Psyllid ID: psy1729

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170
Protein Sequence
MDIESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDRRNCNC
Secondary Structure (PSIPRED)
ccccHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHccccHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHccccccccccccccccccHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
cccccccccccccHHHHHHHHHHHHccccccHcHHHHHHHHHHccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccccHcccccccccccccccccccccccccHHHHcHccHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
mdiesekmISTTKLLVTKLLGnewsklslpekkvyLDRAEVDKKRYREELKVTKLLGnewsklslpekkvyLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSlqangteesdiatdatdeideeeedneELYCRVCDQWFTTLHNkrehlngrqhfqrfdrrncnc
Flexible Loop (DISEMBL)
mdiesekmisTTKLLVTKllgnewsklslpekkvyldraevdkkryreelkvtkllgnewsklslpekkvyldraevdkkryreelkvyrksdayqsylrrkrvkslqangteesdiatdatdeidEEEEDNEELYCRVCDQWFTTLHNKREhlngrqhfqrfdrrncnc
Low Complexity Region (SEG)
MDIESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANGTEESdiatdatdeideeeedneeLYCRVCDQWFTTLHNKREHLNGRQHFQRFDRRNCNC
Disordered region (IsUnstruct)
**********TTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK**AY***************************************************************************
Disordered Region (DISOPRED)
********************************KVYLDRAE*************KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY*************************************************VCDQWFT*************************
Disordered Region (DISEMBL)
*********STTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANGTEESDIATDA************ELYCRVCDQWFTTLHNKREHLNGRQHFQRFDRRNCNC
Disordered Region (DISPRO)
******KMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVK***************************EELYCRVCDQWFTTLHNKREHLNGRQHFQRFDRR****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDIESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYxxxxxxxxxxxxxxxxxxxxxGNEWSKLSLPEKKVYxxxxxxxxxxxxxxxxxxxxxDAYQSYLRRKRVKSLQANGTEESDIxxxxxxxxxxxxxxxxxxxxxVCDQWFTTLHNKREHLNGRQHFQRFDRRNCNC
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	170	2.2.26 [Sep-21-2011]
Q6AZF8	345	High mobility group prote	N/A	N/A	0.317	0.156	0.5	3e-09
Q6DIJ5	345	High mobility group prote	yes	N/A	0.294	0.144	0.54	3e-09
Q9NP66	347	High mobility group prote	yes	N/A	0.452	0.221	0.417	8e-09
Q9DC33	346	High mobility group prote	yes	N/A	0.452	0.222	0.417	8e-09
Q5ZKF4	348	High mobility group prote	yes	N/A	0.294	0.143	0.52	3e-08
Q32L68	317	SWI/SNF-related matrix-as	no	N/A	0.258	0.138	0.545	5e-07
Q9P0W2	317	SWI/SNF-related matrix-as	no	N/A	0.258	0.138	0.545	7e-07
Q9Z104	317	SWI/SNF-related matrix-as	no	N/A	0.258	0.138	0.545	4e-06
Q65WY8	640	FACT complex subunit SSRP	yes	N/A	0.358	0.095	0.384	0.0001
Q9LEF5	639	FACT complex subunit SSRP	N/A	N/A	0.235	0.062	0.5	0.0003

>sp|Q6AZF8|HM20A_XENLA High mobility group protein 20A OS=Xenopus laevis GN=hmg20a PE=2 SV=1

 Score = 61.2 bits (147), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/54 (50%), Positives = 42/54 (77%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVK 105
           +T+++G+EWSKL   EK+ YLD AE DK+RY +EL+ Y+ +DAYQ+Y R+ + +
Sbjct: 131 ITRIVGSEWSKLPAHEKQHYLDEAEKDKERYTKELQKYQNTDAYQTYSRKAKSR 184

Plays a role in neuronal differentiation.
Xenopus laevis (taxid: 8355)

>sp|Q6DIJ5|HM20A_XENTR High mobility group protein 20A OS=Xenopus tropicalis GN=hmg20a PE=2 SV=1

 Score = 61.2 bits (147), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 40/50 (80%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
           +T+++G+EWSKL   EK+ YLD AE DK+RY +EL+ Y+ +DAYQ+Y R+
Sbjct: 131 ITRIVGSEWSKLPAHEKQHYLDEAEKDKERYTKELQQYQNTDAYQTYSRK 180

Plays a role in neuronal differentiation.

Xenopus tropicalis (taxid: 8364)

>sp|Q9NP66|HM20A_HUMAN High mobility group protein 20A OS=Homo sapiens GN=HMG20A PE=1 SV=1

 Score = 59.7 bits (143), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 52/79 (65%), Gaps = 2/79 (2%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANG 111
           +T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R  + +  Q   
Sbjct: 133 ITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSR--KTQDRQKGK 190

Query: 112 TEESDIATDATDEIDEEEE 130
           +   D A  AT + ++E E
Sbjct: 191 SHRQDAARQATHDHEKETE 209

Plays a role in neuronal differentiation as chromatin-associated protein. Acts as inhibitor of HMG20B. Overcomes the repressive effects of the neuronal silencer REST and induces the activation of neuronal-specific genes. Involved in the recruitment of the histone methyltransferase MLL and consequent increased methylation of histone H3 lysine 4.

Homo sapiens (taxid: 9606)

>sp|Q9DC33|HM20A_MOUSE High mobility group protein 20A OS=Mus musculus GN=Hmg20a PE=2 SV=1

 Score = 59.7 bits (143), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 52/79 (65%), Gaps = 2/79 (2%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANG 111
           +T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R  + +  Q   
Sbjct: 132 ITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSR--KTQDRQKGK 189

Query: 112 TEESDIATDATDEIDEEEE 130
           +   D A  AT + ++E E
Sbjct: 190 SHRQDAARQATHDHEKETE 208

Plays a role in neuronal differentiation as chromatin-associated protein. Acts as inhibitor of HMG20B. Overcomes the repressive effects of the neuronal silencer REST and induces the activation of neuronal-specific genes. Involved in the recruitment of the histone methyltransferase MLL and consequent increased methylation of histone H3 lysine 4.

Mus musculus (taxid: 10090)

>sp|Q5ZKF4|HM20A_CHICK High mobility group protein 20A OS=Gallus gallus GN=HMG20A PE=2 SV=1

 Score = 58.2 bits (139), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 39/50 (78%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
           +T++LGNEWSKL   EK+ YLD A+ DK+RY  EL+ Y+K++AY+ + R+
Sbjct: 134 ITRMLGNEWSKLPPEEKRRYLDEADRDKERYMRELEQYQKTEAYKVFSRK 183

Plays a role in neuronal differentiation.

Gallus gallus (taxid: 9031)

>sp|Q32L68|HM20B_BOVIN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related OS=Bos taurus GN=HMG20B PE=2 SV=1

 Score = 53.9 bits (128), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 35/44 (79%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 95
           +TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY
Sbjct: 100 ITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQSEAY 143

Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.

Bos taurus (taxid: 9913)

>sp|Q9P0W2|HM20B_HUMAN SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related OS=Homo sapiens GN=HMG20B PE=1 SV=1

 Score = 53.5 bits (127), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 35/44 (79%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 95
           +TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY
Sbjct: 100 ITKMLGAEWSKLQPTEKQRYLDEAEREKQQYMKELRAYQQSEAY 143

Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.

Homo sapiens (taxid: 9606)

>sp|Q9Z104|HM20B_MOUSE SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related OS=Mus musculus GN=Hmg20b PE=1 SV=1

 Score = 50.8 bits (120), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/44 (54%), Positives = 34/44 (77%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 95
           +TK+LG EWSKL   EK+ YLD AE +K++Y +EL  Y++S+AY
Sbjct: 100 ITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAY 143

Required for correct progression through G2 phase of the cell cycle and entry into mitosis. Required for RCOR1/CoREST mediated repression of neuronal specific gene promoters.

Mus musculus (taxid: 10090)

>sp|Q65WY8|SSP1B_ORYSJ FACT complex subunit SSRP1-B OS=Oryza sativa subsp. japonica GN=SSRP1-B PE=2 SV=1

 Score = 45.8 bits (107), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 4/65 (6%)

Query: 34  VYLDRAE-VDKKRYREELKVTKL---LGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
           +Y  +AE  + K    EL  T++   LG  W K++  EK+ Y+++++VDKKRY EE   Y
Sbjct: 566 MYFSKAERANLKNSNPELATTEIAKKLGERWQKMTAEEKQPYVEQSQVDKKRYAEESAAY 625

Query: 90  RKSDA 94
           R + A
Sbjct: 626 RGAAA 630

Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II. Binds specifically to double-stranded DNA.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9LEF5|SSRP1_MAIZE FACT complex subunit SSRP1 OS=Zea mays GN=SSRP1 PE=1 SV=1

 Score = 45.1 bits (105), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/40 (50%), Positives = 28/40 (70%)

Query: 51  KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90
           ++ K LG  W K+S  EK+ Y+ +A+VDKKRY +E  VYR
Sbjct: 586 EIAKKLGEMWQKMSGEEKQPYIQQAQVDKKRYEKESAVYR 625

Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II (By similarity). Binds specifically to double-stranded DNA.

Zea mays (taxid: 4577)

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	170
91091658	452	PREDICTED: similar to predicted protein	0.623	0.234	0.663	3e-27
405965825	718	Phospholysine phosphohistidine inorganic	0.629	0.149	0.530	7e-23
260828085	410	hypothetical protein BRAFLDRAFT_124005 [	0.652	0.270	0.473	6e-22
196009580	363	hypothetical protein TRIADDRAFT_58720 [T	0.611	0.286	0.444	6e-21
296486384	363	TPA: high-mobility group 20A-like [Bos t	0.7	0.327	0.373	1e-17
426232287	447	PREDICTED: uncharacterized protein LOC10	0.688	0.261	0.390	3e-17
359066596	256	PREDICTED: uncharacterized protein LOC10	0.682	0.453	0.365	6e-16
351700745	570	High mobility group protein 20A [Heteroc	0.652	0.194	0.375	8e-16
443727481	409	hypothetical protein CAPTEDRAFT_191691 [	0.594	0.246	0.380	1e-15
390337111	694	PREDICTED: uncharacterized protein LOC57	0.858	0.210	0.282	4e-11

>gi|91091658|ref|XP_971261.1| PREDICTED: similar to predicted protein [Tribolium castaneum] gi|270000885|gb|EEZ97332.1| hypothetical protein TcasGA2_TC011144 [Tribolium castaneum]

 Score =  126 bits (317), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 73/110 (66%), Positives = 86/110 (78%), Gaps = 4/110 (3%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANG 111
           +TK++GN+WS LSL EK+ YL +AE DK+RYREELK YR+SDAY++YL +KR   LQ N 
Sbjct: 211 ITKVIGNKWSNLSLEEKRPYLAKAEEDKRRYREELKQYRQSDAYRAYLAKKRRNRLQNNV 270

Query: 112 TEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQ 161
             ESD+  DATDE   +EEDNEELYCR CDQWF  LHNKREHL GRQH Q
Sbjct: 271 LSESDM--DATDE--IDEEDNEELYCRTCDQWFHNLHNKREHLQGRQHTQ 316

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|405965825|gb|EKC31179.1| Phospholysine phosphohistidine inorganic pyrophosphate phosphatase [Crassostrea gigas]

 Score =  112 bits (279), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 60/113 (53%), Positives = 80/113 (70%), Gaps = 6/113 (5%)

Query: 51  KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQAN 110
           +VTK+LGNEWS L   +K+ YL  AE DKKRY E+LK +++S+AYQS +++K+ K     
Sbjct: 214 EVTKILGNEWSTLDSQKKQKYLLAAEEDKKRYMEQLKTFQQSEAYQSVMKKKKGKGF-LT 272

Query: 111 GTEESDIATDAT--DEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQ 161
           GTE   I  D T    +DE+E    ELYCRVCDQ+F++LHNK+EH+ GRQH Q
Sbjct: 273 GTE---IHVDETFPYSLDEDEGSMNELYCRVCDQYFSSLHNKKEHMFGRQHLQ 322

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|260828085|ref|XP_002608994.1| hypothetical protein BRAFLDRAFT_124005 [Branchiostoma floridae] gi|229294348|gb|EEN65004.1| hypothetical protein BRAFLDRAFT_124005 [Branchiostoma floridae]

 Score =  108 bits (271), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 53/112 (47%), Positives = 80/112 (71%), Gaps = 1/112 (0%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANG 111
           +T+LLG+ WS LS  +K+ YLD AEVDK+RY EELK Y++S+AYQS+L+R+  K L+   
Sbjct: 174 MTRLLGSRWSALSQEDKQKYLDAAEVDKRRYIEELKAYQQSEAYQSWLKRQAAKKLKCLV 233

Query: 112 TEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRF 163
             E+ I  +    + + E+D  +LYC+ C+Q+F++LHNK+EH+ G+QH Q  
Sbjct: 234 DVET-IDGEVDSIVLDLEDDPSDLYCKTCNQYFSSLHNKKEHMYGKQHLQML 284

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|196009580|ref|XP_002114655.1| hypothetical protein TRIADDRAFT_58720 [Trichoplax adhaerens] gi|190582717|gb|EDV22789.1| hypothetical protein TRIADDRAFT_58720 [Trichoplax adhaerens]

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 56/126 (44%), Positives = 76/126 (60%), Gaps = 22/126 (17%)

Query: 52  VTKLLGNEWSKLSLPEKKV-------------YLDRAEVDKKRYREELKVYRKSDAYQSY 98
           +TK LGNEWSK+ L  K+              +LD AE DK+RY EELK Y+ SD Y+S 
Sbjct: 113 ITKFLGNEWSKMKLSAKQARLDFLPYTYRKKKFLDEAEADKRRYVEELKAYQCSDGYRSE 172

Query: 99  LRR---KRVKSLQANGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLN 155
             R   K+ K     G   + IA D       E+++++EL+CRVC+Q+F++LHNKREH+ 
Sbjct: 173 ASRESSKKSKLFTGTGMNSAYIANDF------EDDESDELFCRVCNQYFSSLHNKREHMF 226

Query: 156 GRQHFQ 161
           GRQH Q
Sbjct: 227 GRQHLQ 232

Source: Trichoplax adhaerens

Species: Trichoplax adhaerens

Genus: Trichoplax

Phylum: Placozoa

Superkingdom: Eukaryota

>gi|296486384|tpg|DAA28497.1| TPA: high-mobility group 20A-like [Bos taurus]

 Score = 94.4 bits (233), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 47/126 (37%), Positives = 77/126 (61%), Gaps = 7/126 (5%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQA-- 109
           +TK+L  +W+ L   +K+ Y+  A+ DK+RY  EL+ Y+ S+AY+++LRR+    +QA  
Sbjct: 105 ITKMLAAQWAHLPQEKKQRYVCEADEDKQRYIRELQAYQNSEAYRAFLRRRAALKVQARC 164

Query: 110 -NGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQR----FD 164
             G    +      D    + ++N++LYCR C Q+F++LHNKREHL G+QH Q     F+
Sbjct: 165 GTGAPGYEFEGKGLDFSAVDADENDDLYCRTCRQFFSSLHNKREHLLGKQHLQNLTGEFE 224

Query: 165 RRNCNC 170
           + +  C
Sbjct: 225 KDSAEC 230

Source: Bos taurus

Species: Bos taurus

Genus: Bos

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|426232287|ref|XP_004010163.1| PREDICTED: uncharacterized protein LOC101112981 [Ovis aries]

 Score = 93.2 bits (230), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/128 (39%), Positives = 80/128 (62%), Gaps = 11/128 (8%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQAN- 110
           +TK+L  +W++L   +K+ Y+  A+ DK+RY  ELK Y+ S+AY+++LRR+  + + A  
Sbjct: 120 ITKMLAAQWAQLPQEKKQRYVCEADEDKQRYIRELKAYQNSEAYRAFLRRRAAQKVLARC 179

Query: 111 GTEESDIATDATD----EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQR---- 162
           GT       +  D     +D +E  N++LYCR C Q+F++LHNKREHL G+QH Q     
Sbjct: 180 GTSAPGHEFEGKDLDFSAVDGDE--NDDLYCRTCRQFFSSLHNKREHLLGKQHLQNLTGE 237

Query: 163 FDRRNCNC 170
           F++ +  C
Sbjct: 238 FEKDSAEC 245

Source: Ovis aries

Species: Ovis aries

Genus: Ovis

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|359066596|ref|XP_002688460.2| PREDICTED: uncharacterized protein LOC100298890 [Bos taurus]

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 45/123 (36%), Positives = 74/123 (60%), Gaps = 7/123 (5%)

Query: 55  LLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQA---NG 111
           +L  +W+ L   +K+ Y+  A+ DK+RY  EL+ Y+ S+AY+++LRR+    +QA    G
Sbjct: 1   MLAAQWAHLPQEKKQRYVCEADEDKQRYIRELQAYQNSEAYRAFLRRRAALKVQARCGTG 60

Query: 112 TEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQR----FDRRN 167
               +      D    + ++N++LYCR C Q+F++LHNKREHL G+QH Q     F++ +
Sbjct: 61  APGYEFEGKGLDFSAVDADENDDLYCRTCRQFFSSLHNKREHLLGKQHLQNLTGEFEKDS 120

Query: 168 CNC 170
             C
Sbjct: 121 AEC 123

Source: Bos taurus

Species: Bos taurus

Genus: Bos

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|351700745|gb|EHB03664.1| High mobility group protein 20A [Heterocephalus glaber]

 Score = 88.6 bits (218), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 42/112 (37%), Positives = 71/112 (63%), Gaps = 1/112 (0%)

Query: 51  KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRV-KSLQA 109
           ++TK+L  +W++LS   K+ Y+  A+ DK+RY  EL+ Y+ S+AY+++LRR+   ++L  
Sbjct: 260 EITKILAAQWAQLSQERKQRYIYEADEDKQRYIRELQAYQSSEAYRAFLRRRAAHRALCG 319

Query: 110 NGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQ 161
            G    ++  +  D    +  ++ +L+CR C Q F++ HNKREHL GRQH  
Sbjct: 320 PGAPGGELGREDLDFSAIDGTEDGDLHCRTCHQCFSSRHNKREHLLGRQHLH 371

Source: Heterocephalus glaber

Species: Heterocephalus glaber

Genus: Heterocephalus

Family: Bathyergidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|443727481|gb|ELU14222.1| hypothetical protein CAPTEDRAFT_191691 [Capitella teleta]

 Score = 87.8 bits (216), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 43/113 (38%), Positives = 68/113 (60%), Gaps = 12/113 (10%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANG 111
           +TK+LGNEWS +   EK+ YL  AE DKKRY +EL VY+KS  Y  +++++++K      
Sbjct: 178 ITKILGNEWSSMGTEEKQKYLSDAENDKKRYIDELDVYKKSPQYLEFVKKRKIK------ 231

Query: 112 TEESDIAT-DATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRF 163
                I T D  + +D    +   L+CR+C+ +F++ HNK+EH+ G+ H    
Sbjct: 232 -----ITTDDPLEHLDNSTYEEVGLHCRLCNLYFSSNHNKKEHMLGKLHLTNL 279

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|390337111|ref|XP_782477.3| PREDICTED: uncharacterized protein LOC577135 [Strongylocentrotus purpuratus]

 Score = 72.8 bits (177), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 43/152 (28%), Positives = 74/152 (48%), Gaps = 6/152 (3%)

Query: 23  EWSKLSLPEKKVYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAE 76
           E +K   P    Y       ++ YRE        KV+ LLG  W+ L    KK YLD  +
Sbjct: 424 EMAKAPRPPSSAYAMFLAEQREGYRESHPEVVGRKVSSLLGKMWTGLPPDVKKRYLDMEK 483

Query: 77  VDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANGTEESDIATDATDEIDEEEEDNEELY 136
            DK+RY +E+K Y++S + Q++L+++   +++     E  ++    +    +      L 
Sbjct: 484 KDKERYIKEIKEYQESSSCQAFLKKQTENAVRNFCGSEEAMSEQIVNMSKNDILGCNYLQ 543

Query: 137 CRVCDQWFTTLHNKREHLNGRQHFQRFDRRNC 168
           C+VCD +F + HN  +H+ G+QH      + C
Sbjct: 544 CKVCDMYFHSTHNMSQHVLGKQHMTALAAKIC 575

