP--GIKVTEVAKRGGELWRAMKDKSE--WEAKAAKA 58

Query: 68 KKRYDTEMQSY 78
          K  YD  ++ +
Sbjct: 59 KDDYDRAVKEF 69

>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 Length = 90

 Score = 55.8 bits (135), Expect = 3e-11
 Identities = 14/58 (24%), Positives = 29/58 (50%)

Query: 82  AGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           + EKR +++++ PE    ++ + L + W D+    K KY+      KA+ E++     
Sbjct: 32  SEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPSS 89

>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 Length = 90

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 15/78 (19%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 2  PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFH 61
           K    KP+  ++A   F +  R + +++ P   +  +E ++  A  W  +SEK+K ++ 
Sbjct: 14 GKGGSEKPKRPVSAMFIFSEEKRRQLQEERP--ELSESELTRLLARMWNDLSEKKKAKYK 71

Query: 62 EMADKDKKRYDTEMQSYT 79
                K + + +    +
Sbjct: 72 AREAALKAQSERKSGPSS 89

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

 Score = 55.9 bits (135), Expect = 3e-11
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           EKR K  + +PE    D+ K L KK+ ++    K KY Q  +++K  +E+ +  ++  
Sbjct: 24  EKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED 81

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

 Score = 52.0 bits (125), Expect = 7e-10
 Identities = 15/71 (21%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+  +T Y  F    R ++ K HPE +    + +K  ++++K + EK+K ++ +   ++
Sbjct: 10 FPKKPLTPYFRFFMEKRAKYAKLHPEMS--NLDLTKILSKKYKELPEKKKMKYIQDFQRE 67

Query: 68 KKRYDTEMQSY 78
          K+ ++  +  +
Sbjct: 68 KQEFERNLARF 78

>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 Length = 101

 Score = 48.4 bits (115), Expect = 2e-08
 Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 4/66 (6%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
          M  Y  F Q      +  H        E   +   RW+ +S+ +K+ + ++A++ +++Y 
Sbjct: 13 MNGYQKFSQELLSNGELNHLP----LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYK 68

Query: 73 TEMQSY 78
            +  +
Sbjct: 69 VHLDLW 74

>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 Length = 101

 Score = 37.2 bits (86), Expect = 3e-04
 Identities = 9/40 (22%), Positives = 22/40 (55%)

Query: 100 DIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           +   E+G +W  +  S K  Y+++AE+ + +Y+  +  + 
Sbjct: 36  ERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWV 75

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71

 Score = 43.0 bits (102), Expect = 9e-07
 Identities = 14/56 (25%), Positives = 32/56 (57%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           ++R ++ Q NP+    +++K LGK W  +  + K  + + AE+ + ++ ++   YK
Sbjct: 16  DERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK 71

>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens} Length = 71

 Score = 38.3 bits (90), Expect = 6e-05
 Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  + +  R+   +++P+ +   AE SK   + WK ++  EK+ F E A++ + +
Sbjct: 7  MNAFMVWAKDERKRLAQQNPDLHN--AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Length = 82

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
             R  ++Q++P        K L   WA +DP  K KY  MA++ K  + K    Y+
Sbjct: 21  RHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYR 76

>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX domain, structural genomics, NPPSFA, riken structural genomics/proteomics initiative; NMR {Mus musculus} Length = 82

 Score = 39.5 bits (93), Expect = 2e-05
 Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  F +  R   +++HP  +      +K  A+ W  +  KEK+++ +MA + K  
Sbjct: 12 MNAFLLFCKRHRSLVRQEHPRLDN--RGATKILADWWAVLDPKEKQKYTDMAKEYKDA 67

>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} Length = 87

 Score = 42.0 bits (99), Expect = 4e-06
 Identities = 9/51 (17%), Positives = 18/51 (35%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
           + R +  Q  P      I+  LG +W  +    +  Y   A+      ++ 
Sbjct: 31  KYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRL 81

>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} Length = 87

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 3  KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHE 62
               K +  M A+  F +  R E+ + +P ++      S    +RWK M  +E++ +  
Sbjct: 12 ATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKD--NRAISVILGDRWKKMKNEERRMYTL 69

Query: 63 MADKDKKRY 71
           A    +  
Sbjct: 70 EAKALAEEQ 78

>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: a.21.1.1 Length = 108

 Score = 42.3 bits (99), Expect = 5e-06
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 9  PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
           +    +Y+ +        K           E    C+++WK +S+KEK  +H+  D+ K
Sbjct: 18 TKPPPNSYSLYCAELMANMKDVPS------TERMVLCSQQWKLLSQKEKDAYHKKCDQKK 71

Query: 69 KRYDTEMQSY 78
          K Y+ E+  +
Sbjct: 72 KDYEVELLRF 81

>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* Length = 76

 Score = 41.0 bits (97), Expect = 6e-06
 Identities = 16/56 (28%), Positives = 32/56 (57%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           ++R K+  +NP     +I+K+LG +W  +  + K  + Q A+K +A + ++   YK
Sbjct: 18  DQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK 73

>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* Length = 76

 Score = 39.5 bits (93), Expect = 3e-05
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  + +  R +   ++P      +E SK+   +WK ++E EK  F + A K +  
Sbjct: 9  MNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64

>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 Length = 85

 Score = 41.0 bits (97), Expect = 8e-06
 Identities = 16/56 (28%), Positives = 32/56 (57%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           ++R K+  +NP     +I+K+LG +W  +  + K  + Q A+K +A + ++   YK
Sbjct: 18  DQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK 73

>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 Length = 85

 Score = 39.5 bits (93), Expect = 3e-05
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  + +  R +   ++P      +E SK+   +WK ++E EK  F + A K +  
Sbjct: 9  MNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79

 Score = 41.0 bits (97), Expect = 8e-06
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
            +R KI + +P+    +I+K LGK+W  +  S K  + Q AE+ + ++  +   YK
Sbjct: 16  IERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYK 71

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} Length = 79

 Score = 39.9 bits (94), Expect = 2e-05
 Identities = 15/58 (25%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  + Q+ R +  ++ P+ +   AE SK+  +RWK + + +K  F + A++ + +
Sbjct: 7  MNAFMVWSQIERRKIMEQSPDMHN--AEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Length = 80

 Score = 40.6 bits (96), Expect = 1e-05
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
            +R K+ Q+NP+    +I+K LG +W  +  + K  +   A++ +A + KE   YK
Sbjct: 16  GQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK 71

>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B Length = 80

 Score = 38.7 bits (91), Expect = 5e-05
 Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  + +  R +  +++P+ +   +E SK+    WK +SE EK+ F + A + +  
Sbjct: 7  MNAFMVWSRGQRRKMAQENPKMHN--SEISKRLGAEWKLLSETEKRPFIDEAKRLRAL 62

>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} PDB: 2yul_A Length = 83

 Score = 40.3 bits (95), Expect = 1e-05
 Identities = 14/56 (25%), Positives = 32/56 (57%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           ++R ++ Q NP+    +++K LGK W  +  + K  + + AE+ + ++ ++   YK
Sbjct: 20  DERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK 75

>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} PDB: 2yul_A Length = 83

 Score = 39.5 bits (93), Expect = 3e-05
 Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  + +  R+   +++P+ +   AE SK   + WK ++  EK+ F E A++ + +
Sbjct: 11 MNAFMVWAKDERKRLAQQNPDLHN--AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66

>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 Length = 86

 Score = 40.3 bits (95), Expect = 1e-05
 Identities = 11/58 (18%), Positives = 26/58 (44%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           E R  +  ++       I + LG++W  +    + KY ++A K++  + +    +  R
Sbjct: 16  EMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSAR 73

>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 Length = 81

 Score = 40.2 bits (95), Expect = 1e-05
 Identities = 14/56 (25%), Positives = 27/56 (48%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
           ++R KI Q  P+    +I+K LG +W  +    K  Y +   +   ++ ++   YK
Sbjct: 18  DERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYK 73

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Length = 106

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 15/56 (26%), Positives = 29/56 (51%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
             R K+    P     +++K LGK W  ++ S K  + + AE+ + +++K+   YK
Sbjct: 43  AARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYK 98

>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain, activator, DNA-binding, NUC transcription; HET: DNA; 2.77A {Homo sapiens} Length = 106

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 2/58 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKR 70
          M A+  + Q  R +   ++P  +   AE SK   + W+ ++E EK+ F E A++ + +
Sbjct: 34 MNAFMVWAQAARRKLADQYPHLHN--AELSKTLGKLWRLLNESEKRPFVEEAERLRVQ 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	156
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	100.0
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	100.0
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	100.0
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.98
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.92
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.92
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.89
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.89
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.89
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.89
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.89
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.88
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.88
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.88
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.88
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.88
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.87
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.86
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.86
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.86
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.85
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.85
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.85
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.85
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.85
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.84
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.84
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.84
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.84
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.84
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.84
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.82
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.8
2cto_A	93	Novel protein; high mobility group box domain, hel	99.8
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.79
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.77
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.75
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.67
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.63
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.62
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.6
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.58
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.58
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.57
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.57
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.55
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.55
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.54
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.54
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.54
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.53
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.53
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.53
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.53
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.53
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.52
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.5
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.49
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	99.49
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	99.49
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.48
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	99.47
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.46
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	99.46
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.44
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.4
1wgf_A	90	Upstream binding factor 1; transcription factor, D	99.38
2cto_A	93	Novel protein; high mobility group box domain, hel	99.23
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	99.18
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	99.16

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

Probab=100.00  E-value=4.2e-38  Score=228.65  Aligned_cols=142  Identities=55%  Similarity=0.983  Sum_probs=131.2

Q ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         1 ~~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      |++++|++||||+|||+|||+++|..|+..||++++++.+|+++||++|++||+++|++|.+.|..++.+|.+++..|..
T Consensus         8 ~~k~dp~~PKrp~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   87 (173)
T 2yrq_A            8 MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   87 (173)
T ss_dssp             SSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence            67899999999999999999999999999999965556999999999999999999999999999999999999999975


Q ss_pred             CCcc------------------------ccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          81 PAGE------------------------KRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMT  136 (156)
Q Consensus        81 ~~~~------------------------~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~  136 (156)
                      ..+.                        .++.++.+||++++++|++.||+.|++||+++|++|.++|+.++++|+.+|+
T Consensus        88 ~~~~~kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~  167 (173)
T 2yrq_A           88 PKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA  167 (173)
T ss_dssp             CCCCSSCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhcccccCCccccCcccHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4321                        1666888999999999999999999999999999999999999999999999


Q ss_pred             HHHhcC
Q psy3264         137 AYKNRS  142 (156)
Q Consensus       137 ~~~~~~  142 (156)
                      .|+.++
T Consensus       168 ~y~~k~  173 (173)
T 2yrq_A          168 AYRAKG  173 (173)
T ss_dssp             HHHCCC
T ss_pred             HHHhcC
Confidence            999763

