Psyllid ID: psy1990

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380--
Protein Sequence
VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNSCLSLDESSLDAAPSRTLPNQLPPSPPPLTMEDNIASVVRTMIDQNKEIQLLRSKMKSLQEKRLKKNAYVYFFPFLSRPEQRNSTAPLQNEKSARETAQAEKGIRSAQATGIEPVSKSSEDFALNRGDRKVHPVHLERACLVLTHRVRNVTRWVSESSSNLEYFPSYRTQPFQRKT
Secondary Structure (PSIPRED)
cccHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHccccccHHHHHHHHHccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHccccccccHHHHHHHHHHHHHHHHHHHHcccccccHHHcccccccccccccccccccEEEEEcccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcccccHHHHccccccccccccccccccccccccHcHHHHHHHccccHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEccccccccccccccccccccccccccHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHccEEEEccccccHHccccccccccHccHHHHHHHHHccHHHHHccccccccccHHHHccccccccccccHHHHHEHHHHHHcccEEEEEccccccccccccccccccccc
Coil and Loop (DISEMBL)
vtkllgnewsklslpekkvyLDRAEVDKKRYREELKVYRKSDAYQSYLILLFFQVTKLLgnewsklslpekkvyLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHHCLTAkvfsgtsegrdsgtyktrgglqangteesdiatdatdeideeeedneELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQsghlavnesnsclsldessldaapsrtlpnqlppspppltmednIASVVRTMIDQNKEIQLLRSKMKSLQEKRlkknayvyffpflsrpeqrnstaplqneksARETAQAEKGIRsaqatgiepvskssedfalnrgdrkvhpVHLERACLVLTHRVRNVTRWVsesssnleyfpsyrtqpfqrkt
Flexible Loop (DISEMBL)
vtkllgnewsklslpekkvyldraevdkkryreelkvyrksdayqsYLILLFFQVTKLLGnewsklslpekkvyldraevdkkryreelkvyrksdayqsylrrkrvkkiqhhcltakvfsgtsegrdsgtyktrgglqangteesdiatdaTDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNSCLSLDESSLDAAPSRtlpnqlppsppplTMEDNIASVVRTMIDQNKEIQLLRSKMKSLQEKRLKKNAYVYFFPflsrpeqrnstaplqneksARETAQAEKGirsaqatgiepvsksSEDFALNRGDRKVHPVHLERAclvlthrvrnvtrwvsesssnleyfpsyrtqpfqrkt
Low Complexity Region (SEG)
VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESdiatdatdeideeeedneeLYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNSCLSLDESSLDAAPSRTlpnqlppsppplTMEDNIASVVRTMIDQNKEIQLLRSKMKSLQEKRLKKNAYVYFFPFLSRPEQRNSTAPLQNEKSARETAQAEKGIRSAQATGIEPVSKSSEDFALNRGDRKVHPVHLERACLVLTHRVRNVTRWVSESSSNLEYFPSYRTQPFQRKT
Disordered region (IsUnstruct)
*****************KVYLDRAEVDKKRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHHCLTAKVF*********************************************LYCRVCDQWFTTLHNKREHLN***********************************************************************************LKKNAYVYFFPFL*****************************************************KVHPVHLERACLVLTHRVRNVTRWVS*********************
Disordered Region (DISOPRED)
VTKLLGN*******************DKKRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY**************************************************************************************************************************************************DNIAS*******************************************************************RSAQATGIEPVSKSSEDFALNRGDRKVHPVHLERACLVLTHRVRNVTRWVSESSSNLEYFPSYRTQP*****
Disordered Region (DISEMBL)
VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDA************ELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNSCLSLDESSLDAAPSRTLPNQLPPSPPPLTMEDNIASVVRTMIDQNKEIQLLRSKMKSLQEKRLKKNAYVYFFPFLSRPEQ************************SAQATGIEPVSKSSEDFALNRGDRKVHPVHLERACLVLTHRVRNVTRWVSESSSNLEYFPSYRTQPFQRKT
Disordered Region (DISPRO)
VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK************************************SDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAV***N******E*SLDAAP***LPNQLPPSPPPLTMEDNIASVVRTMIDQNKEIQLLRSKMKSLQEKRLKKNAYVYFFPFLSR*******************************************F*LNRGDRKVHPVHLERACLVLTHRVRNVTRWVSESSSNLEYFPSYRTQ******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VTKLLGNEWSKLSLPEKKVYxxxxxxxxxxxxxxxxxxxxxDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYxxxxxxxxxxxxxxxxxxxxxDAYQSYLRRKRVKKIQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIxxxxxxxxxxxxxxxxxxxxxVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNSCLSLDESSLDAAPSRTLPNQLPPSPPPLTMEDNIASVVRTxxxxxxxxxxxxxxxxxxxxxRLKKNAYVYFFPFLSRPEQRNSTAPLQNEKSARETAQAEKGIRSAQATGIEPVSKSSEDFALNRGDRKVHPVHLERACLVLTHRVRNVTRWVSESSSNLEYFPSYRTQPFQRKT
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	382	2.2.26 [Sep-21-2011]
Q6AZF8	345	High mobility group prote	N/A	N/A	0.151	0.168	0.482	1e-09
Q6DIJ5	345	High mobility group prote	yes	N/A	0.151	0.168	0.482	2e-09
Q9NP66	347	High mobility group prote	yes	N/A	0.138	0.152	0.509	1e-08
Q5ZKF4	348	High mobility group prote	yes	N/A	0.138	0.152	0.509	1e-08
Q9DC33	346	High mobility group prote	yes	N/A	0.138	0.153	0.509	1e-08
Q32L68	317	SWI/SNF-related matrix-as	no	N/A	0.130	0.157	0.52	2e-07
Q9P0W2	317	SWI/SNF-related matrix-as	no	N/A	0.130	0.157	0.52	3e-07
Q9Z104	317	SWI/SNF-related matrix-as	no	N/A	0.130	0.157	0.52	1e-06
Q5B995	106	Non-histone chromosomal p	yes	N/A	0.125	0.452	0.458	0.0001

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

 Score = 64.7 bits (156), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 45/58 (77%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           F ++T+++G+EWSKL   EK+ YLD AE DK+RY +EL+ Y+ +DAYQ+Y R+ + ++
Sbjct: 128 FPEITRIVGSEWSKLPAHEKQHYLDEAEKDKERYTKELQKYQNTDAYQTYSRKAKSRQ 185

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 = 64.3 bits (155), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 45/58 (77%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           F ++T+++G+EWSKL   EK+ YLD AE DK+RY +EL+ Y+ +DAYQ+Y R+ + ++
Sbjct: 128 FPEITRIVGSEWSKLPAHEKQHYLDEAEKDKERYTKELQQYQNTDAYQTYSRKAQSRQ 185

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 = 61.2 bits (147), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 42/53 (79%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
           F ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct: 130 FPEITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 182

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

 Score = 61.2 bits (147), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 41/53 (77%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
           F ++T++LGNEWSKL   EK+ YLD A+ DK+RY  EL+ Y+K++AY+ + R+
Sbjct: 131 FPEITRMLGNEWSKLPPEEKRRYLDEADRDKERYMRELEQYQKTEAYKVFSRK 183

Plays a role in neuronal differentiation.

Gallus gallus (taxid: 9031)

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

 Score = 61.2 bits (147), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 42/53 (79%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
           F ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct: 129 FPEITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 181

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|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 = 57.4 bits (137), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 39/50 (78%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 99
           L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+
Sbjct: 95  LPFPEITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQSEAYK 144

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 = 56.6 bits (135), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 39/50 (78%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 99
           L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+
Sbjct: 95  LPFPEITKMLGAEWSKLQPTEKQRYLDEAEREKQQYMKELRAYQQSEAYK 144

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 = 54.7 bits (130), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 38/50 (76%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 99
           L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL  Y++S+AY+
Sbjct: 95  LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYK 144

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|Q5B995|NHP6_EMENI Non-histone chromosomal protein 6 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=nhp6 PE=3 SV=1

 Score = 48.1 bits (113), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 30/48 (62%)

Query: 50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 97
          + F QV K+LG +W  LS  E+K Y D+A  DKKRY +E   Y+  +A
Sbjct: 52 ISFGQVGKMLGEKWKSLSDKERKPYEDKAAADKKRYEDEKAAYKAGEA 99

DNA-binding protein that induces severe bending of DNA. Required for DNA-binding by 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. Also augments the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

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	382
91091658	452	PREDICTED: similar to predicted protein	0.366	0.309	0.508	1e-28
260828085	410	hypothetical protein BRAFLDRAFT_124005 [	0.507	0.473	0.355	8e-22
405965825	718	Phospholysine phosphohistidine inorganic	0.295	0.157	0.414	3e-21
196009580	363	hypothetical protein TRIADDRAFT_58720 [T	0.298	0.314	0.405	6e-21
426232287	447	PREDICTED: uncharacterized protein LOC10	0.308	0.263	0.370	3e-17
296486384	363	TPA: high-mobility group 20A-like [Bos t	0.308	0.325	0.363	5e-17
351700745	570	High mobility group protein 20A [Heteroc	0.308	0.207	0.351	7e-15
359066596	256	PREDICTED: uncharacterized protein LOC10	0.287	0.429	0.355	8e-15
443727481	409	hypothetical protein CAPTEDRAFT_191691 [	0.272	0.254	0.330	7e-14
291231769	546	PREDICTED: high mobility group 20 B-like	0.214	0.150	0.378	5e-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 =  133 bits (334), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 90/177 (50%), Positives = 111/177 (62%), Gaps = 37/177 (20%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           L F ++TK++GN+WS LSL EK+ YL +AE DK+RYREELK YR+SDAY++YL +KR   
Sbjct: 206 LAFHEITKVIGNKWSNLSLEEKRPYLAKAEEDKRRYREELKQYRQSDAYRAYLAKKR--- 262

Query: 110 IQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCR 169
                                    R  LQ N   ESD+  DATDE   +EEDNEELYCR
Sbjct: 263 -------------------------RNRLQNNVLSESDM--DATDE--IDEEDNEELYCR 293

Query: 170 VCDQWFTTLHNKREHLNGRQHFQAV--EQSGHLAVNESNSCL---SLDESSLDAAPS 221
            CDQWF  LHNKREHL GRQH Q+V  +    L ++ S+S +   SLDESSLDA P+
Sbjct: 294 TCDQWFHNLHNKREHLQGRQHTQSVAGDIKRELDLSASDSGIFSTSLDESSLDAMPN 350

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

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 =  110 bits (276), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 84/236 (35%), Positives = 124/236 (52%), Gaps = 42/236 (17%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           L F ++T+LLG+ WS LS  +K+ YLD AEVDK+RY EELK Y++S+AYQS+L+R+  KK
Sbjct: 169 LPFTEMTRLLGSRWSALSQEDKQKYLDAAEVDKRRYIEELKAYQQSEAYQSWLKRQAAKK 228

Query: 110 IQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCR 169
           ++  CL   V   T +G                 E   I  D        E+D  +LYC+
Sbjct: 229 LK--CL---VDVETIDG-----------------EVDSIVLDL-------EDDPSDLYCK 259

Query: 170 VCDQWFTTLHNKREHLNGRQHFQAV----EQSGHLAVNESNSCLSLDESSLDAAPSRTLP 225
            C+Q+F++LHNK+EH+ G+QH Q +    E+   L   E +  LS      +     T  
Sbjct: 260 TCNQYFSSLHNKKEHMYGKQHLQMLTGEFEREAELTKQEEDRLLSTSVEEPECLDRTTFL 319

Query: 226 NQL--PPSPPPLTMEDNIASVVRTMIDQNKEIQLLRSKMKSLQEK--RLKKNAYVY 277
            +   P S   L M+   A+ +R M     EI  LR  ++  +E+  +L+K A VY
Sbjct: 320 ERYKGPNSTENLKMDIIEANTLREM-----EIGELRRSLEISRERHLQLQKQAQVY 370

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

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

 Score =  109 bits (272), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 61/147 (41%), Positives = 84/147 (57%), Gaps = 34/147 (23%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           L F +VTK+LGNEWS L   +K+ YL  AE DKKRY E+LK +++S+AYQS +++K+ K 
Sbjct: 210 LSFPEVTKILGNEWSTLDSQKKQKYLLAAEEDKKRYMEQLKTFQQSEAYQSVMKKKKGKG 269

Query: 110 IQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATD--EIDEEEEDNEELY 167
                      +GT                       +I  D T    +DE+E    ELY
Sbjct: 270 F---------LTGT-----------------------EIHVDETFPYSLDEDEGSMNELY 297

Query: 168 CRVCDQWFTTLHNKREHLNGRQHFQAV 194
           CRVCDQ+F++LHNK+EH+ GRQH Q +
Sbjct: 298 CRVCDQYFSSLHNKKEHMFGRQHLQNI 324

Source: Crassostrea gigas

Species: Crassostrea gigas

Genus: Crassostrea

Family: Ostreidae

Order: Ostreoida

Class: Bivalvia

Phylum: Mollusca

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 =  108 bits (269), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 87/158 (55%), Gaps = 44/158 (27%)

Query: 50  LLFFQVTKLLGNEWSKLSLP-------------EKKVYLDRAEVDKKRYREELKVYRKSD 96
           L F ++TK LGNEWSK+ L               KK +LD AE DK+RY EELK Y+ SD
Sbjct: 108 LSFPEITKFLGNEWSKMKLSAKQARLDFLPYTYRKKKFLDEAEADKRRYVEELKAYQCSD 167

Query: 97  AYQSYLRRKRVKKIQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEI 156
            Y+S   R+  KK       +K+F+GT                  G   + IA D     
Sbjct: 168 GYRSEASRESSKK-------SKLFTGT------------------GMNSAYIANDF---- 198

Query: 157 DEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAV 194
             E+++++EL+CRVC+Q+F++LHNKREH+ GRQH Q V
Sbjct: 199 --EDDESDELFCRVCNQYFSSLHNKREHMFGRQHLQNV 234

Source: Trichoplax adhaerens

Species: Trichoplax adhaerens

Genus: Trichoplax

Phylum: Placozoa

Superkingdom: Eukaryota

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

 Score = 95.9 bits (237), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 53/143 (37%), Positives = 82/143 (57%), Gaps = 25/143 (17%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           L F ++TK+L  +W++L   +K+ Y+  A+ DK+RY  ELK Y+ S+AY+++LRR+  +K
Sbjct: 115 LPFPEITKMLAAQWAQLPQEKKQRYVCEADEDKQRYIRELKAYQNSEAYRAFLRRRAAQK 174

Query: 110 IQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCR 169
           +   C       GTS                +  E  D+   A D      ++N++LYCR
Sbjct: 175 VLARC-------GTSA-------------PGHEFEGKDLDFSAVD-----GDENDDLYCR 209

Query: 170 VCDQWFTTLHNKREHLNGRQHFQ 192
            C Q+F++LHNKREHL G+QH Q
Sbjct: 210 TCRQFFSSLHNKREHLLGKQHLQ 232

Source: Ovis aries

Species: Ovis aries

Genus: Ovis

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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

 Score = 95.1 bits (235), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 52/143 (36%), Positives = 81/143 (56%), Gaps = 25/143 (17%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           L F ++TK+L  +W+ L   +K+ Y+  A+ DK+RY  EL+ Y+ S+AY+++LRR+   K
Sbjct: 100 LPFPEITKMLAAQWAHLPQEKKQRYVCEADEDKQRYIRELQAYQNSEAYRAFLRRRAALK 159

Query: 110 IQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCR 169
           +Q  C           G  +  Y+  G     G + S +  D          +N++LYCR
Sbjct: 160 VQARC-----------GTGAPGYEFEG----KGLDFSAVDAD----------ENDDLYCR 194

Query: 170 VCDQWFTTLHNKREHLNGRQHFQ 192
            C Q+F++LHNKREHL G+QH Q
Sbjct: 195 TCRQFFSSLHNKREHLLGKQHLQ 217

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 = 87.8 bits (216), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 51/145 (35%), Positives = 75/145 (51%), Gaps = 27/145 (18%)

Query: 47  YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKR 106
           Y  L F ++TK+L  +W++LS   K+ Y+  A+ DK+RY  EL+ Y+ S+AY+++LRR+ 
Sbjct: 253 YPDLPFTEITKILAAQWAQLSQERKQRYIYEADEDKQRYIRELQAYQSSEAYRAFLRRRA 312

Query: 107 VKKIQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEEL 166
                H  L      G   GR+   +        +GTE+ D                  L
Sbjct: 313 A----HRALCGPGAPGGELGREDLDFSA-----IDGTEDGD------------------L 345

Query: 167 YCRVCDQWFTTLHNKREHLNGRQHF 191
           +CR C Q F++ HNKREHL GRQH 
Sbjct: 346 HCRTCHQCFSSRHNKREHLLGRQHL 370

Source: Heterocephalus glaber

Species: Heterocephalus glaber

Genus: Heterocephalus

Family: Bathyergidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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

 Score = 87.8 bits (216), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 48/135 (35%), Positives = 75/135 (55%), Gaps = 25/135 (18%)

Query: 58  LLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHHCLTA 117
           +L  +W+ L   +K+ Y+  A+ DK+RY  EL+ Y+ S+AY+++LRR+   K+Q  C   
Sbjct: 1   MLAAQWAHLPQEKKQRYVCEADEDKQRYIRELQAYQNSEAYRAFLRRRAALKVQARC--- 57

Query: 118 KVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTT 177
                   G  +  Y+  G     G + S +  D          +N++LYCR C Q+F++
Sbjct: 58  --------GTGAPGYEFEG----KGLDFSAVDAD----------ENDDLYCRTCRQFFSS 95

Query: 178 LHNKREHLNGRQHFQ 192
           LHNKREHL G+QH Q
Sbjct: 96  LHNKREHLLGKQHLQ 110

Source: Bos taurus

Species: Bos taurus

Genus: Bos

Family: Bovidae

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

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

 Score = 84.7 bits (208), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 47/142 (33%), Positives = 71/142 (50%), Gaps = 38/142 (26%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           L F  +TK+LGNEWS +   EK+ YL  AE DKKRY +EL VY+KS  Y  +++++++K 
Sbjct: 173 LAFRDITKILGNEWSSMGTEEKQKYLSDAENDKKRYIDELDVYKKSPQYLEFVKKRKIKI 232