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

Superkingdom: Eukaryota

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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	170
UNIPROTKB|F1N8B1	348	LOC100857252 "Uncharacterized	0.376	0.183	0.441	4.1e-10
MGI|MGI:1914117	346	Hmg20a "high mobility group 20	0.3	0.147	0.509	8.5e-10
UNIPROTKB|Q0VCL5	347	HMG20A "High-mobility group 20	0.3	0.146	0.509	8.6e-10
UNIPROTKB|E2RKW6	347	HMG20A "Uncharacterized protei	0.3	0.146	0.509	8.6e-10
UNIPROTKB|Q9NP66	347	HMG20A "High mobility group pr	0.3	0.146	0.509	8.6e-10
UNIPROTKB|Q5ZKF4	348	HMG20A "High mobility group pr	0.3	0.146	0.509	8.7e-10
RGD|1564760	376	Hmg20a "high mobility group 20	0.3	0.135	0.509	1e-09
UNIPROTKB|C9J8X5	215	HMG20B "SWI/SNF-related matrix	0.323	0.255	0.448	2.2e-09
UNIPROTKB|E2R4Z8	316	HMG20B "Uncharacterized protei	0.323	0.174	0.448	8.7e-09
UNIPROTKB|Q32L68	317	HMG20B "SWI/SNF-related matrix	0.323	0.173	0.448	8.8e-09

UNIPROTKB|F1N8B1 LOC100857252 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 150 (57.9 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 30/68 (44%), Positives = 48/68 (70%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLR----RKRVKS 106
             ++T++LGNEWSKL   EK+ YLD A+ DK+RY  EL+ Y+K++AY+ + R    R++ KS
Sbjct:   133 EITRMLGNEWSKLPPEEKRRYLDEADRDKERYMRELEQYQKTEAYKVFSRKAQDRQKGKS 192

Query:   107 LQANGTEE 114
              + +G  +
Sbjct:   193 HRQDGARQ 200

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

MGI|MGI:1914117 Hmg20a "high mobility group 20A" [Mus musculus (taxid:10090)]

 Score = 147 (56.8 bits), Expect = 8.5e-10, P = 8.5e-10
 Identities = 26/51 (50%), Positives = 41/51 (80%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
             ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   131 EITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 181

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0016568 "chromatin modification" evidence=IMP

GO:0045665 "negative regulation of neuron differentiation" evidence=IGI;IDA

GO:0046982 "protein heterodimerization activity" evidence=IPI

UNIPROTKB|Q0VCL5 HMG20A "High-mobility group 20A" [Bos taurus (taxid:9913)]

 Score = 147 (56.8 bits), Expect = 8.6e-10, P = 8.6e-10
 Identities = 26/51 (50%), Positives = 41/51 (80%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
             ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   132 EITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 182

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|E2RKW6 HMG20A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 147 (56.8 bits), Expect = 8.6e-10, P = 8.6e-10
 Identities = 26/51 (50%), Positives = 41/51 (80%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
             ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   132 EITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 182

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|Q9NP66 HMG20A "High mobility group protein 20A" [Homo sapiens (taxid:9606)]

 Score = 147 (56.8 bits), Expect = 8.6e-10, P = 8.6e-10
 Identities = 26/51 (50%), Positives = 41/51 (80%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
             ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   132 EITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 182

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0003677 "DNA binding" evidence=NAS

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

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

GO:0006325 "chromatin organization" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q5ZKF4 HMG20A "High mobility group protein 20A" [Gallus gallus (taxid:9031)]

 Score = 147 (56.8 bits), Expect = 8.7e-10, P = 8.7e-10
 Identities = 26/51 (50%), Positives = 40/51 (78%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
             ++T++LGNEWSKL   EK+ YLD A+ DK+RY  EL+ Y+K++AY+ + R+
Sbjct:   133 EITRMLGNEWSKLPPEEKRRYLDEADRDKERYMRELEQYQKTEAYKVFSRK 183

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

RGD|1564760 Hmg20a "high mobility group 20A" [Rattus norvegicus (taxid:10116)]

 Score = 147 (56.8 bits), Expect = 1.0e-09, P = 1.0e-09
 Identities = 26/51 (50%), Positives = 41/51 (80%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 101
             ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   132 EITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 182

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0016568 "chromatin modification" evidence=ISO

GO:0045665 "negative regulation of neuron differentiation" evidence=ISO

GO:0046982 "protein heterodimerization activity" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|C9J8X5 HMG20B "SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related" [Homo sapiens (taxid:9606)]

 Score = 137 (53.3 bits), Expect = 2.2e-09, P = 2.2e-09
 Identities = 26/58 (44%), Positives = 43/58 (74%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ---SYLRRKRVK 105
             ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+     ++ K++K
Sbjct:    99 EITKMLGAEWSKLQPTEKQRYLDEAEREKQQYMKELRAYQQSEAYKMCTEKIQEKKIK 156

GO:0033234 "negative regulation of protein sumoylation" evidence=IEA

GO:0045666 "positive regulation of neuron differentiation" evidence=IEA

GO:0046982 "protein heterodimerization activity" evidence=IEA

UNIPROTKB|E2R4Z8 HMG20B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 137 (53.3 bits), Expect = 8.7e-09, P = 8.7e-09
 Identities = 26/58 (44%), Positives = 43/58 (74%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ---SYLRRKRVK 105
             ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+     ++ K++K
Sbjct:    99 EITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQSEAYKMCTEKIQEKKIK 156

GO:0046982 "protein heterodimerization activity" evidence=IEA

GO:0045666 "positive regulation of neuron differentiation" evidence=IEA

GO:0033234 "negative regulation of protein sumoylation" evidence=IEA

UNIPROTKB|Q32L68 HMG20B "SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related" [Bos taurus (taxid:9913)]

 Score = 137 (53.3 bits), Expect = 8.8e-09, P = 8.8e-09
 Identities = 26/58 (44%), Positives = 43/58 (74%)

Query:    51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ---SYLRRKRVK 105
             ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+     ++ K++K
Sbjct:    99 EITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQSEAYKMCAEKIQEKKIK 156

GO:0005694 "chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

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

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	170
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	1e-06
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	1e-06
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	1e-05
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	1e-05
smart00398	70	smart00398, HMG, high mobility group	3e-04
smart00398	70	smart00398, HMG, high mobility group	0.001
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	0.001
pfam12874	25	pfam12874, zf-met, Zinc-finger of C2H2 type	0.003

>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 = 43.4 bits (103), Expect = 1e-06
 Identities = 20/36 (55%), Positives = 28/36 (77%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          VTK+LG +W +LS  EKK Y ++AE DK+RY +E+K
Sbjct: 31 VTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 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|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 = 43.4 bits (103), Expect = 1e-06
 Identities = 20/36 (55%), Positives = 28/36 (77%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 87
          VTK+LG +W +LS  EKK Y ++AE DK+RY +E+K
Sbjct: 31 VTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 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 = 40.7 bits (96), Expect = 1e-05
 Identities = 17/36 (47%), Positives = 25/36 (69%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          ++K+LG  W  LS  EKK Y ++AE DK+RY +E+ 
Sbjct: 31 ISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP 66

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

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 17/36 (47%), Positives = 25/36 (69%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 87
          ++K+LG  W  LS  EKK Y ++AE DK+RY +E+ 
Sbjct: 31 ISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP 66

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 = 37.3 bits (87), Expect = 3e-04
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90
          ++K LG  W  LS  EK  Y ++A+ DK+RY EE+  Y+
Sbjct: 32 ISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

Length = 70

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 16/36 (44%), Positives = 23/36 (63%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          ++K LG  W  LS  EK  Y ++A+ DK+RY EE+ 
Sbjct: 32 ISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMP 67

Length = 70

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

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 16/39 (41%), Positives = 25/39 (64%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90
          ++K+LG +W  LS  EKK Y ++AE +K RY +    Y+
Sbjct: 31 ISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69

Length = 69

>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type

 Score = 33.2 bits (77), Expect = 0.003
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 135 LYCRVCDQWFTTLHNKREHLNGRQH 159
            YC +C+  FT+    + HL G++H
Sbjct: 1   FYCELCNVTFTSESQLKSHLRGKKH 25

This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding. Length = 25

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	170
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.38
KOG4715|consensus	410		99.09
PTZ00199	94	high mobility group protein; Provisional	98.94
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	98.93
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	98.91
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	98.88
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	98.81
PTZ00199	94	high mobility group protein; Provisional	98.81
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.8
KOG0381|consensus	96		98.74
smart00398	70	HMG high mobility group.	98.72
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	98.72
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	98.72
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	98.65
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	98.64
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	98.62
smart00398	70	HMG high mobility group.	98.6
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.6
KOG0527|consensus	331		98.46
KOG0381|consensus	96		98.37
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	98.27
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	98.17
KOG0527|consensus	331		98.12
COG5648	211	NHP6B Chromatin-associated proteins containing the	98.03
KOG0526|consensus	615		97.74
KOG3248|consensus	421		97.7
smart00451	35	ZnF_U1 U1-like zinc finger. Family of C2H2-type zi	97.69
KOG0526|consensus	615		97.53
PF12874	25	zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG	97.16
KOG4715|consensus	410		97.11
PF12171	27	zf-C2H2_jaz: Zinc-finger double-stranded RNA-bindi	96.89
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	96.15
KOG0717|consensus	508		95.39
KOG0528|consensus	511		95.36
PF06220	38	zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc fi	95.06
PF13912	27	zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9	93.6
KOG3248|consensus	421		93.46
KOG3408|consensus	129		93.35
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	92.15
PF11304	107	DUF3106: Protein of unknown function (DUF3106); In	92.04
KOG0528|consensus	511		90.82
PF12756	100	zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB:	90.8
KOG2746|consensus	683		90.65
PF00096	23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	89.08
COG5112	126	UFD2 U1-like Zn-finger-containing protein [General	87.91
PF11304	107	DUF3106: Protein of unknown function (DUF3106); In	83.35
PF07535	49	zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc	83.0
smart00586	49	ZnF_DBF Zinc finger in DBF-like proteins.	82.42
KOG4727|consensus	193		81.7
PF03194	254	LUC7: LUC7 N_terminus; InterPro: IPR004882 This fa	81.34
PF13894	24	zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP	80.21
TIGR03481	198	HpnM hopanoid biosynthesis associated membrane pro	80.19

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

Probab=99.38  E-value=1.1e-12  Score=108.87  Aligned_cols=85  Identities=31%  Similarity=0.447  Sum_probs=79.0

Q ss_pred             cccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH--------------------------------
Q psy1729           3 IESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL--------------------------------   50 (170)
Q Consensus         3 ~~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em--------------------------------   50 (170)
                      ++...+|.+++++|++.+|++|++|+++||++|...|..++++|+++.                                
T Consensus        88 ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~~~~~~~e~~~~~r~~~~~~~~  167 (211)
T COG5648          88 EIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSP  167 (211)
T ss_pred             HHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCCCCchhhhccHHhccccCCCCc
Confidence            456789999999999999999999999999999999999999998865                                


Q ss_pred             -----hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHH
Q psy1729          51 -----KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   87 (170)
Q Consensus        51 -----Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~   87 (170)
                           +.++.+|..|+.|+++-|.+|++.+.+++..|...++
T Consensus       168 ~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         168 DKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             chhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence                 7899999999999999999999999999999987653

>KOG4715|consensus

Probab=99.09  E-value=3e-10  Score=99.68  Aligned_cols=106  Identities=25%  Similarity=0.406  Sum_probs=86.3

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhHHHHHHh-hhhh-hhh-CCCCc--c---ccccccc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK-RVKS-LQA-NGTEE--S---DIATDAT  122 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~~~~~~k-~~k~-~~~-~~~~~--~---~~~~d~~  122 (170)
                      +|.|+||.+|.-|+++||+-|+...+..|..|++-|++|+.+++|.++.-.| +++- +-+ .++..  +   ....+++
T Consensus        94 eiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~ayinaKsra~a~le~~sr~~~sr~~~ge~~~~IQ  173 (410)
T KOG4715|consen   94 EIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQ  173 (410)
T ss_pred             HHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHHHHhhhhhhhhhhhccccccccchhhcCCcceecc
Confidence            8999999999999999999999999999999999999999999999996533 3331 101 11111  1   2224889


Q ss_pred             ccccccccCchhHHHHHHHHHhhhhhhhhhhhch
Q psy1729         123 DEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNG  156 (170)
Q Consensus       123 ~~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~  156 (170)
                      +++|+||-|||.+-.|+.+.+|-++|++---+++
T Consensus       174 PaeDeDD~ddg~stkhla~arf~rN~rLIsei~S  207 (410)
T KOG4715|consen  174 PAEDEDDYDDGFSTKHLATARFQRNHRLISEILS  207 (410)
T ss_pred             cccCccccccccchhhhhhhhhhhhhHHHHHHhc
Confidence            9999999999999999999999999998655443

>PTZ00199 high mobility group protein; Provisional

Probab=98.94  E-value=1.8e-09  Score=79.02  Aligned_cols=40  Identities=43%  Similarity=0.668  Sum_probs=21.5

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      +|++.||++|++||+++|.+|+++|+.++.+|..+|.+|.
T Consensus        54 evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~   93 (94)
T PTZ00199         54 AVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA   93 (94)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4455555555555555555555555555555555555553

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

Probab=98.93  E-value=2e-09  Score=71.95  Aligned_cols=47  Identities=40%  Similarity=0.620  Sum_probs=42.7

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .+.++|++++++|++.||..|+.||+++|.+|.+.|..++.+|..+|
T Consensus        19 ~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~   65 (66)
T cd01390          19 LKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             HHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            46788999999999999999999999999999999999999998875

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

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

Probab=98.91  E-value=2.3e-09  Score=74.24  Aligned_cols=47  Identities=23%  Similarity=0.312  Sum_probs=40.9

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .+.++|++++++|++.||+.|+.||+++|++|.+.|..++++|..++
T Consensus        20 ~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~   66 (72)
T cd01388          20 VLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLY   66 (72)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            35688999999999999999999999999999999999999887754

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.

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

Probab=98.88  E-value=3.5e-09  Score=74.14  Aligned_cols=47  Identities=23%  Similarity=0.298  Sum_probs=35.3

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|+++||++|+.||+++|++|.++|..++++|..++
T Consensus        20 ~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~   66 (77)
T cd01389          20 LKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREY   66 (77)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            35677777788888877777777777777777777777777776654

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=98.81  E-value=8.6e-09  Score=69.56  Aligned_cols=48  Identities=31%  Similarity=0.488  Sum_probs=37.0

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .+.++|++++++|++.||..|+.||+++|++|.+.|..++..|..++.
T Consensus        19 ~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~   66 (69)
T PF00505_consen   19 LKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMP   66 (69)
T ss_dssp             HHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456778888888888888888888888888888888888877776653

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 ....

>PTZ00199 high mobility group protein; Provisional

Probab=98.81  E-value=1.9e-08  Score=73.64  Aligned_cols=41  Identities=39%  Similarity=0.548  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhh
Q psy1729          13 KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVT   53 (170)
Q Consensus        13 ~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~   53 (170)
                      +++|++.||++|+.||+++|.+|++.|..++.+|..++..+
T Consensus        52 ~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y   92 (94)
T PTZ00199         52 VAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEY   92 (94)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999999999999999988655

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

Probab=98.80  E-value=7.2e-09  Score=71.93  Aligned_cols=40  Identities=40%  Similarity=0.675  Sum_probs=35.7

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      ++++.||..|++||++||.+|+++|+.++.+|..+|..|+
T Consensus        34 e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen   34 EVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             HHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            7889999999999999999999999999999999999885

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=98.74  E-value=2e-08  Score=72.31  Aligned_cols=48  Identities=29%  Similarity=0.386  Sum_probs=42.0

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      +++++|++++.+|++.+|++|++|++++|.+|...+..++++|..+|.
T Consensus        41 ~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~   88 (96)
T KOG0381|consen   41 IKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELA   88 (96)
T ss_pred             HHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578889999999999999999999988888888888888888888776

>smart00398 HMG high mobility group

Probab=98.72  E-value=2.9e-08  Score=66.49  Aligned_cols=47  Identities=34%  Similarity=0.518  Sum_probs=35.3

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .+.++|++++++|++.||..|+.||+++|.+|.+.|..++++|..++
T Consensus        20 ~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~   66 (70)
T smart00398       20 IKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEM   66 (70)
T ss_pred             HHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567777777777777777777777777777777777777776654

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

Probab=98.72  E-value=2.6e-08  Score=68.97  Aligned_cols=57  Identities=23%  Similarity=0.401  Sum_probs=47.7

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      .|.-...+.+.....+      .++++.||+.|+.||+++|++|.++|+.++++|.+++.+|+
T Consensus         8 af~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388           8 AFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            4555555556555443      38999999999999999999999999999999999999886

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

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

Probab=98.72  E-value=5.8e-08  Score=65.47  Aligned_cols=57  Identities=30%  Similarity=0.585  Sum_probs=47.6

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      +|.-.....+..+..+      .+|++.||++|++||+++|.+|.+.|.+++.+|..++.+|+
T Consensus         7 af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen    7 AFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4555555555555443      28999999999999999999999999999999999999985

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=98.65  E-value=1.1e-07  Score=63.54  Aligned_cols=54  Identities=41%  Similarity=0.713  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   87 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~   87 (170)
                      +|.-.+...+..+..+      .++++.||+.|++||+++|++|.+.|.+++.+|..+|.
T Consensus         7 af~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~   66 (66)
T cd01390           7 AYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK   66 (66)
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            5566666666666543      38999999999999999999999999999999999873

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.

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

Probab=98.64  E-value=5.7e-08  Score=67.95  Aligned_cols=42  Identities=26%  Similarity=0.471  Sum_probs=40.1

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                      +|++.||++|+.||+++|++|.++|+.++++|..++.+|+-.
T Consensus        31 eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~   72 (77)
T cd01389          31 EISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYT   72 (77)
T ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCccc
Confidence            899999999999999999999999999999999999999843

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.

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

Probab=98.62  E-value=7.9e-08  Score=63.64  Aligned_cols=47  Identities=36%  Similarity=0.542  Sum_probs=41.5

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .+.++|++++.+|++.||..|+.||+++|.+|.+.|..++..|..++
T Consensus        19 ~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084          19 VKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             HHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            45678999999999999999999999999999999999999997653

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

>smart00398 HMG high mobility group

Probab=98.60  E-value=2e-07  Score=62.41  Aligned_cols=57  Identities=32%  Similarity=0.609  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      +|.-.....+..+..+      .++++.||.+|+.||+++|++|.+.|..++.+|..++..|+
T Consensus         8 ~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398        8 AFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4444555555554432      37899999999999999999999999999999999999884

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

Probab=98.60  E-value=7.9e-08  Score=66.66  Aligned_cols=45  Identities=36%  Similarity=0.470  Sum_probs=39.4

Q ss_pred             CCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhh
Q psy1729           8 MISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV   52 (170)
Q Consensus         8 ~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi   52 (170)
                      .+..++.++++.||..|++||++||.+|.+.|+.++++|..++..
T Consensus        27 ~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~   71 (73)
T PF09011_consen   27 GQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKE   71 (73)
T ss_dssp             -T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            567889999999999999999999999999999999999998743

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 ....