>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=100.00  E-value=1.1e-33  Score=202.85  Aligned_cols=135  Identities=30%  Similarity=0.492  Sum_probs=124.4

Q ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCCc-
Q psy3264           5 KDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAG-   83 (156)
Q Consensus         5 ~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~~-   83 (156)
                      .|+.|+||+|||+||+.+.+..|...||++++  .+|+++||++|++||+++|.+|.+.|..++.+|..++..|....+ 
T Consensus         1 g~~~~Krp~~af~~~~~~~~~ki~~~~P~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~k~~   78 (159)
T 2gzk_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGE   78 (159)
T ss_dssp             CTTCCCCCCCHHHHHHHHHHHHHHHHCSSCCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCCCCC
T ss_pred             CcCCCCCCCcHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhcccccccc
Confidence            47899999999999999999999999999865  999999999999999999999999999999999999999964321 


Q ss_pred             ----------c-------------ccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy3264          84 ----------E-------------KRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN  140 (156)
Q Consensus        84 ----------~-------------~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~  140 (156)
                                +             .|+.++.+||++++++|++.||++|++||+++|++|.++|+.++++|+.+|++|++
T Consensus        79 ~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A           79 TKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             CGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             ccccccccccccccccccchhhHhhHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence                      1             16668889999999999999999999999999999999999999999999999986


Q ss_pred             c
Q psy3264         141 R  141 (156)
Q Consensus       141 ~  141 (156)
                      +
T Consensus       159 ~  159 (159)
T 2gzk_A          159 K  159 (159)
T ss_dssp             C
T ss_pred             C
Confidence            4

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

Probab=100.00  E-value=2.8e-33  Score=212.43  Aligned_cols=136  Identities=21%  Similarity=0.409  Sum_probs=119.9

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPA   82 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~   82 (156)
                      .++|++||||+|||+|||+++|..|+.+||++++  .+|+++||++|++||+++|.+|.++|..++.+|.++|..|...+
T Consensus        36 ~~~p~~PKrP~say~lF~~e~r~~~k~~~P~~~~--~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~  113 (238)
T 3tmm_A           36 SVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKT--TELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQL  113 (238)
T ss_dssp             CHHHHSCCCCCCHHHHHHHHHHHHHHHHSTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4578899999999999999999999999999975  99999999999999999999999999999999999999984211


Q ss_pred             c--------------------------------cc-------------cccccccCCCCCchhHHHHHHHHhccCChHHH
Q psy3264          83 G--------------------------------EK-------------RGKIKQDNPEYGVGDIAKELGKKWADVDPSVK  117 (156)
Q Consensus        83 ~--------------------------------~~-------------r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK  117 (156)
                      +                                +.             |+.+++.|    .++|++.||++|++||+++|
T Consensus       114 ~p~~~~~~~~~~~~k~~krk~~~kkk~~kdp~~PKrP~say~lF~~e~r~~~k~~~----p~ei~k~lg~~Wk~ls~~eK  189 (238)
T 3tmm_A          114 TPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDS----PQEKLKTVKENWKNLSDSEK  189 (238)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCHHHHHHHHHTTTSCCSS----HHHHHHHHHHHHHTCCTTTT
T ss_pred             CHHHHHHHHHHHhhhhhhhhcccchhhhcccCCCCCCCcHHHHHHHHHHHHHhccC----HHHHHHHHHHHHHhCCHHHH
Confidence            1                                11             44444444    45999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy3264         118 TKYEQMAEKDKARYEKEMTAYKNRSVA  144 (156)
Q Consensus       118 ~~y~~~a~~~k~~y~~e~~~~~~~~~~  144 (156)
                      ++|.++|+.++++|+++|+.|+++++.
T Consensus       190 ~~Y~~~A~~~k~~Y~~e~~~y~~k~~~  216 (238)
T 3tmm_A          190 ELYIQHAKEDETRYHNEMKSWEEQMIE  216 (238)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence            999999999999999999999998644

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

Probab=99.98  E-value=7.2e-33  Score=207.15  Aligned_cols=135  Identities=21%  Similarity=0.411  Sum_probs=119.0

Q ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCC--
Q psy3264           5 KDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPA--   82 (156)
Q Consensus         5 ~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~--   82 (156)
                      .|++||||+|||+|||+++|..|+.+||++++  ++|+++||++|++||+++|.+|.++|..++.+|.+++..|...+  
T Consensus         6 ~p~~PKrP~say~lF~~~~r~~~k~~~P~~~~--~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~tp   83 (214)
T 3tq6_A            6 LASCPKKPVSSYLRFSKEQLPIFKAQNPDAKT--TELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTP   83 (214)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHHHHCTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHhCCCCCH--HHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCCH
Confidence            47899999999999999999999999999975  99999999999999999999999999999999999999984211  


Q ss_pred             ------------------------------ccc-------------cccccccCCCCCchhHHHHHHHHhccCChHHHHH
Q psy3264          83 ------------------------------GEK-------------RGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTK  119 (156)
Q Consensus        83 ------------------------------~~~-------------r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~  119 (156)
                                                    .+.             |+.+++.    .+++|++.||+.|++||+++|++
T Consensus        84 ~q~~~~~~~~~~~~~krk~~kkkk~~kdp~~PKrP~say~lF~~e~r~~~k~~----~p~ei~k~lg~~Wk~ls~~eK~~  159 (214)
T 3tq6_A           84 SQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGD----SPQEKLKTVKENWKNLSDSEKEL  159 (214)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCHHHHHHHHHTTTSSCS----SHHHHHHHHHHHHHTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhcchhhhhhhccccCcccccchhhhhHHHHHHhhccC----CHHHHHHHHHHHHHcCCHHHHHH
Confidence                                          111             3334444    45699999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264         120 YEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus       120 y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      |.++|+.++++|+.+|++|+++++..
T Consensus       160 Y~~~A~~~k~~Y~~e~~~y~~~~~~~  185 (214)
T 3tq6_A          160 YIQHAKEDETRYHNEMKSWEEQMIEV  185 (214)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            99999999999999999999987443

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

Probab=99.92  E-value=1.6e-25  Score=144.94  Aligned_cols=79  Identities=68%  Similarity=1.103  Sum_probs=75.3

Q ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           1 MPKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         1 ~~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      |++++|++||||+|||+|||+++|..|+.+||++++++.+|+++||++|++||+++|.+|.++|..++.+|.++|..|.
T Consensus         8 ~~~kdp~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A            8 MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             CSSCCSSSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            6789999999999999999999999999999999866799999999999999999999999999999999999998873

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

Probab=99.92  E-value=1.5e-25  Score=144.09  Aligned_cols=81  Identities=63%  Similarity=1.091  Sum_probs=76.6

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPP   81 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~   81 (156)
                      ++++|++||||+|||+|||+++|..|+..||++++++.+|+++||++|++||+++|.+|.++|..++.+|.++|..|...
T Consensus         1 ~kkdp~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~   80 (83)
T 1aab_A            1 GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP   80 (83)
T ss_dssp             CCCCTTCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            58899999999999999999999999999999875568999999999999999999999999999999999999999765


Q ss_pred             C
Q psy3264          82 A   82 (156)
Q Consensus        82 ~   82 (156)
                      .
T Consensus        81 ~   81 (83)
T 1aab_A           81 K   81 (83)
T ss_dssp             S
T ss_pred             C
Confidence            4

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

Probab=99.89  E-value=7.4e-24  Score=138.67  Aligned_cols=77  Identities=26%  Similarity=0.525  Sum_probs=73.6

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      |.++|++||||+|||+|||+++|..|+..||++++  .+|+++||++|++||+++|++|.++|..++.+|.+++..|..
T Consensus         1 g~kdp~~pKrP~~af~lF~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   77 (92)
T 2crj_A            1 GSSGSSGPKAPVTGYVRFLNERREQIRTRHPDLPF--PEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQ   77 (92)
T ss_dssp             CCCCCSSSCCCCCHHHHHHHHHHHHHHHHCTTCCH--HHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            67899999999999999999999999999999875  899999999999999999999999999999999999998854

>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=99.89  E-value=4.6e-24  Score=135.21  Aligned_cols=76  Identities=22%  Similarity=0.475  Sum_probs=72.7

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      |+||++|+||+|||+||++++|..++..||++++  .+|+++||.+|++||+++|.+|.++|..++.+|..++..|..
T Consensus         1 kkdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A            1 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSI--GDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CCCSSCCCCCCCTTHHHHHHHHHHHHHHCTTCCH--HHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            6899999999999999999999999999999875  899999999999999999999999999999999999999853

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

Probab=99.89  E-value=2.6e-23  Score=136.09  Aligned_cols=79  Identities=29%  Similarity=0.444  Sum_probs=74.5

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPP   81 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~   81 (156)
                      |..+|++||||+|||+|||+++|..|+.+||++++  .+|+++||++|++||+++|++|.++|..++.+|.+++..|...
T Consensus         1 g~~~p~~pKrP~say~lF~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~   78 (92)
T 2cs1_A            1 GSSGSSGIKKPMSASALFVQDHRPQFLIENPKTSL--EDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQ   78 (92)
T ss_dssp             CCCCCSSSCCCCCHHHHHHHHHHHHHHHHCCSSCH--HHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            56789999999999999999999999999999975  8999999999999999999999999999999999999999754


Q ss_pred             C
Q psy3264          82 A   82 (156)
Q Consensus        82 ~   82 (156)
                      .
T Consensus        79 ~   79 (92)
T 2cs1_A           79 E   79 (92)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.89  E-value=4.1e-23  Score=134.61  Aligned_cols=74  Identities=22%  Similarity=0.356  Sum_probs=70.7

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      +++|++||||+|||+|||+++|..|+..||++++  .+|+++||++|++||+++|++|.++|..++.+|.++|..+
T Consensus        15 ~kdp~~pKrP~say~lF~~~~r~~~k~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~~   88 (90)
T 1wgf_A           15 KGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSE--SELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPS   88 (90)
T ss_dssp             SSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5799999999999999999999999999999875  8999999999999999999999999999999999998765

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

Probab=99.89  E-value=1.6e-23  Score=138.77  Aligned_cols=79  Identities=20%  Similarity=0.378  Sum_probs=74.3

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPA   82 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~   82 (156)
                      +++|++||||+|||+|||+++|..|+.++|++++  .+|+++||++|++||+++|++|.+.|..++.+|..+|.+|....
T Consensus         5 ~kdp~~PKRP~saf~lF~~~~r~~ik~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~~   82 (99)
T 1k99_A            5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSN--LDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH   82 (99)
T ss_dssp             CSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCS--HHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            5799999999999999999999999999999986  89999999999999999999999999999999999999996543


Q ss_pred             c
Q psy3264          83 G   83 (156)
Q Consensus        83 ~   83 (156)
                      +
T Consensus        83 P   83 (99)
T 1k99_A           83 P   83 (99)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.88  E-value=1.1e-22  Score=130.32  Aligned_cols=77  Identities=22%  Similarity=0.392  Sum_probs=73.3