Query: 110 IQHHCLTAKVFSGTSEGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCR 169
                L         E  D+ TY+  G                             L+CR
Sbjct: 233 TTDDPL---------EHLDNSTYEEVG-----------------------------LHCR 254

Query: 170 VCDQWFTTLHNKREHLNGRQHF 191
           +C+ +F++ HNK+EH+ G+ H 
Sbjct: 255 LCNLYFSSNHNKKEHMLGKLHL 276

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|291231769|ref|XP_002735836.1| PREDICTED: high mobility group 20 B-like [Saccoglossus kowalevskii]

 Score = 75.1 bits (183), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 36/95 (37%), Positives = 59/95 (62%), Gaps = 13/95 (13%)

Query: 50  LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           + F +VTKLLG++WS +S  +K+ Y++ AE DKKRY +ELK Y++++AYQ++L+R+  KK
Sbjct: 285 MAFTEVTKLLGSQWSSMSAEDKQKYVEEAENDKKRYIDELKAYQQTEAYQAFLKRQAAKK 344

Query: 110 IQH-------------HCLTAKVFSGTSEGRDSGT 131
           +                 L  ++ +G   GRD G+
Sbjct: 345 LNDGSSIDSEEVASILGALEVEMITGGETGRDVGS 379

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	382
UNIPROTKB|C9J8X5	215	HMG20B "SWI/SNF-related matrix	0.212	0.376	0.382	7e-09
MGI|MGI:1914117	346	Hmg20a "high mobility group 20	0.138	0.153	0.509	5.9e-08
UNIPROTKB|Q0VCL5	347	HMG20A "High-mobility group 20	0.138	0.152	0.509	5.9e-08
UNIPROTKB|E2RKW6	347	HMG20A "Uncharacterized protei	0.138	0.152	0.509	5.9e-08
UNIPROTKB|Q9NP66	347	HMG20A "High mobility group pr	0.138	0.152	0.509	5.9e-08
UNIPROTKB|F1N8B1	348	LOC100857252 "Uncharacterized	0.138	0.152	0.509	6e-08
UNIPROTKB|Q5ZKF4	348	HMG20A "High mobility group pr	0.138	0.152	0.509	6e-08
UNIPROTKB|Q32L68	317	HMG20B "SWI/SNF-related matrix	0.212	0.255	0.382	6.2e-08
UNIPROTKB|Q9P0W2	317	HMG20B "SWI/SNF-related matrix	0.212	0.255	0.382	6.2e-08
UNIPROTKB|C9JQA7	142	HMG20B "SWI/SNF-related matrix	0.125	0.338	0.520	6.5e-08

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

 Score = 149 (57.5 bits), Expect = 7.0e-09, P = 7.0e-09
 Identities = 31/81 (38%), Positives = 51/81 (62%)

Query:    50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
             L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+    + + KK
Sbjct:    95 LPFPEITKMLGAEWSKLQPTEKQRYLDEAEREKQQYMKELRAYQQSEAYKMCTEKIQEKK 154

Query:   110 IQHHCLTAKVFSGTSEGRDSG 130
             I+    ++ + +    G   G
Sbjct:   155 IKKEDSSSGLMNTLLNGHKGG 175

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

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

 Score = 150 (57.9 bits), Expect = 5.9e-08, P = 5.9e-08
 Identities = 27/53 (50%), Positives = 42/53 (79%)

Query:    52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
             F ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   129 FPEITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 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 = 150 (57.9 bits), Expect = 5.9e-08, P = 5.9e-08
 Identities = 27/53 (50%), Positives = 42/53 (79%)

Query:    52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
             F ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   130 FPEITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 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 = 150 (57.9 bits), Expect = 5.9e-08, P = 5.9e-08
 Identities = 27/53 (50%), Positives = 42/53 (79%)

Query:    52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
             F ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   130 FPEITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 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 = 150 (57.9 bits), Expect = 5.9e-08, P = 5.9e-08
 Identities = 27/53 (50%), Positives = 42/53 (79%)

Query:    52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
             F ++T++LGNEWSKL   EK+ YLD A+ DK+RY +EL+ Y+K++AY+ + R+
Sbjct:   130 FPEITRMLGNEWSKLPPEEKQRYLDEADRDKERYMKELEQYQKTEAYKVFSRK 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|F1N8B1 LOC100857252 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 150 (57.9 bits), Expect = 6.0e-08, P = 6.0e-08
 Identities = 27/53 (50%), Positives = 41/53 (77%)

Query:    52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
             F ++T++LGNEWSKL   EK+ YLD A+ DK+RY  EL+ Y+K++AY+ + R+
Sbjct:   131 FPEITRMLGNEWSKLPPEEKRRYLDEADRDKERYMRELEQYQKTEAYKVFSRK 183

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

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

 Score = 150 (57.9 bits), Expect = 6.0e-08, P = 6.0e-08
 Identities = 27/53 (50%), Positives = 41/53 (77%)

Query:    52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRR 104
             F ++T++LGNEWSKL   EK+ YLD A+ DK+RY  EL+ Y+K++AY+ + R+
Sbjct:   131 FPEITRMLGNEWSKLPPEEKRRYLDEADRDKERYMRELEQYQKTEAYKVFSRK 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

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

 Score = 149 (57.5 bits), Expect = 6.2e-08, P = 6.2e-08
 Identities = 31/81 (38%), Positives = 51/81 (62%)

Query:    50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
             L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+    + + KK
Sbjct:    95 LPFPEITKMLGAEWSKLQPAEKQRYLDEAEREKQQYMKELRAYQQSEAYKMCAEKIQEKK 154

Query:   110 IQHHCLTAKVFSGTSEGRDSG 130
             I+    ++ + +    G   G
Sbjct:   155 IKKEDSSSGLMNTLLNGHKGG 175

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

UNIPROTKB|Q9P0W2 HMG20B "SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related" [Homo sapiens (taxid:9606)]

 Score = 149 (57.5 bits), Expect = 6.2e-08, P = 6.2e-08
 Identities = 31/81 (38%), Positives = 51/81 (62%)

Query:    50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
             L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+AY+    + + KK
Sbjct:    95 LPFPEITKMLGAEWSKLQPTEKQRYLDEAEREKQQYMKELRAYQQSEAYKMCTEKIQEKK 154

Query:   110 IQHHCLTAKVFSGTSEGRDSG 130
             I+    ++ + +    G   G
Sbjct:   155 IKKEDSSSGLMNTLLNGHKGG 175

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

GO:0007049 "cell cycle" evidence=IEA

GO:0016568 "chromatin modification" evidence=IEA

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

GO:0005694 "chromosome" evidence=IEA

GO:0005634 "nucleus" evidence=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:0005654 "nucleoplasm" evidence=TAS

GO:0007596 "blood coagulation" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|C9JQA7 HMG20B "SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related" [Homo sapiens (taxid:9606)]

 Score = 130 (50.8 bits), Expect = 6.5e-08, P = 6.5e-08
 Identities = 25/48 (52%), Positives = 37/48 (77%)

Query:    50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 97
             L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL+ Y++S+A
Sbjct:    95 LPFPEITKMLGAEWSKLQPTEKQRYLDEAEREKQQYMKELRAYQQSEA 142

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

---

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!

---

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	382
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	2e-07
cd01390	66	cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class	2e-07
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	2e-06
cd00084	66	cd00084, HMG-box, High Mobility Group (HMG)-box is	3e-06
smart00398	70	smart00398, HMG, high mobility group	3e-05
smart00398	70	smart00398, HMG, high mobility group	3e-05
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	3e-04
pfam00505	69	pfam00505, HMG_box, HMG (high mobility group) box	5e-04
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	0.002
pfam12874	25	pfam12874, zf-met, Zinc-finger of C2H2 type	0.003
PTZ00199	94	PTZ00199, PTZ00199, high mobility group protein; P	0.004

>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 = 47.6 bits (114), Expect = 2e-07
 Identities = 20/37 (54%), Positives = 29/37 (78%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
          +VTK+LG +W +LS  EKK Y ++AE DK+RY +E+K
Sbjct: 30 EVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 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 = 47.2 bits (113), Expect = 2e-07
 Identities = 20/36 (55%), Positives = 28/36 (77%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 36
          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 = 44.5 bits (106), Expect = 2e-06
 Identities = 17/37 (45%), Positives = 26/37 (70%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
          +++K+LG  W  LS  EKK Y ++AE DK+RY +E+ 
Sbjct: 30 EISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEMP 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 = 44.1 bits (105), Expect = 3e-06
 Identities = 17/36 (47%), Positives = 25/36 (69%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 36
          ++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 = 41.1 bits (97), Expect = 3e-05
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93
          +++K LG  W  LS  EK  Y ++A+ DK+RY EE+  Y+
Sbjct: 31 EISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

Length = 70

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39
          ++K LG  W  LS  EK  Y ++A+ DK+RY EE+  Y+
Sbjct: 32 ISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70

Length = 70

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 16/40 (40%), Positives = 26/40 (65%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93
          +++K+LG +W  LS  EKK Y ++AE +K RY +    Y+
Sbjct: 30 EISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69

Length = 69

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

 Score = 37.6 bits (88), Expect = 5e-04
 Identities = 16/39 (41%), Positives = 25/39 (64%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39
          ++K+LG +W  LS  EKK Y ++AE +K RY +    Y+
Sbjct: 31 ISKILGEKWKNLSEEEKKPYEEKAEKEKARYEKAYPAYK 69

Length = 69

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

 Score = 37.1 bits (86), Expect = 0.002
 Identities = 18/41 (43%), Positives = 24/41 (58%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 94
           V K++G  W+KLS  EK  Y  +A+ DK RY +E   Y K
Sbjct: 54 AVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Length = 94

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

 Score = 34.4 bits (80), Expect = 0.003
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 166 LYCRVCDQWFTTLHNKREHLNGRQH 190
            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

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

 Score = 36.0 bits (83), Expect = 0.004
 Identities = 18/40 (45%), Positives = 24/40 (60%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 40
          V K++G  W+KLS  EK  Y  +A+ DK RY +E   Y K
Sbjct: 55 VGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYAK 94

Length = 94

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	382
KOG4715|consensus	410		99.19
COG5648	211	NHP6B Chromatin-associated proteins containing the	99.1
PTZ00199	94	high mobility group protein; Provisional	99.01
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	98.97
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	98.97
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	98.95
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	98.88
smart00398	70	HMG high mobility group.	98.88
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.86
KOG0381|consensus	96		98.64
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	98.59
KOG0527|consensus	331		98.54
PTZ00199	94	high mobility group protein; Provisional	98.39
COG5648	211	NHP6B Chromatin-associated proteins containing the	98.37
PF09011	73	HMG_box_2: HMG-box domain; InterPro: IPR015101 Thi	98.31
cd01389	77	MATA_HMG-box MATA_HMG-box, class I member of the H	98.19
PF00505	69	HMG_box: HMG (high mobility group) box; InterPro:	98.18
cd01390	66	HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and II	98.17
cd01388	72	SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of	98.15
smart00398	70	HMG high mobility group.	98.14
KOG0526|consensus	615		98.07
KOG0381|consensus	96		97.8
cd00084	66	HMG-box High Mobility Group (HMG)-box is found in	97.75
smart00451	35	ZnF_U1 U1-like zinc finger. Family of C2H2-type zi	97.33
KOG3248|consensus	421		97.31
KOG0527|consensus	331		97.08
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	97.03
KOG4715|consensus	410		96.65
PF12874	25	zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG	96.59
PF14887	85	HMG_box_5: HMG (high mobility group) box 5; PDB: 1	96.37
PF12171	27	zf-C2H2_jaz: Zinc-finger double-stranded RNA-bindi	96.33
KOG0528|consensus	511		95.61
PF06220	38	zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc fi	94.62
KOG0717|consensus	508		92.61
PF13912	27	zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9	90.0
KOG3408|consensus	129		88.64
KOG3454|consensus	165		87.93
KOG3248|consensus	421		86.17
PF11304	107	DUF3106: Protein of unknown function (DUF3106); In	84.79
PF12756	100	zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB:	84.57
KOG2746|consensus	683		83.94
PF00096	23	zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR0070	83.78
PF06382	183	DUF1074: Protein of unknown function (DUF1074); In	82.0
KOG0528|consensus	511		81.35

>KOG4715|consensus

Probab=99.19  E-value=4.6e-11  Score=118.21  Aligned_cols=119  Identities=24%  Similarity=0.409  Sum_probs=93.0

Q ss_pred             hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHHHHH-HhhhhhhhccccccccccCCC
Q psy1990          46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLR-RKRVKKIQHHCLTAKVFSGTS  124 (382)
Q Consensus        46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~~~k-rk~~KK~k~~~~~~kv~s~ts  124 (382)
                      .+|.+..-||.|+||.+|..|.++||+.|.+..+.+|..|++-|++|..+++|.+|.- +-.++..        |  .+ 
T Consensus        86 ~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~ayinaKsra~a~--------l--e~-  154 (410)
T KOG4715|consen   86 SNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAA--------L--EE-  154 (410)
T ss_pred             cCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHHHHhhhhhhhhhh--------h--cc-
Confidence            3688999999999999999999999999999999999999999999999999999985 3333332        1  00 


Q ss_pred             CCCCCCCcccCCCccCCCCccccccccCCcccccccCCcchhhhhhhhhhhhhhhhhhhhh
Q psy1990         125 EGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHL  185 (382)
Q Consensus       125 ~~~~ng~~~~~gg~~~dg~~~~di~~d~~~~~d~~~~d~~~~~c~~c~q~fs~~hnk~eh~  185 (382)
                      .....++..-.|+        -.|  ++++|+|+||-|||.+-.|+++.+|-++|++---+
T Consensus       155 ~sr~~~sr~~~ge--------~~~--~IQPaeDeDD~ddg~stkhla~arf~rN~rLIsei  205 (410)
T KOG4715|consen  155 ESRQRQSRMEKGE--------PYM--SIQPAEDEDDYDDGFSTKHLATARFQRNHRLISEI  205 (410)
T ss_pred             ccccccchhhcCC--------cce--ecccccCccccccccchhhhhhhhhhhhhHHHHHH
Confidence            0011112211122        125  78999999999999999999999999999875443

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

Probab=99.10  E-value=1.1e-10  Score=109.59  Aligned_cols=90  Identities=30%  Similarity=0.493  Sum_probs=79.7

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcccc-------hhh------------hhhhhhHHHHhHHHHH
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD-------AYQ------------SYLILLFFQVTKLLGN   61 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~KD-------AY~------------lfPglSftEIsK~LGE   61 (382)
                      |+|++|++|++|+++||++|...|..++++|+.++..|.++.       +|.            ..|+.+..++++.+|.
T Consensus       101 ~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~  180 (211)
T COG5648         101 VGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISK  180 (211)
T ss_pred             HHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhh
Confidence            578999999999999999999999999999999999998752       232            2456678899999999


Q ss_pred             HhcCCCcchhhhhHHHHHHHHHHHHHHHH
Q psy1990          62 EWSKLSLPEKKVYLDRAEVDKKRYREELK   90 (382)
Q Consensus        62 rWK~LSdEEKqpYedkAekdKeRYekEMk   90 (382)
                      .|++|++.-|.+|++.+.+++..|...++
T Consensus       181 ~w~el~~skK~~~~~~~Kk~k~~~~~~~~  209 (211)
T COG5648         181 AWSELDESKKKKYIDKYKKLKEEYDSFYP  209 (211)
T ss_pred             hhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence            99999999999999999999999987654

>PTZ00199 high mobility group protein; Provisional

Probab=99.01  E-value=5.2e-10  Score=91.97  Aligned_cols=47  Identities=38%  Similarity=0.529  Sum_probs=44.2

Q ss_pred             hhhhh--HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILL--FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglS--ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|+++  +++|+++||++|+.||+++|++|.++|+.++++|..+|.+|.
T Consensus        45 ~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~   93 (94)
T PTZ00199         45 NPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA   93 (94)
T ss_pred             CcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46765  899999999999999999999999999999999999999995

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

Probab=98.97  E-value=4e-10  Score=88.22  Aligned_cols=48  Identities=25%  Similarity=0.324  Sum_probs=45.7

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   94 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk   94 (382)
                      +|++++.+|+++||++|+.||+++|++|.++|+.++++|.+++.+|+-
T Consensus        24 ~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky   71 (77)
T cd01389          24 NPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKY   71 (77)
T ss_pred             CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcc
Confidence            578999999999999999999999999999999999999999999963

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

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

Probab=98.97  E-value=4.3e-10  Score=87.22  Aligned_cols=47  Identities=28%  Similarity=0.400  Sum_probs=45.3

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|++++++|++.||++|+.||+++|++|.++|+.++++|.+++.+|+
T Consensus        24 ~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388          24 YPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            68999999999999999999999999999999999999999999885

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=98.95  E-value=1.2e-09  Score=82.09  Aligned_cols=48  Identities=33%  Similarity=0.520  Sum_probs=45.8

Q ss_pred             hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      .+|++++.+|++.||++|++||+++|++|.+.|..++.+|.++|.+|+
T Consensus        22 ~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen   22 ENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             HSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            368999999999999999999999999999999999999999999995

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=98.88  E-value=2.7e-09  Score=79.43  Aligned_cols=44  Identities=45%  Similarity=0.664  Sum_probs=41.6

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   90 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMk   90 (382)
                      +|++++.+|++.||++|++||+++|++|.++|+.++++|..+|.
T Consensus        23 ~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~   66 (66)
T cd01390          23 NPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK   66 (66)
T ss_pred             CcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            57889999999999999999999999999999999999999873

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.