>KOG0527|consensus

Probab=98.46  E-value=8.2e-08  Score=84.92  Aligned_cols=60  Identities=25%  Similarity=0.491  Sum_probs=50.6

Q ss_pred             hHHHHHHHHHHHHHHHH------hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhHH
Q psy1729          34 VYLDRAEVDKKRYREEL------KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS   97 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~Em------Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~~   97 (170)
                      -|.-.+...|.+-.++-      ||+|.||.+||.|+++||.||++.|++++..++++..+|+    |+.
T Consensus        69 AFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK----YRP  134 (331)
T KOG0527|consen   69 AFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK----YRP  134 (331)
T ss_pred             hhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc----ccc
Confidence            45556666665554432      9999999999999999999999999999999999999999    666

>KOG0381|consensus

Probab=98.37  E-value=6.9e-07  Score=64.28  Aligned_cols=42  Identities=38%  Similarity=0.647  Sum_probs=39.7

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHH-HHHcc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK-VYRKS   92 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~-~yk~~   92 (170)
                      ++.+.+|++|++|++++|.+|+..|..++++|..+|. .|+..
T Consensus        52 ~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~   94 (96)
T KOG0381|consen   52 EVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKAS   94 (96)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            8999999999999999999999999999999999999 87754

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

Probab=98.27  E-value=4e-06  Score=55.36  Aligned_cols=53  Identities=36%  Similarity=0.621  Sum_probs=43.4

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   86 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em   86 (170)
                      +|.-.....+..+..+      .+|++.+|.+|+.||+++|.+|.+.|..++.+|..++
T Consensus         7 af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084           7 AYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            4555555555555443      3899999999999999999999999999999999875

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

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

Probab=98.17  E-value=4.6e-06  Score=60.03  Aligned_cols=44  Identities=32%  Similarity=0.544  Sum_probs=39.0

Q ss_pred             hhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhh
Q psy1729          52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY   95 (170)
Q Consensus        52 i~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~   95 (170)
                      ..+.+...|++|++.+|.+|+.+|.++..+|+.+|.+|+...+.
T Consensus        33 ~~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~   76 (85)
T PF14887_consen   33 ALKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPAD   76 (85)
T ss_dssp             HHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCT
T ss_pred             HHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            35689999999999999999999999999999999999876653

>KOG0527|consensus

Probab=98.12  E-value=2.5e-06  Score=75.59  Aligned_cols=46  Identities=28%  Similarity=0.386  Sum_probs=42.1

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      -.++|.|...||+|.||.+||.|+++||.+|++.|++.|....++-
T Consensus        82 a~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~Hmkeh  127 (331)
T KOG0527|consen   82 AKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEY  127 (331)
T ss_pred             HHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhC
Confidence            3579999999999999999999999999999999999999876653

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

Probab=98.03  E-value=1.2e-05  Score=67.19  Aligned_cols=63  Identities=30%  Similarity=0.509  Sum_probs=51.8

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ   96 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~   96 (170)
                      .|.-.++..|.....+      .++.+.+|++|++|+++||+||...|..++++|..++..|..+..+.
T Consensus        77 ayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~  145 (211)
T COG5648          77 AYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNK  145 (211)
T ss_pred             HHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCC
Confidence            4555555555554442      38999999999999999999999999999999999999999875544

>KOG0526|consensus

Probab=97.74  E-value=3.7e-05  Score=71.78  Aligned_cols=38  Identities=42%  Similarity=0.815  Sum_probs=37.3

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      ++.|.+|++|+.||.  |.+|+++|+.+++||+.+|++|+
T Consensus       563 dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk  600 (615)
T KOG0526|consen  563 DVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYK  600 (615)
T ss_pred             HHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhc
Confidence            899999999999999  99999999999999999999999

>KOG3248|consensus

Probab=97.70  E-value=4.4e-05  Score=68.03  Aligned_cols=46  Identities=22%  Similarity=0.426  Sum_probs=43.6

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ   96 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~   96 (170)
                      +|.++||++|.+||-+|..+|.++|.++++-+.+-...|-....|-
T Consensus       221 aiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYg  266 (421)
T KOG3248|consen  221 AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG  266 (421)
T ss_pred             HHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhh
Confidence            7899999999999999999999999999999999999998888776

>smart00451 ZnF_U1 U1-like zinc finger

Probab=97.69  E-value=6.8e-06  Score=48.95  Aligned_cols=32  Identities=28%  Similarity=0.700  Sum_probs=29.1

Q ss_pred             hHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729         134 ELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR  165 (170)
Q Consensus       134 ~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~  165 (170)
                      -.||.+|+.+|.+.+..+.|+.|++|.+++..
T Consensus         3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~   34 (35)
T smart00451        3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK   34 (35)
T ss_pred             CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence            36899999999999999999999999998753

Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.

>KOG0526|consensus

Probab=97.53  E-value=7e-05  Score=69.95  Aligned_cols=43  Identities=37%  Similarity=0.577  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729          10 STTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK   54 (170)
Q Consensus        10 ~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K   54 (170)
                      +.++++|+|.+|++|+.||.  |.+|++.|+.+|.+|+.+|.-++
T Consensus       558 gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk  600 (615)
T KOG0526|consen  558 GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYK  600 (615)
T ss_pred             CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhc
Confidence            89999999999999999999  99999999999999999997666

>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A

Probab=97.16  E-value=3e-05  Score=43.06  Aligned_cols=25  Identities=32%  Similarity=0.939  Sum_probs=23.6

Q ss_pred             HHHHHHHHHhhhhhhhhhhhchhhh
Q psy1729         135 LYCRVCDQWFTTLHNKREHLNGRQH  159 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~~~~~  159 (170)
                      .+|.+|+..|++.-..+.||.|+.|
T Consensus         1 ~~C~~C~~~f~s~~~~~~H~~s~~H   25 (25)
T PF12874_consen    1 FYCDICNKSFSSENSLRQHLRSKKH   25 (25)
T ss_dssp             EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred             CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence            3799999999999999999999998

>KOG4715|consensus

Probab=97.11  E-value=0.0006  Score=60.54  Aligned_cols=48  Identities=25%  Similarity=0.380  Sum_probs=45.5

Q ss_pred             cccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           3 IESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         3 ~~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      --|++||.+.+=+|.|+||.+|..|++.||+.|...+...|..|.+.|
T Consensus        82 ~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~sm  129 (410)
T KOG4715|consen   82 QVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESM  129 (410)
T ss_pred             hhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHH
Confidence            358999999999999999999999999999999999999999998877

>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length

Probab=96.89  E-value=9e-05  Score=42.28  Aligned_cols=26  Identities=27%  Similarity=0.912  Sum_probs=24.3

Q ss_pred             HHHHHHHHHhhhhhhhhhhhchhhhh
Q psy1729         135 LYCRVCDQWFTTLHNKREHLNGRQHF  160 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~~~~~~  160 (170)
                      .||.+|+-+|++....+.||.|+.|.
T Consensus         2 ~~C~~C~k~f~~~~~~~~H~~sk~Hk   27 (27)
T PF12171_consen    2 FYCDACDKYFSSENQLKQHMKSKKHK   27 (27)
T ss_dssp             CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred             CCcccCCCCcCCHHHHHHHHccCCCC
Confidence            47999999999999999999999994

The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.

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

Probab=96.15  E-value=0.01  Score=42.93  Aligned_cols=44  Identities=32%  Similarity=0.545  Sum_probs=36.8

Q ss_pred             cCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           7 KMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         7 ~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .+++-...+ -+.+...|++|+..+|-+|...|.++..+|+++|-
T Consensus        25 ~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~   68 (85)
T PF14887_consen   25 KFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELR   68 (85)
T ss_dssp             HTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence            344444555 45899999999999999999999999999999873

>KOG0717|consensus

Probab=95.39  E-value=0.022  Score=52.94  Aligned_cols=41  Identities=32%  Similarity=0.649  Sum_probs=33.6

Q ss_pred             cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         124 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       124 ~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      +.|+-+.+++.|||.+|+..|-|---+.-|-.+++|.-||.
T Consensus       282 e~de~d~~ge~lyC~vCnKsFKseKq~kNHEnSKKHkenv~  322 (508)
T KOG0717|consen  282 ESDEADNEGEVLYCVVCNKSFKSEKQLKNHENSKKHKENVA  322 (508)
T ss_pred             hhhhhhhcCCceEEeeccccccchHHHHhhHHHHHHHHHHH
Confidence            33443444555999999999999999999999999998874

>KOG0528|consensus

Probab=95.36  E-value=0.0045  Score=57.44  Aligned_cols=60  Identities=22%  Similarity=0.417  Sum_probs=48.4

Q ss_pred             hHHHHHHHHHHHHHHH---H---hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          34 VYLDRAEVDKKRYREE---L---KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E---m---Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      .|.-.|+..|..-...   |   .|+|.||.+||.||..||+||.+.-+++-..+.+....|+-++
T Consensus       332 AFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkP  397 (511)
T KOG0528|consen  332 AFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKP  397 (511)
T ss_pred             hhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCC
Confidence            4555666666554332   2   7999999999999999999999999999999999999998653

>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=95.06  E-value=0.0051  Score=38.29  Aligned_cols=31  Identities=23%  Similarity=0.654  Sum_probs=19.1

Q ss_pred             HHHHHHHHHh--hhhhhhhhhhchhhhhhhhcc
Q psy1729         135 LYCRVCDQWF--TTLHNKREHLNGRQHFQRFDR  165 (170)
Q Consensus       135 ~~~~~~~~~f--~~~h~~~~~~~~~~~~~~~~~  165 (170)
                      -||-.|+-||  .+...-+-|..|.+|..++..
T Consensus         4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~   36 (38)
T PF06220_consen    4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR   36 (38)
T ss_dssp             -B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred             eecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence            3899999999  344566999999999998864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.

>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B

Probab=93.60  E-value=0.0088  Score=33.46  Aligned_cols=19  Identities=37%  Similarity=0.698  Sum_probs=18.0

Q ss_pred             HHHHHHHHhhhhhhhhhhh
Q psy1729         136 YCRVCDQWFTTLHNKREHL  154 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~  154 (170)
                      .|.+|++.|+++.++++|+
T Consensus         3 ~C~~C~~~F~~~~~l~~H~   21 (27)
T PF13912_consen    3 ECDECGKTFSSLSALREHK   21 (27)
T ss_dssp             EETTTTEEESSHHHHHHHH
T ss_pred             CCCccCCccCChhHHHHHh
Confidence            4899999999999999999

>KOG3248|consensus

Probab=93.46  E-value=0.095  Score=47.22  Aligned_cols=34  Identities=24%  Similarity=0.480  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHH
Q psy1729          13 KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRY   46 (170)
Q Consensus        13 ~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY   46 (170)
                      -++|.++||.+|-.||-+|..+|+++|.++|+..
T Consensus       219 SAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH  252 (421)
T KOG3248|consen  219 SAAINQILGRRWHALSREEQAKYYELARKERQLH  252 (421)
T ss_pred             HHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999998764

>KOG3408|consensus

Probab=93.35  E-value=0.063  Score=41.77  Aligned_cols=40  Identities=25%  Similarity=0.586  Sum_probs=35.5

Q ss_pred             cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729         124 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRF  163 (170)
Q Consensus       124 ~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~  163 (170)
                      ++|.|=+-.+.-||..|..||++--++..|.-|+-|-..|
T Consensus        47 ~~D~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRv   86 (129)
T KOG3408|consen   47 EIDPDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRV   86 (129)
T ss_pred             cCCCCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHH
Confidence            4577777788899999999999999999999999998765

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

Probab=92.15  E-value=0.16  Score=41.75  Aligned_cols=39  Identities=21%  Similarity=0.225  Sum_probs=33.2

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDK   43 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dK   43 (170)
                      +.+|.++++.|++...+..|..||+.+|..|...+....
T Consensus        94 Rrkh~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~~~  132 (183)
T PF06382_consen   94 RRKHCGLSPQDLIQRAARAWCRLSEAEKNRYRRMAPSVR  132 (183)
T ss_pred             HHHccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcchhh
Confidence            457889999999999999999999999999998765444

The function of this family is unknown.

>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=92.04  E-value=1  Score=33.71  Aligned_cols=60  Identities=17%  Similarity=0.219  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHH
Q psy1729          14 LLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLD   73 (170)
Q Consensus        14 ~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~   73 (170)
                      .++..-++..|..|++..+..+...+..-..--..+-+-+..--..|.+||++++..-..
T Consensus        10 q~~L~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~rm~~W~~LspeqR~~~R~   69 (107)
T PF11304_consen   10 QQALAPLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRERMRRWAALSPEQRQQARE   69 (107)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            456788999999999999999988776521111112233333335788888888765444

Currently no function is known.

>KOG0528|consensus

Probab=90.82  E-value=0.082  Score=49.29  Aligned_cols=37  Identities=24%  Similarity=0.427  Sum_probs=32.3

Q ss_pred             CCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHH
Q psy1729           8 MISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKK   44 (170)
Q Consensus         8 ~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKe   44 (170)
                      .|+|....|+|+||.+|+.|+..||++|++.-...-.
T Consensus       348 ~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk  384 (511)
T KOG0528|consen  348 FPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSK  384 (511)
T ss_pred             CccccccchhHHhcccccccccccccchHHHHHHHHH
Confidence            5889999999999999999999999999986655443

>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A

Probab=90.80  E-value=0.033  Score=38.90  Aligned_cols=31  Identities=23%  Similarity=0.544  Sum_probs=26.3

Q ss_pred             hHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         134 ELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       134 ~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      ...|.+|++.|++...+++||.+..|.++..
T Consensus        50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~   80 (100)
T PF12756_consen   50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS   80 (100)
T ss_dssp             SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred             CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence            5889999999999999999999999988653

>KOG2746|consensus

Probab=90.65  E-value=0.31  Score=47.03  Aligned_cols=54  Identities=28%  Similarity=0.331  Sum_probs=45.2

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLP   66 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~   66 (170)
                      -...+|+....-|+++||+.|-+|.+.||+.|.++|.+.++.+.+.         .|+..+..
T Consensus       202 vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka---------e~~k~sk~  255 (683)
T KOG2746|consen  202 VHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA---------EWKKDSKE  255 (683)
T ss_pred             hhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh---------hcccccch
Confidence            3457889999999999999999999999999999999988876442         77777654

>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=89.08  E-value=0.049  Score=29.18  Aligned_cols=20  Identities=25%  Similarity=0.735  Sum_probs=18.4

Q ss_pred             HHHHHHHhhhhhhhhhhhch
Q psy1729         137 CRVCDQWFTTLHNKREHLNG  156 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~~~  156 (170)
                      |..|+..|++..+++.||..
T Consensus         3 C~~C~~~f~~~~~l~~H~~~   22 (23)
T PF00096_consen    3 CPICGKSFSSKSNLKRHMRR   22 (23)
T ss_dssp             ETTTTEEESSHHHHHHHHHH
T ss_pred             CCCCCCccCCHHHHHHHHhH
Confidence            88999999999999999864

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....

>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]

Probab=87.91  E-value=0.2  Score=38.46  Aligned_cols=56  Identities=27%  Similarity=0.421  Sum_probs=42.5

Q ss_pred             hhCCCCcccccccccc-------cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729         108 QANGTEESDIATDATD-------EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRF  163 (170)
Q Consensus       108 ~~~~~~~~~~~~d~~~-------~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~  163 (170)
                      +-+|-..+.|-+|...       .+|.+-+--|.-||.-|..||-+---+-||.-|+-|...+
T Consensus        22 r~~grDlDqi~nDls~~Es~~Klp~Dp~lPGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~   84 (126)
T COG5112          22 RLFGRDLDQIKNDLSTKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGKVHKRRA   84 (126)
T ss_pred             HHhcccHHHHHHhcchhhhhccCCCCCCCCCCceeeeehhHHHHHHHHHHHHHhccchhHHHH
Confidence            3345445667677621       2366666678899999999999999999999999997665

>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=83.35  E-value=3.9  Score=30.59  Aligned_cols=50  Identities=18%  Similarity=0.245  Sum_probs=23.6

Q ss_pred             hcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHH
Q psy1729          24 WSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLD   73 (170)
Q Consensus        24 Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~   73 (170)
                      |..||+.++..+.-++..=..--...-.-...++..|..||++++..+..
T Consensus         2 W~~L~~~Qq~~L~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~   51 (107)
T PF11304_consen    2 WSSLSPAQQQALAPLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRE   51 (107)
T ss_pred             hhhCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            77777777766543333211000011123334555666666665554433

Currently no function is known.

>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=83.00  E-value=0.38  Score=31.64  Aligned_cols=29  Identities=21%  Similarity=0.464  Sum_probs=24.1

Q ss_pred             hhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         133 EELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       133 ~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      -.-||-.|...|.+   +.+|+.+++|+.-++
T Consensus         4 k~GYCE~C~~ky~~---l~~Hi~s~~Hr~FA~   32 (49)
T PF07535_consen    4 KPGYCENCRVKYDD---LEEHIQSEKHRKFAE   32 (49)
T ss_pred             CCccCccccchhhh---HHHHhCCHHHHHHHc
Confidence            34599999999985   579999999987653

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding

>smart00586 ZnF_DBF Zinc finger in DBF-like proteins

Probab=82.42  E-value=0.61  Score=30.75  Aligned_cols=32  Identities=19%  Similarity=0.429  Sum_probs=25.7

Q ss_pred             CchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729         131 DNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR  165 (170)
Q Consensus       131 ~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~  165 (170)
                      |+-.-||-.|...|..   +.+|+.|++|+.-+..
T Consensus         2 ~~k~GYCE~Cr~kfd~---l~~Hi~s~~Hr~FA~~   33 (49)
T smart00586        2 EKKPGYCENCREKYDD---LETHLLSEKHRRFAEN   33 (49)
T ss_pred             CCCCcccccHhHHHhh---HHHHhccHHHHHHHcC
Confidence            4456799999999985   5689999999876543

>KOG4727|consensus

Probab=81.70  E-value=0.35  Score=39.82  Aligned_cols=32  Identities=31%  Similarity=0.629  Sum_probs=29.0

Q ss_pred             chhHHHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729         132 NEELYCRVCDQWFTTLHNKREHLNGRQHFQRF  163 (170)
Q Consensus       132 ~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~  163 (170)
                      -+--||.||+--|----|.-.|++|+.|..+|
T Consensus        73 ~~GyyCdVCdcvvKDSinflDHiNgKkHqrnl  104 (193)
T KOG4727|consen   73 KGGYYCDVCDCVVKDSINFLDHINGKKHQRNL  104 (193)
T ss_pred             cCceeeeecceeehhhHHHHHHhccHHHHHHH
Confidence            35679999999999999999999999998776

>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes

Probab=81.34  E-value=0.71  Score=39.54  Aligned_cols=31  Identities=23%  Similarity=0.508  Sum_probs=25.3

Q ss_pred             hHHHHHHHHHhhhhh---hhhhhhchhhhhhhhc
Q psy1729         134 ELYCRVCDQWFTTLH---NKREHLNGRQHFQRFD  164 (170)
Q Consensus       134 ~~~~~~~~~~f~~~h---~~~~~~~~~~~~~~~~  164 (170)
                      --.|-||+.+-|++-   +.-.|+.|++|+-.+.
T Consensus       190 l~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~~  223 (254)
T PF03194_consen  190 LEVCEVCGAFLSVGDNDRRLADHFGGKQHLGYAK  223 (254)
T ss_pred             ccchhhhhhHHhccchHHHHHHHhccchhhhHHH
Confidence            367999999998875   5669999999986543

LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].

>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A

Probab=80.21  E-value=0.27  Score=25.68  Aligned_cols=19  Identities=26%  Similarity=0.768  Sum_probs=15.8

Q ss_pred             HHHHHHHhhhhhhhhhhhc
Q psy1729         137 CRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~~  155 (170)
                      |..|+..|++.-.++.||.
T Consensus         3 C~~C~~~~~~~~~l~~H~~   21 (24)
T PF13894_consen    3 CPICGKSFRSKSELRQHMR   21 (24)
T ss_dssp             -SSTS-EESSHHHHHHHHH
T ss_pred             CcCCCCcCCcHHHHHHHHH
Confidence            8899999999999999985

...