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      |..+|++||||+|||+|||+++|..|+.+||++++  .+|+++||++|++||+++|++|.++|..++.+|..++..|..
T Consensus         1 g~~~~~~pkrP~~af~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~   77 (82)
T 1wz6_A            1 GSSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDN--RGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRS   77 (82)
T ss_dssp             CCSSCCCSCCCCCHHHHHHHHHHHHHHHHCSSSCT--THHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhc
Confidence            45789999999999999999999999999999876  899999999999999999999999999999999999999964

>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=99.88  E-value=2.7e-23  Score=129.61  Aligned_cols=71  Identities=69%  Similarity=1.236  Sum_probs=68.1

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      +||||+|||+|||+++|..++..||++++++.+|+++||++|++||+++|.+|.++|..++.+|.++|..|
T Consensus         1 kPKrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            59999999999999999999999999986679999999999999999999999999999999999999876

>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=99.88  E-value=7.5e-23  Score=129.26  Aligned_cols=73  Identities=22%  Similarity=0.321  Sum_probs=68.9

Q ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           5 KDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         5 ~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      +|++||||+|||+|||+++|..|+.+||++++  .+|+++||++|++||+++|++|.++|..++.+|.+++..|.
T Consensus         1 dp~~pkrP~~af~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   73 (76)
T 1hry_A            1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (76)
T ss_dssp             --CCCCCCCCHHHHHHHHHHHHHHHHCSCCSS--SHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CcCCCCCCCCHHHHHHHHHHHHHHHHCcCCCH--HHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            68999999999999999999999999999976  79999999999999999999999999999999999999885

>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=99.88  E-value=8.2e-23  Score=132.36  Aligned_cols=76  Identities=18%  Similarity=0.240  Sum_probs=72.2

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      .+++|+.||||+|||+|||+++|..|+.+||++++  .+|+++||++|++||+++|++|.++|..++.+|.+++..|.
T Consensus        11 ~~kdp~~pKrP~~af~lf~~~~r~~~~~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           11 SATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDN--RAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             CCCCCSSCCCCCCHHHHHHHHTHHHHHHHCTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            56899999999999999999999999999999875  89999999999999999999999999999999999988874

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

Probab=99.88  E-value=6.6e-23  Score=136.54  Aligned_cols=77  Identities=25%  Similarity=0.487  Sum_probs=73.0

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      .+++|++||||+|||+|||+++|..|+..||++++  .+|+++||.+|++||+++|++|.++|..++.+|..++..|..
T Consensus        11 ~~kdp~~pKrP~say~lF~~~~r~~i~~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   87 (102)
T 2co9_A           11 KKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATF--GEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA   87 (102)
T ss_dssp             SCCCCCSCCCCCCHHHHTHHHHHHHHHHHCTTSCH--HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            35799999999999999999999999999999875  899999999999999999999999999999999999999853

>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=99.87  E-value=4.6e-22  Score=128.27  Aligned_cols=74  Identities=22%  Similarity=0.304  Sum_probs=70.9

Q ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           5 KDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         5 ~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      .|+.|+||+|||+|||+++|..|+..||++++  .+|+++||++|++||+++|++|.+.|..++.+|..++..|..
T Consensus         1 ~p~~pKRP~~af~lf~~~~r~~~~~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~   74 (85)
T 1j46_A            1 MQDRVKRPMNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (85)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHHHHSTTSCH--HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CcCcCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCccccc
Confidence            48899999999999999999999999999876  899999999999999999999999999999999999999964

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

Probab=99.86  E-value=5.2e-22  Score=124.50  Aligned_cols=71  Identities=37%  Similarity=0.689  Sum_probs=68.1

Q ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           6 DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         6 p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      |++||||+|||+||++++|..|+..||++++  .+|+++||++|++|  ++|.+|.++|..++.+|.+++..|..
T Consensus         1 P~~pKrP~say~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~   71 (73)
T 1wxl_A            1 SHMPKRATTAFMLWLNDTRESIKRENPGIKV--TEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKP   71 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTCCH--HHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTT
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHc
Confidence            7899999999999999999999999999875  89999999999999  88999999999999999999999964

>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=99.86  E-value=6.3e-23  Score=134.47  Aligned_cols=75  Identities=31%  Similarity=0.627  Sum_probs=71.7

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      +++|+.|+||+|||+|||+++|..|+.+||++++  .+|+++||++|++||+++|++|.+.|..++.+|..++..|.
T Consensus        15 ~kdp~~pKrP~saf~lF~~~~r~~~~~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~   89 (93)
T 1cg7_A           15 KKDPNAPKRALSAYMFFANENRDIVRSENPDITF--GQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYN   89 (93)
T ss_dssp             CCCSSCCCSCCCHHHHHHHHHTSTTTTTCTTSCH--HHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999999999999875  89999999999999999999999999999999999998874

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

Probab=99.86  E-value=1.3e-21  Score=131.15  Aligned_cols=77  Identities=22%  Similarity=0.384  Sum_probs=69.6

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      ..++|+.||||+|||+|||+++|..|+.++|++++  .+|+++||++|++||+++|++|.++|..++.+|.+++..|.-
T Consensus        23 ~~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky   99 (106)
T 4euw_A           23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHN--AELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKY   99 (106)
T ss_dssp             -----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCH--HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             ccCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCc
Confidence            35789999999999999999999999999999876  899999999999999999999999999999999999999964

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

Probab=99.85  E-value=1e-21  Score=122.34  Aligned_cols=70  Identities=24%  Similarity=0.382  Sum_probs=62.6

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      ++||||+|||+||++++|..++..+|++++  .+|+++||++|++||+++|.+|.++|..++.+|.+++..|
T Consensus         1 gk~krP~~af~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Y   70 (71)
T 4a3n_A            1 GSIRRPMNAFMVWAKDERKRLAQQNPDLHN--AELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY   70 (71)
T ss_dssp             ----CCCCHHHHHHHHHHHHHHTTCTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC--
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCc
Confidence            469999999999999999999999999976  8999999999999999999999999999999999999887

>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=99.85  E-value=3.5e-22  Score=125.27  Aligned_cols=70  Identities=30%  Similarity=0.609  Sum_probs=66.6

Q ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           6 DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         6 p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      +++||||+|||+|||+++|..|+.+||++++  .+|+++||++|++||+  |++|.++|..++.+|.+++..|.
T Consensus         1 s~~PKrP~say~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~   70 (73)
T 3nm9_A            1 SDKPKRPLSAYALWLNSARESIKRENPGIKV--TEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFE   70 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSSSCCH--HHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999976  8999999999999998  99999999999999999998874

>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=99.85  E-value=1.6e-21  Score=125.13  Aligned_cols=74  Identities=23%  Similarity=0.355  Sum_probs=67.7

Q ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           5 KDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         5 ~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      .++.||||+|||+|||+++|..|+..||+++.  .+|+++||++|++||+++|++|.++|..++.+|..++..|.-
T Consensus         3 ~~~~pKrP~~af~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky   76 (83)
T 3f27_D            3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHN--AELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKY   76 (83)
T ss_dssp             ----CCCCCCHHHHHHHHHHHHHHHHCSSSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            57889999999999999999999999999976  899999999999999999999999999999999999999864

>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=99.85  E-value=1.9e-21  Score=123.97  Aligned_cols=72  Identities=24%  Similarity=0.368  Sum_probs=68.8

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      +.|+||+|||+|||+++|..|+..||++++  .+|+++||.+|++||+++|++|.+.|..++.+|..++..|..
T Consensus         1 ~~pkrP~~af~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~   72 (80)
T 1gt0_D            1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHN--SEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKY   72 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCH--HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCccccc
Confidence            479999999999999999999999999875  899999999999999999999999999999999999999964

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

Probab=99.85  E-value=1.8e-23  Score=138.07  Aligned_cols=78  Identities=29%  Similarity=0.549  Sum_probs=73.1

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      .+++|++|+||+|||+|||+++|..|+.+||+++.++.+|+++||++|++||+++|++|.++|..++.+|.+++..|.
T Consensus        16 ~~kdp~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y~   93 (97)
T 2lhj_A           16 AKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYA   93 (97)
T ss_dssp             TTSCCCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999833489999999999999999999999999999999999998874

>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=99.84  E-value=5.5e-21  Score=123.44  Aligned_cols=71  Identities=14%  Similarity=0.343  Sum_probs=68.1

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      ..|+||+|||+|||+++|..|..+||++++  .+|+++||++|++||+++|++|.++|..++.+|..++..|.
T Consensus         1 ~~pKRP~naf~lf~~~~r~~~~~~~P~~~~--~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (86)
T 2lef_A            1 MHIKKPLNAFMLYMKEMRANVVAESTLKES--AAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS   71 (86)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHHHSSCCCH--HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            369999999999999999999999999865  89999999999999999999999999999999999999996

>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=99.84  E-value=6.8e-21  Score=121.53  Aligned_cols=64  Identities=16%  Similarity=0.232  Sum_probs=60.4

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhh
Q psy3264           4 EKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK   68 (156)
Q Consensus         4 ~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k   68 (156)
                      |+|+.||||+|||+|||+++|..|+.+||+++ ++.+|+++||++|++||+++|++|.++|..+.
T Consensus         1 ~~~~~PKRP~say~lF~~e~R~~ik~~~P~~~-~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A            1 GSSGSSGRPKTGFQMWLEENRSNILSDNPDFS-DEADIIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHHHHHCTTCC-SHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCc-hhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            57999999999999999999999999999997 34999999999999999999999999999874

>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=99.84  E-value=5.3e-21  Score=121.54  Aligned_cols=72  Identities=22%  Similarity=0.392  Sum_probs=68.7

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      +.||||+|||+|||+++|..|+.++|++++  .+|+++||++|++||+++|++|.++|..++.+|..++..|.-
T Consensus         1 G~iKRP~naf~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky   72 (79)
T 3u2b_C            1 GHIKRPMNAFMVWSQIERRKIMEQSPDMHN--AEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKY   72 (79)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCcCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            479999999999999999999999999976  899999999999999999999999999999999999999864

>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=99.84  E-value=3.9e-21  Score=124.41  Aligned_cols=74  Identities=22%  Similarity=0.323  Sum_probs=69.4

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCCc
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPAG   83 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~~   83 (156)
                      ++|+||+|||+||+++.|..++..+|+ .  +++|++.||++|++||+++|.+|.++|..++.+|+++|..|.....
T Consensus         3 ~kPKrP~SAy~lf~~~~r~~~k~~~p~-~--~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~   76 (91)
T 1l8y_A            3 KLPESPKRAEEIWQQSVIGDYLARFKN-D--RVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPA   76 (91)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHHTTS-T--HHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCC-C--HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            589999999999999999999999998 4  4999999999999999999999999999999999999999976443