>smart00398 HMG high mobility group

Probab=98.88  E-value=2.9e-09  Score=79.27  Aligned_cols=47  Identities=38%  Similarity=0.570  Sum_probs=44.8

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|++++++|++.||.+|+.||+++|++|.++|+.++++|.+++..|+
T Consensus        24 ~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398       24 NPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             CcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            57889999999999999999999999999999999999999999884

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

Probab=98.86  E-value=3.3e-09  Score=82.49  Aligned_cols=44  Identities=39%  Similarity=0.619  Sum_probs=40.5

Q ss_pred             hhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        50 lSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      .++.|+++.||.+|++||++||.+|.++|+.++++|+.+|..|.
T Consensus        30 ~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen   30 QSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            46889999999999999999999999999999999999999984

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=98.64  E-value=4.2e-08  Score=78.82  Aligned_cols=50  Identities=34%  Similarity=0.473  Sum_probs=46.8

Q ss_pred             hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHH-HHHhh
Q psy1990          46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK-VYRKS   95 (382)
Q Consensus        46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMk-eYkks   95 (382)
                      .+|++++.+|++.+|++|++|++++|++|...|..++++|..+|. .|+.+
T Consensus        44 ~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~   94 (96)
T KOG0381|consen   44 ENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKAS   94 (96)
T ss_pred             hCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            368899999999999999999999999999999999999999999 88764

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

Probab=98.59  E-value=7.4e-08  Score=70.94  Aligned_cols=43  Identities=42%  Similarity=0.623  Sum_probs=40.7

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   89 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEM   89 (382)
                      +|++++.+|++.||.+|+.|++++|++|.+.|+.++.+|.+++
T Consensus        23 ~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084          23 NPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             CcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            5788999999999999999999999999999999999999875

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

>KOG0527|consensus

Probab=98.54  E-value=2.5e-08  Score=99.24  Aligned_cols=52  Identities=29%  Similarity=0.418  Sum_probs=48.8

Q ss_pred             hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHHH
Q psy1990          46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY  101 (382)
Q Consensus        46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~~  101 (382)
                      .+|+|-+.||+|.||.+||.|+++||.||+++|++.|..+.+|..+|+    |+.-
T Consensus        84 qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK----YRPR  135 (331)
T KOG0527|consen   84 QNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK----YRPR  135 (331)
T ss_pred             hCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc----cccc
Confidence            378999999999999999999999999999999999999999999994    7773

>PTZ00199 high mobility group protein; Provisional

Probab=98.39  E-value=3.3e-07  Score=75.44  Aligned_cols=39  Identities=44%  Similarity=0.688  Sum_probs=37.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|+.||+++|.+|+++|..++.+|..+|..|.
T Consensus        55 vsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~   93 (94)
T PTZ00199         55 VGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA   93 (94)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999999999999985

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

Probab=98.37  E-value=3e-07  Score=86.77  Aligned_cols=54  Identities=33%  Similarity=0.512  Sum_probs=50.2

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS  100 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~  100 (382)
                      +|.++|.+|++.+|++|++|+++||++|...|..++++|..++..|..+..+..
T Consensus        93 ~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~  146 (211)
T COG5648          93 NPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKA  146 (211)
T ss_pred             CCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCC
Confidence            468899999999999999999999999999999999999999999998876554

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

Probab=98.31  E-value=5.2e-07  Score=70.18  Aligned_cols=39  Identities=41%  Similarity=0.682  Sum_probs=35.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |++.||..|++||++||.+|+++|+.++++|..+|..|.
T Consensus        35 ~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~   73 (73)
T PF09011_consen   35 VMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN   73 (73)
T ss_dssp             HHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            468899999999999999999999999999999999873

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 ....

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

Probab=98.19  E-value=1.1e-06  Score=68.86  Aligned_cols=39  Identities=28%  Similarity=0.502  Sum_probs=37.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|+.||+++|++|.++|+.++++|..++..|+
T Consensus        32 isk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yk   70 (77)
T cd01389          32 ISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYK   70 (77)
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCc
Confidence            689999999999999999999999999999999999885

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=98.18  E-value=1.4e-06  Score=65.52  Aligned_cols=39  Identities=38%  Similarity=0.726  Sum_probs=37.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|.+.|.+++.+|.++|..|+
T Consensus        31 i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~   69 (69)
T PF00505_consen   31 ISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK   69 (69)
T ss_dssp             HHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            578999999999999999999999999999999999884

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=98.17  E-value=1.7e-06  Score=64.41  Aligned_cols=36  Identities=56%  Similarity=0.914  Sum_probs=33.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHH
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK   36 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMe   36 (382)
                      |++.||++|+.||+++|++|.++|.+++++|.++|.
T Consensus        31 i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~   66 (66)
T cd01390          31 VTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK   66 (66)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence            578999999999999999999999999999999873

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=98.15  E-value=1.6e-06  Score=67.29  Aligned_cols=39  Identities=31%  Similarity=0.508  Sum_probs=36.8

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+|+||++|+.||+++|++|.++|..++++|.+++-.|+
T Consensus        32 isk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~   70 (72)
T cd01388          32 ISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK   70 (72)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            578999999999999999999999999999999998874

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.

>smart00398 HMG high mobility group

Probab=98.14  E-value=2.8e-06  Score=63.18  Aligned_cols=39  Identities=44%  Similarity=0.766  Sum_probs=36.8

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||.+|+.||+++|++|.++|..++++|.++|..|+
T Consensus        32 i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~   70 (70)
T smart00398       32 ISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK   70 (70)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            578999999999999999999999999999999999874

>KOG0526|consensus

Probab=98.07  E-value=2.5e-06  Score=89.56  Aligned_cols=44  Identities=36%  Similarity=0.646  Sum_probs=42.1

Q ss_pred             hhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990          49 ILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   94 (382)
Q Consensus        49 glSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk   94 (382)
                      |.+++||+|.+|++|+.||.  |.+|+++|+.+|.+|+.||++|+.
T Consensus       558 gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk~  601 (615)
T KOG0526|consen  558 GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYKN  601 (615)
T ss_pred             CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhcC
Confidence            67899999999999999999  999999999999999999999983

>KOG0381|consensus

Probab=97.80  E-value=2.3e-05  Score=63.04  Aligned_cols=40  Identities=38%  Similarity=0.651  Sum_probs=37.5

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHH-hhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK-VYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMe-eYk~   40 (382)
                      |+|++|++|++|++++|.+|+..+..++++|..+|. .|+.
T Consensus        53 v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~   93 (96)
T KOG0381|consen   53 VAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKA   93 (96)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            578999999999999999999999999999999999 8754

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

Probab=97.75  E-value=3.1e-05  Score=56.92  Aligned_cols=35  Identities=49%  Similarity=0.857  Sum_probs=32.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHH
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   35 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEM   35 (382)
                      |++.||++|+.||+++|++|.+.|+.++..|.+++
T Consensus        31 i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~   65 (66)
T cd00084          31 ISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM   65 (66)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence            57899999999999999999999999999998875

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

>smart00451 ZnF_U1 U1-like zinc finger

Probab=97.33  E-value=5.4e-05  Score=50.81  Aligned_cols=32  Identities=31%  Similarity=0.723  Sum_probs=29.4

Q ss_pred             hhhhhhhhhhhhhhhhhhhhhchhhhHHhhhh
Q psy1990         165 ELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQ  196 (382)
Q Consensus       165 ~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~  196 (382)
                      -.||.+|+.+|.+.+..+.|+.|++|..++..
T Consensus         3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~   34 (35)
T smart00451        3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK   34 (35)
T ss_pred             CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence            46899999999999999999999999998863

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

>KOG3248|consensus

Probab=97.31  E-value=0.00022  Score=72.16  Aligned_cols=57  Identities=25%  Similarity=0.388  Sum_probs=50.3

Q ss_pred             HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhhhh
Q psy1990          52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVK  108 (382)
Q Consensus        52 ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~~~krk~~K  108 (382)
                      ..+|.++||++|.+||-+|..+|.++|.++++-+.+....|-+..+|-...+|+++|
T Consensus       219 SAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYgKKkKrkReK  275 (421)
T KOG3248|consen  219 SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK  275 (421)
T ss_pred             HHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhhhhhhhhc
Confidence            457999999999999999999999999999999999999999988888555555554

>KOG0527|consensus

Probab=97.08  E-value=0.00027  Score=70.88  Aligned_cols=39  Identities=36%  Similarity=0.565  Sum_probs=36.4

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+|.||++||.|+++||.+|++.|++.|....++.=+||
T Consensus        93 ISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK  131 (331)
T KOG0527|consen   93 ISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK  131 (331)
T ss_pred             HHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc
Confidence            799999999999999999999999999999988887774

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

Probab=97.03  E-value=0.00065  Score=56.32  Aligned_cols=50  Identities=26%  Similarity=0.396  Sum_probs=43.1

Q ss_pred             hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      .|+.....+ .+.+...|++|++.+|-+|+.+|.++.++|+.+|.+|+..+
T Consensus        25 ~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~   74 (85)
T PF14887_consen   25 KFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAP   74 (85)
T ss_dssp             HTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CC
T ss_pred             HhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            567666665 56999999999999999999999999999999999997654

>KOG4715|consensus

Probab=96.65  E-value=0.0019  Score=65.07  Aligned_cols=49  Identities=37%  Similarity=0.687  Sum_probs=46.0

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLI   49 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~KDAY~lfPg   49 (382)
                      |.|+||.+|+.|+++||+.|...++.+|..|.+.|+.|..+-+|+.|.+
T Consensus        95 iGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~ayin  143 (410)
T KOG4715|consen   95 IGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYIN  143 (410)
T ss_pred             HHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHHHHhh
Confidence            6799999999999999999999999999999999999998888887765

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

Probab=96.59  E-value=0.00035  Score=44.00  Aligned_cols=25  Identities=32%  Similarity=0.939  Sum_probs=23.7

Q ss_pred             hhhhhhhhhhhhhhhhhhhhchhhh
Q psy1990         166 LYCRVCDQWFTTLHNKREHLNGRQH  190 (382)
Q Consensus       166 ~~c~~c~q~fs~~hnk~eh~~~~~h  190 (382)
                      .+|.+|+..|++.-..+.||.|+.|
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

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

Probab=96.37  E-value=0.0046  Score=51.41  Aligned_cols=38  Identities=34%  Similarity=0.640  Sum_probs=34.9

Q ss_pred             chHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           3 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         3 KiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      +.+...|++|++.+|-+|...|.+|.++|+.+|.+|+.
T Consensus        35 kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~   72 (85)
T PF14887_consen   35 KAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRS   72 (85)
T ss_dssp             HHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-
T ss_pred             HHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhc
Confidence            45788999999999999999999999999999999975

>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=96.33  E-value=0.00081  Score=43.71  Aligned_cols=26  Identities=27%  Similarity=0.912  Sum_probs=24.4

Q ss_pred             hhhhhhhhhhhhhhhhhhhhchhhhH
Q psy1990         166 LYCRVCDQWFTTLHNKREHLNGRQHF  191 (382)
Q Consensus       166 ~~c~~c~q~fs~~hnk~eh~~~~~h~  191 (382)
                      .||.+|+.+|++....+.||.|+.|.
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            48999999999999999999999994

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.

>KOG0528|consensus

Probab=95.61  E-value=0.0029  Score=66.34  Aligned_cols=50  Identities=24%  Similarity=0.361  Sum_probs=46.0

Q ss_pred             hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      .|||+-...|+|+||.+||.||..||+||.++-.+.-+.+.+....|+=+
T Consensus       347 A~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYk  396 (511)
T KOG0528|consen  347 AFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYK  396 (511)
T ss_pred             cCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccC
Confidence            38999999999999999999999999999999999988999988888755

>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=94.62  E-value=0.014  Score=41.75  Aligned_cols=32  Identities=22%  Similarity=0.616  Sum_probs=20.2

Q ss_pred             hhhhhhhhhh--hhhhhhhhhhchhhhHHhhhhc
Q psy1990         166 LYCRVCDQWF--TTLHNKREHLNGRQHFQAVEQS  197 (382)
Q Consensus       166 ~~c~~c~q~f--s~~hnk~eh~~~~~h~~~~~~~  197 (382)
                      -||-.|+.||  .+....+-|..|.+|..+++..
T Consensus         4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~   37 (38)
T PF06220_consen    4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY   37 (38)
T ss_dssp             -B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred             eecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence            3899999999  3445669999999999999764

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.

>KOG0717|consensus

Probab=92.61  E-value=0.034  Score=58.57  Aligned_cols=37  Identities=30%  Similarity=0.627  Sum_probs=32.2

Q ss_pred             CCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhc
Q psy1990         161 EDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQS  197 (382)
Q Consensus       161 ~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~  197 (382)
                      .+++.|||-+|+..|-|---+.-|-.+++|.-||+.-
T Consensus       288 ~~ge~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eL  324 (508)
T KOG0717|consen  288 NEGEVLYCVVCNKSFKSEKQLKNHENSKKHKENVAEL  324 (508)
T ss_pred             hcCCceEEeeccccccchHHHHhhHHHHHHHHHHHHH
Confidence            3344499999999999999999999999999998753

>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=90.00  E-value=0.057  Score=34.41  Aligned_cols=19  Identities=37%  Similarity=0.698  Sum_probs=18.2

Q ss_pred             hhhhhhhhhhhhhhhhhhh
Q psy1990         167 YCRVCDQWFTTLHNKREHL  185 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~  185 (382)
                      .|.+|++.|++..+.++|+
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            5999999999999999999

>KOG3408|consensus

Probab=88.64  E-value=0.3  Score=43.69  Aligned_cols=53  Identities=19%  Similarity=0.468  Sum_probs=44.5

Q ss_pred             ccccccCCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhccccccccccc
Q psy1990         155 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNS  207 (382)
Q Consensus       155 ~~d~~~~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~~l~~~~~~~  207 (382)
                      +||.|=|-.|--||-.|..||.+--++..|.-|+-|..-|-.--+.+-.+++.
T Consensus        47 ~~D~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~PySQeeA   99 (129)
T KOG3408|consen   47 EIDPDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELREVPYSQEEA   99 (129)
T ss_pred             cCCCCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcccCCccHHHH
Confidence            56888899999999999999999999999999999998887655555554443

>KOG3454|consensus

Probab=87.93  E-value=0.28  Score=45.55  Aligned_cols=33  Identities=33%  Similarity=0.724  Sum_probs=29.5

Q ss_pred             hhhhhhhhhhh--hhhhhhhhhchhhhHHhhhhcc
Q psy1990         166 LYCRVCDQWFT--TLHNKREHLNGRQHFQAVEQSG  198 (382)
Q Consensus       166 ~~c~~c~q~fs--~~hnk~eh~~~~~h~~~~~~~~  198 (382)
                      -||--|+-|-+  |+|+-+-|+.||+|++|+.-+.
T Consensus         4 YyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY   38 (165)
T KOG3454|consen    4 YYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYY   38 (165)
T ss_pred             chhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHH
Confidence            48999998875  7999999999999999998775

>KOG3248|consensus

Probab=86.17  E-value=0.48  Score=48.69  Aligned_cols=31  Identities=26%  Similarity=0.551  Sum_probs=28.6

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHH
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRY   31 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRY   31 (382)
                      |-++||.+|-.||-+|..+|.++|.++|+-.
T Consensus       222 iNqiLGrRWH~LSrEEQAKYyElArKerqlH  252 (421)
T KOG3248|consen  222 INQILGRRWHALSREEQAKYYELARKERQLH  252 (421)
T ss_pred             HHHHHhHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999998776

>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=84.79  E-value=4.2  Score=34.79  Aligned_cols=71  Identities=24%  Similarity=0.440  Sum_probs=44.9

Q ss_pred             chHHHHhcCCChHHHHHHHHHHH-------HHHHHHHHHHHhhccc---------chhhhhhhhhHHHHhHHHHHHh---
Q psy1990           3 KLLGNEWSKLSLPEKKVYLDRAE-------VDKKRYREELKVYRKS---------DAYQSYLILLFFQVTKLLGNEW---   63 (382)
Q Consensus         3 KiLGEkWK~LSdeEKqkYedkAk-------eDKeRYeeEMeeYk~K---------DAY~lfPglSftEIsK~LGErW---   63 (382)
                      .-+...|..|++..|.++...+.       +++.++..-|..|..=         ..|..|..++..+.. .|...|   
T Consensus        14 ~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~rm~~W~~LspeqR~~~R~~~~~~~~Lpp~qR~-~lr~~w~~y   92 (107)
T PF11304_consen   14 APLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRERMRRWAALSPEQRQQARENYQRFKQLPPEQRQ-ALRARWEAY   92 (107)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHcCCHHHHH-HHHHHHHHH
Confidence            45788999999999987766654       4666677777766431         134445555544433 456666   


Q ss_pred             cCCCcchhhhh
Q psy1990          64 SKLSLPEKKVY   74 (382)
Q Consensus        64 K~LSdEEKqpY   74 (382)
                      ..||+++|+..
T Consensus        93 q~l~~eeR~~l  103 (107)
T PF11304_consen   93 QQLPPEERQAL  103 (107)
T ss_pred             HcCCHHHHHHH
Confidence            67777776543

Currently no function is known.

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

Probab=84.57  E-value=0.18  Score=39.43  Aligned_cols=31  Identities=19%  Similarity=0.493  Sum_probs=26.3

Q ss_pred             hhhhhhhhhhhhhhhhhhhhhchhhhHHhhh
Q psy1990         165 ELYCRVCDQWFTTLHNKREHLNGRQHFQAVE  195 (382)
Q Consensus       165 ~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~  195 (382)
                      ...|.+|++.|.+...+++||.+..|.+...
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            5899999999999999999999999988754

>KOG2746|consensus

Probab=83.94  E-value=0.83  Score=50.13  Aligned_cols=43  Identities=26%  Similarity=0.162  Sum_probs=39.3

Q ss_pred             hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHH
Q psy1990          46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   88 (382)
Q Consensus        46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekE   88 (382)
                      .||+..+.-|+|+||+.|-.|.+.||++|.++|.+.|+.+-+.
T Consensus       205 ~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka  247 (683)
T KOG2746|consen  205 RHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA  247 (683)
T ss_pred             cCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence            3678888999999999999999999999999999999888775

>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=83.78  E-value=0.23  Score=30.44  Aligned_cols=20  Identities=25%  Similarity=0.735  Sum_probs=18.5

Q ss_pred             hhhhhhhhhhhhhhhhhhch
Q psy1990         168 CRVCDQWFTTLHNKREHLNG  187 (382)
Q Consensus       168 c~~c~q~fs~~hnk~eh~~~  187 (382)
                      |..|+..|++..+++.||.-
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            89999999999999999864

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 ....

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

Probab=82.00  E-value=1.1  Score=42.36  Aligned_cols=32  Identities=25%  Similarity=0.216  Sum_probs=29.4

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRA   78 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkA   78 (382)
                      |.+|+..|+....+..|..||+.||..|..++
T Consensus        97 h~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~  128 (183)
T PF06382_consen   97 HCGLSPQDLIQRAARAWCRLSEAEKNRYRRMA  128 (183)
T ss_pred             ccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhc
Confidence            46899999999999999999999999998864

The function of this family is unknown.