>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM

Probab=80.19  E-value=8.5  Score=31.59  Aligned_cols=39  Identities=21%  Similarity=0.459  Sum_probs=34.8

Q ss_pred             hhHHHHhhCCChhhhhhhHHHHHH-HHHHHHHHHHHHHcc
Q psy1729          54 KLLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRKS   92 (170)
Q Consensus        54 K~lg~~Wk~LS~~EK~~Y~~~A~~-dk~rY~~em~~yk~~   92 (170)
                      ..||.-|+.+|+++++.|.+.... ....|-..+..|...
T Consensus        72 ~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~  111 (198)
T TIGR03481        72 LTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGE  111 (198)
T ss_pred             HHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence            479999999999999999999888 888999999998743

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	170
2crj_A	92	Solution Structure Of The Hmg Domain Of Mouse Hmg D		4e-07

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 35/45 (77%)
Query: 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 95
          ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL  Y++S+AY
Sbjct: 37 EITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAY 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	170
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	6e-11
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	4e-07
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	6e-11
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	7e-07
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	1e-09
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	2e-08
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	1e-09
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	7e-06
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	2e-09
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	1e-06
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	2e-09
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	3e-04
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	6e-09
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	8e-07
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	9e-09
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	7e-07
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	9e-09
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	3e-07
2lhj_A	97	High mobility group protein homolog NHP1; structur	1e-08
2lhj_A	97	High mobility group protein homolog NHP1; structur	2e-06
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	2e-08
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	2e-08
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	5e-05
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	6e-08
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	6e-07
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	1e-07
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	8e-06
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	1e-07
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	2e-05
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-07
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	1e-04
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	6e-04
1ckt_A	71	High mobility group 1 protein; high-mobility group	1e-07
1ckt_A	71	High mobility group 1 protein; high-mobility group	1e-06
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	5e-07
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	1e-04
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	2e-04
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	2e-04
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	1e-06
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	5e-04
1wgf_A	90	Upstream binding factor 1; transcription factor, D	5e-06
1wgf_A	90	Upstream binding factor 1; transcription factor, D	2e-05

>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 = 55.1 bits (133), Expect = 6e-11
 Identities = 24/51 (47%), Positives = 35/51 (68%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 102
           +TK+LG EWSKL   EK+ YLD AE +K++Y +EL  Y++S+AY+      
Sbjct: 38  ITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCTESG 88

>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 = 45.1 bits (107), Expect = 4e-07
 Identities = 20/36 (55%), Positives = 27/36 (75%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          +TK+LG EWSKL   EK+ YLD AE +K++Y +EL 
Sbjct: 38 ITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELW 73

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

 Score = 55.5 bits (134), Expect = 6e-11
 Identities = 17/51 (33%), Positives = 27/51 (52%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 102
           V+K++ + W  L   +K+VY  + E  KK Y ++L  YR S   +SY    
Sbjct: 48  VSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSYTDSG 98

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

 Score = 44.3 bits (105), Expect = 7e-07
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          V+K++ + W  L   +K+VY  + E  KK Y ++L 
Sbjct: 48 VSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLA 83

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

 Score = 51.1 bits (123), Expect = 1e-09
 Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 6/52 (11%)

Query: 44 KRYREELK------VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
              +E K        K +   W  LS  EK++Y+  A+ D+ RY  E+K +
Sbjct: 15 AERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66

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

 Score = 47.7 bits (114), Expect = 2e-08
 Identities = 13/46 (28%), Positives = 23/46 (50%)

Query: 6  EKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          ++    +     K +   W  LS  EK++Y+  A+ D+ RY  E+K
Sbjct: 19 QEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMK 64

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

 Score = 51.6 bits (124), Expect = 1e-09
 Identities = 10/59 (16%), Positives = 25/59 (42%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQAN 110
           +TK+L  ++ +L   +K  Y+   + +K+ +   L  +R+         +K       +
Sbjct: 41  LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKKLEHHHHHH 99

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

 Score = 41.6 bits (98), Expect = 7e-06
 Identities = 8/36 (22%), Positives = 19/36 (52%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          +TK+L  ++ +L   +K  Y+   + +K+ +   L 
Sbjct: 41 LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLA 76

>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 = 51.2 bits (123), Expect = 2e-09
 Identities = 18/43 (41%), Positives = 26/43 (60%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 94
          V K LG +W  L+  EK+ Y  +A+ DKKRY  E ++Y  + A
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 93

>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 = 43.8 bits (104), Expect = 1e-06
 Identities = 16/36 (44%), Positives = 22/36 (61%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          V K LG +W  L+  EK+ Y  +A+ DKKRY  E +
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKE 86

>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 = 52.5 bits (126), Expect = 2e-09
 Identities = 22/124 (17%), Positives = 41/124 (33%), Gaps = 48/124 (38%)

Query: 16  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK------------------------ 51
           ++K LG +W  L+  EK  +   A+  +  +RE+                          
Sbjct: 35  ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPS 94

Query: 52  ------------------------VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 87
                                   V K LG  W+  +  +K+ Y  +A   K++Y +++ 
Sbjct: 95  AFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA 154

Query: 88  VYRK 91
            YR 
Sbjct: 155 AYRA 158

>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 = 38.3 bits (89), Expect = 3e-04
 Identities = 11/45 (24%), Positives = 21/45 (46%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 96
          ++K LG +W  L+  EK  +   A+  +  +RE+   Y+      
Sbjct: 35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGET 79

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

 Score = 49.7 bits (119), Expect = 6e-09
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS 97
           T  +   W  LS  EK  Y ++A  D +RY  ++K   + ++  S
Sbjct: 38 ATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMS 83

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

 Score = 44.0 bits (104), Expect = 8e-07
 Identities = 12/36 (33%), Positives = 18/36 (50%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
           T  +   W  LS  EK  Y ++A  D +RY  ++K
Sbjct: 38 ATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMK 73

>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 = 48.8 bits (117), Expect = 9e-09
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 91
          V K LG  W+  +  +K+ Y  +A   K++Y +++  YR 
Sbjct: 37 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 76

>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 = 43.8 bits (104), Expect = 7e-07
 Identities = 10/36 (27%), Positives = 20/36 (55%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          V K LG  W+  +  +K+ Y  +A   K++Y +++ 
Sbjct: 37 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA 72

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

 Score = 49.2 bits (118), Expect = 9e-09
 Identities = 14/41 (34%), Positives = 19/41 (46%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 92
           +K     W  +S  EK  + D A+ DK RY  E+K Y   
Sbjct: 40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP 80

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

 Score = 45.0 bits (107), Expect = 3e-07
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
           +K     W  +S  EK  + D A+ DK RY  E+K
Sbjct: 40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK 75

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

 Score = 48.9 bits (117), Expect = 1e-08
 Identities = 14/41 (34%), Positives = 22/41 (53%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 92
          + K++G  W+ LS  EKK Y   ++ D+ RY  E   Y + 
Sbjct: 55 IGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR 95

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

 Score = 43.5 bits (103), Expect = 2e-06
 Identities = 13/36 (36%), Positives = 20/36 (55%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          + K++G  W+ LS  EKK Y   ++ D+ RY  E  
Sbjct: 55 IGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKA 90

>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 = 50.4 bits (120), Expect = 2e-08
 Identities = 25/124 (20%), Positives = 41/124 (33%), Gaps = 48/124 (38%)

Query: 16  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRY----------------------------- 46
            +K     W  +S  EK  + D A+ DK RY                             
Sbjct: 48  FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPS 107

Query: 47  ---------REELK----------VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 87
                    R ++K          V K LG  W+  +  +K+ Y  +A   K++Y +++ 
Sbjct: 108 AFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA 167

Query: 88  VYRK 91
            YR 
Sbjct: 168 AYRA 171

>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 = 14/70 (20%), Positives = 31/70 (44%)

Query: 37  DRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 96
           +     +  +    +    +G+ W ++S  +K+ Y   AE  +++Y+  L ++ KS + Q
Sbjct: 22  ELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ 81

Query: 97  SYLRRKRVKS 106
                K   S
Sbjct: 82  DRAAYKEYIS 91

>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 = 39.5 bits (92), Expect = 5e-05
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 17/79 (21%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRA 75
              +G+ W ++S  +K+ Y   AE  +++Y+  L         W K   P+        
Sbjct: 37 RMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLD-------LWVKSLSPQ-------- 81

Query: 76 EVDKKRYREELKVYRKSDA 94
            D+  Y+E +   RKS  
Sbjct: 82 --DRAAYKEYISNKRKSGP 98

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

 Score = 47.0 bits (112), Expect = 6e-08
 Identities = 13/38 (34%), Positives = 19/38 (50%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
           +K     W  +S  EK  + + A+ DK RY  E+K Y
Sbjct: 48 FSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY 85

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

 Score = 44.3 bits (105), Expect = 6e-07
 Identities = 12/36 (33%), Positives = 18/36 (50%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
           +K     W  +S  EK  + + A+ DK RY  E+K
Sbjct: 48 FSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMK 83

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

 Score = 46.1 bits (110), Expect = 1e-07
 Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 2/41 (4%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 92
          + K  G  W +L   +K  + D A  DK+RY +E++ Y+  
Sbjct: 34 IAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYKPE 72

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

 Score = 41.1 bits (97), Expect = 8e-06
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          + K  G  W +L   +K  + D A  DK+RY +E++
Sbjct: 34 IAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMR 67

>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 = 46.1 bits (110), Expect = 1e-07
 Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 2/41 (4%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 92
          V K  G  W  +   +K  +  +A   K  Y   +K +  +
Sbjct: 34 VAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEAN 72

>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 = 40.0 bits (94), Expect = 2e-05
 Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 2/36 (5%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          V K  G  W  +   +K  +  +A   K  Y   +K
Sbjct: 34 VAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVK 67

>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 = 48.7 bits (115), Expect = 1e-07
 Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 2/66 (3%)

Query: 51  KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS--DAYQSYLRRKRVKSLQ 108
           +  K +   W  LS  EK++Y+  A+ D+ RY  E+K + +   +  +  L R+ +K  +
Sbjct: 172 EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKKQR 231

Query: 109 ANGTEE 114
             G EE
Sbjct: 232 KYGAEE 237

>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 = 39.8 bits (92), Expect = 1e-04
 Identities = 13/36 (36%), Positives = 20/36 (55%)

Query: 16  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
             K +   W  LS  EK++Y+  A+ D+ RY  E+K
Sbjct: 173 KLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMK 208

>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 = 38.3 bits (88), Expect = 6e-04
 Identities = 19/117 (16%), Positives = 45/117 (38%), Gaps = 3/117 (2%)

Query: 16  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRA 75
           + + +   W +L   +KK+Y D    + + Y+EE+   K        +SL ++ +     
Sbjct: 72  LIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLK 131

Query: 76  EVDKKRYREELKVY---RKSDAYQSYLRRKRVKSLQANGTEESDIATDATDEIDEEE 129
                + +E   +    R   AY  Y+  +  ++   +  E+     +    + + E
Sbjct: 132 RKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSE 188

>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 = 45.5 bits (108), Expect = 1e-07
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
           +K     W  +S  EK  + D A+ DK RY  E+K Y
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 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 = 43.1 bits (102), Expect = 1e-06
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
           +K     W  +S  EK  + D A+ DK RY  E+K
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK 69

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

 Score = 46.7 bits (110), Expect = 5e-07
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 51  KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS--DAYQSYLRRKRVKSLQ 108
           +  K +   W  LS  EK++Y+  A+ D+ RY  E+K + +   +  +  L R+ +K  +
Sbjct: 140 EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKKQR 199

Query: 109 ANGTEES 115
             G EE 
Sbjct: 200 KYGAEEC 206

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 12/82 (14%)

Query: 16  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRA 75
             K +   W  LS  EK++Y+  A+ D+ RY  E+K  +            E+ + + R 
Sbjct: 141 KLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWE------------EQMIEVGRK 188

Query: 76  EVDKKRYREELKVYRKSDAYQS 97
           ++ ++  +++ K   +      
Sbjct: 189 DLLRRTIKKQRKYGAEECLQHH 210

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

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 9/47 (19%), Positives = 22/47 (46%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 98
          + + +   W +L   +KK+Y D    + + Y+EE+  +++       
Sbjct: 40 LIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQI 86

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

 Score = 39.4 bits (91), Expect = 2e-04
 Identities = 21/117 (17%), Positives = 41/117 (35%), Gaps = 3/117 (2%)

Query: 16  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV---TKLLGNEWSKLSLPEKKVYL 72
           + + +   W +L   +KK+Y D    + + Y+EE+             S       K   
Sbjct: 40  LIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLK 99

Query: 73  DRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQANGTEESDIATDATDEIDEEE 129
            +A   KK      K  R   AY  Y+  +  ++   +  E+     +    + + E
Sbjct: 100 RKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSE 156

>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 = 44.2 bits (104), Expect = 1e-06
 Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLR-RKRVKSLQAN 110
              L   +W  LS  EK  Y  + +  KK Y  EL  + +S   +   R     K L  +
Sbjct: 44  RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEEKMLNIS 103

Query: 111 GT 112
           G 
Sbjct: 104 GP 105

>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 = 36.9 bits (85), Expect = 5e-04
 Identities = 12/36 (33%), Positives = 15/36 (41%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
             L   +W  LS  EK  Y  + +  KK Y  EL 
Sbjct: 44 RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELL 79

>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 = 42.0 bits (99), Expect = 5e-06
 Identities = 10/39 (25%), Positives = 16/39 (41%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90
          +T+LL   W+ LS  +K  Y  R    K +   +     
Sbjct: 51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPSS 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 = 40.1 bits (94), Expect = 2e-05
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 49
          +T+LL   W+ LS  +K  Y  R    K +   +
Sbjct: 51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	170
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.81
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.8
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.79
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.78
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.2
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.09
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.06
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.06
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.04
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.01
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.01
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.01
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.01
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.0
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	98.99
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	98.98
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	98.98
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	98.97
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	98.97
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	98.97
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	98.96
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	98.96
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	98.96
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	98.94
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	98.94
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	98.93
1wgf_A	90	Upstream binding factor 1; transcription factor, D	98.93
1ckt_A	71	High mobility group 1 protein; high-mobility group	98.93
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	98.92
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	98.92
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	98.91
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	98.91
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	98.9
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	98.9
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	98.9
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	98.88
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	98.88
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	98.87
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	98.87
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	98.85
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	98.85
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	98.84
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	98.82
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	98.82
2lhj_A	97	High mobility group protein homolog NHP1; structur	98.81
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	98.8
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	98.8
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	98.8
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	98.79
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	98.77
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	98.76
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	98.76
2lhj_A	97	High mobility group protein homolog NHP1; structur	98.75
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	98.73
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	98.72
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.71
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	98.69
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	98.69
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	98.68
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	98.66
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	98.66
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	98.61
2cto_A	93	Novel protein; high mobility group box domain, hel	98.51
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	98.44
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.44
1wgf_A	90	Upstream binding factor 1; transcription factor, D	98.44
2cto_A	93	Novel protein; high mobility group box domain, hel	98.38
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	98.28
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	97.81
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	97.72
1zu1_A	127	DSRBP-ZFA, RNA binding protein ZFA; zinc finger pr	96.81
1zr9_A	124	Zinc finger protein 593; DNA binding, structural g	96.16
1zu1_A	127	DSRBP-ZFA, RNA binding protein ZFA; zinc finger pr	94.82
3cw1_L	77	U1 small nuclear ribonucleoprotein C; PRE-mRNA spl	93.77
2lvu_A	26	Zinc finger and BTB domain-containing protein 17;	90.38
2lvt_A	29	Zinc finger and BTB domain-containing protein 17;	88.74
2yrk_A	55	Zinc finger homeobox protein 4; structure genomics	87.91
2lvr_A	30	Zinc finger and BTB domain-containing protein 17;	87.5
1ard_A	29	Yeast transcription factor ADR1; transcription reg	86.42
2kfq_A	32	FP1; protein, de novo protein; NMR {Synthetic}	86.39
2kvg_A	27	Zinc finger and BTB domain-containing protein 32;	86.17
2kvf_A	28	Zinc finger and BTB domain-containing protein 32;	86.05
4dgw_A	402	PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A	85.47
2m0f_A	29	Zinc finger and BTB domain-containing protein 17;	84.84
2elo_A	37	Zinc finger protein 406; ZFAT zinc finger 1, struc	84.06
1znf_A	27	31ST zinc finger from XFIN; zinc finger DNA bindin	83.75
2m0d_A	30	Zinc finger and BTB domain-containing protein 17;	83.37
1fv5_A	36	First zinc finger of U-shaped; CCHC, protein inter	82.94
2kvh_A	27	Zinc finger and BTB domain-containing protein 32;	82.9
2elx_A	35	Zinc finger protein 406; ZFAT zinc finger 1, struc	82.72
1rim_A	33	E6APC2 peptide; E6-binding domain, zinc finger, hu	82.71
2elq_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	81.65
1rik_A	29	E6APC1 peptide; E6-binding domain, zinc finger, hu	81.03
2els_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	80.97
1njq_A	39	Superman protein; zinc-finger, peptide-zinc comple	80.94
1srk_A	35	Zinc finger protein ZFPM1; classical zinc finger,	80.92
2elv_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	80.75
2elr_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	80.6
2ytb_A	42	Zinc finger protein 32; zinc-finger domain, C2H2,	80.49
2elt_A	36	Zinc finger protein 406; ZFAT zinc finger 1, struc	80.34
2m0e_A	29	Zinc finger and BTB domain-containing protein 17;	80.24

>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=99.81  E-value=7.9e-20  Score=142.09  Aligned_cols=87  Identities=25%  Similarity=0.426  Sum_probs=82.4

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH----------------------------------
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL----------------------------------   50 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em----------------------------------   50 (170)
                      +.++|++++++|++.||++|++||+++|.+|.+.|..++++|..++                                  
T Consensus        24 ~~~~P~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~k~~~kk~~kdp~~pKrp~say~lf~~~~  103 (159)
T 2gzk_A           24 ALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEY  103 (159)
T ss_dssp             HHHCSSCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCCCCCCGGGSCCTTCCCCCCCHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccchhhHhh
Confidence            4789999999999999999999999999999999999999987644                                  


Q ss_pred             --------------hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHc
Q psy1729          51 --------------KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   91 (170)
Q Consensus        51 --------------Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~   91 (170)
                                    +|++.||++|++||+++|++|+++|+.++++|..+|.+|+.
T Consensus       104 r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A          104 RPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence                          78999999999999999999999999999999999999985

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

Probab=99.80  E-value=1.8e-19  Score=142.11  Aligned_cols=89  Identities=28%  Similarity=0.480  Sum_probs=83.7

Q ss_pred             ccccCCC--CCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH-------------------------------
Q psy1729           4 ESEKMIS--TTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL-------------------------------   50 (170)
Q Consensus         4 ~k~~~p~--~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em-------------------------------   50 (170)
                      .+.++|+  +++++|++.||++|++||++||++|.+.|..++++|..++                               
T Consensus        34 ~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~~~~kk~~kdp~~pKrP~saf~lf~  113 (173)
T 2yrq_A           34 HKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFC  113 (173)
T ss_dssp             HHHHCTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCCCCCCSSCSCCCSSSCCCCCCHHHHHH
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccccCCccccCcccHHHHHH
Confidence            4678999  6999999999999999999999999999999999997765                               


Q ss_pred             -----------------hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          51 -----------------KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        51 -----------------Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                                       +|++.||++|++||+++|++|+++|+.++++|..+|.+|+.+
T Consensus       114 ~~~r~~~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~k  172 (173)
T 2yrq_A          114 SEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK  172 (173)
T ss_dssp             HHHHHHHHHHCSSSCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence                             789999999999999999999999999999999999999865

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

Probab=99.79  E-value=4.7e-19  Score=145.21  Aligned_cols=90  Identities=24%  Similarity=0.468  Sum_probs=83.2

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH---------------------------------
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL---------------------------------   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em---------------------------------   50 (170)
                      .+.++|++++++|++.||++|++||+++|.+|++.|..++++|..+|                                 
T Consensus        28 ~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~tp~q~~~~~~~~~~~~~krk~~kkkk  107 (214)
T 3tq6_A           28 FKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKK  107 (214)
T ss_dssp             HHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHHHHHhhhcchhhhh
Confidence            46789999999999999999999999999999999999998874421                                 


Q ss_pred             --------------------------------hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 --------------------------------KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 --------------------------------Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                                                      +|++.||++|++||+++|+||+++|++++++|..+|.+|+...
T Consensus       108 ~~kdp~~PKrP~say~lF~~e~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~~  182 (214)
T 3tq6_A          108 ELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  182 (214)
T ss_dssp             HHHHTTCCCCCCCHHHHHHHHHTTTSSCSSHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhccccCcccccchhhhhHHHHHHhhccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence                                            6899999999999999999999999999999999999999764

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

Probab=99.78  E-value=5.1e-19  Score=147.05  Aligned_cols=90  Identities=24%  Similarity=0.468  Sum_probs=83.3

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH---------------------------------
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL---------------------------------   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em---------------------------------   50 (170)
                      .+.++|++++++|++.||++|++||++||.+|++.|..++++|..+|                                 
T Consensus        60 ~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~~p~~~~~~~~~~~~k~~krk~~~kkk  139 (238)
T 3tmm_A           60 FKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKK  139 (238)
T ss_dssp             HHHHSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhcccchh
Confidence            46789999999999999999999999999999999999998874422                                 


Q ss_pred             --------------------------------hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 --------------------------------KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 --------------------------------Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                                                      +|++.||++|++||+++|+||+++|++++++|+.+|.+|+...
T Consensus       140 ~~kdp~~PKrP~say~lF~~e~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k~  214 (238)
T 3tmm_A          140 ELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  214 (238)
T ss_dssp             HHHHTTCCCCCCCHHHHHHHHHTTTSCCSSHHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhcccCCCCCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence                                            6899999999999999999999999999999999999999764

>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=99.20  E-value=2.2e-11  Score=88.44  Aligned_cols=65  Identities=25%  Similarity=0.339  Sum_probs=53.3