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

Probab=99.84  E-value=2.2e-21  Score=119.69  Aligned_cols=67  Identities=34%  Similarity=0.563  Sum_probs=62.0

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      +.||||+|||+|||+++|..++..||      .+|+++||++|++||+++|.+|.++|..++.+|.++|..|+
T Consensus         1 g~PKrP~say~~F~~~~r~~~k~~~p------~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y~   67 (67)
T 3fgh_A            1 GKPKRPRSAYNVYVAERFQEAKGDSP------QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWA   67 (67)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSSH------HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHhcCH------HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            57999999999999999999976554      69999999999999999999999999999999999999884

>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=99.84  E-value=4e-21  Score=122.75  Aligned_cols=73  Identities=21%  Similarity=0.304  Sum_probs=67.9

Q ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           6 DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         6 p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      ++.||||+|||+||++++|..|+..+|++++  .+|+++||.+|++||+++|++|.+.|..++..|.+++..|.-
T Consensus         2 ~~~pkRP~naf~lf~~~~r~~~~~~~p~~~~--~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky   74 (81)
T 1i11_A            2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHN--SNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKY   74 (81)
T ss_dssp             -CCSCCSCCHHHHHHHHHHHHHHTTCSSCCH--HHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC--
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            5789999999999999999999999999875  899999999999999999999999999999999999999864

>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=99.82  E-value=1.8e-20  Score=133.86  Aligned_cols=75  Identities=23%  Similarity=0.480  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      .++|+.||||+|||+|||+++|..|+.+||++++  ++|+++||++|++||+++|++|.++|..++.+|..++..|.
T Consensus        83 ~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~~~--~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~  157 (159)
T 2gzk_A           83 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSI--GDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR  157 (159)
T ss_dssp             SCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCCCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccccccccccchhhHhhHHHHHHhCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3689999999999999999999999999999875  89999999999999999999999999999999999998874

>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=99.80  E-value=3.2e-20  Score=124.63  Aligned_cols=74  Identities=24%  Similarity=0.479  Sum_probs=67.9

Q ss_pred             CCCCCCC-CCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCC
Q psy3264           3 KEKDVKP-RGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPP   81 (156)
Q Consensus         3 k~~p~~P-krP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~   81 (156)
                      .++|+.| |||+|||+|||+++|..|+    +++  +.+|+++||++|++||+++|.+|.++|..++.+|.+++..|...
T Consensus        11 ~kd~~~P~KrP~say~lF~~e~r~~~k----~~~--~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~   84 (108)
T 1v64_A           11 DKFDGRPTKPPPNSYSLYCAELMANMK----DVP--STERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLES   84 (108)
T ss_dssp             CCTTTSCCCCCSSHHHHHHHHHHHHCT----TSC--HHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHHHh----CCC--HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            5799999 9999999999999999876    454  48999999999999999999999999999999999999999754


Q ss_pred             C
Q psy3264          82 A   82 (156)
Q Consensus        82 ~   82 (156)
                      .
T Consensus        85 ~   85 (108)
T 1v64_A           85 L   85 (108)
T ss_dssp             S
T ss_pred             C
Confidence            3

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

Probab=99.80  E-value=6.8e-20  Score=119.54  Aligned_cols=72  Identities=22%  Similarity=0.319  Sum_probs=65.9

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHH---HHHhccCCHHHHHHHHHhhhhhhhhhcccccc
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKC---AERWKTMSEKEKKRFHEMADKDKKRYDTEMQS   77 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l---~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~   77 (156)
                      +..+++.||||+|||+|||+++|..|+.+  ++++  .+|+++|   |++|++||+++|++|.++|..++..|..++..
T Consensus         4 ~~~~~~~PKRP~sAf~lF~~e~R~~ik~e--~~~~--~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~~   78 (93)
T 2cto_A            4 GSSGMPNRKASRNAYYFFVQEKIPELRRR--GLPV--ARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGP   78 (93)
T ss_dssp             CCCCCCCCCSSCCHHHHHHHTTHHHHHHH--TCCC--SSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHc--CCCH--HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccccc
Confidence            45688999999999999999999999988  5554  7999999   99999999999999999999999999988754

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

Probab=99.79  E-value=6.9e-20  Score=132.59  Aligned_cols=75  Identities=23%  Similarity=0.480  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      .++|+.||||+|||+|||+++|..|+..||++++  .+|+++||.+|++||+++|++|.++|..++.+|..++..|.
T Consensus        96 ~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~~~--~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~  170 (173)
T 2yrq_A           96 FKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSI--GDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR  170 (173)
T ss_dssp             CCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSSCH--HHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCccccCcccHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3689999999999999999999999999999875  89999999999999999999999999999999999998884

>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=99.77  E-value=3.1e-19  Score=118.47  Aligned_cols=75  Identities=15%  Similarity=0.321  Sum_probs=64.5

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCC
Q psy3264           4 EKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPA   82 (156)
Q Consensus         4 ~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~   82 (156)
                      +...+||||+|||+|||++++.  ...+++++  +.+|+++||++|++||+++|++|.++|..++.+|.++|..|....
T Consensus         4 ~~~~~PKrP~say~lF~~e~~~--~p~~~~~~--~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~   78 (101)
T 1v63_A            4 GSSGPKKPPMNGYQKFSQELLS--NGELNHLP--LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSL   78 (101)
T ss_dssp             CCCSSCCCCSSSHHHHHHHHHH--HCTTTTSC--HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHh--CCCCCCCC--HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            5678999999999999999964  12233343  589999999999999999999999999999999999999996543

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

Probab=99.75  E-value=6.4e-20  Score=118.67  Aligned_cols=69  Identities=10%  Similarity=0.236  Sum_probs=61.2

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhcccc
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEM   75 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~   75 (156)
                      ++||+.||||+|||+|||+++|..|+.+||+++..+.+|+    ++|++||+++|++|.++|..++..|....
T Consensus        17 ~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~~~   85 (90)
T 2yuk_A           17 EKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRINK   85 (90)
T ss_dssp             HHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             cCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHhhH
Confidence            3689999999999999999999999999999861126776    99999999999999999999999887543

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

Probab=99.67  E-value=5.6e-18  Score=126.39  Aligned_cols=71  Identities=32%  Similarity=0.497  Sum_probs=65.1

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           4 EKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         4 ~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      ++|+.||||+|||+|||+++|..++..+|      .+|+++||++|++||+++|++|.++|..++.+|..+|..|..
T Consensus       110 kdp~~PKrP~say~lF~~e~r~~~k~~~p------~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  180 (214)
T 3tq6_A          110 TLLGKPKRPRSAYNVYVAERFQEAKGDSP------QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  180 (214)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSSCSSH------HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccCcccccchhhhhHHHHHHhhccCCH------HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47999999999999999999988765443      599999999999999999999999999999999999999964

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

Probab=99.63  E-value=9.9e-18  Score=126.90  Aligned_cols=71  Identities=32%  Similarity=0.497  Sum_probs=65.2

Q ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           4 EKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         4 ~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      ++|+.||||+|||+|||+++|..++..+|      .+|+++||++|++||+++|++|.++|..++.+|..+|..|..
T Consensus       142 kdp~~PKrP~say~lF~~e~r~~~k~~~p------~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~  212 (238)
T 3tmm_A          142 TLLGKPKRPRSAYNVYVAERFQEAKGDSP------QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEE  212 (238)
T ss_dssp             HHTTCCCCCCCHHHHHHHHHTTTSCCSSH------HHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccCCCCCCCcHHHHHHHHHHHHHhccCH------HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47999999999999999999988765443      599999999999999999999999999999999999999954

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

Probab=99.62  E-value=2.1e-16  Score=104.98  Aligned_cols=84  Identities=20%  Similarity=0.381  Sum_probs=76.2

Q ss_pred             hhhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q psy3264          68 KKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPVN  147 (156)
Q Consensus        68 k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~~~  147 (156)
                      -....+.+.+|+.|+...|+.++.+||++++.+|+++||++|++||+++|++|.++|+.++++|..+|+.|+.+......
T Consensus        15 p~~pKrP~say~lF~~~~r~~i~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~~   94 (102)
T 2co9_A           15 PNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSY   94 (102)
T ss_dssp             CCSCCCCCCHHHHTHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            34456778888888888899999999999999999999999999999999999999999999999999999999988877


Q ss_pred             Cccc
Q psy3264         148 EEAD  151 (156)
Q Consensus       148 ~~~~  151 (156)
                      .+..
T Consensus        95 ~e~~   98 (102)
T 2co9_A           95 TDSG   98 (102)
T ss_dssp             CCCS
T ss_pred             cccc
Confidence            6654

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

Probab=99.60  E-value=1.8e-16  Score=103.39  Aligned_cols=76  Identities=21%  Similarity=0.322  Sum_probs=69.6

Q ss_pred             hccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q psy3264          71 YDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPV  146 (156)
Q Consensus        71 y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~~  146 (156)
                      -.+.+.+|+.+....|+.++.+||++++.+|+++||+.|++||+++|++|.++|++++++|.++|+.|+.+.....
T Consensus         8 pKrP~say~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~~~~~   83 (92)
T 2cs1_A            8 IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMS   83 (92)
T ss_dssp             SCCCCCHHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTTTCCC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
Confidence            3567778888888889999999999999999999999999999999999999999999999999999999876643

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

Probab=99.58  E-value=2.7e-16  Score=103.88  Aligned_cols=77  Identities=23%  Similarity=0.316  Sum_probs=70.4

Q ss_pred             hhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264          69 KRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus        69 ~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      ..-.+.+.+|+.++...|+.++.+||++++++|+++||++|++||+++|++|.++|+.++++|+.+|..|..+.+.-
T Consensus         9 ~~PKRP~saf~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~~P~~   85 (99)
T 1k99_A            9 DFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDL   85 (99)
T ss_dssp             SSCCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCc
Confidence            34566788888888888999999999999999999999999999999999999999999999999999999987643

>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=99.58  E-value=3.1e-16  Score=97.96  Aligned_cols=69  Identities=25%  Similarity=0.483  Sum_probs=63.8

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      .+.+.+|..++.+.|+.++.+||++++++|++.||+.|++||+  |++|.++|+.++++|+++|+.|++++
T Consensus         5 KrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~kg   73 (73)
T 3nm9_A            5 KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEANG   73 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4567778888888899999999999999999999999999998  99999999999999999999999864

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

Probab=99.57  E-value=7.2e-16  Score=100.48  Aligned_cols=75  Identities=29%  Similarity=0.535  Sum_probs=68.2

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVA  144 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~  144 (156)
                      .-.+.+.+|+.++...|+.++.+||++++.+|+++||++|++||+++|++|.++|+.++++|..+|+.|+.+...
T Consensus         7 ~pKrP~~af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~   81 (92)
T 2crj_A            7 GPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAY   81 (92)
T ss_dssp             SSCCCCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHHH
Confidence            345677888888888899999999999999999999999999999999999999999999999999999876443