>KOG0528|consensus

Probab=81.35  E-value=0.42  Score=50.78  Aligned_cols=38  Identities=29%  Similarity=0.488  Sum_probs=29.6

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   38 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeY   38 (382)
                      |+|+||-+||.||-.||++|.+.-..--+...+..-.|
T Consensus       356 ISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdY  393 (511)
T KOG0528|consen  356 ISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDY  393 (511)
T ss_pred             hhHHhcccccccccccccchHHHHHHHHHhhhccCccc
Confidence            78999999999999999999877666555444444444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	382
2crj_A	92	Solution Structure Of The Hmg Domain Of Mouse Hmg D		6e-08

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 26/50 (52%), Positives = 38/50 (76%)
Query: 50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 99
          L F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL  Y++S+AY+
Sbjct: 33 LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYK 82

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	382
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	6e-14
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	5e-05
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	9e-14
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	7e-06
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	1e-12
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	4e-09
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	2e-12
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	2e-04
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	1e-11
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	3e-11
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	1e-11
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	2e-11
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	5e-11
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	2e-10
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	4e-10
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	8e-10
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	2e-09
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	9e-10
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	2e-09
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	9e-10
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	9e-10
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	1e-09
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	2e-09
2lhj_A	97	High mobility group protein homolog NHP1; structur	2e-09
2lhj_A	97	High mobility group protein homolog NHP1; structur	3e-09
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	5e-09
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	1e-08
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	9e-09
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	4e-08
1ckt_A	71	High mobility group 1 protein; high-mobility group	9e-09
1ckt_A	71	High mobility group 1 protein; high-mobility group	2e-08
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	1e-08
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	3e-08
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	2e-08
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	3e-08
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	9e-08
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	1e-06
1wgf_A	90	Upstream binding factor 1; transcription factor, D	3e-06
1wgf_A	90	Upstream binding factor 1; transcription factor, D	5e-06
3cw1_L	77	U1 small nuclear ribonucleoprotein C; PRE-mRNA spl	4e-04

>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX, amphoterin, DNA/structural protein complex; NMR {Homo sapiens} SCOP: a.21.1.1 a.21.1.1 Length = 159

 Score = 67.9 bits (166), Expect = 6e-14
 Identities = 25/124 (20%), Positives = 45/124 (36%), Gaps = 30/124 (24%)

Query: 1   VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILL--------- 51
           ++K LG +W  L+  EK  +   A+  +  +RE+   Y+                     
Sbjct: 35  ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPS 94

Query: 52  -FF--------------------QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
            FF                     V K LG  W+  +  +K+ Y  +A   K++Y +++ 
Sbjct: 95  AFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA 154

Query: 91  VYRK 94
            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 = 42.5 bits (100), Expect = 5e-05
 Identities = 11/48 (22%), Positives = 22/48 (45%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 99
            +++K LG +W  L+  EK  +   A+  +  +RE+   Y+      
Sbjct: 32 NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGET 79

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

 Score = 69.0 bits (168), Expect = 9e-14
 Identities = 26/158 (16%), Positives = 55/158 (34%), Gaps = 49/158 (31%)

Query: 1   VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLI----------- 49
           + + +   W +L   +KK+Y D    + + Y+EE+  +++       +            
Sbjct: 40  LIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLK 99

Query: 50  -----------------------LLFFQ-------------VTKLLGNEWSKLSLPEKKV 73
                                   ++                 K +   W  LS  EK++
Sbjct: 100 RKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKEL 159

Query: 74  YLDRAEVDKKRYREELKVYRKS--DAYQSYLRRKRVKK 109
           Y+  A+ D+ RY  E+K + +   +  +  L R+ +KK
Sbjct: 160 YIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKK 197

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

 Score = 45.5 bits (107), Expect = 7e-06
 Identities = 10/62 (16%), Positives = 28/62 (45%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQ 111
             ++ + +   W +L   +KK+Y D    + + Y+EE+  +++       +  ++    +
Sbjct: 37  TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDK 96

Query: 112 HH 113
           H 
Sbjct: 97  HL 98

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

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 12/62 (19%), Positives = 26/62 (41%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQ 111
              +TK+L  ++ +L   +K  Y+   + +K+ +   L  +R+         +K      
Sbjct: 38  NLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKKLEHHHH 97

Query: 112 HH 113
           HH
Sbjct: 98  HH 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 = 52.8 bits (127), Expect = 4e-09
 Identities = 9/47 (19%), Positives = 22/47 (46%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 47
          +TK+L  ++ +L   +K  Y+   + +K+ +   L  +R+       
Sbjct: 41 LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQ 87

>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 = 65.6 bits (159), Expect = 2e-12
 Identities = 26/158 (16%), Positives = 55/158 (34%), Gaps = 49/158 (31%)

Query: 1   VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLI----------- 49
           + + +   W +L   +KK+Y D    + + Y+EE+  +++       +            
Sbjct: 72  LIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLK 131

Query: 50  -----------------------LLFFQ-------------VTKLLGNEWSKLSLPEKKV 73
                                   ++                 K +   W  LS  EK++
Sbjct: 132 RKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKEL 191

Query: 74  YLDRAEVDKKRYREELKVYRKS--DAYQSYLRRKRVKK 109
           Y+  A+ D+ RY  E+K + +   +  +  L R+ +KK
Sbjct: 192 YIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTIKK 229

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

 Score = 41.7 bits (97), Expect = 2e-04
 Identities = 10/62 (16%), Positives = 28/62 (45%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQ 111
             ++ + +   W +L   +KK+Y D    + + Y+EE+  +++       +  ++    +
Sbjct: 69  TTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDK 128

Query: 112 HH 113
           H 
Sbjct: 129 HL 130

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

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 18/54 (33%), Positives = 29/54 (53%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 105
           F +V+K++ + W  L   +K+VY  + E  KK Y ++L  YR S   +SY    
Sbjct: 45  FGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSYTDSG 98

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

 Score = 58.6 bits (142), Expect = 3e-11
 Identities = 17/47 (36%), Positives = 27/47 (57%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 47
          V+K++ + W  L   +K+VY  + E  KK Y ++L  YR S   +SY
Sbjct: 48 VSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKSY 94

>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 = 61.9 bits (150), Expect = 1e-11
 Identities = 28/124 (22%), Positives = 43/124 (34%), Gaps = 30/124 (24%)

Query: 1   VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLI----------- 49
            +K     W  +S  EK  + D A+ DK RY  E+K Y                      
Sbjct: 48  FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPS 107

Query: 50  --LLFFQ-----------------VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90
              LF                   V K LG  W+  +  +K+ Y  +A   K++Y +++ 
Sbjct: 108 AFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIA 167

Query: 91  VYRK 94
            YR 
Sbjct: 168 AYRA 171

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

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 25/54 (46%), Positives = 37/54 (68%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 105
           F ++TK+LG EWSKL   EK+ YLD AE +K++Y +EL  Y++S+AY+      
Sbjct: 35  FPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCTESG 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 = 57.8 bits (140), Expect = 5e-11
 Identities = 24/47 (51%), Positives = 35/47 (74%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 47
          +TK+LG EWSKL   EK+ YLD AE +K++Y +EL  Y++S+AY+  
Sbjct: 38 ITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVC 84

>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 = 55.8 bits (135), Expect = 2e-10
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 97
          QV K LG +W  L+  EK+ Y  +A+ DKKRY  E ++Y  + A
Sbjct: 50 QVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 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 = 55.4 bits (134), Expect = 4e-10
 Identities = 18/43 (41%), Positives = 26/43 (60%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 43
          V K LG +W  L+  EK+ Y  +A+ DKKRY  E ++Y  + A
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 93

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

 Score = 53.8 bits (130), Expect = 8e-10
 Identities = 15/44 (34%), Positives = 21/44 (47%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 95
          F + +K     W  +S  EK  + D A+ DK RY  E+K Y   
Sbjct: 37 FSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP 80

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 14/41 (34%), Positives = 19/41 (46%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 41
           +K     W  +S  EK  + D A+ DK RY  E+K Y   
Sbjct: 40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP 80

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

 Score = 54.4 bits (131), Expect = 9e-10
 Identities = 13/49 (26%), Positives = 22/49 (44%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS 100
               T  +   W  LS  EK  Y ++A  D +RY  ++K   + ++  S
Sbjct: 35  LEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMS 83

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

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS 46
           T  +   W  LS  EK  Y ++A  D +RY  ++K   + ++  S
Sbjct: 38 ATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMS 83

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

 Score = 53.4 bits (129), Expect = 9e-10
 Identities = 13/39 (33%), Positives = 22/39 (56%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
          +  K +   W  LS  EK++Y+  A+ D+ RY  E+K +
Sbjct: 28 EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66

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

 Score = 53.4 bits (129), Expect = 9e-10
 Identities = 13/38 (34%), Positives = 21/38 (55%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
            K +   W  LS  EK++Y+  A+ D+ RY  E+K +
Sbjct: 29 KLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66

>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 = 53.4 bits (129), Expect = 1e-09
 Identities = 12/41 (29%), Positives = 22/41 (53%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 94
           V K LG  W+  +  +K+ Y  +A   K++Y +++  YR 
Sbjct: 36 DVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 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 = 52.6 bits (127), Expect = 2e-09
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 40
          V K LG  W+  +  +K+ Y  +A   K++Y +++  YR 
Sbjct: 37 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 76

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 14/44 (31%), Positives = 22/44 (50%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 95
             + K++G  W+ LS  EKK Y   ++ D+ RY  E   Y + 
Sbjct: 52 VAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR 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 = 52.8 bits (127), Expect = 3e-09
 Identities = 14/41 (34%), Positives = 22/41 (53%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 41
          + K++G  W+ LS  EKK Y   ++ D+ RY  E   Y + 
Sbjct: 55 IGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR 95

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

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 14/41 (34%), Positives = 21/41 (51%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
          F + +K     W  +S  EK  + + A+ DK RY  E+K Y
Sbjct: 45 FAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY 85

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 13/38 (34%), Positives = 19/38 (50%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
           +K     W  +S  EK  + + A+ DK RY  E+K Y
Sbjct: 48 FSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY 85

>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 = 51.8 bits (124), Expect = 9e-09
 Identities = 13/56 (23%), Positives = 27/56 (48%)

Query: 54  QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKK 109
           +    +G+ W ++S  +K+ Y   AE  +++Y+  L ++ KS + Q     K    
Sbjct: 36  ERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDRAAYKEYIS 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 = 49.9 bits (119), Expect = 4e-08
 Identities = 12/51 (23%), Positives = 25/51 (49%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILL 51
              +G+ W ++S  +K+ Y   AE  +++Y+  L ++ KS + Q      
Sbjct: 37 RMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDRAAYK 87

>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 = 50.8 bits (122), Expect = 9e-09
 Identities = 15/41 (36%), Positives = 21/41 (51%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
          F + +K     W  +S  EK  + D A+ DK RY  E+K Y
Sbjct: 31 FSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 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 = 49.7 bits (119), Expect = 2e-08
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
           +K     W  +S  EK  + D A+ DK RY  E+K Y
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71

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

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 2/44 (4%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 95
            ++ K  G  W +L   +K  + D A  DK+RY +E++ Y+  
Sbjct: 31 VTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYKPE 72

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

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 2/41 (4%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 41
          + K  G  W +L   +K  + D A  DK+RY +E++ Y+  
Sbjct: 34 IAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYKPE 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 = 50.0 bits (120), Expect = 2e-08
 Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 2/42 (4%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 95
          +V K  G  W  +   +K  +  +A   K  Y   +K +  +
Sbjct: 33 EVAKRGGELWRAMK--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 = 49.2 bits (118), Expect = 3e-08
 Identities = 9/41 (21%), Positives = 16/41 (39%), Gaps = 2/41 (4%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 41
          V K  G  W  +   +K  +  +A   K  Y   +K +  +
Sbjct: 34 VAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEAN 72

>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 = 48.8 bits (116), Expect = 9e-08
 Identities = 15/60 (25%), Positives = 25/60 (41%)

Query: 54  QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHH 113
           +   L   +W  LS  EK  Y  + +  KK Y  EL  + +S   +   R    +K+ + 
Sbjct: 43  ERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEEKMLNI 102

>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 = 45.7 bits (108), Expect = 1e-06
 Identities = 14/51 (27%), Positives = 21/51 (41%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILL 51
             L   +W  LS  EK  Y  + +  KK Y  EL  + +S   +    +L
Sbjct: 44 RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVL 94

>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 = 44.3 bits (105), Expect = 3e-06
 Identities = 10/40 (25%), Positives = 17/40 (42%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93
          ++T+LL   W+ LS  +K  Y  R    K +   +     
Sbjct: 50 ELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPSS 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 = 43.5 bits (103), Expect = 5e-06
 Identities = 10/39 (25%), Positives = 16/39 (41%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39
          +T+LL   W+ LS  +K  Y  R    K +   +     
Sbjct: 51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPSS 89

>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 Length = 77

 Score = 37.7 bits (87), Expect = 4e-04
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 167 YCRVCDQWFT--TLHNKREHLNGRQHFQAVEQSGHLAVNESNSCLSLDESSLDAAPSRTL 224
           YC  CD + T  +   ++ H +GR+H + V+      + E    L +D+++      +  
Sbjct: 5   YCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYCKWMEEQAQSL-IDKTTAAFQQGKIP 63

Query: 225 PNQLPPSPPPLTM 237
           P      PP   M
Sbjct: 64  PTPFSAPPPAGAM 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	382
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	99.8
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	99.79
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	99.75
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	99.75
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	99.32
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	99.21
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	99.19
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	99.16
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	99.15
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	99.15
1ckt_A	71	High mobility group 1 protein; high-mobility group	99.13
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	99.12
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	99.12
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	99.11
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	99.11
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	99.1
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	99.09
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	99.09
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	99.07
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	99.07
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	99.04
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	99.04
2lhj_A	97	High mobility group protein homolog NHP1; structur	99.03
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	99.03
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	99.02
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	99.02
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	99.02
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	98.98
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	98.98
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	98.97
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	98.96
1wgf_A	90	Upstream binding factor 1; transcription factor, D	98.82
3tq6_A	214	Transcription factor A, mitochondrial; transcripti	98.73
3tmm_A	238	Transcription factor A, mitochondrial; HMG, high m	98.72
2yrq_A	173	High mobility group protein B1; HMG box domain, DN	98.66
1l8y_A	91	Upstream binding factor 1; HUBF, HMG box 5, DNA bi	98.65
3fgh_A	67	Transcription factor A, mitochondrial; HMG domain,	98.65
1ckt_A	71	High mobility group 1 protein; high-mobility group	98.59
2cto_A	93	Novel protein; high mobility group box domain, hel	98.58
2eqz_A	86	High mobility group protein B3; HMG-box domain, mo	98.56
1aab_A	83	High mobility group protein; HMG-BOX, DNA-binding;	98.55
2crj_A	92	SWI/SNF-related matrix-associated actin- dependent	98.54
1v63_A	101	Nucleolar transcription factor 1; DNA binding, str	98.52
2cs1_A	92	PMS1 protein homolog 1; DNA mismatch repair protei	98.48
1hme_A	77	High mobility group protein fragment-B; DNA-bindin	98.45
2gzk_A	159	Sex-determining region on Y / HMGB1; protein-DNA c	98.42
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	98.38
1k99_A	99	Upstream binding factor 1; alpha-helix, L-shape, D	98.38
1gt0_D	80	Transcription factor SOX-2; POU factors, SOX prote	98.37
1hry_A	76	Human SRY; DNA, DNA-binding protein, DNA binding p	98.37
4a3n_A	71	Transcription factor SOX-17; 2.40A {Homo sapiens}	98.35
2co9_A	102	Thymus high mobility group box protein TOX; TOX pr	98.34
1v64_A	108	Nucleolar transcription factor 1; DNA binding, str	98.33
2lef_A	86	LEF-1 HMG, protein (lymphoid enhancer-binding fact	98.28
1j46_A	85	SRY, sex-determining region Y protein; MALE sex de	98.27
3f27_D	83	Transcription factor SOX-17; protein-DNA complex,	98.27
1wz6_A	82	HMG-box transcription factor BBX; bobby SOX homolo	98.26
1cg7_A	93	Protein (NON histone protein 6 A); HMG BOX, DNA be	98.25
3u2b_C	79	Transcription factor SOX-4; HMG domain, transcript	98.24
4euw_A	106	Transcription factor SOX-9; protein-DNA complex, H	98.22
3nm9_A	73	HMG-D, high mobility group protein D; DNA bending,	98.22
1wxl_A	73	Single-strand recognition protein; FACT, SSRP1, HM	98.19
2lhj_A	97	High mobility group protein homolog NHP1; structur	98.19
2e6o_A	87	HMG box-containing protein 1; HMG-box domain, HMG-	98.14
1i11_A	81	Transcription factor SOX-5; HMG BOX, DNA bending,	98.09
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	98.04
1wgf_A	90	Upstream binding factor 1; transcription factor, D	97.97
2cto_A	93	Novel protein; high mobility group box domain, hel	97.85
2d7l_A	81	WD repeat and HMG-box DNA binding protein 1; high	97.19
2yuk_A	90	Myeloid/lymphoid or mixed-lineage leukemia protein	96.68
1zu1_A	127	DSRBP-ZFA, RNA binding protein ZFA; zinc finger pr	96.36
1zr9_A	124	Zinc finger protein 593; DNA binding, structural g	95.73
1zu1_A	127	DSRBP-ZFA, RNA binding protein ZFA; zinc finger pr	94.22
3cw1_L	77	U1 small nuclear ribonucleoprotein C; PRE-mRNA spl	93.16
4dgw_A	402	PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A	88.49
2lvu_A	26	Zinc finger and BTB domain-containing protein 17;	86.53
2lvt_A	29	Zinc finger and BTB domain-containing protein 17;	83.98
1ard_A	29	Yeast transcription factor ADR1; transcription reg	83.06
2kfq_A	32	FP1; protein, de novo protein; NMR {Synthetic}	82.45
2kvf_A	28	Zinc finger and BTB domain-containing protein 32;	82.2
2kvg_A	27	Zinc finger and BTB domain-containing protein 32;	81.94
2yrk_A	55	Zinc finger homeobox protein 4; structure genomics	81.63
2lvr_A	30	Zinc finger and BTB domain-containing protein 17;	82.12
2m0f_A	29	Zinc finger and BTB domain-containing protein 17;	80.74
1znf_A	27	31ST zinc finger from XFIN; zinc finger DNA bindin	80.28

>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=6.1e-20  Score=160.74  Aligned_cols=95  Identities=29%  Similarity=0.474  Sum_probs=87.8