Q ss_pred             HHHhHHHHHHHHHHHHHHH-----HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhh
Q psy1729          31 EKKVYLDRAEVDKKRYREE-----LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY   95 (170)
Q Consensus        31 EK~~Ye~~Ak~dKerY~~E-----mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~   95 (170)
                      -...|.-.....+..|..+     .+|++.||++|++||++||+||+++|+.++++|+++|.+|+.+.+.
T Consensus         8 P~SAy~lf~~~~r~~~k~~~p~~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~~   77 (91)
T 1l8y_A            8 PKRAEEIWQQSVIGDYLARFKNDRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAA   77 (91)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTSTHHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGGS
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            3344555555666666554     3899999999999999999999999999999999999999876553

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

Probab=99.09  E-value=1.8e-10  Score=82.27  Aligned_cols=66  Identities=39%  Similarity=0.648  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYL   99 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~~~~   99 (170)
                      .|.-.....+.....+      .+|++.||++|++||+++|++|+++|..++++|..+|.+|+.+.+|+.+.
T Consensus        14 af~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~~~   85 (92)
T 2crj_A           14 GYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCT   85 (92)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHCSS
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHH
Confidence            3444455555554443      38999999999999999999999999999999999999999999987654

>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=99.06  E-value=3.6e-10  Score=82.54  Aligned_cols=44  Identities=25%  Similarity=0.489  Sum_probs=35.8

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchh
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA   94 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~   94 (170)
                      +|++.||++|++||++||+||+++|++++++|..+|++|..+..
T Consensus        36 eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~   79 (101)
T 1v63_A           36 ERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLS   79 (101)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            67888888888888888888888888888888888888886543

>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=99.06  E-value=1e-10  Score=79.13  Aligned_cols=48  Identities=29%  Similarity=0.424  Sum_probs=39.8

Q ss_pred             ccccCCCCCH--HHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTK--LLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~--~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .++++|++++  ++|++.||++|++||+++|.+|.+.|..++++|..+|.
T Consensus        20 ~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~   69 (71)
T 1ckt_A           20 HKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK   69 (71)
T ss_dssp             HHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHCCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3567888765  88888888888888888888888888888888887763

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

Probab=99.04  E-value=2.1e-10  Score=81.97  Aligned_cols=46  Identities=26%  Similarity=0.280  Sum_probs=26.6

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      ++++|++++++|++.||++|+.||+++|++|.+.|..++++|..+|
T Consensus        27 ~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~   72 (92)
T 2cs1_A           27 LIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQM   72 (92)
T ss_dssp             HHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455666666666665555555555555555555555555555544

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

Probab=99.01  E-value=3.6e-10  Score=79.65  Aligned_cols=47  Identities=28%  Similarity=0.352  Sum_probs=26.5

Q ss_pred             cccCCCCC--HHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           5 SEKMISTT--KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         5 k~~~p~~s--~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      ++++|+++  +++|++.||++|++||+++|++|++.|..++++|..+|.
T Consensus        35 k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~   83 (86)
T 2eqz_A           35 KKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMK   83 (86)
T ss_dssp             HHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34555554  355666555555555555555555555555555555543

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

Probab=99.01  E-value=2.5e-10  Score=82.92  Aligned_cols=49  Identities=18%  Similarity=0.306  Sum_probs=33.5

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV   52 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi   52 (170)
                      +++++|++++++|++.||++|+.||+++|++|.+.|..++++|..+|..
T Consensus        29 ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~   77 (99)
T 1k99_A           29 YAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLAR   77 (99)
T ss_dssp             HHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGG
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3556777777777777777777777777777777777777766666543

>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=99.01  E-value=4.5e-10  Score=77.81  Aligned_cols=48  Identities=25%  Similarity=0.309  Sum_probs=36.9

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++.
T Consensus        21 ~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~   68 (80)
T 1gt0_D           21 MAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHP   68 (80)
T ss_dssp             HHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            356778888888888888888888888888888888888777776653

>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=99.01  E-value=3.3e-10  Score=82.27  Aligned_cols=50  Identities=22%  Similarity=0.444  Sum_probs=46.1

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhh
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKL   55 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~   55 (170)
                      ++++|+ ++++|++.||++|++||+++|++|++.|+.++++|.++|..++.
T Consensus        24 k~~~p~-~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~   73 (91)
T 1l8y_A           24 LARFKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRA   73 (91)
T ss_dssp             HHHTTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             HHHcCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            578899 99999999999999999999999999999999999999966543

>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=99.00  E-value=3.1e-10  Score=78.03  Aligned_cols=48  Identities=21%  Similarity=0.311  Sum_probs=34.5

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++.
T Consensus        25 ~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~   72 (77)
T 1hme_A           25 IKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA   72 (77)
T ss_dssp             HHHHCTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345677777777777777777777777777777777777777766653

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

Probab=98.99  E-value=3.1e-10  Score=76.49  Aligned_cols=47  Identities=21%  Similarity=0.397  Sum_probs=41.6

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|++.||+.|++||+++|++|.+.|..++++|..++
T Consensus        21 ~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   67 (71)
T 4a3n_A           21 LAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDH   67 (71)
T ss_dssp             HHTTCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            46789999999999999999999999999999999999999987754

>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=98.98  E-value=9.9e-10  Score=80.19  Aligned_cols=64  Identities=19%  Similarity=0.312  Sum_probs=55.0

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDR   74 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~~   74 (170)
                      .+++|+++++||++.||++|+.||++||++|+++|+.++++|..+|..+..      .|++.++..|.+.
T Consensus        26 ~p~~~~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~------~~~~~~~~~~~~~   89 (101)
T 1v63_A           26 NGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVK------SLSPQDRAAYKEY   89 (101)
T ss_dssp             HCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHH------HSCTTHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh------hCCHHHHHHHHHH
Confidence            356778999999999999999999999999999999999999998876544      6788877766553

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

Probab=98.98  E-value=6.4e-10  Score=79.38  Aligned_cols=51  Identities=39%  Similarity=0.530  Sum_probs=47.1

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK   54 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K   54 (170)
                      +++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++..++
T Consensus        26 ~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~   76 (92)
T 2crj_A           26 IRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQ   76 (92)
T ss_dssp             HHHHCTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999999999999885443

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

Probab=98.97  E-value=4.8e-10  Score=75.36  Aligned_cols=39  Identities=33%  Similarity=0.655  Sum_probs=36.6

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   89 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~y   89 (170)
                      ++++.||++|++||+++|++|+++|..++++|..+|++|
T Consensus        28 ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A           28 EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            789999999999999999999999999999999999887

>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=98.97  E-value=4e-10  Score=77.29  Aligned_cols=47  Identities=21%  Similarity=0.254  Sum_probs=36.6

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++
T Consensus        23 ~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   69 (76)
T 1hry_A           23 MALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY   69 (76)
T ss_dssp             HHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            35677888888888888888888888888888888888888877654

>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=98.97  E-value=7.4e-10  Score=77.93  Aligned_cols=45  Identities=22%  Similarity=0.442  Sum_probs=30.4

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhh
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY   95 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~   95 (170)
                      +|++.||++|++||+++|++|++.|+.++++|..++.+|+.++.+
T Consensus        32 eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~   76 (86)
T 2lef_A           32 AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY   76 (86)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSST
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCC
Confidence            555666666666666666677777777777777777777765553

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

Probab=98.96  E-value=9.9e-10  Score=78.38  Aligned_cols=60  Identities=22%  Similarity=0.260  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      .|.-.+...+.....+      .+|++.||++|++||+++|++|+++|++++++|..+|.+|+.+.
T Consensus        14 ay~lF~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~~   79 (92)
T 2cs1_A           14 ASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQE   79 (92)
T ss_dssp             HHHHHHHHHHHHHHHHCCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTSTT
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            4555556666555543      38999999999999999999999999999999999999998653

>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=98.96  E-value=8e-10  Score=77.72  Aligned_cols=47  Identities=21%  Similarity=0.254  Sum_probs=33.4

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++
T Consensus        23 ~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~   69 (85)
T 1j46_A           23 MALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY   69 (85)
T ss_dssp             HHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            34567777777777777777777777777777777777777776654

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

Probab=98.96  E-value=1e-09  Score=79.84  Aligned_cols=44  Identities=34%  Similarity=0.607  Sum_probs=28.5

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchh
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA   94 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~   94 (170)
                      +|++.||++|++||+++|++|+++|..++++|..+|.+|+.+..
T Consensus        47 eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~   90 (102)
T 2co9_A           47 EVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLV   90 (102)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            55666666666666666666666666666666666666665544

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

Probab=98.94  E-value=2.3e-09  Score=75.49  Aligned_cols=57  Identities=25%  Similarity=0.384  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHHHHHHH--------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE--------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E--------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      .|.-.....+.....+        .+|++.||++|++||+++|++|+++|+.++++|..+|++|+
T Consensus        22 ay~lF~~~~r~~~k~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A           22 AYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             HHHHHHHHHHHHHHHHCTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            4555555555554332        48999999999999999999999999999999999999984

>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=98.94  E-value=8.8e-10  Score=75.94  Aligned_cols=47  Identities=19%  Similarity=0.263  Sum_probs=37.4

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++
T Consensus        21 ~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   67 (79)
T 3u2b_C           21 IMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADY   67 (79)
T ss_dssp             HHTTSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            45678888888888888888888888888888888888888877654

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=98.93  E-value=6e-10  Score=76.15  Aligned_cols=39  Identities=23%  Similarity=0.377  Sum_probs=20.4

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   91 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~   91 (170)
                      +|++.||++|++||+  |++|+++|++++++|..+|++|+.
T Consensus        33 eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~   71 (73)
T 3nm9_A           33 EVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             HHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHh
Confidence            444455555555554  555555555555555555555543

>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=98.93  E-value=2.9e-10  Score=80.96  Aligned_cols=48  Identities=23%  Similarity=0.255  Sum_probs=45.0

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..+|.
T Consensus        39 ~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~   86 (90)
T 1wgf_A           39 LQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSG   86 (90)
T ss_dssp             HHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCS
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999999999988764

>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=98.93  E-value=1.3e-09  Score=73.63  Aligned_cols=40  Identities=35%  Similarity=0.591  Sum_probs=38.2

Q ss_pred             HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHH
Q psy1729          50 LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   89 (170)
Q Consensus        50 mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~y   89 (170)
                      .+|++.||++|++||+++|++|+++|+.++++|..+|++|
T Consensus        32 ~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A           32 SEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             HHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            5899999999999999999999999999999999999876

>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=98.92  E-value=9e-10  Score=76.68  Aligned_cols=47  Identities=21%  Similarity=0.397  Sum_probs=32.2

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++
T Consensus        25 ~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   71 (83)
T 3f27_D           25 LAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDH   71 (83)
T ss_dssp             HHHHCSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            35567777777777777777777777777777777777666666554

>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=98.92  E-value=6e-10  Score=78.40  Aligned_cols=42  Identities=19%  Similarity=0.336  Sum_probs=39.3

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhh
Q psy1729          11 TTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV   52 (170)
Q Consensus        11 ~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi   52 (170)
                      +++++|++.||++|++||+++|++|.+.|..++++|..++..
T Consensus        28 ~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~   69 (86)
T 2lef_A           28 KESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPG   69 (86)
T ss_dssp             CCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTT
T ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHccc
Confidence            689999999999999999999999999999999999887643

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

Probab=98.91  E-value=5.8e-10  Score=77.73  Aligned_cols=47  Identities=23%  Similarity=0.254  Sum_probs=37.0

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|..++++|..++
T Consensus        26 ~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~   72 (82)
T 1wz6_A           26 VRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKAN   72 (82)
T ss_dssp             HHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45677888888888888888888888888888888888888876654

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

Probab=98.91  E-value=1.2e-09  Score=74.68  Aligned_cols=48  Identities=25%  Similarity=0.374  Sum_probs=34.8

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVT   53 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~   53 (170)
                      .+.++|++++++|++.||++|++|  ++|++|++.|..++++|..+|..+
T Consensus        22 ~~~~~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y   69 (73)
T 1wxl_A           22 IKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNY   69 (73)
T ss_dssp             HHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGG
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHH
Confidence            356677777777777777777777  777777777777777777766443

>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=98.90  E-value=5.5e-10  Score=79.99  Aligned_cols=48  Identities=35%  Similarity=0.480  Sum_probs=28.4

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhh
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV   52 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi   52 (170)
                      ++++|++++++|++.||++|++||+++|++|.+.|..++++|..++..
T Consensus        40 ~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~   87 (93)
T 1cg7_A           40 RSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKEL   87 (93)
T ss_dssp             TTTCTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            455666666666666666666666666666666666666665555433

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

Probab=98.90  E-value=5.5e-10  Score=78.00  Aligned_cols=41  Identities=34%  Similarity=0.569  Sum_probs=21.1

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   91 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~   91 (170)
                      +|++.||++|++||+++|++|+++|..++++|..+|.+|+.
T Consensus        39 eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   79 (83)
T 1aab_A           39 EFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIP   79 (83)
T ss_dssp             SSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCC
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            44455555555555555555555555555555555555543

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

Probab=98.90  E-value=2.7e-09  Score=77.61  Aligned_cols=44  Identities=30%  Similarity=0.470  Sum_probs=41.1

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729          11 TTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK   54 (170)
Q Consensus        11 ~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K   54 (170)
                      +++++|++.||++|++||+++|++|.+.|..++++|..++..++
T Consensus        43 ~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~   86 (102)
T 2co9_A           43 ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYR   86 (102)
T ss_dssp             SCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67999999999999999999999999999999999999886654

>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=98.88  E-value=1.5e-09  Score=75.40  Aligned_cols=47  Identities=19%  Similarity=0.304  Sum_probs=36.0

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .++++|++++++|++.||++|+.||+++|++|.+.|+.++++|..++
T Consensus        23 ~~~~~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~   69 (81)
T 1i11_A           23 ILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKY   69 (81)
T ss_dssp             HHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHCCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            35677888888888888888888888888888888887777776543

>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=98.88  E-value=1.5e-09  Score=76.65  Aligned_cols=47  Identities=15%  Similarity=0.285  Sum_probs=39.5

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      .+.++|++++++|++.||++|+.||+++|++|+++|..++++|.+++
T Consensus        36 ~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~   82 (87)
T 2e6o_A           36 YTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLN   82 (87)
T ss_dssp             HHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            45678888888898888888888888888888888888888887653

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

Probab=98.87  E-value=2.4e-09  Score=78.59  Aligned_cols=45  Identities=20%  Similarity=0.374  Sum_probs=22.4

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   49 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~E   49 (170)
                      ++++|++++++|++.||++|+.||+++|++|+++|..++++|..+
T Consensus        49 k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e   93 (106)
T 4euw_A           49 ADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKD   93 (106)
T ss_dssp             HHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence            344555555555555555555555555555544444444444443

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

Probab=98.87  E-value=5.8e-10  Score=77.89  Aligned_cols=51  Identities=27%  Similarity=0.373  Sum_probs=46.1

Q ss_pred             ccccCCCCCH--HHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729           4 ESEKMISTTK--LLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK   54 (170)
Q Consensus         4 ~k~~~p~~s~--~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K   54 (170)
                      ++.++|++++  ++|++.||++|++||+++|.+|.+.|..++++|..+|..++
T Consensus        26 ~~~~~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~   78 (83)
T 1aab_A           26 HKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYI   78 (83)
T ss_dssp             HTTSCTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCC
T ss_pred             HHHHCCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4678999874  99999999999999999999999999999999999886543

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

Probab=98.85  E-value=2e-09  Score=73.94  Aligned_cols=41  Identities=29%  Similarity=0.596  Sum_probs=39.6

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   91 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~   91 (170)
                      +|++.||++|++||+++|++|+++|+.++++|..+|.+|+.
T Consensus        36 eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A           36 DVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             HHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            89999999999999999999999999999999999999874

>3nm9_A HMG-D, high mobility group protein D; DNA bending, non-sequence-specific, HMG chromosomal protein; HET: DNA; 2.85A {Drosophila melanogaster} SCOP: a.21.1.1 PDB: 1e7j_A* 1hma_A 1qrv_A*

Probab=98.85  E-value=5.2e-09  Score=71.44  Aligned_cols=42  Identities=21%  Similarity=0.243  Sum_probs=39.0

Q ss_pred             CCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729          11 TTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK   54 (170)
Q Consensus        11 ~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K   54 (170)
                      +++++|++.||++|+.||+  |++|++.|..++++|..++..++
T Consensus        29 ~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~   70 (73)
T 3nm9_A           29 IKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFE   70 (73)
T ss_dssp             CCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999998  99999999999999999886654

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

Probab=98.84  E-value=2.9e-09  Score=77.26  Aligned_cols=59  Identities=20%  Similarity=0.423  Sum_probs=48.8

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                      .|.-.+...+.....+      .+|++.||++|++||+++|++|+++|+.++++|..+|++|...
T Consensus        17 af~lF~~~~r~~ik~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~   81 (99)
T 1k99_A           17 PYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (99)
T ss_dssp             HHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4445555555554432      3899999999999999999999999999999999999999875

>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=98.82  E-value=3e-09  Score=73.65  Aligned_cols=43  Identities=30%  Similarity=0.449  Sum_probs=40.8

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      +|++.||++|++||+++|++|+++|..++++|..+|.+|+-++
T Consensus        32 eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   74 (80)
T 1gt0_D           32 EISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRP   74 (80)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccCC
Confidence            8999999999999999999999999999999999999998544

>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=98.82  E-value=4e-09  Score=81.43  Aligned_cols=50  Identities=20%  Similarity=0.286  Sum_probs=46.7

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVT   53 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~   53 (170)
                      +++++|++++++|++.||++|++||+++|++|.+.|..++++|..+|..+
T Consensus       107 ~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y  156 (159)
T 2gzk_A          107 IKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAY  156 (159)
T ss_dssp             HHHHCSCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999999999999999999988554

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

Probab=98.81  E-value=9.6e-10  Score=79.18  Aligned_cols=46  Identities=28%  Similarity=0.420  Sum_probs=23.2

Q ss_pred             cccCCCCC--HHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTT--KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         5 k~~~p~~s--~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      ++++|+++  +++|++.||++|++||+++|++|.+.|..++++|..++
T Consensus        42 k~~~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~   89 (97)
T 2lhj_A           42 IAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREK   89 (97)
T ss_dssp             HHHCTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            34455555  55555555555555555544444444444444444444

>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=98.80  E-value=4.2e-09  Score=72.09  Aligned_cols=57  Identities=21%  Similarity=0.374  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHc
Q psy1729          35 YLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   91 (170)
Q Consensus        35 Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~   91 (170)
                      |.-.....+.....+      .+|++.||++|++||+++|++|+++|+.++++|..++.+|+-
T Consensus        12 f~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky   74 (76)
T 1hry_A           12 FIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (76)
T ss_dssp             HHHHHHHHHHHHHHHCSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             HHHHHHHHHHHHHHHCcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCCC
Confidence            444444444444432      289999999999999999999999999999999999998874

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

Probab=98.80  E-value=5.5e-09  Score=70.11  Aligned_cols=40  Identities=33%  Similarity=0.574  Sum_probs=37.6

Q ss_pred             CHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729          12 TKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus        12 s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .+++|++.||++|++||+++|.+|.+.|..++++|..+|.
T Consensus        25 ~p~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~   64 (67)
T 3fgh_A           25 SPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMK   64 (67)
T ss_dssp             SHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4589999999999999999999999999999999999874

>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=98.80  E-value=4.1e-09  Score=77.82  Aligned_cols=45  Identities=29%  Similarity=0.403  Sum_probs=41.9

Q ss_pred             HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchh
Q psy1729          50 LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA   94 (170)
Q Consensus        50 mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~   94 (170)
                      .+|++.||++|++||++||++|+++|+.++++|..+|.+|..+..
T Consensus        42 ~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~   86 (108)
T 1v64_A           42 TERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLP   86 (108)
T ss_dssp             HHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence            389999999999999999999999999999999999999997543

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

Probab=98.79  E-value=3.2e-09  Score=71.45  Aligned_cols=40  Identities=28%  Similarity=0.603  Sum_probs=36.4

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      +|++.||++|++||+++|++|+++|+.++++|..++++|+
T Consensus        32 eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A           32 ELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            8999999999999999999999999999999999998885

>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=98.77  E-value=2.5e-09  Score=76.53  Aligned_cols=43  Identities=40%  Similarity=0.669  Sum_probs=41.0

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      +|++.||++|++||+++|++|+++|..++++|..+|.+|+.+.
T Consensus        50 eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~~~~   92 (93)
T 1cg7_A           50 QVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATL   92 (93)
T ss_dssp             HHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            8999999999999999999999999999999999999998653

>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=98.76  E-value=7.2e-09  Score=72.78  Aligned_cols=43  Identities=26%  Similarity=0.419  Sum_probs=40.7