>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=99.57  E-value=2.1e-16  Score=99.68  Aligned_cols=72  Identities=33%  Similarity=0.572  Sum_probs=66.5

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR  141 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~  141 (156)
                      ...+.+.+|+.+....|+.++..||++++++|+++||+.|++||+++|++|.++|+.++++|..+|+.|+++
T Consensus         6 ~pKrP~saf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~k   77 (77)
T 1hme_A            6 APKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK   77 (77)
T ss_dssp             CCCCCCCTTHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            445678888888888899999999999999999999999999999999999999999999999999999753

>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=99.55  E-value=3.4e-16  Score=97.21  Aligned_cols=67  Identities=34%  Similarity=0.595  Sum_probs=60.8

Q ss_pred             ccccccCCCCCccccccccccCCCCCc--hhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY  138 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~--~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~  138 (156)
                      .+.+.+|..+....|+.++.+||++++  ++|++.||+.|++||+++|++|.++|+.++++|.++|..|
T Consensus         3 KrP~say~~F~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A            3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            456777777777889999999999876  9999999999999999999999999999999999999876

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

Probab=99.55  E-value=8.3e-16  Score=98.98  Aligned_cols=71  Identities=30%  Similarity=0.549  Sum_probs=64.2

Q ss_pred             hhhccccccCCCCCccccccccccCCCCC--chhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          69 KRYDTEMQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        69 ~~y~~~~~~~~~~~~~~r~~~~~~~p~~~--~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      ..-.+.+.+|+.++...|+.++.+||+++  +.+|++.||+.|++||+++|++|.++|+.++++|..+|..|+
T Consensus        14 ~~PKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A           14 KKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             SSCCCCCCHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            34556777888888888999999999987  599999999999999999999999999999999999999984

>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=99.54  E-value=4.6e-16  Score=101.60  Aligned_cols=73  Identities=33%  Similarity=0.593  Sum_probs=66.6

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      ...+.+.+|+.|+...|+.++.+||++++.+|+++||+.|++||+++|++|.++|+.++++|..+|+.|..+.
T Consensus        20 ~pKrP~saf~lF~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~~~~   92 (93)
T 1cg7_A           20 APKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATL   92 (93)
T ss_dssp             CCCSCCCHHHHHHHHHTSTTTTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHHHHT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            4456677777777788999999999999999999999999999999999999999999999999999999865

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

Probab=99.54  E-value=4.4e-16  Score=96.59  Aligned_cols=68  Identities=24%  Similarity=0.437  Sum_probs=60.6

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      .+.+++|+.+....|+.++..+|++++++|++.||+.|++||+++|++|.++|+.++++|..+++.|+
T Consensus         4 krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A            4 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             -CCCCHHHHHHHHHHHHHHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            45777888888888999999999999999999999999999999999999999999999999999885

>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=99.54  E-value=4.9e-16  Score=97.72  Aligned_cols=71  Identities=25%  Similarity=0.380  Sum_probs=64.9

Q ss_pred             hccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3264          71 YDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR  141 (156)
Q Consensus        71 y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~  141 (156)
                      -.+.+++|+.++...|+.++.+||++++++|+++||+.|++||+++|++|.++|+.++++|..++++|+.+
T Consensus         5 pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~   75 (76)
T 1hry_A            5 VKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCCC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence            35677788888888899999999999999999999999999999999999999999999999999988753

>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=99.53  E-value=9.4e-16  Score=98.69  Aligned_cols=73  Identities=15%  Similarity=0.291  Sum_probs=66.9

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVA  144 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~  144 (156)
                      .+.+++|+.++...|+.+..+||++++++|+++||+.|++||+++|++|.++|+.++++|..+|+.|..+...
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~   76 (86)
T 2lef_A            4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY   76 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSST
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCC
Confidence            4567788888888899999999999999999999999999999999999999999999999999999866543

>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=99.53  E-value=1.2e-15  Score=96.88  Aligned_cols=72  Identities=26%  Similarity=0.393  Sum_probs=65.9

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV  143 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~  143 (156)
                      .+.+.+|+.++...|+.++..||++++++|+++||+.|++||+++|++|.++|+.++++|..+|+.|+....
T Consensus         4 krP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~   75 (80)
T 1gt0_D            4 KRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPR   75 (80)
T ss_dssp             CCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccCCC
Confidence            456777888888889999999999999999999999999999999999999999999999999999987543

>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=99.53  E-value=1.1e-15  Score=98.73  Aligned_cols=71  Identities=15%  Similarity=0.214  Sum_probs=61.6

Q ss_pred             cccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy3264          73 TEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVA  144 (156)
Q Consensus        73 ~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~  144 (156)
                      +.+.+|..+....|..++..+|+ ++.+|++.||++|++||+++|++|+++|+.++++|+++|..|+.++..
T Consensus         7 rP~SAy~lf~~~~r~~~k~~~p~-~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~~   77 (91)
T 1l8y_A            7 SPKRAEEIWQQSVIGDYLARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAA   77 (91)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGS
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            34445544555568889999999 899999999999999999999999999999999999999999987665

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

Probab=99.53  E-value=7.1e-16  Score=98.61  Aligned_cols=74  Identities=31%  Similarity=0.532  Sum_probs=66.7

Q ss_pred             hhhccccccCCCCCccccccccccCCCCC--chhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          69 KRYDTEMQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        69 ~~y~~~~~~~~~~~~~~r~~~~~~~p~~~--~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      ..-.+.+.+|+.++...|+.++.+||+++  +.+|++.||+.|++||+++|++|.++|+.++++|..+|..|....
T Consensus         6 ~~PKrP~say~lF~~~~r~~~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~   81 (83)
T 1aab_A            6 KKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK   81 (83)
T ss_dssp             TCCCCCCCHHHHHHHHHHHHHTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCCS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence            34456778888888888999999999986  499999999999999999999999999999999999999998764

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

Probab=99.53  E-value=1.5e-15  Score=99.95  Aligned_cols=75  Identities=35%  Similarity=0.577  Sum_probs=69.2

Q ss_pred             hhhhccccccCCCCCccccccccccCCCCC--chhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          68 KKRYDTEMQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        68 k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~--~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      -....+.+.+|+.|+...|+.++.+||+++  +.+|+++||+.|++||+++|++|.++|+.++++|..+|..|+.+.
T Consensus        20 p~~pKrP~say~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~~   96 (97)
T 2lhj_A           20 PNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQRK   96 (97)
T ss_dssp             CCCCCCCCCSSTHHHHGGGGGHHHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            344567888999999999999999999999  999999999999999999999999999999999999999998753

>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=99.52  E-value=1.6e-15  Score=97.43  Aligned_cols=72  Identities=25%  Similarity=0.373  Sum_probs=66.2

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV  143 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~  143 (156)
                      .+.+++|+.++...|+.++.+||++++++|+++||+.|++||+++|++|.++|+.++++|..++++|+.+..
T Consensus         6 KRP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~pr   77 (85)
T 1j46_A            6 KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPR   77 (85)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccCCC
Confidence            456777888888889999999999999999999999999999999999999999999999999999987654

>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=99.50  E-value=1.5e-15  Score=96.10  Aligned_cols=72  Identities=26%  Similarity=0.396  Sum_probs=66.0

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV  143 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~  143 (156)
                      .+.+++|+.++...|+.++.++|++++++|+++||+.|++||+++|++|.++|+.++++|..++++|+.+-.
T Consensus         4 KRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~Pr   75 (79)
T 3u2b_C            4 KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRPR   75 (79)
T ss_dssp             CCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCCC
Confidence            457778888888889999999999999999999999999999999999999999999999999999986543

>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=99.49  E-value=1.7e-15  Score=96.77  Aligned_cols=72  Identities=24%  Similarity=0.427  Sum_probs=66.4

Q ss_pred             hccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          71 YDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        71 y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      -.+.+++|+.++...|+.++..||++++++|+++||+.|++||+++|++|.++|+.++++|..+|+.|+.+-
T Consensus         7 pKrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~P   78 (83)
T 3f27_D            7 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRP   78 (83)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCC
Confidence            456778888888888999999999999999999999999999999999999999999999999999998654

>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=99.49  E-value=1.6e-15  Score=97.89  Aligned_cols=71  Identities=15%  Similarity=0.166  Sum_probs=65.3

Q ss_pred             hhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          69 KRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK  139 (156)
Q Consensus        69 ~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~  139 (156)
                      ....+.+++|+.++...|+.++.+||++++.+|+++||++|++||+++|++|.++|+.++++|..++++|+
T Consensus        16 ~~pKrP~~af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           16 NKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             SSCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            35567788888888888999999999999999999999999999999999999999999999999998875

>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=99.49  E-value=7.1e-16  Score=98.42  Aligned_cols=73  Identities=25%  Similarity=0.400  Sum_probs=66.3

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      .-.+.+.+|+.++...|+.++.+||++++.+|+++||+.|++||+++|++|.++|+.++++|..+|+.|+.+-
T Consensus         7 ~pkrP~~af~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~p   79 (82)
T 1wz6_A            7 GARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSGP   79 (82)
T ss_dssp             CSCCCCCHHHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCCT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcCC
Confidence            3456778888888888999999999999999999999999999999999999999999999999999997653

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

Probab=99.48  E-value=2.1e-15  Score=94.13  Aligned_cols=68  Identities=35%  Similarity=0.579  Sum_probs=62.7

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR  141 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~  141 (156)
                      .+.+.+|..+....|+.++.+||++++++|++.||+.|++|  ++|++|.++|+.++++|..+|..|+.+
T Consensus         5 KrP~say~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A            5 KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            45677777788888999999999999999999999999999  999999999999999999999999864

>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=99.47  E-value=2.1e-15  Score=95.94  Aligned_cols=72  Identities=22%  Similarity=0.332  Sum_probs=63.5

Q ss_pred             hccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          71 YDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        71 y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      -.+.+++|+.+....++.++..+|++++++|+++||+.|++||+++|++|.++|+.++++|..++++|+.+.
T Consensus         5 pkRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~p   76 (81)
T 1i11_A            5 IKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKP   76 (81)
T ss_dssp             SCCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC----
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCeecc
Confidence            356778888888888999999999999999999999999999999999999999999999999999987653

>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=99.46  E-value=3.4e-14  Score=94.02  Aligned_cols=72  Identities=17%  Similarity=0.349  Sum_probs=58.7

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      .+.+.+|..|+.+.+.  ...++++++++|++.||++|++||+++|++|.++|++++++|+++|+.|..++.+.
T Consensus        10 KrP~say~lF~~e~~~--~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~~   81 (101)
T 1v63_A           10 KPPMNGYQKFSQELLS--NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             CCCSSSHHHHHHHHHH--HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCCCHHHHHHHHHHh--CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHH
Confidence            3455566555555432  23456688999999999999999999999999999999999999999999987654