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhccc------------------chhhh------------hhhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS------------------DAYQS------------YLIL   50 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~K------------------DAY~l------------fPgl   50 (382)
                      |+++||++|++||++||++|+++|..++++|..+|..|.+.                  +||++            +|++
T Consensus        48 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~~~~kk~~kdp~~pKrP~saf~lf~~~~r~~~~~~~p~~  127 (173)
T 2yrq_A           48 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL  127 (173)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCCCCCCSSCSCCCSSSCCCCCCHHHHHHHHHHHHHHHHCSSS
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccccCCccccCcccHHHHHHHHHHHHHHHHCCCC
Confidence            57999999999999999999999999999999999999531                  37754            4789


Q ss_pred             hHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          51 LFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        51 SftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      ++.+|++.||++|++||+++|++|.++|+.++++|.++|.+|+.+
T Consensus       128 ~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~k  172 (173)
T 2yrq_A          128 SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK  172 (173)
T ss_dssp             CHHHHHHHHHHHHHHSCGGGHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999864

>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=99.79  E-value=6.7e-20  Score=157.98  Aligned_cols=94  Identities=27%  Similarity=0.425  Sum_probs=86.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc------------------cchhhh------------hhhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK------------------SDAYQS------------YLIL   50 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~------------------KDAY~l------------fPgl   50 (382)
                      |+++||++|++||+++|++|+++|..++++|..+|..|..                  .+||++            +|++
T Consensus        35 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~k~~~kk~~kdp~~pKrp~say~lf~~~~r~~~~~~~p~~  114 (159)
T 2gzk_A           35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL  114 (159)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCCCCCCGGGSCCTTCCCCCCCHHHHHHHHHHHHHHHHCSCC
T ss_pred             HHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccccccccccccccccccccccccchhhHhhHHHHHHhCCCC
Confidence            6899999999999999999999999999999999999952                  137754            5789


Q ss_pred             hHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990          51 LFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   94 (382)
Q Consensus        51 SftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk   94 (382)
                      ++++|++.||++|++||+++|++|+++|+.++++|.++|.+|++
T Consensus       115 ~~~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~  158 (159)
T 2gzk_A          115 SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA  158 (159)
T ss_dssp             CHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999999999999999999999999975

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

Probab=99.75  E-value=2.3e-18  Score=159.43  Aligned_cols=96  Identities=26%  Similarity=0.509  Sum_probs=86.6

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc---------------------------------------c
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK---------------------------------------S   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~---------------------------------------K   41 (382)
                      |+|+||++|++||++||.+|+++|+.++++|+++|..|..                                       .
T Consensus        72 isk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~~p~~~~~~~~~~~~k~~krk~~~kkk~~kdp~~PKrP~  151 (238)
T 3tmm_A           72 LIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPR  151 (238)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhcccchhhhcccCCCCCCC
Confidence            5799999999999999999999999999999999999930                                       1


Q ss_pred             chhhhhh--------hhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          42 DAYQSYL--------ILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        42 DAY~lfP--------glSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +||++|.        +....+|++.||++|++|++++|++|+++|+.++++|+++|++|+.+.
T Consensus       152 say~lF~~e~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~k~  214 (238)
T 3tmm_A          152 SAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  214 (238)
T ss_dssp             CHHHHHHHHHTTTSCCSSHHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            3887764        456779999999999999999999999999999999999999998754

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

Probab=99.75  E-value=2.5e-18  Score=156.95  Aligned_cols=96  Identities=26%  Similarity=0.509  Sum_probs=86.8

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc---------------------------------------c
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK---------------------------------------S   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~---------------------------------------K   41 (382)
                      |+|+||++|++||++||.+|+++|..++++|.++|..|..                                       .
T Consensus        40 isk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~tp~q~~~~~~~~~~~~~krk~~kkkk~~kdp~~PKrP~  119 (214)
T 3tq6_A           40 LIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPR  119 (214)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCC
T ss_pred             HHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHHHHHhhhcchhhhhhhccccCccccc
Confidence            5899999999999999999999999999999999999931                                       1


Q ss_pred             chhhhhh--------hhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          42 DAYQSYL--------ILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        42 DAY~lfP--------glSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +||++|.        +..+.+|++.||++|++||+++|++|+++|+.++++|+++|++|+++.
T Consensus       120 say~lF~~e~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~y~~~~  182 (214)
T 3tq6_A          120 SAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQM  182 (214)
T ss_dssp             CHHHHHHHHHTTTSSCSSHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhhhhHHHHHHhhccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            3887763        456789999999999999999999999999999999999999998764

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

Probab=99.32  E-value=7.1e-13  Score=105.95  Aligned_cols=57  Identities=46%  Similarity=0.690  Sum_probs=53.6

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLR  103 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~~~k  103 (382)
                      +|++++++|+++||++|++||+++|++|.++|+.++++|.++|.+|+.+.+|+.+.+
T Consensus        30 ~p~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~~~~   86 (92)
T 2crj_A           30 HPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVCTE   86 (92)
T ss_dssp             CTTCCHHHHHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHCSSC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHh
Confidence            578999999999999999999999999999999999999999999999999987643

>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=99.21  E-value=3e-11  Score=98.98  Aligned_cols=50  Identities=24%  Similarity=0.401  Sum_probs=46.8

Q ss_pred             hhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhh
Q psy1990          49 ILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY   98 (382)
Q Consensus        49 glSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aY   98 (382)
                      +++++||+|.||++|+.|+++||++|+++|++++++|+++|++|..+...
T Consensus        31 ~~~~~eisK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~~~   80 (101)
T 1v63_A           31 HLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSP   80 (101)
T ss_dssp             TSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCT
T ss_pred             CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCH
Confidence            47899999999999999999999999999999999999999999987543

>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=99.19  E-value=1.4e-11  Score=101.02  Aligned_cols=50  Identities=26%  Similarity=0.420  Sum_probs=46.3

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA   97 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~a   97 (382)
                      +|+ +++||+|.||++|++||++||++|+++|+.+|++|+++|++|+.+.+
T Consensus        27 ~p~-~~~evsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~~~   76 (91)
T 1l8y_A           27 FKN-DRVKALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPA   76 (91)
T ss_dssp             TTS-THHHHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCGGG
T ss_pred             cCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcccc
Confidence            467 89999999999999999999999999999999999999999987544

>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=99.16  E-value=1.5e-11  Score=94.38  Aligned_cols=48  Identities=27%  Similarity=0.434  Sum_probs=46.0

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   94 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk   94 (382)
                      +|++++++|++.||++|++||+++|++|.++|+.++++|.++|.+|+.
T Consensus        29 ~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A           29 HPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             CTTCCHHHHHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            578999999999999999999999999999999999999999999975

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

Probab=99.15  E-value=3.5e-11  Score=98.05  Aligned_cols=53  Identities=30%  Similarity=0.460  Sum_probs=48.9

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ   99 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk   99 (382)
                      +|++++.+|+++||++|++|++++|++|.++|+.++++|.++|.+|+.+..++
T Consensus        40 ~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~   92 (102)
T 2co9_A           40 NPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSK   92 (102)
T ss_dssp             CTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS
T ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            57899999999999999999999999999999999999999999998765443

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

Probab=99.15  E-value=1.9e-11  Score=97.62  Aligned_cols=49  Identities=24%  Similarity=0.270  Sum_probs=46.7

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++.||+++||++|++|++++|++|.++|+.++++|.++|++|+..
T Consensus        30 ~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~   78 (92)
T 2cs1_A           30 NPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQ   78 (92)
T ss_dssp             CCSSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTST
T ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999999999999999764

>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=99.13  E-value=2.3e-11  Score=91.83  Aligned_cols=46  Identities=33%  Similarity=0.479  Sum_probs=42.9

Q ss_pred             hhhhh--HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILL--FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   92 (382)
Q Consensus        47 fPglS--ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeY   92 (382)
                      +|+++  ++||++.||++|++||+++|++|.++|+.++++|.++|++|
T Consensus        24 ~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A           24 HPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CTTCCCCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCcHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            57775  59999999999999999999999999999999999999876

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

Probab=99.12  E-value=5.7e-12  Score=99.17  Aligned_cols=53  Identities=19%  Similarity=0.306  Sum_probs=49.7

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ   99 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk   99 (382)
                      +|++++++|+++||++|++||+++|++|.++|+.++++|.++|.+|+..+.|.
T Consensus        25 ~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~p~~~   77 (86)
T 2lef_A           25 STLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG   77 (86)
T ss_dssp             SSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSSTT
T ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHcccccCCCCCC
Confidence            57899999999999999999999999999999999999999999998777654

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

Probab=99.12  E-value=5.2e-11  Score=91.12  Aligned_cols=47  Identities=19%  Similarity=0.256  Sum_probs=44.7

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|+++++||++.||++|++|++  |++|.++|++++++|+++|++|+++
T Consensus        26 ~p~~~~~eisk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~k   72 (73)
T 3nm9_A           26 NPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             SSSCCHHHHHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999998  9999999999999999999999864

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

Probab=99.11  E-value=3.6e-11  Score=97.87  Aligned_cols=49  Identities=18%  Similarity=0.369  Sum_probs=46.9

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|+++++||+++||++|++||+++|++|.++|+.++++|.++|++|...
T Consensus        33 ~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~   81 (99)
T 1k99_A           33 HPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (99)
T ss_dssp             CTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999875

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

Probab=99.11  E-value=7.1e-11  Score=93.08  Aligned_cols=47  Identities=30%  Similarity=0.427  Sum_probs=44.1

Q ss_pred             hhhhh--HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILL--FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglS--ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|+++  +.||++.||++|++||+++|++|.++|+.++++|.++|++|+
T Consensus        38 ~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A           38 NPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             CTTSCCCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            46775  799999999999999999999999999999999999999994

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

Probab=99.10  E-value=2.3e-11  Score=91.49  Aligned_cols=47  Identities=26%  Similarity=0.441  Sum_probs=42.7

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|++++++|++.||++|++||+++|++|.++|+.++++|.+++.+|+
T Consensus        25 ~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A           25 NPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            57999999999999999999999999999999999999999998884

>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=99.09  E-value=3.9e-11  Score=92.92  Aligned_cols=49  Identities=27%  Similarity=0.329  Sum_probs=46.4

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++++|+++||++|++||+++|++|.++|+.++++|.++|.+|+-.
T Consensus        25 ~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~   73 (80)
T 1gt0_D           25 NPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR   73 (80)
T ss_dssp             STTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccccC
Confidence            5789999999999999999999999999999999999999999999643

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

Probab=99.09  E-value=1e-10  Score=87.99  Aligned_cols=51  Identities=31%  Similarity=0.524  Sum_probs=45.9

Q ss_pred             chhhhhh--------hhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHH
Q psy1990          42 DAYQSYL--------ILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   92 (382)
Q Consensus        42 DAY~lfP--------glSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeY   92 (382)
                      +||++|.        +..+++|++.||++|++||+++|++|.++|+.++++|+++|++|
T Consensus         8 say~~F~~~~r~~~k~~~p~ei~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A            8 SAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             CHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5777653        34568999999999999999999999999999999999999998

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

Probab=99.07  E-value=2.2e-10  Score=94.91  Aligned_cols=55  Identities=27%  Similarity=0.377  Sum_probs=50.6

Q ss_pred             chhhhhh--------hhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          42 DAYQSYL--------ILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        42 DAY~lfP--------glSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +||++|.        +++++||++.||++|++|+++||++|.++|+.++++|.++|.+|..+.
T Consensus        23 say~lF~~e~r~~~k~~~~~eisk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~~~   85 (108)
T 1v64_A           23 NSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESL   85 (108)
T ss_dssp             SHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            5887664        688999999999999999999999999999999999999999998764

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

Probab=99.07  E-value=3.7e-11  Score=96.32  Aligned_cols=50  Identities=38%  Similarity=0.555  Sum_probs=47.5

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +|++++.||++.||++|++||+++|++|.++|+.++++|.++|.+|+.+.
T Consensus        43 ~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~~~~   92 (93)
T 1cg7_A           43 NPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATL   92 (93)
T ss_dssp             CTTSCHHHHTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            57899999999999999999999999999999999999999999998753

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

Probab=99.04  E-value=9.2e-11  Score=89.71  Aligned_cols=47  Identities=28%  Similarity=0.494  Sum_probs=44.6

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|+++++||++.||++|++|  ++|++|.++|+.++++|.++|.+|+++
T Consensus        26 ~p~~~~~eisk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~~   72 (73)
T 1wxl_A           26 NPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKPE   72 (73)
T ss_dssp             STTCCHHHHHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTTC
T ss_pred             CCCCCHHHHHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            58999999999999999999  899999999999999999999999764

>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor, SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1j47_A

Probab=99.04  E-value=8.3e-11  Score=92.51  Aligned_cols=49  Identities=22%  Similarity=0.299  Sum_probs=46.3

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++++|+++||++|++||+++|++|.++|+.++++|..++.+|+-.
T Consensus        27 ~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk~~   75 (85)
T 1j46_A           27 NPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (85)
T ss_dssp             STTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccccC
Confidence            5789999999999999999999999999999999999999999999643

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

Probab=99.03  E-value=8.5e-11  Score=94.68  Aligned_cols=49  Identities=29%  Similarity=0.451  Sum_probs=46.6

Q ss_pred             hhhhh--HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILL--FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglS--ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|+++  +++|++.||++|++||+++|++|.++|+.++++|.++|.+|+.+
T Consensus        45 ~p~~~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~~   95 (97)
T 2lhj_A           45 NPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR   95 (97)
T ss_dssp             CTTSTTCSSHHHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            47888  99999999999999999999999999999999999999999865

>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1 PDB: 1hrz_A*

Probab=99.03  E-value=4.3e-11  Score=91.63  Aligned_cols=47  Identities=23%  Similarity=0.328  Sum_probs=45.0

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|++++++|+++||++|++||+++|++|.++|+.++++|.+++.+|+
T Consensus        27 ~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   73 (76)
T 1hry_A           27 NPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (76)
T ss_dssp             CSCCSSSHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             CcCCCHHHHHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            57889999999999999999999999999999999999999999886

>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus musculus} SCOP: a.21.1.1

Probab=99.02  E-value=7.3e-11  Score=90.80  Aligned_cols=48  Identities=19%  Similarity=0.262  Sum_probs=45.8

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   94 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk   94 (382)
                      +|++++++|+++||++|++||+++|++|.++|+.++++|.+++.+|+-
T Consensus        25 ~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yky   72 (79)
T 3u2b_C           25 SPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKY   72 (79)
T ss_dssp             STTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCCC
T ss_pred             CcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCee
Confidence            578999999999999999999999999999999999999999999964

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

Probab=99.02  E-value=7.7e-11  Score=91.62  Aligned_cols=49  Identities=24%  Similarity=0.407  Sum_probs=46.2

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++++|+++||++|++|++++|++|.++|+.++++|.++|.+|+-+
T Consensus        29 ~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yky~   77 (83)
T 3f27_D           29 NPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYR   77 (83)
T ss_dssp             CSSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCeeC
Confidence            4789999999999999999999999999999999999999999999643

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

Probab=99.02  E-value=4.7e-11  Score=93.22  Aligned_cols=49  Identities=31%  Similarity=0.432  Sum_probs=45.4

Q ss_pred             hhhhh--HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILL--FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglS--ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|+++  ++||++.||++|++||+++|++|.++|+.++++|.++|.+|+.+
T Consensus        30 ~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~   80 (83)
T 1aab_A           30 HPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP   80 (83)
T ss_dssp             CTTTCCCSSSSHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             CCCCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            46775  59999999999999999999999999999999999999999765

>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=98.98  E-value=4.1e-11  Score=93.37  Aligned_cols=49  Identities=29%  Similarity=0.279  Sum_probs=46.1

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++.+|+++||++|++||+++|++|.++|+.++++|.++|.+|+..
T Consensus        30 ~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk~~   78 (82)
T 1wz6_A           30 HPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSG   78 (82)
T ss_dssp             CSSSCTTHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCCCC
T ss_pred             CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhhcC
Confidence            5788999999999999999999999999999999999999999999754

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

Probab=98.98  E-value=2e-10  Score=94.50  Aligned_cols=48  Identities=25%  Similarity=0.400  Sum_probs=45.7

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   94 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk   94 (382)
                      +|++++.+|+++||++|+.|++++|++|.++|+.++++|.++|.+|+-
T Consensus        52 ~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yky   99 (106)
T 4euw_A           52 YPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKY   99 (106)
T ss_dssp             CTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcCc
Confidence            478999999999999999999999999999999999999999999963

>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=98.97  E-value=1.6e-10  Score=89.81  Aligned_cols=47  Identities=21%  Similarity=0.381  Sum_probs=44.4

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|++++++|+++||++|++||+++|++|.++|+.++++|.+++.+|+
T Consensus        27 ~p~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yk   73 (81)
T 1i11_A           27 FPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYK   73 (81)
T ss_dssp             CSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC-
T ss_pred             CCCCCHHHHHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            57899999999999999999999999999999999999999999885

>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=98.96  E-value=1.5e-10  Score=91.52  Aligned_cols=47  Identities=17%  Similarity=0.205  Sum_probs=44.5

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   93 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk   93 (382)
                      +|++++.+|+++||++|++|++++|++|.++|+.++++|.+++.+|+
T Consensus        40 ~P~~~~~eisk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           40 YPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            57899999999999999999999999999999999999999988774

>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=98.82  E-value=2e-10  Score=91.57  Aligned_cols=45  Identities=24%  Similarity=0.225  Sum_probs=42.2

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV   91 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMke   91 (382)
                      +|++++.||+++||++|++|++++|++|.++|+.++++|.++|..
T Consensus        43 ~P~~~~~eisk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~   87 (90)
T 1wgf_A           43 RPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGP   87 (90)
T ss_dssp             CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSS
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999988754

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

Probab=98.73  E-value=7.9e-09  Score=94.32  Aligned_cols=50  Identities=18%  Similarity=0.337  Sum_probs=47.4

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +|+++++||++.||++|+.||++||++|+++|..++++|.++|..|..+.
T Consensus        32 ~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~   81 (214)
T 3tq6_A           32 NPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQL   81 (214)
T ss_dssp             CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHccCHHhhhHHHHHHHHHHHHHHHHhhhhcccC
Confidence            48999999999999999999999999999999999999999999998653