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      +|++.||++|++||+++|++|++.|+.++++|..++.+|+-++
T Consensus        34 eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p   76 (85)
T 1j46_A           34 EISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccCC
Confidence            8999999999999999999999999999999999999998544

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

Probab=98.76  E-value=2.5e-09  Score=74.45  Aligned_cols=59  Identities=27%  Similarity=0.355  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          35 YLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        35 Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      |.-.....+.....+      .+|++.||++|++||+++|++|+++|+.++++|..+|.+|+.++
T Consensus        15 f~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~p   79 (82)
T 1wz6_A           15 FLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSGP   79 (82)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCCT
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcCC
Confidence            444444444444443      28999999999999999999999999999999999999998654

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

Probab=98.75  E-value=3.2e-09  Score=76.41  Aligned_cols=42  Identities=33%  Similarity=0.579  Sum_probs=40.5

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                      +|++.||++|++||+++|++|+++|..++++|..+|.+|+.+
T Consensus        54 eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~   95 (97)
T 2lhj_A           54 AIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR   95 (97)
T ss_dssp             HHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            899999999999999999999999999999999999999864

>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=98.73  E-value=1.8e-08  Score=74.31  Aligned_cols=46  Identities=26%  Similarity=0.301  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhh
Q psy1729          10 STTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKL   55 (170)
Q Consensus        10 ~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~   55 (170)
                      ++++++|++.||++|++||+++|++|.+.|..++++|..+|..++.
T Consensus        38 ~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~   83 (108)
T 1v64_A           38 DVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             TSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            7899999999999999999999999999999999999998865543

>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=98.72  E-value=8.6e-09  Score=71.65  Aligned_cols=43  Identities=26%  Similarity=0.538  Sum_probs=40.7

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      +|++.||++|++||+++|++|+++|+.++++|..++.+|+-++
T Consensus        36 eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~P   78 (83)
T 3f27_D           36 ELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRP   78 (83)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCC
Confidence            8999999999999999999999999999999999999998544

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

Probab=98.71  E-value=1.3e-08  Score=79.75  Aligned_cols=51  Identities=20%  Similarity=0.298  Sum_probs=47.3

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK   54 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K   54 (170)
                      +++++|++++++|++.||++|++||+++|++|.+.|..++++|..++..++
T Consensus       120 ~~~~~p~~~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~  170 (173)
T 2yrq_A          120 IKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR  170 (173)
T ss_dssp             HHHHCSSSCHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999999999999999999999886544

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

Probab=98.69  E-value=1.4e-08  Score=74.40  Aligned_cols=59  Identities=19%  Similarity=0.427  Sum_probs=48.4

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                      .|.-.....+.....+      .+|++.||++|++||+++|++|+++|++++++|..++++|+-+
T Consensus        36 af~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky~  100 (106)
T 4euw_A           36 AFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQ  100 (106)
T ss_dssp             HHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC-
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCcC
Confidence            4555555555555443      3899999999999999999999999999999999999999843

>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=98.69  E-value=8.6e-09  Score=70.90  Aligned_cols=43  Identities=21%  Similarity=0.378  Sum_probs=40.6

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      +|++.||++|++||+++|++|+++|+.++++|..++.+|+-++
T Consensus        32 eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky~P   74 (79)
T 3u2b_C           32 EISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRP   74 (79)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCCCC
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCeeCC
Confidence            8999999999999999999999999999999999999998543

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

Probab=98.68  E-value=1.5e-08  Score=69.06  Aligned_cols=57  Identities=25%  Similarity=0.505  Sum_probs=45.9

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                      .|.-.....+.....+      .+|++.||++|++|  ++|++|+++|..++++|..+|.+|+.+
T Consensus        10 ay~lf~~~~r~~~~~~~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A           10 AFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             HHHHHHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            3444445555554443      38999999999999  889999999999999999999999864

>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=98.66  E-value=1e-08  Score=72.26  Aligned_cols=40  Identities=18%  Similarity=0.081  Sum_probs=37.5

Q ss_pred             ccccCCCCC-HHHHHHHHHHHhcCCChHHHHhHHHHHHHHH
Q psy1729           4 ESEKMISTT-KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDK   43 (170)
Q Consensus         4 ~k~~~p~~s-~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dK   43 (170)
                      ++.+||+++ +++|++.||++|++||+++|++|++.|+.+.
T Consensus        24 ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A           24 ILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             HHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             HHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            578899998 9999999999999999999999999999874

>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=98.66  E-value=1.3e-08  Score=71.91  Aligned_cols=57  Identities=16%  Similarity=0.272  Sum_probs=46.3

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   90 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk   90 (170)
                      .|.-.....+.....+      .+|++.||++|++||+++|++|+++|+.++++|..++.+|+
T Consensus        24 af~lf~~~~r~~~~~~~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           24 AFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             HHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            4555555555555442      38999999999999999999999999999999999987775

>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=98.61  E-value=1.6e-08  Score=70.22  Aligned_cols=41  Identities=24%  Similarity=0.468  Sum_probs=38.2

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHc
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   91 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~   91 (170)
                      +|++.||++|++||+++|++|.+.|+.++++|..++.+|+-
T Consensus        34 eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky   74 (81)
T 1i11_A           34 NISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKY   74 (81)
T ss_dssp             HHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC--
T ss_pred             HHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            89999999999999999999999999999999999998873

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

Probab=98.51  E-value=2.6e-08  Score=72.18  Aligned_cols=41  Identities=17%  Similarity=0.230  Sum_probs=25.1

Q ss_pred             CCCHHHHHHHH---HHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729          10 STTKLLVTKLL---GNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus        10 ~~s~~evsK~l---ge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      ++++++|++.|   |++|++|+++||++|+++|..+|+.|..++
T Consensus        33 ~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A           33 GLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             TCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            45566666666   666666666666666666666666665543

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

Probab=98.44  E-value=3.4e-07  Score=74.56  Aligned_cols=58  Identities=19%  Similarity=0.471  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          35 YLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        35 Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                      |.-.....+..+..+      .+|++.||++|++||++||.+|++.|..++++|..+|..|..+
T Consensus        17 y~lF~~~~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~   80 (214)
T 3tq6_A           17 YLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQ   80 (214)
T ss_dssp             HHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhccc
Confidence            555555555555543      3899999999999999999999999999999999999999864

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

Probab=98.44  E-value=3.4e-07  Score=75.73  Aligned_cols=59  Identities=19%  Similarity=0.458  Sum_probs=51.8

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   92 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~   92 (170)
                      .|.-.....+..+..+      .+|++.||++|++||++||.+|+++|..++++|+.+|..|..+
T Consensus        48 ay~lF~~e~r~~~k~~~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~  112 (238)
T 3tmm_A           48 SYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQ  112 (238)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4777777777777654      2899999999999999999999999999999999999999754

>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=98.44  E-value=4e-08  Score=69.78  Aligned_cols=55  Identities=24%  Similarity=0.323  Sum_probs=44.3

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV   88 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~   88 (170)
                      .|.-.....+.....+      .+|++.||++|++||+++|++|+++|+.++++|..+|..
T Consensus        27 ay~lF~~~~r~~~k~~~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~   87 (90)
T 1wgf_A           27 AMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGP   87 (90)
T ss_dssp             HHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSS
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555443      389999999999999999999999999999999887643

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

Probab=98.38  E-value=1.1e-07  Score=68.94  Aligned_cols=36  Identities=19%  Similarity=0.341  Sum_probs=34.2

Q ss_pred             hhhhhH---HHHhhCCChhhhhhhHHHHHHHHHHHHHHH
Q psy1729          51 KVTKLL---GNEWSKLSLPEKKVYLDRAEVDKKRYREEL   86 (170)
Q Consensus        51 Ei~K~l---g~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em   86 (170)
                      +|++.|   |++|++||++||+||+++|++++++|++++
T Consensus        38 eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A           38 RVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             SHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            788888   999999999999999999999999999886

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

Probab=98.28  E-value=3e-07  Score=66.39  Aligned_cols=41  Identities=22%  Similarity=0.294  Sum_probs=36.9

Q ss_pred             ccccCCCCC--HHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTT--KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYRE   48 (170)
Q Consensus         4 ~k~~~p~~s--~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~   48 (170)
                      ++.+||+++  +++|+    ++|+.|++++|++|++.|..+++.|..
T Consensus        41 ik~enP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~   83 (90)
T 2yuk_A           41 LKEEFPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRI   83 (90)
T ss_dssp             HHHHCCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence            578999999  99998    999999999999999999999998864

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

Probab=97.81  E-value=1.2e-05  Score=56.45  Aligned_cols=45  Identities=20%  Similarity=0.180  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHHHHH-------HHhhhhhHHHHhhCCChhhhhhhHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYRE-------ELKVTKLLGNEWSKLSLPEKKVYLDRAEVD   78 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~-------EmEi~K~lg~~Wk~LS~~EK~~Y~~~A~~d   78 (170)
                      .|.-.....+.....       ..+|++.||++|++||+++|++|+++|+.+
T Consensus        12 ay~lF~~e~R~~ik~~~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A           12 GFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHHHHHCCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344455555555443       248999999999999999999999999887

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

Probab=97.72  E-value=2.6e-05  Score=56.11  Aligned_cols=51  Identities=20%  Similarity=0.324  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHH-h---hhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHH
Q psy1729          35 YLDRAEVDKKRYREEL-K---VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   85 (170)
Q Consensus        35 Ye~~Ak~dKerY~~Em-E---i~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~e   85 (170)
                      |.-.+...+.....+. .   ....|+++|++||+++|+||+++|++++++|..+
T Consensus        30 f~lf~~e~R~kik~enP~~s~~~~eIse~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           30 PVLYTNINFPNLKEEFPDWTTRVKQIAKLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             HHHHHHHHCTTHHHHCCSHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHhHHHHHHHCcCccchHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            4445555555554432 1   1345669999999999999999999999999753

>1zu1_A DSRBP-ZFA, RNA binding protein ZFA; zinc finger protein, helix-loop-helix, helix-turn-helix; NMR {Xenopus laevis} SCOP: g.37.1.4 g.37.1.4

Probab=96.81  E-value=0.00011  Score=55.18  Aligned_cols=36  Identities=19%  Similarity=0.507  Sum_probs=33.0

Q ss_pred             ccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         129 EEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       129 ~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      +..+...||.+|+.+|+|.....-|+.|+.|..++.
T Consensus        88 ~~~~~~~~C~~C~~~f~s~~~~~~H~~gk~H~~~~~  123 (127)
T 1zu1_A           88 DGEDRSKCCPVCNMTFSSPVVAESHYIGKTHIKNLR  123 (127)
T ss_dssp             SCCCTTTEETTTTEECSSHHHHHHHHTSHHHHHHHH
T ss_pred             cCCCCCeEcCCCCCEeCCHHHHHHHHCCHHHHHHHH
Confidence            456788999999999999999999999999998875

>1zr9_A Zinc finger protein 593; DNA binding, structural genomics, PSI, protein structure initiative, center for eukaryotic structural genomics, CESG; NMR {Homo sapiens} SCOP: g.37.1.4

Probab=96.16  E-value=0.00052  Score=52.10  Aligned_cols=41  Identities=22%  Similarity=0.485  Sum_probs=35.3

Q ss_pred             cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         124 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       124 ~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      .+|+|=+.....||..|+.+|++..++.-|+.++.|..++.
T Consensus        40 ~~ded~tGekpfyC~~C~K~F~~~~~L~~H~rsK~HKrrvk   80 (124)
T 1zr9_A           40 EFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLK   80 (124)
T ss_dssp             SSCSSSGGGGCSEETTTTEECSSHHHHHHHTTCHHHHHHHH
T ss_pred             cccccCCCCcceEcccCcchhCCHHHHHHHHhhhhhhHHHH
Confidence            34666566788999999999999999999999999998764

>1zu1_A DSRBP-ZFA, RNA binding protein ZFA; zinc finger protein, helix-loop-helix, helix-turn-helix; NMR {Xenopus laevis} SCOP: g.37.1.4 g.37.1.4

Probab=94.82  E-value=0.002  Score=48.17  Aligned_cols=33  Identities=21%  Similarity=0.460  Sum_probs=30.0

Q ss_pred             chhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         132 NEELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       132 ~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      ...+||.+|+..|.|-...+.|..|+.|..+|.
T Consensus        30 ~~~~~C~~C~v~~~S~s~~~~H~~gkkH~~~v~   62 (127)
T 1zu1_A           30 FSDTQCKVCSAVLISESQKLAHYQSRKHANKVR   62 (127)
T ss_dssp             BCSSEETTTTEECCSHHHHHHHHHCHHHHHHHH
T ss_pred             CCCCcCcCCCCEeCCHHHHHHHHCcHHHHHHHH
Confidence            456899999999999999999999999998864

>3cw1_L U1 small nuclear ribonucleoprotein C; PRE-mRNA splicing, spliceosome, RNA-binding domain, SM fold, finger, RNA recognition motif, 5' splice site; 5.49A {Homo sapiens} PDB: 1uw2_A 2vrd_A

Probab=93.77  E-value=0.0083  Score=42.03  Aligned_cols=31  Identities=26%  Similarity=0.726  Sum_probs=26.5

Q ss_pred             HHHHHHHHHh--hhhhhhhhhhchhhhhhhhcc
Q psy1729         135 LYCRVCDQWF--TTLHNKREHLNGRQHFQRFDR  165 (170)
Q Consensus       135 ~~~~~~~~~f--~~~h~~~~~~~~~~~~~~~~~  165 (170)
                      -||-.|+-||  .|...-+.|..|++|..++..
T Consensus         4 YyCdYCd~~lt~Ds~s~Rk~H~~G~kH~~nv~~   36 (77)
T 3cw1_L            4 FYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKD   36 (77)
T ss_pred             cccccCCceecCCCHHHHHHHHccHHHHHHHHH
Confidence            4899999999  557768899999999998753

>2lvu_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, transcription; NMR {Homo sapiens}

Probab=90.38  E-value=0.042  Score=27.89  Aligned_cols=20  Identities=20%  Similarity=0.551  Sum_probs=18.2

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.||.
T Consensus         4 ~C~~C~k~f~~~~~l~~H~~   23 (26)
T 2lvu_A            4 VCERCGKRFVQSSQLANHIR   23 (26)
Confidence            48999999999999999974

>2lvt_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, transcription; NMR {Homo sapiens}

Probab=88.74  E-value=0.074  Score=27.45  Aligned_cols=20  Identities=25%  Similarity=0.526  Sum_probs=18.2

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.|+.
T Consensus         4 ~C~~C~k~f~~~~~l~~H~~   23 (29)
T 2lvt_A            4 QCVMCGKAFTQASSLIAHVR   23 (29)
Confidence            59999999999999999974

>2yrk_A Zinc finger homeobox protein 4; structure genomics, ZF-C2H2 domain, ZFH-4, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.37.1.4

Probab=87.91  E-value=0.053  Score=35.60  Aligned_cols=30  Identities=20%  Similarity=0.503  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      .-|..|+--||..-..|.|++.+||+..|.
T Consensus        14 ~eC~lC~vkYs~r~slqDHIFs~qHI~~vk   43 (55)
T 2yrk_A           14 PECTLCGVKYSARLSIRDHIFSKQHISKVR   43 (55)
T ss_dssp             SCCTTTTCCCCSSSCHHHHHTSHHHHHHHH
T ss_pred             ccccccCcccccccchhhhhccHHHHHHHH
Confidence            469999999999999999999999998764

>2lvr_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc finger, classical zinc finger, transcription; NMR {Homo sapiens}

Probab=87.50  E-value=0.11  Score=26.78  Aligned_cols=21  Identities=19%  Similarity=0.456  Sum_probs=18.6

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.|+.
T Consensus         4 ~~C~~C~k~f~~~~~l~~H~~   24 (30)
T 2lvr_A            4 YVCIHCQRQFADPGALQRHVR   24 (30)
Confidence            359999999999999999974

>1ard_A Yeast transcription factor ADR1; transcription regulation; NMR {Saccharomyces cerevisiae} SCOP: g.37.1.1 PDB: 1arf_A 1are_A

Probab=86.42  E-value=0.057  Score=27.65  Aligned_cols=20  Identities=25%  Similarity=0.639  Sum_probs=18.0

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.|+.
T Consensus         4 ~C~~C~~~f~~~~~l~~H~~   23 (29)
T 1ard_A            4 VCEVCTRAFARQEHLKRHYR   23 (29)
T ss_dssp             BCTTTCCBCSSHHHHHHHHH
T ss_pred             ECCCCCcccCCHHHHHHHHH
Confidence            48899999999999999974

>2kfq_A FP1; protein, de novo protein; NMR {Synthetic}

Probab=86.39  E-value=0.064  Score=28.98  Aligned_cols=20  Identities=20%  Similarity=0.532  Sum_probs=17.9

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.||.
T Consensus         4 ~C~~C~k~f~~~~~L~~H~~   23 (32)
T 2kfq_A            4 ACPACPKRFMRSDALSKHIK   23 (32)
T ss_dssp             SSSSSCTTHHHHHTTSSSTT
T ss_pred             CCCCCCcccCCHHHHHHHHH
Confidence            38899999999999999984

>2kvg_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=86.17  E-value=0.058  Score=27.84  Aligned_cols=20  Identities=20%  Similarity=0.529  Sum_probs=18.0

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.|+.
T Consensus         5 ~C~~C~k~f~~~~~l~~H~~   24 (27)
T 2kvg_A            5 RCPLCRAGCPSLASMQAHMR   24 (27)
T ss_dssp             EETTTTEEESCHHHHHHHHT
T ss_pred             CCCCCCcccCCHHHHHHHHH
Confidence            38899999999999999974

>2kvf_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=86.05  E-value=0.044  Score=28.14  Aligned_cols=20  Identities=30%  Similarity=0.688  Sum_probs=17.8

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|.+|+..|++..+++.|+.
T Consensus         5 ~C~~C~k~f~~~~~l~~H~~   24 (28)
T 2kvf_A            5 SCSVCGKRFSLKHQMETHYR   24 (28)
T ss_dssp             ECSSSCCEESCHHHHHHHHT
T ss_pred             cCCCCCcccCCHHHHHHHHH
Confidence            38899999999999999974

>4dgw_A PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A {Saccharomyces cerevisiae}

Probab=85.47  E-value=0.08  Score=47.06  Aligned_cols=36  Identities=28%  Similarity=0.680  Sum_probs=31.5

Q ss_pred             cCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729         130 EDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR  165 (170)
Q Consensus       130 ~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~  165 (170)
                      .+.+.+||..|..+|++..-...||.|+.|...+.+
T Consensus       288 ~~~~~l~C~~c~K~Fs~~~v~~~hL~GKkh~K~~~~  323 (402)
T 4dgw_A          288 SEAKGIYCPFCSRWFKTSSVFESHLVGKIHKKNESK  323 (402)
T ss_dssp             ETTTEECBTTTTBCBSSHHHHHTTSSSHHHHHHHHH
T ss_pred             CCCcCeeehhhhhhhccccccHHHhcccccchhHHH
Confidence            345679999999999999999999999999887643

>2m0f_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=84.84  E-value=0.072  Score=27.13  Aligned_cols=20  Identities=45%  Similarity=0.770  Sum_probs=17.8

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.|+.
T Consensus         4 ~C~~C~k~f~~~~~l~~H~~   23 (29)
T 2m0f_A            4 KCRECGKQFTTSGNLKRHLR   23 (29)
T ss_dssp             ECTTTSCEESCHHHHHHHHH
T ss_pred             cCCCCCCccCChhHHHHHHH
Confidence            48899999999999999974

>2elo_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=84.06  E-value=0.091  Score=28.80  Aligned_cols=21  Identities=24%  Similarity=0.586  Sum_probs=18.8

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.|+.
T Consensus        10 ~~C~~C~k~f~~~~~l~~H~~   30 (37)
T 2elo_A           10 YSCPVCEKSFSEDRLIKSHIK   30 (37)
T ss_dssp             CEETTTTEECSSHHHHHHHHH
T ss_pred             cCCCCCCCccCCHHHHHHHHH
Confidence            359999999999999999985

>1znf_A 31ST zinc finger from XFIN; zinc finger DNA binding domain; NMR {Xenopus laevis} SCOP: g.37.1.1

Probab=83.75  E-value=0.073  Score=26.90  Aligned_cols=19  Identities=21%  Similarity=0.558  Sum_probs=17.3