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

Probab=99.46  E-value=4.6e-15  Score=99.10  Aligned_cols=78  Identities=24%  Similarity=0.391  Sum_probs=68.5

Q ss_pred             hhhhhhhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          65 DKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        65 ~~~k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      ..+.....+.+.+|+.++...|+.++..+|++++++|+++||+.|++||+++|++|.++|+.++++|+.+++.|+.+-
T Consensus        24 ~k~~~~pKRP~naf~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~P  101 (106)
T 4euw_A           24 SKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQP  101 (106)
T ss_dssp             ----CCCCCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC--
T ss_pred             cCCCCcCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcCC
Confidence            344566778889999999999999999999999999999999999999999999999999999999999999998653

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

Probab=99.44  E-value=1.6e-14  Score=88.62  Aligned_cols=63  Identities=27%  Similarity=0.472  Sum_probs=55.4

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY  138 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~  138 (156)
                      .+.+.+|..+....|+.++..||    ++|++.||+.|++||+++|++|.++|+.++++|+++|..|
T Consensus         4 KrP~say~~F~~~~r~~~k~~~p----~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            4 KRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSSSH----HHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHHhcCH----HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34566677777777888877765    6999999999999999999999999999999999999988

>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=99.40  E-value=8.3e-14  Score=93.22  Aligned_cols=69  Identities=16%  Similarity=0.244  Sum_probs=60.2

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVA  144 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~  144 (156)
                      .+.+.+|..|+.+.|+.++    ++++.+|++.||+.|++||+++|++|.++|+.++++|..+|..|..+...
T Consensus        19 KrP~say~lF~~e~r~~~k----~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~   87 (108)
T 1v64_A           19 KPPPNSYSLYCAELMANMK----DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPE   87 (108)
T ss_dssp             CCCSSHHHHHHHHHHHHCT----TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             CCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            4556667666767677766    78999999999999999999999999999999999999999999987643

>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=99.38  E-value=8.5e-15  Score=94.99  Aligned_cols=67  Identities=21%  Similarity=0.376  Sum_probs=60.8

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMT  136 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~  136 (156)
                      .-.+.+.+|+.|+...|+.++.+||++++.+|+++||+.|++||+++|++|.++|+.++++|+++|.
T Consensus        20 ~pKrP~say~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A           20 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             CCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456777788888888999999999999999999999999999999999999999999999988764

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

Probab=99.23  E-value=8.5e-13  Score=85.82  Aligned_cols=64  Identities=22%  Similarity=0.290  Sum_probs=57.8

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHH---HHHhccCChHHHHHHHHHHHHHHHHHHHHH
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKEL---GKKWADVDPSVKTKYEQMAEKDKARYEKEM  135 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~---~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~  135 (156)
                      ...+.+.+|..|+.+.|+.++.+  ++++.+|++.|   |++|++||++||++|.++|++++++|++++
T Consensus        10 ~PKRP~sAf~lF~~e~R~~ik~e--~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A           10 NRKASRNAYYFFVQEKIPELRRR--GLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             CCCSSCCHHHHHHHTTHHHHHHH--TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            34567788888888889999887  89999999999   999999999999999999999999999886

>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=99.18  E-value=1.1e-12  Score=83.36  Aligned_cols=57  Identities=19%  Similarity=0.267  Sum_probs=52.4

Q ss_pred             hccccccCCCCCccccccccccCCCCC-chhHHHHHHHHhccCChHHHHHHHHHHHHH
Q psy3264          71 YDTEMQSYTPPAGEKRGKIKQDNPEYG-VGDIAKELGKKWADVDPSVKTKYEQMAEKD  127 (156)
Q Consensus        71 y~~~~~~~~~~~~~~r~~~~~~~p~~~-~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~  127 (156)
                      ..+.+.+|..++...|+.++.+||+++ +++|+++||++|++||+++|++|.++|+.+
T Consensus         6 PKRP~say~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A            6 SGRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            356778888888888999999999998 999999999999999999999999999987

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

Probab=99.16  E-value=5.8e-12  Score=81.25  Aligned_cols=68  Identities=18%  Similarity=0.245  Sum_probs=61.2

Q ss_pred             hhhhhhhhhccccccCCCCCccccccccccCCCCC--chhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHH
Q psy3264          63 MADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE  134 (156)
Q Consensus        63 ~a~~~k~~y~~~~~~~~~~~~~~r~~~~~~~p~~~--~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e  134 (156)
                      ...+|-..-.+.+.+|..++...|+.|+.+||+++  +++|+    ++|++||+++|+||+++|++++++|..+
T Consensus        15 k~~kDpnaPKRp~sAf~lf~~e~R~kik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           15 KWEKEEALGEMATVAPVLYTNINFPNLKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             HHHHHHHHGGGCSSSHHHHHHHHCTTHHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             hccCCCCCCCCCccHHHHHHHHhHHHHHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            34456667788999999999999999999999999  99998    9999999999999999999999999753

---

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	156
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	8e-14
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	7e-07
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	7e-10
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-08
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	7e-09
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	1e-07
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-08
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-06
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	2e-08
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	5e-07
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	2e-08
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	1e-06
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-08
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-06
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	3e-07
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	5e-07
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	6e-07
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	7e-06
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	7e-07
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	4e-05
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	8e-07
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	5e-06
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	8e-06
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-04

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

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]

 Score = 60.7 bits (147), Expect = 8e-14
 Identities = 49/71 (69%), Positives = 61/71 (85%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA  D
Sbjct: 1  KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60

Query: 68 KKRYDTEMQSY 78
          K RY+ EM++Y
Sbjct: 61 KARYEREMKTY 71

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

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]

 Score = 42.2 bits (99), Expect = 7e-07
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 84  EKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY 138
             R + K+ +P+  V   + +K+  ++W  +    K K+E MA+ DKARYE+EM  Y
Sbjct: 15  TCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71

>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 = 50.6 bits (121), Expect = 7e-10
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+   +A+  F    R + K +HP  +    + +KK  E W   +  +K+ + + A K 
Sbjct: 2  APKRPPSAFFLFCSEYRPKIKGEHPGLS--IGDVAKKLGEMWNNTAADDKQPYEKKAAKL 59

Query: 68 KKRYDTEMQSY 78
          K++Y+ ++ +Y
Sbjct: 60 KEKYEKDIAAY 70

>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 = 47.1 bits (112), Expect = 2e-08
 Identities = 24/58 (41%), Positives = 37/58 (63%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           E R KIK ++P   +GD+AK+LG+ W +     K  YE+ A K K +YEK++ AY+ +
Sbjct: 16  EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 73

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

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

 Score = 47.5 bits (113), Expect = 7e-09
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 4/71 (5%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          KP+  ++AY  ++   RE  K+++P       E +K+  E W+ M +K +  +   A K 
Sbjct: 3  KPKRPLSAYMLWLNSARESIKRENPGIK--VTEVAKRGGELWRAMKDKSE--WEAKAAKA 58

Query: 68 KKRYDTEMQSY 78
          K  YD  ++ +
Sbjct: 59 KDDYDRAVKEF 69

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

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

 Score = 44.4 bits (105), Expect = 1e-07
 Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN 140
             R  IK++NP   V ++AK  G+ W       K+++E  A K K  Y++ +  ++ 
Sbjct: 17  SARESIKRENPGIKVTEVAKRGGELWRA--MKDKSEWEAKAAKAKDDYDRAVKEFEA 71

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

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

 Score = 47.6 bits (113), Expect = 1e-08
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 3  KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHE 62
          K    KP+  ++A   F +  R + +++ PE +   +E ++  A  W  +SEK+K ++  
Sbjct: 15 KGGSEKPKRPVSAMFIFSEEKRRQLQEERPELS--ESELTRLLARMWNDLSEKKKAKYKA 72

Query: 63 MADKDKKRYDTEMQSYT 79
               K + + +    +
Sbjct: 73 REAALKAQSERKSGPSS 89

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

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

 Score = 41.9 bits (98), Expect = 1e-06
 Identities = 17/87 (19%), Positives = 36/87 (41%)

Query: 53  SEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADV 112
           S    K   E      ++    + +    + EKR +++++ PE    ++ + L + W D+
Sbjct: 3   SGSSGKPSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDL 62

Query: 113 DPSVKTKYEQMAEKDKARYEKEMTAYK 139
               K KY+      KA+ E++     
Sbjct: 63  SEKKKAKYKAREAALKAQSERKSGPSS 89

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

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

 Score = 47.2 bits (112), Expect = 2e-08
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+  ++AY FF    R+  + ++P  ++ F +  KK  E+WK ++ +EK+ +   A  D
Sbjct: 20 APKRALSAYMFFANENRDIVRSENP--DITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77

Query: 68 KKRYDTEMQSY 78
          KKRY++E + Y
Sbjct: 78 KKRYESEKELY 88

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

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

 Score = 43.3 bits (102), Expect = 5e-07
 Identities = 28/87 (32%), Positives = 42/87 (48%)

Query: 53  SEKEKKRFHEMADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADV 112
           + +E K+      KD       + +Y   A E R  ++ +NP+   G + K+LG+KW  +
Sbjct: 3   TPREPKKRTTRKKKDPNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKAL 62

Query: 113 DPSVKTKYEQMAEKDKARYEKEMTAYK 139
            P  K  YE  A+ DK RYE E   Y 
Sbjct: 63  TPEEKQPYEAKAQADKKRYESEKELYN 89

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.7 bits (111), Expect = 2e-08
 Identities = 17/56 (30%), Positives = 31/56 (55%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
            +R K+ Q+NP+    +I+K LG +W  +  + K  +   A++ +A + KE   YK
Sbjct: 16  GQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK 71

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 80

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.1 bits (99), Expect = 1e-06
 Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          + +  M A+  + +  R +  +++P+ +   +E SK+    WK +SE EK+ F + A + 
Sbjct: 2  RVKRPMNAFMVWSRGQRRKMAQENPKMH--NSEISKRLGAEWKLLSETEKRPFIDEAKRL 59

Query: 68 KKRYDTEMQSY 78
          +  +  E   Y
Sbjct: 60 RALHMKEHPDY 70

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101

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

 Score = 47.2 bits (112), Expect = 2e-08
 Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
            +  M  Y  F Q      +  H        E   +   RW+ +S+ +K+ + ++A++ 
Sbjct: 8  PKKPPMNGYQKFSQELLSNGELNHLP----LKERMVEIGSRWQRISQSQKEHYKKLAEEQ 63

Query: 68 KKRYDTEMQSYTPPAGEKR 86
          +++Y   +  +      + 
Sbjct: 64 QRQYKVHLDLWVKSLSPQD 82

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 101

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

 Score = 41.0 bits (96), Expect = 4e-06
 Identities = 10/58 (17%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           E     + ++    + +   E+G +W  +  S K  Y+++AE+ + +Y+  +  +   
Sbjct: 22  ELLSNGELNHLP--LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKS 77