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

Probab=98.72  E-value=8.5e-09  Score=95.44  Aligned_cols=50  Identities=18%  Similarity=0.337  Sum_probs=47.4

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +|+++++||++.||++|+.||++||++|+++|+.++++|+++|+.|..+.
T Consensus        64 ~P~~~~~eisk~lge~Wk~Ls~~EK~~y~~~A~~~k~~y~~e~~~y~~~~  113 (238)
T 3tmm_A           64 NPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQL  113 (238)
T ss_dssp             STTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            57899999999999999999999999999999999999999999998653

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

Probab=98.66  E-value=1.1e-08  Score=89.48  Aligned_cols=50  Identities=30%  Similarity=0.441  Sum_probs=46.5

Q ss_pred             hhh--hhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          47 YLI--LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        47 fPg--lSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +|+  +++.||++.||++|+.||++||++|.++|+.++++|.++|.+|....
T Consensus        38 ~p~~~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~~   89 (173)
T 2yrq_A           38 HPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK   89 (173)
T ss_dssp             CTTCCCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTHHHHHHCCCCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence            477  58999999999999999999999999999999999999999997653

>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=98.65  E-value=1.3e-08  Score=83.47  Aligned_cols=41  Identities=29%  Similarity=0.542  Sum_probs=39.2

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~K   41 (382)
                      |+|+||++|++||++||++|+++|.++|++|+++|..|+++
T Consensus        34 vsK~lGe~Wk~ls~~eK~pye~kA~~dK~rYekEm~~Y~~~   74 (91)
T 1l8y_A           34 ALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRAP   74 (91)
T ss_dssp             HHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSCG
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence            58999999999999999999999999999999999999865

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

Probab=98.65  E-value=1.8e-08  Score=75.65  Aligned_cols=38  Identities=34%  Similarity=0.662  Sum_probs=36.8

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   38 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeY   38 (382)
                      |+|+||++|++||+++|++|+++|.+++++|+++|..|
T Consensus        29 i~k~lg~~Wk~ls~~eK~~y~~~A~~~k~~Y~~e~~~y   66 (67)
T 3fgh_A           29 KLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW   66 (67)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            57999999999999999999999999999999999988

>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=98.59  E-value=1.8e-08  Score=75.99  Aligned_cols=38  Identities=37%  Similarity=0.629  Sum_probs=36.5

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   38 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeY   38 (382)
                      |+|+||++|++||+++|++|+++|+.++++|.++|..|
T Consensus        34 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y   71 (71)
T 1ckt_A           34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             HHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            58999999999999999999999999999999999876

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

Probab=98.58  E-value=8e-09  Score=84.51  Aligned_cols=48  Identities=21%  Similarity=0.316  Sum_probs=43.3

Q ss_pred             chhhhhh----------hhhHHHHhHHH---HHHhcCCCcchhhhhHHHHHHHHHHHHHHH
Q psy1990          42 DAYQSYL----------ILLFFQVTKLL---GNEWSKLSLPEKKVYLDRAEVDKKRYREEL   89 (382)
Q Consensus        42 DAY~lfP----------glSftEIsK~L---GErWK~LSdEEKqpYedkAekdKeRYekEM   89 (382)
                      +||++|.          +++++||++.|   |++|+.|+++||++|+++|+++|++|++++
T Consensus        16 sAf~lF~~e~R~~ik~e~~~~~eisK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~   76 (93)
T 2cto_A           16 NAYYFFVQEKIPELRRRGLPVARVADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDP   76 (93)
T ss_dssp             CHHHHHHHTTHHHHHHHTCCCSSHHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCS
T ss_pred             CHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccc
Confidence            5787653          57889999999   999999999999999999999999999885

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

Probab=98.56  E-value=4.2e-08  Score=77.21  Aligned_cols=39  Identities=33%  Similarity=0.519  Sum_probs=37.4

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|+++|+.++++|.++|..|+
T Consensus        48 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~Y~   86 (86)
T 2eqz_A           48 FSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDYG   86 (86)
T ss_dssp             HHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            579999999999999999999999999999999999984

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

Probab=98.55  E-value=4.1e-08  Score=76.46  Aligned_cols=41  Identities=34%  Similarity=0.562  Sum_probs=38.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~K   41 (382)
                      |+|+||++|++||+++|++|+++|..++++|.++|..|..+
T Consensus        40 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~~   80 (83)
T 1aab_A           40 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPP   80 (83)
T ss_dssp             SHHHHHHHHTTSCTTHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            68999999999999999999999999999999999999753

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

Probab=98.54  E-value=4.1e-08  Score=78.26  Aligned_cols=47  Identities=51%  Similarity=0.855  Sum_probs=42.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY   47 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~KDAY~lf   47 (382)
                      |+|+||++|++||+++|++|+++|..++++|.++|..|+.+.+|..|
T Consensus        38 isk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~~~~~~~~   84 (92)
T 2crj_A           38 ITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYKVC   84 (92)
T ss_dssp             HHHHHHHHHHTCCTTHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHCS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHH
Confidence            68999999999999999999999999999999999999887666543

>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=98.52  E-value=5.9e-08  Score=79.36  Aligned_cols=40  Identities=25%  Similarity=0.533  Sum_probs=38.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+|+||++|++|+++||++|+++|+++|++|.++|..|..
T Consensus        37 isK~lge~Wk~ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~   76 (101)
T 1v63_A           37 RMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVK   76 (101)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5899999999999999999999999999999999999964

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

Probab=98.48  E-value=6.3e-08  Score=77.19  Aligned_cols=41  Identities=29%  Similarity=0.404  Sum_probs=38.8

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~K   41 (382)
                      |+|+||++|++||+++|++|+++|++++++|.++|..|+..
T Consensus        38 isk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~y~~~   78 (92)
T 2cs1_A           38 ATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQ   78 (92)
T ss_dssp             HHHHHHHHHHSSCHHHHHHHHHHHHTTTHHHHHHHHHHTST
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999999999753

>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=98.45  E-value=7.3e-08  Score=73.78  Aligned_cols=40  Identities=30%  Similarity=0.606  Sum_probs=38.2

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||+++|++|.++|..++++|.++|..|+.
T Consensus        37 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~e~~~y~~   76 (77)
T 1hme_A           37 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   76 (77)
T ss_dssp             HHHHHHHHHHHSCGGGSHHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5899999999999999999999999999999999999964

>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=98.42  E-value=4.9e-08  Score=83.89  Aligned_cols=49  Identities=22%  Similarity=0.299  Sum_probs=46.5

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|+++++||++.||++|+.||+++|++|.++|..++++|..+|..|...
T Consensus        27 ~P~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~y~~~   75 (159)
T 2gzk_A           27 NPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR   75 (159)
T ss_dssp             CSSCCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCSSCSCC
T ss_pred             CCCCCHHHHHHHHHHHHHHhhHHHhccHHHHHHHHHHHHHHHhhccccc
Confidence            6899999999999999999999999999999999999999999998654

>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=98.38  E-value=8.5e-08  Score=76.06  Aligned_cols=35  Identities=20%  Similarity=0.093  Sum_probs=33.3

Q ss_pred             hhhhh-HHHHhHHHHHHhcCCCcchhhhhHHHHHHH
Q psy1990          47 YLILL-FFQVTKLLGNEWSKLSLPEKKVYLDRAEVD   81 (382)
Q Consensus        47 fPglS-ftEIsK~LGErWK~LSdEEKqpYedkAekd   81 (382)
                      +|+++ ++||+|.||++|++||++||++|+++|+.+
T Consensus        28 ~P~~~~~~eisK~lge~Wk~ls~eeK~~y~~~A~~d   63 (81)
T 2d7l_A           28 NPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGE   63 (81)
T ss_dssp             CTTCCSHHHHHHHHHHHHSSSCHHHHHHHHHHTTSS
T ss_pred             CCCCchhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            58998 999999999999999999999999999887

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

Probab=98.38  E-value=1.4e-07  Score=76.56  Aligned_cols=41  Identities=22%  Similarity=0.494  Sum_probs=38.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~K   41 (382)
                      |+++||++|++||+++|++|+++|..++++|.++|..|...
T Consensus        41 isk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~Y~~e~~~y~~~   81 (99)
T 1k99_A           41 LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (99)
T ss_dssp             HHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999754

>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=98.37  E-value=1.5e-07  Score=72.65  Aligned_cols=39  Identities=33%  Similarity=0.510  Sum_probs=37.5

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|+++|..++++|..+|..|+
T Consensus        33 isk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (80)
T 1gt0_D           33 ISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK   71 (80)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            689999999999999999999999999999999999985

>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=98.37  E-value=1.4e-07  Score=72.03  Aligned_cols=39  Identities=28%  Similarity=0.477  Sum_probs=37.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+|+||++|++||+++|++|.++|+.++++|.++|..|+
T Consensus        35 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   73 (76)
T 1hry_A           35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (76)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             HHHHHHhHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCC
Confidence            689999999999999999999999999999999999885

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

Probab=98.35  E-value=8.7e-08  Score=71.84  Aligned_cols=39  Identities=28%  Similarity=0.608  Sum_probs=34.8

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|+++|..++++|.++|..|+
T Consensus        33 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~YK   71 (71)
T 4a3n_A           33 LSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   71 (71)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHTTCC---
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCcCcC
Confidence            589999999999999999999999999999999998874

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

Probab=98.34  E-value=3e-07  Score=74.79  Aligned_cols=40  Identities=35%  Similarity=0.672  Sum_probs=38.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||+++|++|+++|..++++|.++|..|+.
T Consensus        48 isk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Y~~   87 (102)
T 2co9_A           48 VSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRA   87 (102)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999999999964

>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=98.33  E-value=2.5e-07  Score=76.60  Aligned_cols=40  Identities=30%  Similarity=0.467  Sum_probs=38.2

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+|+||++|++||++||++|+++|+.++++|.++|..|..
T Consensus        44 isk~lg~~Wk~Ls~~eK~~Y~~~A~~~k~~Y~~e~~~Y~~   83 (108)
T 1v64_A           44 RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5899999999999999999999999999999999999965

>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=98.28  E-value=3.4e-07  Score=71.83  Aligned_cols=39  Identities=21%  Similarity=0.415  Sum_probs=37.7

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|.++|..++++|.++|..|+
T Consensus        33 isk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   71 (86)
T 2lef_A           33 INQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWS   71 (86)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            689999999999999999999999999999999999996

>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=98.27  E-value=3.5e-07  Score=71.77  Aligned_cols=39  Identities=28%  Similarity=0.477  Sum_probs=37.5

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|.++|..++++|..+|..|+
T Consensus        35 isk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~~~~~Yk   73 (85)
T 1j46_A           35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYK   73 (85)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            689999999999999999999999999999999999985

>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=98.27  E-value=2.9e-07  Score=71.40  Aligned_cols=39  Identities=28%  Similarity=0.608  Sum_probs=37.4

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|.++|..++++|.++|..|+
T Consensus        37 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~Yk   75 (83)
T 3f27_D           37 LSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK   75 (83)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            689999999999999999999999999999999999985

>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=98.26  E-value=1.4e-07  Score=73.32  Aligned_cols=39  Identities=33%  Similarity=0.467  Sum_probs=37.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+|+||++|++||+++|++|+++|+.++++|.++|..|+
T Consensus        38 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~~~yk   76 (82)
T 1wz6_A           38 ATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYR   76 (82)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHCCSCSSCC
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHhHHhh
Confidence            589999999999999999999999999999999999886

>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=98.25  E-value=2.4e-07  Score=74.12  Aligned_cols=40  Identities=43%  Similarity=0.727  Sum_probs=38.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||+++|++|+++|..++++|.++|..|..
T Consensus        51 isk~lg~~Wk~ls~eeK~~y~~~A~~~k~~y~~e~~~Y~~   90 (93)
T 1cg7_A           51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA   90 (93)
T ss_dssp             HTTTHHHHHHTTHHHHHHHHHHHHTTHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999964

>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=98.24  E-value=3.1e-07  Score=70.42  Aligned_cols=39  Identities=23%  Similarity=0.432  Sum_probs=37.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|.++|..++++|.+++..|+
T Consensus        33 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~y~~~~p~Yk   71 (79)
T 3u2b_C           33 ISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYK   71 (79)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHSSSCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            689999999999999999999999999999999999885

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

Probab=98.22  E-value=5.1e-07  Score=74.17  Aligned_cols=39  Identities=26%  Similarity=0.496  Sum_probs=37.4

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+|+||++|+.||+++|++|+++|.+++++|.++|..|+
T Consensus        60 isk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~Yk   98 (106)
T 4euw_A           60 LSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYK   98 (106)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence            689999999999999999999999999999999999985

>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=98.22  E-value=4.4e-07  Score=69.21  Aligned_cols=38  Identities=24%  Similarity=0.377  Sum_probs=35.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+|+||++|++||+  |++|+++|.+++++|.++|..|+.
T Consensus        34 isk~lg~~Wk~ls~--K~~y~~~A~~~k~~y~~~~~~Y~~   71 (73)
T 3nm9_A           34 VAKRGGELWRAMKD--KSEWEAKAAKAKDDYDRAVKEFEA   71 (73)
T ss_dssp             HHHHHHHHHHHCSC--CHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCc--hHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999998  999999999999999999999964

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

Probab=98.19  E-value=4.8e-07  Score=69.02  Aligned_cols=38  Identities=34%  Similarity=0.677  Sum_probs=36.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+|+||++|++|  ++|++|+++|..++++|.++|..|+.
T Consensus        34 isk~lg~~Wk~l--~eK~~y~~~A~~~k~~y~~e~~~Y~~   71 (73)
T 1wxl_A           34 IAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEMRNYKP   71 (73)
T ss_dssp             HHHHHHHHHHTC--TTHHHHHHHHHHHHHHHHTTTGGGTT
T ss_pred             HHHHHHHHHHhh--HhhHHHHHHHHHHHHHHHHHHHHHHc
Confidence            589999999999  99999999999999999999999975

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

Probab=98.19  E-value=2.1e-07  Score=74.82  Aligned_cols=40  Identities=35%  Similarity=0.613  Sum_probs=38.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||+++|++|+++|..++++|.++|..|+.
T Consensus        55 isk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~y~~   94 (97)
T 2lhj_A           55 IGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQ   94 (97)
T ss_dssp             HHHHHHHTSSSSCSTTTSSSSHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5799999999999999999999999999999999999964

>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=98.14  E-value=6.5e-07  Score=70.65  Aligned_cols=39  Identities=18%  Similarity=0.345  Sum_probs=36.6

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+|+||++|++||+++|++|+++|++++++|.+++-+|+
T Consensus        48 isk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~P~Yk   86 (87)
T 2e6o_A           48 ISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCW   86 (87)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence            689999999999999999999999999999999987774

>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=98.09  E-value=6.9e-07  Score=69.23  Aligned_cols=39  Identities=26%  Similarity=0.503  Sum_probs=36.3

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|.++|.+++++|.+++-.|+
T Consensus        35 isk~lg~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yk   73 (81)
T 1i11_A           35 ISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYK   73 (81)
T ss_dssp             HHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC-
T ss_pred             HHHHHHhhhhhCCHHHHHHHHHHHHHHHHHHHHHCCCCe
Confidence            689999999999999999999999999999999998874

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

Probab=98.04  E-value=1.8e-06  Score=70.46  Aligned_cols=38  Identities=21%  Similarity=0.336  Sum_probs=35.0

Q ss_pred             hhhhh--HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHH
Q psy1990          47 YLILL--FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   88 (382)
Q Consensus        47 fPglS--ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekE   88 (382)
                      ||+++  ++||+    ++|++|++++|+||+++|+++|++|..+
T Consensus        45 nP~~s~~~~eIs----e~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           45 FPDWTTRVKQIA----KLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             CCSHHHHHHHHH----HHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             CcCccchHHHHH----HHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            57888  99998    9999999999999999999999999763

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

Probab=97.97  E-value=3.8e-07  Score=72.53  Aligned_cols=38  Identities=26%  Similarity=0.337  Sum_probs=35.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   38 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeY   38 (382)
                      |+|+||++|++||+++|++|+++|..++++|.++|..+
T Consensus        51 isk~lg~~Wk~ls~eeK~~Y~~~A~~~k~~y~~e~~~~   88 (90)
T 1wgf_A           51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPS   88 (90)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCCSSC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            68999999999999999999999999999999887653

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

Probab=97.85  E-value=4.1e-06  Score=68.43  Aligned_cols=37  Identities=19%  Similarity=0.282  Sum_probs=33.5

Q ss_pred             CcchH---HHHhcCCChHHHHHHHHHHHHHHHHHHHHHHh
Q psy1990           1 VTKLL---GNEWSKLSLPEKKVYLDRAEVDKKRYREELKV   37 (382)
Q Consensus         1 ISKiL---GEkWK~LSdeEKqkYedkAkeDKeRYeeEMee   37 (382)
                      |+|+|   |++|++|+++||++|+++|.++|++|.+++..
T Consensus        39 isK~l~~cGe~Wk~ls~eEK~pYe~~A~~~K~~y~kd~~~   78 (93)
T 2cto_A           39 VADAIPYCSSDWALLREEEKEKYAEMAREWRAAQGKDPGP   78 (93)
T ss_dssp             HHHHTGGGHHHHHHSCHHHHHHHHHHHHHHHHHHHHCSSC
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccccc
Confidence            46677   99999999999999999999999999988754

>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=97.19  E-value=8.1e-05  Score=58.90  Aligned_cols=28  Identities=25%  Similarity=0.269  Sum_probs=26.2

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHH
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDK   28 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDK   28 (382)
                      |+|+||++|++||+++|++|+++|+.+.
T Consensus        37 isK~lge~Wk~ls~eeK~~y~~~A~~d~   64 (81)
T 2d7l_A           37 IIKEGMIRFRVLSTEERKVWANKAKGET   64 (81)
T ss_dssp             HHHHHHHHHSSSCHHHHHHHHHHTTSSS
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            6899999999999999999999999874

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

Probab=96.68  E-value=0.001  Score=54.23  Aligned_cols=32  Identities=25%  Similarity=0.447  Sum_probs=28.5

Q ss_pred             chHHHHhcCCChHHHHHHHHHHHHHHHHHHHH
Q psy1990           3 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE   34 (382)
Q Consensus         3 KiLGEkWK~LSdeEKqkYedkAkeDKeRYeeE   34 (382)
                      ..|+++|+.|++++|++|+++|.++|++|..+
T Consensus        53 ~eIse~Wk~ls~eeK~pY~~kA~~~K~~h~~~   84 (90)
T 2yuk_A           53 KQIAKLWRKASSQERAPYVQKARDNRAALRIN   84 (90)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHhh
Confidence            45679999999999999999999999999643