Q ss_pred             HHHHHHHhhhhhhhhhhhc
Q psy1729         137 CRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~~  155 (170)
                      |..|+..|++..+++.|+.
T Consensus         4 C~~C~k~f~~~~~l~~H~~   22 (27)
T 1znf_A            4 CGLCERSFVEKSALSRHQR   22 (27)
T ss_dssp             CSSSCCBCSSHHHHHHHGG
T ss_pred             CCCCCCcCCCHHHHHHHHH
Confidence            7889999999999999983

>2m0d_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=83.37  E-value=0.088  Score=26.91  Aligned_cols=20  Identities=30%  Similarity=0.630  Sum_probs=17.8

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.|+.
T Consensus         5 ~C~~C~~~f~~~~~l~~H~~   24 (30)
T 2m0d_A            5 QCDYCGRSFSDPTSKMRHLE   24 (30)
T ss_dssp             ECTTTCCEESCHHHHHHHHH
T ss_pred             cCCCCCcccCCHHHHHHHHH
Confidence            38899999999999999974

>1fv5_A First zinc finger of U-shaped; CCHC, protein interaction, transcription; NMR {Drosophila melanogaster} SCOP: g.37.1.2 PDB: 1y0j_B 2l6z_B

Probab=82.94  E-value=0.11  Score=30.49  Aligned_cols=19  Identities=21%  Similarity=0.424  Sum_probs=17.9

Q ss_pred             HHHHHHHHhhhhhhhhhhh
Q psy1729         136 YCRVCDQWFTTLHNKREHL  154 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~  154 (170)
                      -|..|+..|++..+++-||
T Consensus        10 ~C~~CgK~F~~~s~L~~H~   28 (36)
T 1fv5_A           10 MCLPCGIAFSSPSTLEAHQ   28 (36)
T ss_dssp             EETTTTEECSCHHHHHHHH
T ss_pred             ECCCCCCccCCHhHccCcC
Confidence            4899999999999999998

>2kvh_A Zinc finger and BTB domain-containing protein 32; protein/DNA, metal-binding, transcription; NMR {Mus musculus}

Probab=82.90  E-value=0.077  Score=27.07  Aligned_cols=20  Identities=25%  Similarity=0.526  Sum_probs=17.8

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.|+.
T Consensus         5 ~C~~C~k~f~~~~~l~~H~~   24 (27)
T 2kvh_A            5 SCSLCPQRSRDFSAMTKHLR   24 (27)
T ss_dssp             ECSSSSCEESSHHHHHHHHH
T ss_pred             cCCCcChhhCCHHHHHHHHH
Confidence            38899999999999999974

>2elx_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=82.72  E-value=0.08  Score=28.48  Aligned_cols=21  Identities=24%  Similarity=0.532  Sum_probs=18.7

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.|+.
T Consensus         8 ~~C~~C~k~f~~~~~L~~H~~   28 (35)
T 2elx_A            8 YVCALCLKKFVSSIRLRSHIR   28 (35)
T ss_dssp             EECSSSCCEESSHHHHHHHHH
T ss_pred             eECCCCcchhCCHHHHHHHHH
Confidence            459999999999999999974

>1rim_A E6APC2 peptide; E6-binding domain, zinc finger, human papillomavirus, HPV E6 protein, de novo protein; NMR {Synthetic} SCOP: k.12.1.1

Probab=82.71  E-value=0.086  Score=28.72  Aligned_cols=20  Identities=20%  Similarity=0.519  Sum_probs=17.9

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|.+|+..|++..+++.||.
T Consensus         4 ~C~~C~k~F~~~~~L~~H~~   23 (33)
T 1rim_A            4 ACPECPKRFMRSDHLSKHIT   23 (33)
T ss_dssp             CCSSSCCCCSSHHHHHHHHH
T ss_pred             cCCCCCchhCCHHHHHHHHH
Confidence            38899999999999999984

>2elq_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=81.65  E-value=0.096  Score=28.61  Aligned_cols=21  Identities=24%  Similarity=0.567  Sum_probs=18.6

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.|+.
T Consensus        10 ~~C~~C~k~f~~~~~l~~H~~   30 (36)
T 2elq_A           10 FKCSLCEYATRSKSNLKAHMN   30 (36)
T ss_dssp             EECSSSSCEESCHHHHHHHHH
T ss_pred             ccCCCCCchhCCHHHHHHHHH
Confidence            358999999999999999984

>1rik_A E6APC1 peptide; E6-binding domain, zinc finger, human papillomavirus, HPV E6 protein, de novo protein; NMR {Synthetic} SCOP: k.12.1.1 PDB: 1sp1_A 1va3_A

Probab=81.03  E-value=0.093  Score=26.86  Aligned_cols=20  Identities=20%  Similarity=0.395  Sum_probs=17.8

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..+++.|+.
T Consensus         4 ~C~~C~k~f~~~~~l~~H~~   23 (29)
T 1rik_A            4 ACPECPKRFMRSDHLTLHIL   23 (29)
T ss_dssp             ECSSSSCEESCSHHHHHHHT
T ss_pred             cCCCCCchhCCHHHHHHHHH
Confidence            38889999999999999984

>2els_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.97  E-value=0.13  Score=28.03  Aligned_cols=21  Identities=29%  Similarity=0.681  Sum_probs=18.6

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.|+.
T Consensus        10 ~~C~~C~k~f~~~~~l~~H~~   30 (36)
T 2els_A           10 FTCEYCNKVFKFKHSLQAHLR   30 (36)
T ss_dssp             EECTTTCCEESSHHHHHHHHH
T ss_pred             EECCCCCceeCCHHHHHHHHH
Confidence            359999999999999999974

>1njq_A Superman protein; zinc-finger, peptide-zinc complex, beta-BETA-ALFA motif, metal binding protein; NMR {Synthetic} SCOP: g.37.1.3 PDB: 2l1o_A

Probab=80.94  E-value=0.13  Score=28.69  Aligned_cols=21  Identities=24%  Similarity=0.563  Sum_probs=18.7

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|.+|+..|++..+++.||.
T Consensus         7 ~~C~~C~k~f~~~~~L~~H~~   27 (39)
T 1njq_A            7 YTCSFCKREFRSAQALGGHMN   27 (39)
T ss_dssp             EECTTTCCEESSHHHHHHHHH
T ss_pred             eECCCCCcccCCHHHHHHHHH
Confidence            359999999999999999984

>1srk_A Zinc finger protein ZFPM1; classical zinc finger, transcription; NMR {Mus musculus} SCOP: g.37.1.1

Probab=80.92  E-value=0.1  Score=28.20  Aligned_cols=21  Identities=43%  Similarity=0.714  Sum_probs=18.5

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.||.
T Consensus         8 ~~C~~C~k~f~~~~~l~~H~~   28 (35)
T 1srk_A            8 FVCRICLSAFTTKANCARHLK   28 (35)
T ss_dssp             EECSSSCCEESSHHHHHHHHG
T ss_pred             eeCCCCCcccCCHHHHHHHHH
Confidence            348999999999999999984

>2elv_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.75  E-value=0.11  Score=28.42  Aligned_cols=21  Identities=19%  Similarity=0.608  Sum_probs=18.8

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|.+|+..|++..+++.||.
T Consensus        10 ~~C~~C~k~f~~~~~l~~H~~   30 (36)
T 2elv_A           10 YDCHICERKFKNELDRDRHML   30 (36)
T ss_dssp             EECSSSCCEESSHHHHHHHHT
T ss_pred             eECCCCCCccCCHHHHHHHHH
Confidence            459999999999999999984

>2elr_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.60  E-value=0.14  Score=27.67  Aligned_cols=21  Identities=19%  Similarity=0.442  Sum_probs=18.6

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.|+.
T Consensus        10 ~~C~~C~k~f~~~~~l~~H~~   30 (36)
T 2elr_A           10 HLCDMCGKKFKSKGTLKSHKL   30 (36)
T ss_dssp             CBCTTTCCBCSSHHHHHHHHH
T ss_pred             eecCcCCCCcCchHHHHHHHH
Confidence            459999999999999999974

>2ytb_A Zinc finger protein 32; zinc-finger domain, C2H2, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: k.12.1.1

Probab=80.49  E-value=0.18  Score=28.37  Aligned_cols=21  Identities=19%  Similarity=0.414  Sum_probs=18.8

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.|+.
T Consensus        12 ~~C~~C~k~f~~~~~L~~H~~   32 (42)
T 2ytb_A           12 YRCDQCGKAFSQKGSLIVHIR   32 (42)
T ss_dssp             BCCTTTTCCBSSHHHHHTTGG
T ss_pred             eeCCCccchhCCHHHHHHHHH
Confidence            459999999999999999984

>2elt_A Zinc finger protein 406; ZFAT zinc finger 1, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=80.34  E-value=0.11  Score=28.10  Aligned_cols=21  Identities=24%  Similarity=0.294  Sum_probs=18.6

Q ss_pred             HHHHHHHHHhhhhhhhhhhhc
Q psy1729         135 LYCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       135 ~~~~~~~~~f~~~h~~~~~~~  155 (170)
                      .-|..|+..|++..+++.||.
T Consensus        10 ~~C~~C~k~f~~~~~l~~H~~   30 (36)
T 2elt_A           10 YKCPQCSYASAIKANLNVHLR   30 (36)
T ss_dssp             EECSSSSCEESSHHHHHHHHH
T ss_pred             CCCCCCCcccCCHHHHHHHHH
Confidence            458999999999999999984

>2m0e_A Zinc finger and BTB domain-containing protein 17; C2H2 zinc fingers, transcription; NMR {Homo sapiens}

Probab=80.24  E-value=0.12  Score=26.21  Aligned_cols=19  Identities=37%  Similarity=0.805  Sum_probs=17.3

Q ss_pred             HHHHHHHhhhhhhhhhhhc
Q psy1729         137 CRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~~  155 (170)
                      |..|+..|++..+++.|+.
T Consensus         5 C~~C~~~f~~~~~l~~H~~   23 (29)
T 2m0e_A            5 CPHCDKKFNQVGNLKAHLK   23 (29)
T ss_dssp             CSSCCCCCCTTTHHHHHHH
T ss_pred             CCCCCcccCCHHHHHHHHH
Confidence            8889999999999999984

---

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	170
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-07
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	7e-05
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	1e-06
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	4e-04
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-06
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-04
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	7e-06
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-05
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	6e-04
d1zr9a1	67	g.37.1.4 (A:28-94) Zinc finger protein 593, ZNF593	2e-05
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	2e-04
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	2e-04
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-04
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	0.002
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	5e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	6e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	0.001
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	7e-04
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	7e-04
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	7e-04

>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 = 45.3 bits (107), Expect = 1e-07
 Identities = 14/57 (24%), Positives = 28/57 (49%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKSLQ 108
               +G+ W ++S  +K+ Y   AE  +++Y+  L ++ KS + Q     K   S +
Sbjct: 37  RMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDRAAYKEYISNK 93

>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 = 37.9 bits (88), Expect = 7e-05
 Identities = 10/54 (18%), Positives = 24/54 (44%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKK 69
              +G+ W ++S  +K+ Y   AE  +++Y+  L +     +   + +  E  
Sbjct: 37 RMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDRAAYKEYI 90

>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 = 42.2 bits (99), Expect = 1e-06
 Identities = 18/44 (40%), Positives = 27/44 (61%)

Query: 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 94
          +V K LG +W  L+  EK+ Y  +A+ DKKRY  E ++Y  + A
Sbjct: 50 QVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 93

>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 = 35.6 bits (82), Expect = 4e-04
 Identities = 16/36 (44%), Positives = 22/36 (61%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          V K LG +W  L+  EK+ Y  +A+ DKKRY  E +
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKE 86

>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 = 41.5 bits (97), Expect = 4e-06
 Identities = 14/52 (26%), Positives = 20/52 (38%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKR 103
              L   +W  LS  EK  Y  + +  KK Y  EL  + +S   +   R   
Sbjct: 44  RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLG 95

>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 = 36.1 bits (83), Expect = 4e-04
 Identities = 12/36 (33%), Positives = 15/36 (41%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
             L   +W  LS  EK  Y  + +  KK Y  EL 
Sbjct: 44 RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELL 79

>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 = 40.2 bits (94), Expect = 7e-06
 Identities = 14/54 (25%), Positives = 26/54 (48%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVK 105
           + ++LG  W  LS  E+  Y + A  +++ + +    +   D Y    +RKR K
Sbjct: 33  INQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 86

>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 = 38.7 bits (90), Expect = 2e-05
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 91
          V K LG  W+  +  +K+ Y  +A   K++Y +++  YR 
Sbjct: 33 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 72

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

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

 Score = 34.8 bits (80), Expect = 6e-04
 Identities = 10/36 (27%), Positives = 20/36 (55%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
          V K LG  W+  +  +K+ Y  +A   K++Y +++ 
Sbjct: 33 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA 68

>d1zr9a1 g.37.1.4 (A:28-94) Zinc finger protein 593, ZNF593 {Human (Homo sapiens) [TaxId: 9606]} Length = 67

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Zinc finger protein 593, ZNF593
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (90), Expect = 2e-05
 Identities = 10/43 (23%), Positives = 16/43 (37%)

Query: 120 DATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQR 162
           D   E D +        C  C ++F    N + H   + H +R
Sbjct: 1   DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKR 43

>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 = 36.7 bits (85), Expect = 2e-04
 Identities = 12/51 (23%), Positives = 25/51 (49%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 102
           ++K LG +W  L+  EK  +   A+  +  +RE+   Y+     ++ +  K
Sbjct: 35  ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK 85

>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 = 36.3 bits (84), Expect = 2e-04
 Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 2/41 (4%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 92
          V K  G  W   ++ +K  +  +A   K  Y   +K +  +
Sbjct: 34 VAKRGGELWR--AMKDKSEWEAKAAKAKDDYDRAVKEFEAN 72

>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 = 35.6 bits (82), Expect = 3e-04
 Identities = 14/39 (35%), Positives = 20/39 (51%)

Query: 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
          + +K     W  +S  EK  + D A+ DK RY  E+K Y
Sbjct: 33 EFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 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 = 33.3 bits (76), Expect = 0.002
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51
           +K     W  +S  EK  + D A+ DK RY  E+K
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMK 69

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

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

 Score = 35.3 bits (81), Expect = 5e-04
 Identities = 10/51 (19%), Positives = 24/51 (47%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 102
           +TK+L  ++ +L   +K  Y+   + +K+ +   L  +R+         +K
Sbjct: 41  LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK 91

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

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

 Score = 34.9 bits (80), Expect = 6e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89
          +T+LL   W+ LS  +K  Y  R    K +   +    
Sbjct: 51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPS 88

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

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

 Score = 34.6 bits (79), Expect = 0.001
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 49
          +T+LL   W+ LS  +K  Y  R    K +   +
Sbjct: 51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 84

>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 = 34.8 bits (80), Expect = 7e-04
 Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 7/55 (12%)

Query: 52  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKS 106
           ++K LG EW  LS  EK+ ++D A+  +  + +E   Y+       Y  R++ K+
Sbjct: 33  ISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK-------YRPRRKTKT 80

>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 = 34.4 bits (79), Expect = 7e-04
 Identities = 9/34 (26%), Positives = 20/34 (58%)

Query: 16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 49
          ++K+LG+ W  ++  EK+ Y +      K++ E+
Sbjct: 33 ISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 66

>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 = 34.4 bits (79), Expect = 7e-04
 Identities = 9/34 (26%), Positives = 20/34 (58%)

Query: 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 85
          ++K+LG+ W  ++  EK+ Y +      K++ E+
Sbjct: 33 ISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	170
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	98.98
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	98.98
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	98.95
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	98.93
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	98.91
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	98.91
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	98.9
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	98.89
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	98.86
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	98.8
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	98.79
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	98.79
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.77
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	98.77
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	98.74
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	98.73
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	98.72
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.71
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	98.71
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	98.7
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	98.68
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.62
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	98.53
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.15
d1zr9a1	67	Zinc finger protein 593, ZNF593 {Human (Homo sapie	97.38
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	97.23
d1zu1a2	55	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	96.48
d1srka_	35	Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musc	93.87
d2vrda1	61	Spliceosomal protein U1C {Human (Homo sapiens) [Ta	93.65
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	93.53
d2dmda2	26	Zinc finger protein 64, ZFP68 {Human (Homo sapiens	91.69
d1a1ia2	28	ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	91.22
d2adra1	29	ADR1 {Synthetic, based on Saccharomyces cerevisiae	90.56
d1p7aa_	37	Kruppel-like factor 3, Bklf {Mouse (Mus musculus)	90.55
d2yrka1	48	Zinc finger homeobox protein 4, ZFHX4 {Human (Homo	89.69
d2ct1a2	36	Transcriptional repressor CTCF {Human (Homo sapien	85.15
d1zu1a1	72	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	83.39
d1sp1a_	29	Transcription factor sp1 {Human (Homo sapiens) [Ta	82.29
d2epsa1	39	PATZ1 {Human (Homo sapiens) [TaxId: 9606]}	80.91

>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=98.98  E-value=1.4e-10  Score=79.06  Aligned_cols=46  Identities=22%  Similarity=0.346  Sum_probs=22.7

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      +.++|++++++|++.||.+|+.||+++|.+|.+.|..++++|..+|
T Consensus        22 ~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~   67 (79)
T d1hsma_          22 KGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI   67 (79)
T ss_dssp             HHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445555555555555555555554444444444444444444444

>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=98.98  E-value=2.2e-10  Score=76.76  Aligned_cols=46  Identities=20%  Similarity=0.310  Sum_probs=42.8

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   49 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~E   49 (170)
                      +++++|++++++|++.||.+|++||+++|++|.+.|..++++|.++
T Consensus        21 i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~   66 (70)
T d1i11a_          21 ILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK   66 (70)
T ss_dssp             HHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTT
T ss_pred             HHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999999764

>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=98.95  E-value=4.4e-10  Score=77.35  Aligned_cols=48  Identities=25%  Similarity=0.309  Sum_probs=39.1

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      .++++|++++++|++.||++|++||+++|++|+++|..++++|..++.
T Consensus        21 ~~~~~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p   68 (80)
T d1gt0d_          21 MAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHP   68 (80)
T ss_dssp             HHTTSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHcCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCc
Confidence            467788888888888888888888888888888888888888877653

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

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

Probab=98.93  E-value=7e-10  Score=77.89  Aligned_cols=48  Identities=35%  Similarity=0.455  Sum_probs=27.5

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      +++++|++++++|++.||++|++||+++|.+|.+.|..++++|..+|.
T Consensus        39 ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~   86 (93)
T d1lwma_          39 VRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKE   86 (93)
T ss_dssp             HHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345556666666666655555555555555555555555555555543

>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=98.91  E-value=7.1e-10  Score=76.77  Aligned_cols=48  Identities=21%  Similarity=0.245  Sum_probs=35.9

Q ss_pred             ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729           4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus         4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      ++.++|++++++|++.||+.|++||+++|.+|.+.|..++++|..++.
T Consensus        23 i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~   70 (85)
T d1j46a_          23 MALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYP   70 (85)
T ss_dssp             HHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhH
Confidence            456778888888887777777777777777777777777777776553

>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=98.91  E-value=7.5e-10  Score=76.79  Aligned_cols=46  Identities=17%  Similarity=0.307  Sum_probs=35.9

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      +.++|++++++|++.||..|++||+++|++|.++|..++++|..++
T Consensus        22 ~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~   67 (86)
T d2lefa_          22 VAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLY   67 (86)
T ss_dssp             HHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence            5678888888888888888888888888888888877777776654

>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=98.90  E-value=1.4e-09  Score=73.91  Aligned_cols=59  Identities=22%  Similarity=0.422  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          35 YLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        35 Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      |.-.....+..+..+      .+|++.||++|++||+++|.+|.+.|..++++|..+|.+|+.+.
T Consensus        10 y~~f~~~~r~~i~~~~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~   74 (79)
T d1hsma_          10 FFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG   74 (79)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence            444455555555443      28999999999999999999999999999999999999998654

>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=98.89  E-value=7.7e-10  Score=73.71  Aligned_cols=47  Identities=28%  Similarity=0.388  Sum_probs=34.2

Q ss_pred             ccccCCC--CCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           4 ESEKMIS--TTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         4 ~k~~~p~--~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      ++.++|+  +++++|++.||.+|+.||+++|++|.+.|..++++|..+|
T Consensus        20 ~k~~~p~~~~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~   68 (71)
T d1ckta_          20 HKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREM   68 (71)
T ss_dssp             HHHHCTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4566675  4567777777777777777777777777777777777665

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

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

Probab=98.86  E-value=3.1e-09  Score=74.49  Aligned_cols=60  Identities=35%  Similarity=0.537  Sum_probs=50.0