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70

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

 Score = 43.3 bits (102), Expect = 3e-07
 Identities = 13/55 (23%), Positives = 26/55 (47%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY 138
           ++R KI Q  P+    +I+K LG +W  +    K  Y +   +   ++ ++   Y
Sbjct: 16  DERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY 70

>d1i11a_ a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId: 10090]} Length = 70

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

 Score = 42.9 bits (101), Expect = 5e-07
 Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
          M A+  + +  R +  +  P+ +   +  SK    RWK M+  EK+ ++E   +  K++ 
Sbjct: 7  MNAFMVWAKDERRKILQAFPDMH--NSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHL 64

Query: 73 TEMQSY 78
           +   Y
Sbjct: 65 EKYPDY 70

>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 = 43.0 bits (101), Expect = 6e-07
 Identities = 15/71 (21%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
           P+  +T Y  F    R ++ K HPE +    + +K  ++++K + EK+K ++ +   ++
Sbjct: 10 FPKKPLTPYFRFFMEKRAKYAKLHPEMS--NLDLTKILSKKYKELPEKKKMKYIQDFQRE 67

Query: 68 KKRYDTEMQSY 78
          K+ ++  +  +
Sbjct: 68 KQEFERNLARF 78

>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 = 40.3 bits (94), Expect = 7e-06
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           EKR K  + +PE    D+ K L KK+ ++    K KY Q  +++K  +E+ +  ++  
Sbjct: 24  EKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED 81

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

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]

 Score = 42.5 bits (100), Expect = 7e-07
 Identities = 11/58 (18%), Positives = 26/58 (44%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           E R  +  ++       I + LG++W  +    + KY ++A K++  + +    +  R
Sbjct: 16  EMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSAR 73

>d2lefa_ a.21.1.1 (A:) Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

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]

 Score = 37.9 bits (88), Expect = 4e-05
 Identities = 11/76 (14%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
          + A+  +++  R     +   +    A  ++    RW  +S +E+ +++E+A K+++ + 
Sbjct: 7  LNAFMLYMKEMRANVVAESTLKE--SAAINQILGRRWHALSREEQAKYYELARKERQLHM 64

Query: 73 TEMQSYTPPAGEKRGK 88
               ++      + K
Sbjct: 65 QLYPGWSARDNYGKKK 80

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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

 Score = 42.5 bits (100), Expect = 8e-07
 Identities = 17/58 (29%), Positives = 33/58 (56%)

Query: 84  EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           ++R K+  +NP     +I+K+LG +W  +  + K  + Q A+K +A + ++   YK R
Sbjct: 18  DQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75

>d1j46a_ a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 9606]} Length = 85

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

 Score = 40.2 bits (94), Expect = 5e-06
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 8  KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
          + +  M A+  + +  R +   ++P      +E SK+   +WK ++E EK  F + A K 
Sbjct: 4  RVKRPMNAFIVWSRDQRRKMALENPRMR--NSEISKQLGYQWKMLTEAEKWPFFQEAQKL 61

Query: 68 KKRYDTEMQSY 78
          +  +  +  +Y
Sbjct: 62 QAMHREKYPNY 72

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108

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

 Score = 40.3 bits (94), Expect = 8e-06
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 2  PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFH 61
           K      +    +Y+ +        K           E    C+++WK +S+KEK  +H
Sbjct: 11 DKFDGRPTKPPPNSYSLYCAELMANMKDVP------STERMVLCSQQWKLLSQKEKDAYH 64

Query: 62 EMADKDKKRYDTEMQSY 78
          +  D+ KK Y+ E+  +
Sbjct: 65 KKCDQKKKDYEVELLRF 81

>d1v64a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 108

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

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 7/54 (12%), Positives = 20/54 (37%)

Query: 88  KIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
           ++  +  +    +      ++W  +    K  Y +  ++ K  YE E+  +   
Sbjct: 31  ELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLES 84

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	156
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.87
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.87
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.86
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.86
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.86
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.85
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.85
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.82
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.81
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.77
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.75
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.61
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.55
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.55
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.52
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.51
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	99.47
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	99.46
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.44
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.36
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.21
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	99.19
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	97.75
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	97.54

>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=99.87  E-value=4e-23  Score=127.48  Aligned_cols=71  Identities=69%  Similarity=1.236  Sum_probs=68.0

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      +||||+|||+|||+++|..|+.+||+..+++++|+++||.+|++||+++|++|.++|..++.+|..+|..|
T Consensus         1 KPKrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            59999999999999999999999999877779999999999999999999999999999999999999876

>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=99.87  E-value=1.8e-22  Score=130.67  Aligned_cols=76  Identities=30%  Similarity=0.616  Sum_probs=72.1

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      .+++|++||||+|||+|||.++|..|+.++|+++.  .+|++.||.+|++||+++|..|.+.|..++.+|..+|..|.
T Consensus        14 ~~k~p~~PKrP~saf~lF~~e~r~~ik~~~p~~~~--~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~   89 (93)
T d1lwma_          14 KKKDPNAPKRALSAYMFFANENRDIVRSENPDITF--GQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYN   89 (93)
T ss_dssp             CCCCSSCCCCCCCHHHHHHHHHHHHHHHHCTTSCH--HHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcCCCCCCCCHHHHHHHHHHHHHHHhCCCCcH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35799999999999999999999999999999875  89999999999999999999999999999999999998874

>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=99.86  E-value=3.6e-22  Score=125.74  Aligned_cols=72  Identities=24%  Similarity=0.368  Sum_probs=68.9

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      ++||||+|||+||++++|..|+.+||+++.  .+|+++||.+|++||+++|.+|.++|..++.+|..++..|..
T Consensus         1 ~kiKRP~nAy~lF~~~~r~~~~~~~p~~~~--~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~   72 (80)
T d1gt0d_           1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHN--SEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKY   72 (80)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHHTTSTTSCH--HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHcCCCCH--HHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccC
Confidence            579999999999999999999999999876  899999999999999999999999999999999999999963

>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=99.86  E-value=1.4e-22  Score=130.69  Aligned_cols=79  Identities=20%  Similarity=0.378  Sum_probs=74.7

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPA   82 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~   82 (156)
                      +++|+.|+||+|||+||++++|..++..||++++  .+|++.||..|+.||+++|++|.+.|..++.+|..++..|...+
T Consensus         5 kk~p~~PKrP~say~lf~~~~r~~~~~~~p~~~~--~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~~   82 (91)
T d1k99a_           5 KKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSN--LDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH   82 (91)
T ss_dssp             CSSSSSCCCSCCHHHHHHHHHHHHHHTTCTTSCS--HHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCC
T ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            6899999999999999999999999999999986  89999999999999999999999999999999999999996544


Q ss_pred             c
Q psy3264          83 G   83 (156)
Q Consensus        83 ~   83 (156)
                      +
T Consensus        83 p   83 (91)
T d1k99a_          83 P   83 (91)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.86  E-value=9.2e-22  Score=126.59  Aligned_cols=75  Identities=21%  Similarity=0.344  Sum_probs=70.7

Q ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           2 PKEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         2 ~k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      ++++|+.||||+|||+|||+++|..|+..||++++  .+|+++||.+|+.||+++|++|.++|..++..|.+....+
T Consensus        14 ~~~~~~~PKrP~say~lF~~e~r~~~~~~~p~~~~--~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~~~~~   88 (90)
T d1wgfa_          14 GKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSE--SELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPS   88 (90)
T ss_dssp             CSSCCCCCCCCCCHHHHHHHHTHHHHHHHCTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSSC
T ss_pred             CCCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            57799999999999999999999999999999875  8999999999999999999999999999999999887654

>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=99.85  E-value=1e-21  Score=125.09  Aligned_cols=73  Identities=22%  Similarity=0.315  Sum_probs=69.6

Q ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           6 DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         6 p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      -++||||+|||+||++++|..|+.+||+++.  .+|+++||..|++||+++|.+|.++|..++.+|..++..|..
T Consensus         2 ~~~iKRP~nay~lF~~~~r~~i~~~~p~~~~--~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~   74 (85)
T d1j46a_           2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (85)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHHHHSTTSCH--HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHhccCCH--HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhcc
Confidence            3789999999999999999999999999875  899999999999999999999999999999999999999964

>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=99.85  E-value=9e-23  Score=128.37  Aligned_cols=71  Identities=24%  Similarity=0.518  Sum_probs=68.4

Q ss_pred             CCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           7 VKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         7 ~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      |.||||+|||+|||+++|..|+.+||++++  ++|+++||.+|++||+++|..|...|..++.+|.++|..|.
T Consensus         1 NaPKrP~say~~f~~~~r~~i~~~~p~~~~--~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~   71 (79)
T d1hsma_           1 NAPKRPPSAFFLFCSEYRPKIKGEHPGLSI--GDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR   71 (79)
T ss_dssp             CCCCCCCCSHHHHHHHHHHHHHHHCTTCCT--TTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCcHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            679999999999999999999999999976  89999999999999999999999999999999999999984

>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=99.84  E-value=1.3e-21  Score=120.17  Aligned_cols=69  Identities=22%  Similarity=0.342  Sum_probs=65.0

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY   78 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~   78 (156)
                      ++|||+|||+|||+++|..|+.+||+++.  ++|+++||.+|++||+++|++|.++|..++.+|.+++..|
T Consensus         2 ~iKRP~nay~lf~~~~r~~i~~~~p~~~~--~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           2 HIKRPMNAFMVWAKDERRKILQAFPDMHN--SNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CSCCSCCHHHHHHHHHHHHHHTTCSSCCH--HHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHhccCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            46899999999999999999999999876  8999999999999999999999999999999999887765

>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=99.82  E-value=5.1e-21  Score=118.46  Aligned_cols=71  Identities=28%  Similarity=0.587  Sum_probs=66.2

Q ss_pred             CCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           6 DVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         6 p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      .+.||||+|||+|||+++|..|+.+||++++  .+|+++||.+|++|++  |++|.++|..++.+|..++..|..
T Consensus         1 sn~PKrP~say~lf~~~~r~~~k~~~p~~~~--~eisk~l~~~Wk~~~e--K~~y~~~a~~~k~~y~~~~~~y~~   71 (73)
T d1qrva_           1 SDKPKRPLSAYMLWLNSARESIKRENPGIKV--TEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             CCSCCCCCCHHHHHHHHHHHHHHHTSTTCCH--HHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CccCCCCCcHHHHHHHHHHHHHHHHcCCCCH--HHHHHHHHHHhcChhH--HHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999999999876  8999999999999974  899999999999999999998854

>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=99.81  E-value=4.1e-20  Score=117.76  Aligned_cols=71  Identities=14%  Similarity=0.337  Sum_probs=67.4