>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=96.36  E-value=0.00069  Score=57.20  Aligned_cols=36  Identities=19%  Similarity=0.467  Sum_probs=33.1

Q ss_pred             CCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhh
Q psy1990         161 EDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQ  196 (382)
Q Consensus       161 ~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~  196 (382)
                      ..+...||.+|+.+|+|.....-|+.||.|..+|..
T Consensus        89 ~~~~~~~C~~C~~~f~s~~~~~~H~~gk~H~~~~~~  124 (127)
T 1zu1_A           89 GEDRSKCCPVCNMTFSSPVVAESHYIGKTHIKNLRL  124 (127)
T ss_dssp             CCCTTTEETTTTEECSSHHHHHHHHTSHHHHHHHHH
T ss_pred             CCCCCeEcCCCCCEeCCHHHHHHHHCCHHHHHHHHH
Confidence            467789999999999999999999999999998864

>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=95.73  E-value=0.003  Score=54.38  Aligned_cols=44  Identities=18%  Similarity=0.382  Sum_probs=38.4

Q ss_pred             cccccCCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhccc
Q psy1990         156 IDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGH  199 (382)
Q Consensus       156 ~d~~~~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~~  199 (382)
                      .|+|=+.....||-+|+.+|++..++.-|+.++.|...|..--+
T Consensus        41 ~ded~tGekpfyC~~C~K~F~~~~~L~~H~rsK~HKrrvk~l~~   84 (124)
T 1zr9_A           41 FDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLSV   84 (124)
T ss_dssp             SCSSSGGGGCSEETTTTEECSSHHHHHHHTTCHHHHHHHHHHTS
T ss_pred             ccccCCCCcceEcccCcchhCCHHHHHHHHhhhhhhHHHHHhcc
Confidence            45566777889999999999999999999999999999887543

>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=94.22  E-value=0.0065  Score=51.20  Aligned_cols=41  Identities=22%  Similarity=0.383  Sum_probs=34.0

Q ss_pred             ccccCCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhc
Q psy1990         157 DEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQS  197 (382)
Q Consensus       157 d~~~~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~  197 (382)
                      .|..+-...+||.+|+..|.|....+.|+.|+.|..+|...
T Consensus        24 ~e~~~~~~~~~C~~C~v~~~S~s~~~~H~~gkkH~~~v~~~   64 (127)
T 1zu1_A           24 RENSHIFSDTQCKVCSAVLISESQKLAHYQSRKHANKVRRY   64 (127)
T ss_dssp             HHTTTTBCSSEETTTTEECCSHHHHHHHHHCHHHHHHHHHH
T ss_pred             ccccccCCCCcCcCCCCEeCCHHHHHHHHCcHHHHHHHHHH
Confidence            33334456699999999999999999999999999987643

>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=93.16  E-value=0.017  Score=46.31  Aligned_cols=33  Identities=27%  Similarity=0.669  Sum_probs=29.2

Q ss_pred             hhhhhhhhhh--hhhhhhhhhhchhhhHHhhhhcc
Q psy1990         166 LYCRVCDQWF--TTLHNKREHLNGRQHFQAVEQSG  198 (382)
Q Consensus       166 ~~c~~c~q~f--s~~hnk~eh~~~~~h~~~~~~~~  198 (382)
                      -||..|+-||  .|...-+.|..|++|..++..++
T Consensus         4 YyCdYCd~~lt~Ds~s~Rk~H~~G~kH~~nv~~yy   38 (77)
T 3cw1_L            4 FYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYY   38 (77)
T ss_pred             cccccCCceecCCCHHHHHHHHccHHHHHHHHHHH
Confidence            4899999999  45666889999999999999888

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

Probab=88.49  E-value=0.28  Score=49.29  Aligned_cols=34  Identities=29%  Similarity=0.690  Sum_probs=30.8

Q ss_pred             cchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhh
Q psy1990         163 NEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQ  196 (382)
Q Consensus       163 ~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~  196 (382)
                      .+.+||..|..+|++..-...||.|+.|..++..
T Consensus       290 ~~~l~C~~c~K~Fs~~~v~~~hL~GKkh~K~~~~  323 (402)
T 4dgw_A          290 AKGIYCPFCSRWFKTSSVFESHLVGKIHKKNESK  323 (402)
T ss_dssp             TTEECBTTTTBCBSSHHHHHTTSSSHHHHHHHHH
T ss_pred             CcCeeehhhhhhhccccccHHHhcccccchhHHH
Confidence            4579999999999999999999999999998654

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

Probab=86.53  E-value=0.13  Score=29.40  Aligned_cols=20  Identities=20%  Similarity=0.551  Sum_probs=18.3

Q ss_pred             hhhhhhhhhhhhhhhhhhhc
Q psy1990         167 YCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~  186 (382)
                      -|.+|+..|++..+++.||.
T Consensus         4 ~C~~C~k~f~~~~~l~~H~~   23 (26)
T 2lvu_A            4 VCERCGKRFVQSSQLANHIR   23 (26)
Confidence            49999999999999999984

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

Probab=83.98  E-value=0.22  Score=28.92  Aligned_cols=21  Identities=24%  Similarity=0.477  Sum_probs=18.7

Q ss_pred             hhhhhhhhhhhhhhhhhhhhc
Q psy1990         166 LYCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       166 ~~c~~c~q~fs~~hnk~eh~~  186 (382)
                      .-|.+|+..|++..+++.||.
T Consensus         3 ~~C~~C~k~f~~~~~l~~H~~   23 (29)
T 2lvt_A            3 CQCVMCGKAFTQASSLIAHVR   23 (29)
Confidence            359999999999999999984

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

Probab=83.06  E-value=0.17  Score=29.10  Aligned_cols=20  Identities=25%  Similarity=0.639  Sum_probs=18.3

Q ss_pred             hhhhhhhhhhhhhhhhhhhc
Q psy1990         167 YCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~  186 (382)
                      -|.+|+..|++..+++.||.
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            49999999999999999974

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

Probab=82.45  E-value=0.2  Score=30.58  Aligned_cols=20  Identities=20%  Similarity=0.532  Sum_probs=18.3

Q ss_pred             hhhhhhhhhhhhhhhhhhhc
Q psy1990         167 YCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~  186 (382)
                      -|.+|+..|++..+++.||.
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            49999999999999999984

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

Probab=82.20  E-value=0.15  Score=29.50  Aligned_cols=20  Identities=30%  Similarity=0.688  Sum_probs=18.2

Q ss_pred             hhhhhhhhhhhhhhhhhhhc
Q psy1990         167 YCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~  186 (382)
                      -|.+|+..|++..+++.|+.
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            49999999999999999974

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

Probab=81.94  E-value=0.19  Score=29.30  Aligned_cols=20  Identities=20%  Similarity=0.529  Sum_probs=18.2

Q ss_pred             hhhhhhhhhhhhhhhhhhhc
Q psy1990         167 YCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~  186 (382)
                      -|.+|+..|++..+++.||.
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            49999999999999999984

>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=81.63  E-value=0.3  Score=37.07  Aligned_cols=32  Identities=22%  Similarity=0.504  Sum_probs=29.4

Q ss_pred             hhhhhhhhhhhhhhhhhhhchhhhHHhhhhcc
Q psy1990         167 YCRVCDQWFTTLHNKREHLNGRQHFQAVEQSG  198 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~  198 (382)
                      -|..|+-.|+..--.|.|++.+||+..|....
T Consensus        15 eC~lC~vkYs~r~slqDHIFs~qHI~~vk~~v   46 (55)
T 2yrk_A           15 ECTLCGVKYSARLSIRDHIFSKQHISKVRETV   46 (55)
T ss_dssp             CCTTTTCCCCSSSCHHHHHTSHHHHHHHHHTT
T ss_pred             cccccCcccccccchhhhhccHHHHHHHHHHH
Confidence            59999999999999999999999999987654

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

Probab=82.12  E-value=0.3  Score=28.21  Aligned_cols=21  Identities=19%  Similarity=0.456  Sum_probs=18.7

Q ss_pred             hhhhhhhhhhhhhhhhhhhhc
Q psy1990         166 LYCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       166 ~~c~~c~q~fs~~hnk~eh~~  186 (382)
                      .-|..|+..|++..+++.|+.
T Consensus         4 ~~C~~C~k~f~~~~~l~~H~~   24 (30)
T 2lvr_A            4 YVCIHCQRQFADPGALQRHVR   24 (30)
Confidence            359999999999999999984

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

Probab=80.74  E-value=0.22  Score=28.53  Aligned_cols=20  Identities=45%  Similarity=0.770  Sum_probs=18.1

Q ss_pred             hhhhhhhhhhhhhhhhhhhc
Q psy1990         167 YCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~  186 (382)
                      -|..|+..|++..+++.|+.
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            49999999999999999974

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

Probab=80.28  E-value=0.22  Score=28.40  Aligned_cols=20  Identities=20%  Similarity=0.496  Sum_probs=18.0

Q ss_pred             hhhhhhhhhhhhhhhhhhhc
Q psy1990         167 YCRVCDQWFTTLHNKREHLN  186 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~  186 (382)
                      -|.+|+..|++..+++.||.
T Consensus         3 ~C~~C~k~f~~~~~l~~H~~   22 (27)
T 1znf_A            3 KCGLCERSFVEKSALSRHQR   22 (27)
T ss_dssp             BCSSSCCBCSSHHHHHHHGG
T ss_pred             cCCCCCCcCCCHHHHHHHHH
Confidence            38999999999999999983

---

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	382
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-08
d1v63a_	101	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-07
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-07
d1v64a_	108	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	1e-06
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	2e-07
d1lwma_	93	a.21.1.1 (A:) NHP6a {Baker's yeast (Saccharomyces	2e-07
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	4e-07
d2lefa_	86	a.21.1.1 (A:) Lymphoid enhancer-binding factor, LE	9e-05
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-06
d1hsma_	79	a.21.1.1 (A:) High mobility group protein 1, HMG1	5e-06
d1zr9a1	67	g.37.1.4 (A:28-94) Zinc finger protein 593, ZNF593	2e-06
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	7e-06
d1j46a_	85	a.21.1.1 (A:) SRY {Human (Homo sapiens) [TaxId: 96	3e-05
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	2e-05
d1ckta_	71	a.21.1.1 (A:) High mobility group protein 1, HMG1	3e-05
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	2e-05
d1qrva_	73	a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxI	3e-05
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	4e-05
d1k99a_	91	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	8e-05
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	1e-04
d1i11a_	70	a.21.1.1 (A:) Sox-5 {Mouse (Mus musculus) [TaxId:	2e-04
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	1e-04
d1gt0d_	80	a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId:	7e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	2e-04
d1wgfa_	90	a.21.1.1 (A:) Nucleolar transcription factor 1 (Up	3e-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 = 49.9 bits (119), Expect = 1e-08
 Identities = 13/59 (22%), Positives = 28/59 (47%)

Query: 54  QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQH 112
           +    +G+ W ++S  +K+ Y   AE  +++Y+  L ++ KS + Q     K     + 
Sbjct: 36  ERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDRAAYKEYISNKR 94

>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 = 46.0 bits (109), Expect = 3e-07
 Identities = 12/47 (25%), Positives = 25/47 (53%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 47
              +G+ W ++S  +K+ Y   AE  +++Y+  L ++ KS + Q  
Sbjct: 37 RMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQDR 83

>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 = 47.6 bits (113), Expect = 1e-07
 Identities = 15/60 (25%), Positives = 25/60 (41%)

Query: 54  QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHH 113
           +   L   +W  LS  EK  Y  + +  KK Y  EL  + +S   +   R    +K+ + 
Sbjct: 43  ERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEEQQRVLGEEKMLNI 102

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 13/45 (28%), Positives = 19/45 (42%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 45
             L   +W  LS  EK  Y  + +  KK Y  EL  + +S   +
Sbjct: 44 RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEE 88

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

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

 Score = 46.8 bits (111), Expect = 2e-07
 Identities = 20/46 (43%), Positives = 28/46 (60%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 97
          F QV K LG +W  L+  EK+ Y  +A+ DKKRY  E ++Y  + A
Sbjct: 48 FGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 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 = 46.0 bits (109), Expect = 2e-07
 Identities = 18/43 (41%), Positives = 26/43 (60%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDA 43
          V K LG +W  L+  EK+ Y  +A+ DKKRY  E ++Y  + A
Sbjct: 51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATLA 93

>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 = 45.2 bits (107), Expect = 4e-07
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVK 108
              + ++LG  W  LS  E+  Y + A  +++ + +    +   D Y    +RKR K
Sbjct: 30  SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 86

>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 = 38.7 bits (90), Expect = 9e-05
 Identities = 10/46 (21%), Positives = 21/46 (45%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS 46
          + ++LG  W  LS  E+  Y + A  +++ + +    +   D Y  
Sbjct: 33 INQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGK 78

>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 = 42.9 bits (101), Expect = 2e-06
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 94
             V K LG  W+  +  +K+ Y  +A   K++Y +++  YR 
Sbjct: 30 IGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 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 = 41.8 bits (98), Expect = 5e-06
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 40
          V K LG  W+  +  +K+ Y  +A   K++Y +++  YR 
Sbjct: 33 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA 72

>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 = 42.4 bits (100), Expect = 2e-06
 Identities = 10/46 (21%), Positives = 18/46 (39%)

Query: 151 DATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQ 196
           D   E D +        C  C ++F    N + H   + H + ++Q
Sbjct: 1   DPNAEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQ 46

>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 = 41.7 bits (98), Expect = 7e-06
 Identities = 12/54 (22%), Positives = 26/54 (48%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 105
             +++K LG +W  L+  EK  +   A+  +  +RE+   Y+     ++ +  K
Sbjct: 32  NSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK 85

>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 = 39.8 bits (93), Expect = 3e-05
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 41
          ++K LG +W  L+  EK  +   A+  +  +RE+   Y+  
Sbjct: 35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75

>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 = 40.2 bits (94), Expect = 2e-05
 Identities = 14/39 (35%), Positives = 20/39 (51%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
          + +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 = 39.5 bits (92), Expect = 3e-05
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
           +K     W  +S  EK  + D A+ DK RY  E+K Y
Sbjct: 34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71

>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 = 40.2 bits (94), Expect = 2e-05
 Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 2/42 (4%)

Query: 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 95
          +V K  G  W   ++ +K  +  +A   K  Y   +K +  +
Sbjct: 33 EVAKRGGELWR--AMKDKSEWEAKAAKAKDDYDRAVKEFEAN 72

>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 = 39.8 bits (93), Expect = 3e-05
 Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 2/41 (4%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 41
          V K  G  W   ++ +K  +  +A   K  Y   +K +  +
Sbjct: 34 VAKRGGELWR--AMKDKSEWEAKAAKAKDDYDRAVKEFEAN 72

>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 = 39.9 bits (93), Expect = 4e-05
 Identities = 10/54 (18%), Positives = 24/54 (44%)

Query: 52  FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK 105
              +TK+L  ++ +L   +K  Y+   + +K+ +   L  +R+         +K
Sbjct: 38  NLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK 91

>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 = 38.8 bits (90), Expect = 8e-05
 Identities = 9/40 (22%), Positives = 22/40 (55%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 40
          +TK+L  ++ +L   +K  Y+   + +K+ +   L  +R+
Sbjct: 41 LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRE 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 = 37.9 bits (88), Expect = 1e-04
 Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 8/60 (13%)

Query: 29 KRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 88
          K  R ++         Q++  +    ++K+LG+ W  ++  EK+ Y +      K++ E+
Sbjct: 15 KDERRKIL--------QAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 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 = 37.1 bits (86), Expect = 2e-04
 Identities = 9/34 (26%), Positives = 20/34 (58%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 34
          ++K+LG+ W  ++  EK+ Y +      K++ E+
Sbjct: 33 ISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 66

>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 = 38.2 bits (89), Expect = 1e-04
 Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 15/80 (18%)

Query: 29  KRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 88
           +  R ++         Q    +   +++K LG EW  LS  EK+ ++D A+  +  + +E
Sbjct: 15  RGQRRKMA--------QENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66

Query: 89  LKVYRKSDAYQSYLRRKRVK 108
              Y+       Y  R++ K
Sbjct: 67  HPDYK-------YRPRRKTK 79

>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 = 35.9 bits (83), Expect = 7e-04
 Identities = 13/41 (31%), Positives = 23/41 (56%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 41
          ++K LG EW  LS  EK+ ++D A+  +  + +E   Y+  
Sbjct: 33 ISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR 73

>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 = 37.6 bits (87), Expect = 2e-04
 Identities = 10/41 (24%), Positives = 17/41 (41%)

Query: 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 92
            ++T+LL   W+ LS  +K  Y  R    K +   +    
Sbjct: 48 ESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPS 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 = 37.2 bits (86), Expect = 3e-04
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 1  VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38
          +T+LL   W+ LS  +K  Y  R    K +   +    
Sbjct: 51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERKSGPS 88

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	382
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	99.15
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	99.13
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	99.09
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	99.07
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	99.05
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	99.04
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	99.04
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	99.04
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	99.0
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	98.91
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.91
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	98.55
d1ckta_	71	High mobility group protein 1, HMG1 {Rat (Rattus n	98.45
d1hsma_	79	High mobility group protein 1, HMG1 {Hamster (Cric	98.33
d1v63a_	101	Nucleolar transcription factor 1 (Upstream binding	98.28
d1lwma_	93	NHP6a {Baker's yeast (Saccharomyces cerevisiae) [T	98.25
d1gt0d_	80	Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}	98.24
d1j46a_	85	SRY {Human (Homo sapiens) [TaxId: 9606]}	98.2
d1i11a_	70	Sox-5 {Mouse (Mus musculus) [TaxId: 10090]}	98.19
d1v64a_	108	Nucleolar transcription factor 1 (Upstream binding	98.17
d2lefa_	86	Lymphoid enhancer-binding factor, LEF1 {Mouse (Mus	98.15
d1k99a_	91	Nucleolar transcription factor 1 (Upstream binding	98.02
d1qrva_	73	HMG-D {Drosophila melanogaster [TaxId: 7227]}	97.8
d1wgfa_	90	Nucleolar transcription factor 1 (Upstream binding	97.48
d1zr9a1	67	Zinc finger protein 593, ZNF593 {Human (Homo sapie	97.24
d1zu1a2	55	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	96.21
d2vrda1	61	Spliceosomal protein U1C {Human (Homo sapiens) [Ta	93.81
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	92.83
d1srka_	35	Zinc finger protein ZFPM1 (FOG-1) {Mouse (Mus musc	91.29
d1l8ya_	84	Nucleolar transcription factor 1 (Upstream binding	90.38
d2dmda2	26	Zinc finger protein 64, ZFP68 {Human (Homo sapiens	89.18
d2adra1	29	ADR1 {Synthetic, based on Saccharomyces cerevisiae	87.27
d1p7aa_	37	Kruppel-like factor 3, Bklf {Mouse (Mus musculus)	86.97
d1a1ia2	28	ZIF268 {Mouse (Mus musculus) [TaxId: 10090]}	86.75
d2yrka1	48	Zinc finger homeobox protein 4, ZFHX4 {Human (Homo	84.49
d1zu1a1	72	dsRNA-binding protein ZFa (ZNF346, JAZ) {African c	82.3