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      .|.-.+...+..+..+      -+|++.||++|++||+++|.+|+++|.+++.+|..+|..|+.+.
T Consensus        27 af~lF~~e~r~~ik~~~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~~~l   92 (93)
T d1lwma_          27 AYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATL   92 (93)
T ss_dssp             HHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4555555655555432      28999999999999999999999999999999999999998653

>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=98.80  E-value=5.1e-09  Score=73.89  Aligned_cols=46  Identities=26%  Similarity=0.465  Sum_probs=41.5

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ   96 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~   96 (170)
                      +|++.||++|++||++||++|.++|.+++++|..+|.+|..+....
T Consensus        36 ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~~   81 (101)
T d1v63a_          36 ERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQ   81 (101)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTT
T ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHH
Confidence            8999999999999999999999999999999999999998764433

>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=98.79  E-value=3e-09  Score=70.75  Aligned_cols=39  Identities=36%  Similarity=0.624  Sum_probs=37.7

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHH
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   89 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~y   89 (170)
                      +|++.||.+|++||+++|++|.++|.+++++|..+|++|
T Consensus        33 ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_          33 EFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             HHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            899999999999999999999999999999999999876

>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=98.79  E-value=7.1e-09  Score=74.35  Aligned_cols=45  Identities=29%  Similarity=0.393  Sum_probs=42.1

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhh
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY   95 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~   95 (170)
                      ++++.||++|++||+++|++|.++|..++.+|..+|.+|..+...
T Consensus        43 e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~~~~   87 (108)
T d1v64a_          43 ERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPE   87 (108)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            889999999999999999999999999999999999999976553

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

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

Probab=98.77  E-value=2.9e-09  Score=74.01  Aligned_cols=46  Identities=20%  Similarity=0.362  Sum_probs=29.1

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      ++++|++++.+|++.||+.|+.||+++|++|.+.|..++.+|..++
T Consensus        30 ~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~   75 (91)
T d1k99a_          30 AKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNL   75 (91)
T ss_dssp             HTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4556666666666666666666666666666666666666665554

>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=98.77  E-value=8.5e-10  Score=76.51  Aligned_cols=61  Identities=18%  Similarity=0.325  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhh
Q psy1729          35 YLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY   95 (170)
Q Consensus        35 Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~   95 (170)
                      |.-.+...+.....+      .+|++.||.+|++||+++|++|.++|.+++++|..++.+|+.++..
T Consensus        10 f~lF~~~~r~~~~~~~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~   76 (86)
T d2lefa_          10 FMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY   76 (86)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSST
T ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCC
Confidence            444555555555443      2899999999999999999999999999999999999999765543

>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=98.74  E-value=4.3e-09  Score=72.69  Aligned_cols=60  Identities=20%  Similarity=0.351  Sum_probs=49.5

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      .|.-.+...+.....+      .+|++.||.+|++||+++|.+|.++|+.++.+|..+|.+|+.++
T Consensus        11 ay~lF~~~~r~~i~~~~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p   76 (85)
T d1j46a_          11 AFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCC
Confidence            3444555555555543      28999999999999999999999999999999999999998654

>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=98.73  E-value=1.7e-08  Score=71.06  Aligned_cols=61  Identities=20%  Similarity=0.337  Sum_probs=49.2

Q ss_pred             cCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHH
Q psy1729           7 KMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLD   73 (170)
Q Consensus         7 ~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~   73 (170)
                      +.+++++++|++.||++|+.||+++|++|.+.|..++++|..+|...+.      .+++.++..+..
T Consensus        28 ~~~~~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~------~~~~~~~~~~~~   88 (101)
T d1v63a_          28 ELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVK------SLSPQDRAAYKE   88 (101)
T ss_dssp             TTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHH------HSCTTHHHHHHH
T ss_pred             HhcCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh------cCCHHHHHHHHH
Confidence            4566789999999999999999999999999999999999998854432      356655544443

>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=98.72  E-value=3.8e-09  Score=72.50  Aligned_cols=43  Identities=30%  Similarity=0.449  Sum_probs=40.9

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      +|++.||.+|++||+++|++|.++|+.++++|..++++|+..+
T Consensus        32 eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~p   74 (80)
T d1gt0d_          32 EISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRP   74 (80)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             HHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCCC
Confidence            8999999999999999999999999999999999999998554

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

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

Probab=98.71  E-value=2.4e-09  Score=74.26  Aligned_cols=47  Identities=23%  Similarity=0.270  Sum_probs=43.3

Q ss_pred             cccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHH
Q psy1729           3 IESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   49 (170)
Q Consensus         3 ~~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~E   49 (170)
                      .++.++|++++++|++.||.+|+.||+++|++|.++|..+++.|.++
T Consensus        38 ~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          38 QLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             HHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            35788999999999999999999999999999999999999999754

>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=98.71  E-value=2.6e-09  Score=71.32  Aligned_cols=56  Identities=20%  Similarity=0.409  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   89 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~y   89 (170)
                      .|.-.+...+.....+      .+|++.||++|++||+++|++|.++|++++++|.+++.+|
T Consensus         9 ay~lf~~~~r~~i~~~~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_           9 AFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             HHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             HHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            3555556666665543      3899999999999999999999999999999998876544

>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=98.70  E-value=6e-09  Score=69.85  Aligned_cols=44  Identities=18%  Similarity=0.260  Sum_probs=21.8

Q ss_pred             cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729           5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   50 (170)
Q Consensus         5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em   50 (170)
                      ++++|++++++|++.||++|++|+  +|++|++.|..++++|..++
T Consensus        23 k~~~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~   66 (73)
T d1qrva_          23 KRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAV   66 (73)
T ss_dssp             HHTSTTCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHH
Confidence            445555555555555555555443  24444444444444444443

>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=98.68  E-value=1.6e-08  Score=72.45  Aligned_cols=49  Identities=27%  Similarity=0.322  Sum_probs=45.2

Q ss_pred             ccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729           6 EKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK   54 (170)
Q Consensus         6 ~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K   54 (170)
                      ++.|++++.+|++.||..|+.||+++|++|.++|..++.+|..+|..+.
T Consensus        34 ~~~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~   82 (108)
T d1v64a_          34 ANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFL   82 (108)
T ss_dssp             HHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5689999999999999999999999999999999999999999885443

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

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

Probab=98.62  E-value=1.6e-08  Score=70.07  Aligned_cols=60  Identities=20%  Similarity=0.418  Sum_probs=50.3

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      .|.-.+...+..+..+      .+|++.||+.|+.||+++|.+|++.|..++.+|..+|.+|....
T Consensus        17 ay~lf~~~~r~~~~~~~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~~   82 (91)
T d1k99a_          17 PYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH   82 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGCC
T ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            5555556666555443      28999999999999999999999999999999999999998763

>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=98.53  E-value=6.7e-08  Score=64.55  Aligned_cols=58  Identities=19%  Similarity=0.367  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   93 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~   93 (170)
                      .|.-.+...+.....+      .+|++.||++|++|+  +|++|.++|+.++++|..+|..|+.++
T Consensus        10 ay~lf~~~~r~~~k~~~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~g   73 (73)
T d1qrva_          10 AYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEANG   73 (73)
T ss_dssp             HHHHHHHHHHHHHHHTSTTCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            3444555555555442      389999999999886  599999999999999999999998754

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

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

Probab=98.15  E-value=2.6e-07  Score=63.66  Aligned_cols=52  Identities=25%  Similarity=0.373  Sum_probs=42.1

Q ss_pred             hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHH
Q psy1729          34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   85 (170)
Q Consensus        34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~e   85 (170)
                      .|.-.....+..+..+      .+|++.||.+|+.||+++|++|+++|.+++++|.++
T Consensus        27 ay~lF~~e~r~~~~~~~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~   84 (90)
T d1wgfa_          27 AMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK   84 (90)
T ss_dssp             HHHHHHHHTHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCC
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence            4555556655555443      289999999999999999999999999999998754

>d1zr9a1 g.37.1.4 (A:28-94) Zinc finger protein 593, ZNF593 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Zinc finger protein 593, ZNF593
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.38  E-value=6.8e-06  Score=54.79  Aligned_cols=41  Identities=22%  Similarity=0.485  Sum_probs=36.3

Q ss_pred             cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         124 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       124 ~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      ++|+|-+..+-.||..|+.+|.|-..+..|+.++.|..+|.
T Consensus         5 e~D~D~pG~gqfYCv~C~K~F~se~~l~~H~ksKkHKrrvk   45 (67)
T d1zr9a1           5 EFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLK   45 (67)
T ss_dssp             SSCSSSGGGGCSEETTTTEECSSHHHHHHHTTCHHHHHHHH
T ss_pred             CCCCCCCCCCEEecccccCccCCHHHHHHHHcccHHHHHHH
Confidence            56777777888899999999999999999999999988763

>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=97.23  E-value=0.00014  Score=49.33  Aligned_cols=44  Identities=32%  Similarity=0.542  Sum_probs=38.3

Q ss_pred             hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchh
Q psy1729          51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA   94 (170)
Q Consensus        51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~   94 (170)
                      ...+.+...|++|...||.+|+.+|++|..||++++.+.+..++
T Consensus        32 KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~~~a   75 (84)
T d1l8ya_          32 KALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPA   75 (84)
T ss_dssp             HHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGG
T ss_pred             HHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhccCCC
Confidence            34556777899999999999999999999999999988876655

>d1zu1a2 g.37.1.4 (A:74-128) dsRNA-binding protein ZFa (ZNF346, JAZ) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: dsRNA-binding protein ZFa (ZNF346, JAZ)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=96.48  E-value=0.00012  Score=46.83  Aligned_cols=34  Identities=21%  Similarity=0.471  Sum_probs=29.8

Q ss_pred             chhHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729         132 NEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR  165 (170)
Q Consensus       132 ~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~  165 (170)
                      |.+-||.+|+.+|+|.--=+-|..|+-|..+|..
T Consensus        19 d~nk~C~lCn~~Fns~~~AqsHY~GK~H~K~lk~   52 (55)
T d1zu1a2          19 DRSKCCPVCNMTFSSPVVAESHYIGKTHIKNLRL   52 (55)
T ss_dssp             CTTTEETTTTEECSSHHHHHHHHTSHHHHHHHHH
T ss_pred             CchhhhhhhhcccCCHHHHHHHhhhhHHHHHHHH
Confidence            3444999999999999999999999999988753

>d1srka_ g.37.1.1 (A:) Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein ZFPM1 (FOG-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.87  E-value=0.002  Score=37.20  Aligned_cols=26  Identities=38%  Similarity=0.640  Sum_probs=22.3

Q ss_pred             HHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729         136 YCRVCDQWFTTLHNKREHLNGRQHFQRF  163 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~~~~~~~~~  163 (170)
                      -|.+|+..|++..|++-||  |-|...+
T Consensus         9 ~C~~C~k~F~~~~~L~~H~--r~Ht~~~   34 (35)
T d1srka_           9 VCRICLSAFTTKANCARHL--KVHTDTL   34 (35)
T ss_dssp             ECSSSCCEESSHHHHHHHH--GGGTSCC
T ss_pred             cCCCCCCcccChHHHHHHc--cccCCcC
Confidence            4999999999999999998  6776543

>d2vrda1 g.37.1.4 (A:1-61) Spliceosomal protein U1C {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Spliceosomal protein U1C
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.65  E-value=0.0027  Score=41.11  Aligned_cols=30  Identities=30%  Similarity=0.781  Sum_probs=24.9

Q ss_pred             HHHHHHHHHhh--hhhhhhhhhchhhhhhhhc
Q psy1729         135 LYCRVCDQWFT--TLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       135 ~~~~~~~~~f~--~~h~~~~~~~~~~~~~~~~  164 (170)
                      -||--|+-||+  |+..-+-|+.|++|+.++.
T Consensus         4 yyCdYC~~~lt~ds~s~RK~H~~G~kH~~n~~   35 (61)
T d2vrda1           4 FYCDYCDTYLTHDSPSVRKTHCSGRKHKENVK   35 (61)
T ss_dssp             CEETTTTEECSCCSHHHHHHHTCCTHHHHHHH
T ss_pred             hhhhhhcchhccCChhHHHHHhccHHHHHHHH
Confidence            37899999994  5666678999999999874

>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=93.53  E-value=0.044  Score=36.62  Aligned_cols=36  Identities=31%  Similarity=0.593  Sum_probs=32.4

Q ss_pred             HHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729          16 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   51 (170)
Q Consensus        16 vsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE   51 (170)
                      ..+.+...|++|...||-+|...|+++..+|++|+-
T Consensus        33 aqkaMeatW~~meKkEki~wikkaaedqkryerel~   68 (84)
T d1l8ya_          33 ALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELS   68 (84)
T ss_dssp             HHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence            456778899999999999999999999999999763

>d2dmda2 g.37.1.1 (A:8-33) Zinc finger protein 64, ZFP68 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Zinc finger protein 64, ZFP68
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.69  E-value=0.0084  Score=32.01  Aligned_cols=19  Identities=26%  Similarity=0.779  Sum_probs=17.6

Q ss_pred             HHHHHHHhhhhhhhhhhhc
Q psy1729         137 CRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~~  155 (170)
                      |.+|+.+||+.-++.-||-
T Consensus         4 c~~c~kcfsrkdklk~hmr   22 (26)
T d2dmda2           4 CEVCGKCFSRKDKLKTHMR   22 (26)
T ss_dssp             BTTTTBCCCCHHHHHHHGG
T ss_pred             cchhhhHhcchhHHHHHhh
Confidence            8899999999999999984

>d1a1ia2 g.37.1.1 (A:132-159) ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: ZIF268
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.22  E-value=0.0073  Score=33.09  Aligned_cols=18  Identities=28%  Similarity=0.739  Sum_probs=17.1

Q ss_pred             HHHHHHHhhhhhhhhhhh
Q psy1729         137 CRVCDQWFTTLHNKREHL  154 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~  154 (170)
                      |.+|+..|+...|+..||
T Consensus         6 C~~C~k~F~~~~~L~~H~   23 (28)
T d1a1ia2           6 CRICMRNFSRSDHLTTHI   23 (28)
T ss_dssp             CTTTCCEESCHHHHHHHH
T ss_pred             CCCCcCEecccccccccC
Confidence            899999999999999887

>d2adra1 g.37.1.1 (A:102-130) ADR1 {Synthetic, based on Saccharomyces cerevisiae sequence}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: ADR1
species: Synthetic, based on Saccharomyces cerevisiae sequence

Probab=90.56  E-value=0.01  Score=32.64  Aligned_cols=18  Identities=28%  Similarity=0.724  Sum_probs=17.2

Q ss_pred             HHHHHHHhhhhhhhhhhh
Q psy1729         137 CRVCDQWFTTLHNKREHL  154 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~  154 (170)
                      |.+|+..|++..+++.||
T Consensus         5 C~~C~k~F~~~~~L~~H~   22 (29)
T d2adra1           5 CEVCTRAFARQEHLKRHY   22 (29)
T ss_dssp             CTTTCCCBSCHHHHHHHH
T ss_pred             CCCCCCCCCCchHccccc
Confidence            889999999999999998

>d1p7aa_ g.37.1.1 (A:) Kruppel-like factor 3, Bklf {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Kruppel-like factor 3, Bklf
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=90.55  E-value=0.013  Score=33.77  Aligned_cols=24  Identities=25%  Similarity=0.510  Sum_probs=20.7

Q ss_pred             HHHHHHHHhhhhhhhhhhhchhhhhh
Q psy1729         136 YCRVCDQWFTTLHNKREHLNGRQHFQ  161 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~~~~~~~  161 (170)
                      -|..|+..|++..+++.|+  |-|+.
T Consensus        13 ~C~~C~k~F~~~~~L~~H~--r~H~~   36 (37)
T d1p7aa_          13 QCPDCDRSFSRSDHLALHR--KRHML   36 (37)
T ss_dssp             CCTTTCCCBSSHHHHHHHH--GGGTC
T ss_pred             EeCCCCCEecCHHHHHHHH--hcCcC
Confidence            4899999999999999998  56664

>d2yrka1 g.37.1.4 (A:8-55) Zinc finger homeobox protein 4, ZFHX4 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: Zinc finger homeobox protein 4, ZFHX4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.69  E-value=0.016  Score=35.58  Aligned_cols=28  Identities=21%  Similarity=0.598  Sum_probs=25.8

Q ss_pred             HHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         137 CRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      |..|+--+|+.-..|.|++.+||+..|.
T Consensus         9 C~lC~vKYs~~~SvrdHiFskqHI~~Vk   36 (48)
T d2yrka1           9 CTLCGVKYSARLSIRDHIFSKQHISKVR   36 (48)
T ss_dssp             CTTTTCCCCSSSCHHHHHTSHHHHHHHH
T ss_pred             CcccceeeeeecchHhhhhhHHHHHHHH
Confidence            8999999999999999999999998763

>d2ct1a2 g.37.1.1 (A:8-43) Transcriptional repressor CTCF {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcriptional repressor CTCF
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.15  E-value=0.03  Score=31.98  Aligned_cols=25  Identities=24%  Similarity=0.505  Sum_probs=20.3

Q ss_pred             HHHHHHHHhhhhhhhhhhhchhhhhh
Q psy1729         136 YCRVCDQWFTTLHNKREHLNGRQHFQ  161 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~~~~~~~  161 (170)
                      -|..|+..|+...|++-||.- .|..
T Consensus        10 ~C~~C~k~F~~~~~L~~H~~~-~H~~   34 (36)
T d2ct1a2          10 ECYICHARFTQSGTMKMHILQ-KHTE   34 (36)
T ss_dssp             ECTTTCCEESCHHHHHHHHHH-HSSS
T ss_pred             eCCCCcccccchHHHHHHccc-ccCC
Confidence            389999999999999999754 2543

>d1zu1a1 g.37.1.4 (A:2-73) dsRNA-binding protein ZFa (ZNF346, JAZ) {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: HkH motif-containing C2H2 finger
domain: dsRNA-binding protein ZFa (ZNF346, JAZ)
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=83.39  E-value=0.04  Score=36.22  Aligned_cols=32  Identities=22%  Similarity=0.506  Sum_probs=28.6

Q ss_pred             hhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729         133 EELYCRVCDQWFTTLHNKREHLNGRQHFQRFD  164 (170)
Q Consensus       133 ~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~  164 (170)
                      -++||.+|+.-.-|-.-+--|..|+.|-+++.
T Consensus        31 td~~CkvC~a~L~seSQriaHYeskkHa~kvr   62 (72)
T d1zu1a1          31 SDTQCKVCSAVLISESQKLAHYQSRKHANKVR   62 (72)
T ss_dssp             CSSEETTTTEECCSHHHHHHHHHCHHHHHHHH
T ss_pred             chhhHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35789999999999999999999999999874

>d1sp1a_ g.37.1.1 (A:) Transcription factor sp1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: Transcription factor sp1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.29  E-value=0.057  Score=29.48  Aligned_cols=19  Identities=21%  Similarity=0.590  Sum_probs=17.3

Q ss_pred             HHHHHHHhhhhhhhhhhhc
Q psy1729         137 CRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       137 ~~~~~~~f~~~h~~~~~~~  155 (170)
                      |..|+..|+..+++..|+-
T Consensus         5 C~~C~k~F~~~s~L~~H~r   23 (29)
T d1sp1a_           5 CPECPKRFMRSDHLSKHIK   23 (29)
T ss_dssp             CTTTTCCCSCSHHHHHHHH
T ss_pred             CCcCCCeecchHHhhhhcC
Confidence            8899999999999998873

>d2epsa1 g.37.1.1 (A:408-446) PATZ1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: beta-beta-alpha zinc fingers
superfamily: beta-beta-alpha zinc fingers
family: Classic zinc finger, C2H2
domain: PATZ1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.91  E-value=0.05  Score=31.68  Aligned_cols=20  Identities=20%  Similarity=0.584  Sum_probs=17.8

Q ss_pred             HHHHHHHHhhhhhhhhhhhc
Q psy1729         136 YCRVCDQWFTTLHNKREHLN  155 (170)
Q Consensus       136 ~~~~~~~~f~~~h~~~~~~~  155 (170)
                      -|..|+..|++..|++.||.
T Consensus         7 ~C~~Cgk~F~~~~~L~~H~r   26 (39)
T d2epsa1           7 ICQSCGKGFSRPDHLNGHIK   26 (39)
T ss_dssp             ECSSSCCEESSHHHHHHHHH
T ss_pred             cCCCCCCCcCChHHhhccCc
Confidence            38899999999999999974