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTP   80 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~   80 (156)
                      ..|||+|||+||+++.|..|..+||+++.  ++|+++||.+|++||+++|.+|.++|.+++..|...+..|..
T Consensus         2 hikRP~naf~lF~~~~r~~~~~~~P~~~~--~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~   72 (86)
T d2lefa_           2 HIKKPLNAFMLYMKEMRANVVAESTLKES--AAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA   72 (86)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSSCCCH--HHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHCCCCCH--HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            46899999999999999999999999876  899999999999999999999999999999999999999864

>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=99.77  E-value=1.2e-19  Score=118.83  Aligned_cols=75  Identities=16%  Similarity=0.360  Sum_probs=67.2

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPP   81 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~   81 (156)
                      .+...|||||+|||+|||+++|..+...|+  +  +.+|+++||.+|++||+++|++|.++|..++.+|..+|..|...
T Consensus         3 ~~~~~p~KrP~~ay~~F~~e~r~~~~~~~~--~--~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~   77 (101)
T d1v63a_           3 SGSSGPKKPPMNGYQKFSQELLSNGELNHL--P--LKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKS   77 (101)
T ss_dssp             CCCCSSCCCCSSSHHHHHHHHHHHCTTTTS--C--HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHhcCC--C--HHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            356788999999999999999998876554  3  48999999999999999999999999999999999999999643

>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=99.75  E-value=5.7e-19  Score=116.97  Aligned_cols=74  Identities=22%  Similarity=0.413  Sum_probs=66.3

Q ss_pred             CCCCCCCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCCCCC
Q psy3264           3 KEKDVKPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYTPPA   82 (156)
Q Consensus         3 k~~p~~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~~~~   82 (156)
                      +.++.|||+|+|||+|||+++|..    +|+++.  .+|+++||.+|++||+++|++|.++|..++.+|..+|..|....
T Consensus        12 ~~~~~p~K~P~~ay~lF~~~~r~~----~~~~~~--~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~~   85 (108)
T d1v64a_          12 KFDGRPTKPPPNSYSLYCAELMAN----MKDVPS--TERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESL   85 (108)
T ss_dssp             CTTTSCCCCCSSHHHHHHHHHHHH----CTTSCH--HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             cCCCCCCCCCCcHHHHHHHHHHHH----ccCCCH--HHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            457888999999999999998864    577655  89999999999999999999999999999999999999996543

>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=99.61  E-value=9.8e-17  Score=100.26  Aligned_cols=74  Identities=32%  Similarity=0.566  Sum_probs=68.0

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      .+.+.+|+.+....|+.++.+||++++++|++.||..|++||+++|.+|.+.|+.++++|..+|+.|+.+..+.
T Consensus         4 KrP~say~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~~~~   77 (79)
T d1hsma_           4 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPD   77 (79)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHTTTT
T ss_pred             CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCC
Confidence            45677788888888999999999999999999999999999999999999999999999999999999987654

>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=99.55  E-value=3.1e-16  Score=98.14  Aligned_cols=73  Identities=26%  Similarity=0.383  Sum_probs=67.5

Q ss_pred             hccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy3264          71 YDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV  143 (156)
Q Consensus        71 y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~  143 (156)
                      ..+.+++|+.+....|+.++.+||++++++|+++||..|++||+++|++|.++|+.++++|..+|+.|+....
T Consensus         3 iKRP~nAy~lF~~~~r~~~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p~   75 (80)
T d1gt0d_           3 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPR   75 (80)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCCC
Confidence            3567888888888889999999999999999999999999999999999999999999999999999986643

>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=99.55  E-value=9e-17  Score=98.20  Aligned_cols=67  Identities=22%  Similarity=0.335  Sum_probs=62.3

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY  138 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~  138 (156)
                      .+.+++|+.++...|+.++.+||++++++|++.||..|++||+++|++|.++|+.++++|.+++++|
T Consensus         4 KRP~nay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           4 KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CCSCCHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            5678888888889999999999999999999999999999999999999999999999999887654

>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=99.55  E-value=2.6e-16  Score=99.60  Aligned_cols=74  Identities=26%  Similarity=0.379  Sum_probs=68.9

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV  143 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~  143 (156)
                      +..+.+++|+.+....|+.++.+||++++++|+++||..|++||+++|.+|.++|+.++++|..+|+.|+.+..
T Consensus         4 ~iKRP~nay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p~   77 (85)
T d1j46a_           4 RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPR   77 (85)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCCC
Confidence            45678888988899999999999999999999999999999999999999999999999999999999987654

>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=99.52  E-value=7.1e-16  Score=97.77  Aligned_cols=74  Identities=15%  Similarity=0.280  Sum_probs=67.5

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      .+.+++|+.|....|+.+..+||++++++|+++||..|++||+++|++|.++|+.++++|..++++|+......
T Consensus         4 kRP~naf~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~~   77 (86)
T d2lefa_           4 KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG   77 (86)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCCC
Confidence            46778888888888999999999999999999999999999999999999999999999999999997654433

>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=99.51  E-value=1.7e-15  Score=97.36  Aligned_cols=71  Identities=34%  Similarity=0.627  Sum_probs=63.9

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      .+.+.+|+.+..+.|+.++.++|++++.+|++.||+.|++||+++|.+|.+.|+.++++|..+|..|++++
T Consensus        22 KrP~saf~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~~~l   92 (93)
T d1lwma_          22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATL   92 (93)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            35566666666677899999999999999999999999999999999999999999999999999999764

>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=99.47  E-value=4.8e-15  Score=91.04  Aligned_cols=69  Identities=25%  Similarity=0.467  Sum_probs=63.1

Q ss_pred             ccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS  142 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~  142 (156)
                      .+.+.+|+.+....|+.++.+||++++.+|+++||+.|++|+  +|++|.++|+.++++|..+|+.|++++
T Consensus         5 KrP~say~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~g   73 (73)
T d1qrva_           5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEANG   73 (73)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCcHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            467778888888889999999999999999999999999986  599999999999999999999998864

>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=99.46  E-value=5.7e-15  Score=94.43  Aligned_cols=77  Identities=23%  Similarity=0.344  Sum_probs=69.4

Q ss_pred             hccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC
Q psy3264          71 YDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAPVN  147 (156)
Q Consensus        71 y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~~~  147 (156)
                      -.+.+..|+.+....+..++..||++++++|++.||..|+.||+++|.+|+++|+.++.+|..+|..|..+.+..+.
T Consensus        11 PKrP~say~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~~pe~~~   87 (91)
T d1k99a_          11 PKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQ   87 (91)
T ss_dssp             CCCSCCHHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCCCCCSC
T ss_pred             CCCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCccccc
Confidence            34567777777777899999999999999999999999999999999999999999999999999999999876543

>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=99.44  E-value=4e-15  Score=90.88  Aligned_cols=67  Identities=33%  Similarity=0.584  Sum_probs=59.9

Q ss_pred             ccccccCCCCCccccccccccCCC--CCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHH
Q psy3264          72 DTEMQSYTPPAGEKRGKIKQDNPE--YGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAY  138 (156)
Q Consensus        72 ~~~~~~~~~~~~~~r~~~~~~~p~--~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~  138 (156)
                      .+.+.+|+.+....|+.++.+||+  +++.+|+++||..|++||+++|++|.++|+.++++|+.+|+.|
T Consensus         3 KrP~say~~f~~~~r~~~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_           3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            356777777788889999999997  5567999999999999999999999999999999999999876

>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=99.36  E-value=2e-13  Score=88.67  Aligned_cols=71  Identities=17%  Similarity=0.353  Sum_probs=61.3

Q ss_pred             cccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy3264          73 TEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVAP  145 (156)
Q Consensus        73 ~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~~  145 (156)
                      +.+..|+.|+.+.++.+...+  +++.+|++.||+.|+.||+++|++|.++|+.++++|..+|..|.......
T Consensus        11 rP~~ay~~F~~e~r~~~~~~~--~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~~   81 (101)
T d1v63a_          11 PPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             CCSSSHHHHHHHHHHHCTTTT--SCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             CCCCHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHH
Confidence            466777777777777776544  57899999999999999999999999999999999999999999887653

>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=99.21  E-value=1e-11  Score=81.40  Aligned_cols=55  Identities=13%  Similarity=0.218  Sum_probs=50.8

Q ss_pred             cccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q psy3264          90 KQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSVA  144 (156)
Q Consensus        90 ~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~~  144 (156)
                      ...++++++.+|++.||..|++||+++|++|.++|+.++.+|..+|+.|......
T Consensus        33 r~~~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~~~~   87 (108)
T d1v64a_          33 MANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPE   87 (108)
T ss_dssp             HHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             HHHccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            3457889999999999999999999999999999999999999999999987654

>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=99.19  E-value=2.7e-13  Score=86.26  Aligned_cols=65  Identities=22%  Similarity=0.401  Sum_probs=58.6

Q ss_pred             hhccccccCCCCCccccccccccCCCCCchhHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHH
Q psy3264          70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE  134 (156)
Q Consensus        70 ~y~~~~~~~~~~~~~~r~~~~~~~p~~~~~e~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e  134 (156)
                      .-.+.+..|+.|+.+.|+.++..||++++.+|++.|+..|+.||+++|++|.++|+.++++|+++
T Consensus        20 ~PKrP~say~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          20 KPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             CCCCCCCHHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            34567778888888889999999999999999999999999999999999999999999988754

>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.75  E-value=3.2e-05  Score=45.37  Aligned_cols=69  Identities=22%  Similarity=0.331  Sum_probs=60.0

Q ss_pred             CCCCCCcHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHhccCCHHHHHHHHHhhhhhhhhhccccccCC
Q psy3264           8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT   79 (156)
Q Consensus         8 ~PkrP~say~lF~~e~r~~~~~~~p~~~~~~~ei~k~l~~~Wk~Ls~~eK~~y~~~a~~~k~~y~~~~~~~~   79 (156)
                      .|..|.+|--+|-+.....+...+.+-.   ....+.+..-|++|...|+-.|+..|.++..+|++++....
T Consensus         3 lpetpktaeeiWQqsvIgdYlA~fk~DR---~KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr   71 (84)
T d1l8ya_           3 LPESPKRAEEIWQQSVIGDYLARFKNDR---VKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMR   71 (84)
T ss_dssp             CCCCCCHHHHHHHHHHHHHHHHHTTSTH---HHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHhhH---HHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence            3566778899999999999999987654   47778888899999999999999999999999999887764

>d1l8ya_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.54  E-value=4.8e-05  Score=44.58  Aligned_cols=43  Identities=21%  Similarity=0.465  Sum_probs=37.3

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy3264         101 IAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV  143 (156)
Q Consensus       101 ~~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~~~~~~~  143 (156)
                      ..+.+...|++|...||-+|+..|..|..+|++||-+.+.-..
T Consensus        33 aqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~~~a   75 (84)
T d1l8ya_          33 ALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPA   75 (84)
T ss_dssp             HHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGG
T ss_pred             HHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence            4466778899999999999999999999999999988765443