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

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

Probab=99.15  E-value=1.2e-11  Score=94.37  Aligned_cols=50  Identities=26%  Similarity=0.418  Sum_probs=47.3

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +|++++++|++.||++|++||+++|++|.++|..++++|.++|.+|+.+.
T Consensus        25 ~p~~~~~ei~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~k~   74 (79)
T d1hsma_          25 HPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG   74 (79)
T ss_dssp             CTTCCTTTHHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence            58999999999999999999999999999999999999999999997653

>d1v63a_ a.21.1.1 (A:) Nucleolar transcription factor 1 (Upstream binding factor 1, UBF-1) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=99.13  E-value=5.6e-11  Score=94.12  Aligned_cols=59  Identities=25%  Similarity=0.445  Sum_probs=52.3

Q ss_pred             chhhhh----------hhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHH
Q psy1990          42 DAYQSY----------LILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS  100 (382)
Q Consensus        42 DAY~lf----------PglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~  100 (382)
                      +||++|          +++++.||++.||++|+.||++||++|.++|..++++|..+|.+|..+.....
T Consensus        14 ~ay~~F~~e~r~~~~~~~~~~~ei~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~~~~~~~   82 (101)
T d1v63a_          14 NGYQKFSQELLSNGELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQD   82 (101)
T ss_dssp             SSHHHHHHHHHHHCTTTTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTTH
T ss_pred             CHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHH
Confidence            577765          37789999999999999999999999999999999999999999988755443

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

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

Probab=99.09  E-value=5.3e-11  Score=93.79  Aligned_cols=50  Identities=38%  Similarity=0.555  Sum_probs=47.5

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +|++++.+|++.||++|++||+++|++|+++|+.++++|..+|.+|+++.
T Consensus        43 ~p~~~~~ei~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~~~l   92 (93)
T d1lwma_          43 NPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNATL   92 (93)
T ss_dssp             CTTSCHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            47899999999999999999999999999999999999999999998764

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

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

Probab=99.07  E-value=6.4e-12  Score=98.05  Aligned_cols=52  Identities=19%  Similarity=0.318  Sum_probs=47.8

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY   98 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aY   98 (382)
                      +|++++++|+++||.+|++||++||++|.++|+.++++|.+++.+|+....+
T Consensus        25 ~P~~~~~~Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~~~~~   76 (86)
T d2lefa_          25 STLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNY   76 (86)
T ss_dssp             SSCCCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCSCSST
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCCCCCC
Confidence            5899999999999999999999999999999999999999999999755433

>d1gt0d_ a.21.1.1 (D:) Sox-2 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: Sox-2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.05  E-value=3.1e-11  Score=93.52  Aligned_cols=49  Identities=27%  Similarity=0.329  Sum_probs=46.3

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++++|+++||++|++|++++|++|.++|+.++++|.++|++|+..
T Consensus        25 ~p~~~~~eisk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk~~   73 (80)
T d1gt0d_          25 NPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYR   73 (80)
T ss_dssp             STTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCC
T ss_pred             cCCCCHHHHHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCccccCC
Confidence            5799999999999999999999999999999999999999999999643

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

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

Probab=99.04  E-value=2.8e-11  Score=91.08  Aligned_cols=46  Identities=22%  Similarity=0.369  Sum_probs=42.8

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   92 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeY   92 (382)
                      +|++++++|++.||++|++||+++|++|.++|++++++|.+++.+|
T Consensus        25 ~p~~~~~eisk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_          25 FPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             CSSCCHHHHHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             hccCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            5799999999999999999999999999999999999998877654

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

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

Probab=99.04  E-value=1.4e-10  Score=93.48  Aligned_cols=59  Identities=25%  Similarity=0.345  Sum_probs=52.8

Q ss_pred             chhhhh--------hhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHH
Q psy1990          42 DAYQSY--------LILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS  100 (382)
Q Consensus        42 DAY~lf--------PglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~  100 (382)
                      +||++|        |++++.||++.||++|++||++||++|.++|+.++++|..+|.+|..+.....
T Consensus        23 ~ay~lF~~~~r~~~~~~~~~e~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~~~~~~~   89 (108)
T d1v64a_          23 NSYSLYCAELMANMKDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEE   89 (108)
T ss_dssp             SHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCHHH
T ss_pred             cHHHHHHHHHHHHccCCCHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCHHH
Confidence            578765        68899999999999999999999999999999999999999999987765433

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

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

Probab=99.04  E-value=3.8e-11  Score=93.40  Aligned_cols=50  Identities=22%  Similarity=0.288  Sum_probs=47.0

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD   96 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~   96 (382)
                      +|++++.||+++||++|++||+++|++|.++|..++++|.++|.+|+.++
T Consensus        27 ~p~~~~~eisk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~~p   76 (85)
T d1j46a_          27 NPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP   76 (85)
T ss_dssp             STTSCHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCCCC
T ss_pred             hccCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhccCC
Confidence            47999999999999999999999999999999999999999999997543

>d1ckta_ a.21.1.1 (A:) High mobility group protein 1, HMG1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: High mobility group protein 1, HMG1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.00  E-value=1.2e-10  Score=87.03  Aligned_cols=43  Identities=35%  Similarity=0.593  Sum_probs=41.1

Q ss_pred             hhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHH
Q psy1990          50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   92 (382)
Q Consensus        50 lSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeY   92 (382)
                      +++++|+++||++|++||+++|++|.++|+.++++|.++|++|
T Consensus        29 ~~~~ei~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_          29 VNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             CCHHHHHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            5689999999999999999999999999999999999999876

>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=98.91  E-value=5.2e-10  Score=84.35  Aligned_cols=47  Identities=19%  Similarity=0.303  Sum_probs=43.8

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++.+|++.||++|++|+  +|++|.++|+.++++|.++|.+|+.+
T Consensus        26 ~p~~~~~eisk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~   72 (73)
T d1qrva_          26 NPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             STTCCHHHHHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             cCCCCHHHHHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            589999999999999999885  59999999999999999999999875

>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=98.91  E-value=3.3e-10  Score=88.25  Aligned_cols=49  Identities=18%  Similarity=0.369  Sum_probs=47.0

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   95 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks   95 (382)
                      +|++++.+|++.||++|+.||+++|++|.++|+.++.+|..+|.+|..+
T Consensus        33 ~p~~~~~ev~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~   81 (91)
T d1k99a_          33 HPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (91)
T ss_dssp             CTTSCSHHHHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             CCCCCHHHHHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999865

>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=98.55  E-value=4.2e-09  Score=81.70  Aligned_cols=43  Identities=26%  Similarity=0.258  Sum_probs=39.8

Q ss_pred             hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHH
Q psy1990          47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   89 (382)
Q Consensus        47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEM   89 (382)
                      +|++++.+|++.||++|+.|+++||++|.++|..++++|+++.
T Consensus        43 ~p~~~~~ei~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~~   85 (90)
T d1wgfa_          43 RPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKS   85 (90)
T ss_dssp             CTTSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCC
T ss_pred             CCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            4789999999999999999999999999999999999987653

>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=98.45  E-value=3.2e-08  Score=73.53  Aligned_cols=38  Identities=37%  Similarity=0.629  Sum_probs=36.5

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   38 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeY   38 (382)
                      |+|+||++|+.||+++|++|+++|++++++|..+|..|
T Consensus        34 i~k~~~~~Wk~ls~~eK~~y~~~a~~~k~~y~~e~~~Y   71 (71)
T d1ckta_          34 FSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY   71 (71)
T ss_dssp             HHHHHHHHHHTCCTTTSHHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            58999999999999999999999999999999999877

>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=98.33  E-value=1.1e-07  Score=72.09  Aligned_cols=40  Identities=30%  Similarity=0.606  Sum_probs=38.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||+++|++|+++|..++++|.++|..|+.
T Consensus        33 i~k~~~~~W~~ls~~eK~~y~~~a~~~k~~Y~~e~~~y~~   72 (79)
T d1hsma_          33 VAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRA   72 (79)
T ss_dssp             HHHHHHHHHHTSCSTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            5799999999999999999999999999999999999964

>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=98.28  E-value=2.3e-07  Score=72.82  Aligned_cols=40  Identities=25%  Similarity=0.533  Sum_probs=38.0

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|+.||++||++|.++|.+++++|..+|..|..
T Consensus        37 i~k~~g~~Wk~ls~~eK~~Y~~~a~~~~~~y~~e~~~y~~   76 (101)
T d1v63a_          37 RMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVK   76 (101)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5799999999999999999999999999999999999964

>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=98.25  E-value=2.9e-07  Score=72.00  Aligned_cols=40  Identities=43%  Similarity=0.727  Sum_probs=38.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||+++|.+|+++|.+++++|.++|..|+.
T Consensus        51 i~k~l~~~W~~ls~~eK~~y~~~a~~~k~~y~~e~~~y~~   90 (93)
T d1lwma_          51 VGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYNA   90 (93)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5799999999999999999999999999999999999964

>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=98.24  E-value=2.1e-07  Score=71.54  Aligned_cols=39  Identities=33%  Similarity=0.510  Sum_probs=37.7

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR   39 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk   39 (382)
                      |+++||++|++||+++|++|+++|..++++|..+|..|+
T Consensus        33 isk~~g~~W~~l~~eeK~~y~~~A~~~k~~y~~~~p~Yk   71 (80)
T d1gt0d_          33 ISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYK   71 (80)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCC
T ss_pred             HHHHHHHHHCcCCHHHHHHHHHHHHHHHHHHHHHCcccc
Confidence            689999999999999999999999999999999999996

>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=98.20  E-value=3e-07  Score=70.94  Aligned_cols=40  Identities=28%  Similarity=0.448  Sum_probs=38.1

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||+++|.+|+++|.+++++|..+|..|+.
T Consensus        35 isk~ig~~W~~L~~eeK~~y~~~A~~~k~~y~~~~~~yk~   74 (85)
T d1j46a_          35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKY   74 (85)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhHHhcc
Confidence            6899999999999999999999999999999999999963

>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=98.19  E-value=1.5e-07  Score=70.22  Aligned_cols=38  Identities=26%  Similarity=0.493  Sum_probs=34.6

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY   38 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeY   38 (382)
                      |+|+||++|++||+++|++|+++|++++++|.+++-+|
T Consensus        33 isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~Y   70 (70)
T d1i11a_          33 ISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDY   70 (70)
T ss_dssp             HHHHHHHHHTTSCSGGGHHHHHHHHHHHHHHHTTCSCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCC
Confidence            68999999999999999999999999999998776544

>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=98.17  E-value=4.1e-07  Score=72.73  Aligned_cols=40  Identities=30%  Similarity=0.467  Sum_probs=38.0

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||++||++|+++|..++++|..+|..|..
T Consensus        44 ~~k~ig~~W~~Ls~~eK~~Y~~~a~~~k~~Y~~~~~~y~~   83 (108)
T d1v64a_          44 RMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLE   83 (108)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            5789999999999999999999999999999999999964

>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=98.15  E-value=4.3e-07  Score=70.15  Aligned_cols=40  Identities=20%  Similarity=0.401  Sum_probs=38.0

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      |+++||++|++||++||++|.++|.+++++|.+++..|+.
T Consensus        33 Isk~lg~~Wk~ls~~eK~~y~~~A~~~k~~~~~~~p~yk~   72 (86)
T d2lefa_          33 INQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSA   72 (86)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHSTTCCS
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHCcCCCC
Confidence            6899999999999999999999999999999999999864

>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=98.02  E-value=1.2e-06  Score=67.64  Aligned_cols=41  Identities=22%  Similarity=0.494  Sum_probs=38.6

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~K   41 (382)
                      |+++||+.|+.||+++|++|.++|..++.+|.++|..|..+
T Consensus        41 v~k~l~~~W~~ls~~eK~~y~~~a~~~~~~y~~~~~~y~~~   81 (91)
T d1k99a_          41 LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFRED   81 (91)
T ss_dssp             HHHHHHHHHHHSCSTTHHHHHHHHHHHHHHHHHHHGGGGGC
T ss_pred             HHHHHHhHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999754

>d1qrva_ a.21.1.1 (A:) HMG-D {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: HMG-box
superfamily: HMG-box
family: HMG-box
domain: HMG-D
species: Drosophila melanogaster [TaxId: 7227]

Probab=97.80  E-value=4.4e-06  Score=62.28  Aligned_cols=39  Identities=23%  Similarity=0.432  Sum_probs=35.5

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhccc
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS   41 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~K   41 (382)
                      |+++||++|++|+  +|++|+++|.+++++|.++|..|+.+
T Consensus        34 isk~l~~~Wk~~~--eK~~y~~~a~~~k~~y~~~~~~y~~~   72 (73)
T d1qrva_          34 VAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFEAN   72 (73)
T ss_dssp             HHHHHHHHHHHCS--CCHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhcChh--HHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            6899999999886  59999999999999999999999753

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

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

Probab=97.48  E-value=2.9e-06  Score=65.24  Aligned_cols=35  Identities=29%  Similarity=0.411  Sum_probs=31.9

Q ss_pred             CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHH
Q psy1990           1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL   35 (382)
Q Consensus         1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEM   35 (382)
                      |+++||++|+.|++++|++|+++|.+++++|.++.
T Consensus        51 i~k~l~~~W~~Ls~~eK~~Y~~~A~~~k~~y~~~~   85 (90)
T d1wgfa_          51 LTRLLARMWNDLSEKKKAKYKAREAALKAQSERKS   85 (90)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTCCCC
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            67999999999999999999999999999887554

>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=97.24  E-value=2.9e-05  Score=58.93  Aligned_cols=45  Identities=20%  Similarity=0.412  Sum_probs=40.0

Q ss_pred             cccccccCCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhcc
Q psy1990         154 DEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSG  198 (382)
Q Consensus       154 ~~~d~~~~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~  198 (382)
                      .++|+|.|..|-.||-+|+.+|.|-..+..|+.++.|...|..--
T Consensus         4 ~e~D~D~pG~gqfYCv~C~K~F~se~~l~~H~ksKkHKrrvk~L~   48 (67)
T d1zr9a1           4 AEFDPDLPGGGLHRCLACARYFIDSTNLKTHFRSKDHKKRLKQLS   48 (67)
T ss_dssp             CSSCSSSGGGGCSEETTTTEECSSHHHHHHHTTCHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCEEecccccCccCCHHHHHHHHcccHHHHHHHHhc
Confidence            456777788899999999999999999999999999999987643

>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=96.21  E-value=0.00046  Score=50.62  Aligned_cols=33  Identities=21%  Similarity=0.506  Sum_probs=29.2

Q ss_pred             cchhhhhhhhhhhhhhhhhhhhhchhhhHHhhh
Q psy1990         163 NEELYCRVCDQWFTTLHNKREHLNGRQHFQAVE  195 (382)
Q Consensus       163 ~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~  195 (382)
                      |.+-||.+|+.+|++.---+-|..|+.|..+|-
T Consensus        19 d~nk~C~lCn~~Fns~~~AqsHY~GK~H~K~lk   51 (55)
T d1zu1a2          19 DRSKCCPVCNMTFSSPVVAESHYIGKTHIKNLR   51 (55)
T ss_dssp             CTTTEETTTTEECSSHHHHHHHHTSHHHHHHHH
T ss_pred             CchhhhhhhhcccCCHHHHHHHhhhhHHHHHHH
Confidence            344499999999999999999999999998764

>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=93.81  E-value=0.005  Score=45.62  Aligned_cols=34  Identities=29%  Similarity=0.685  Sum_probs=29.1

Q ss_pred             hhhhhhhhhhh--hhhhhhhhhchhhhHHhhhhccc
Q psy1990         166 LYCRVCDQWFT--TLHNKREHLNGRQHFQAVEQSGH  199 (382)
Q Consensus       166 ~~c~~c~q~fs--~~hnk~eh~~~~~h~~~~~~~~~  199 (382)
                      -||--|+-||+  +.+.-+-|+.|++|..|+..++.
T Consensus         4 yyCdYC~~~lt~ds~s~RK~H~~G~kH~~n~~~yy~   39 (61)
T d2vrda1           4 FYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQ   39 (61)
T ss_dssp             CEETTTTEECSCCSHHHHHHHTCCTHHHHHHHHHTS
T ss_pred             hhhhhhcchhccCChhHHHHHhccHHHHHHHHHHHH
Confidence            48999999995  45666789999999999999883

>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=92.83  E-value=0.046  Score=42.21  Aligned_cols=41  Identities=29%  Similarity=0.551  Sum_probs=35.7

Q ss_pred             HHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990          54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   94 (382)
Q Consensus        54 EIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk   94 (382)
                      ...+.+-..|++|.-+||-+|+.+|.+|.++|++|+-+-+.
T Consensus        32 KaqkaMeatW~~meKkEki~wikkaaedqkryerel~emr~   72 (84)
T d1l8ya_          32 KALKAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRA   72 (84)
T ss_dssp             HHHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            45566778999999999999999999999999999876654

>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=91.29  E-value=0.0087  Score=39.60  Aligned_cols=26  Identities=38%  Similarity=0.650  Sum_probs=22.3

Q ss_pred             hhhhhhhhhhhhhhhhhhhhchhhhHHh
Q psy1990         166 LYCRVCDQWFTTLHNKREHLNGRQHFQA  193 (382)
Q Consensus       166 ~~c~~c~q~fs~~hnk~eh~~~~~h~~~  193 (382)
                      --|.+|+..|+...|++-||  |-|...
T Consensus         8 y~C~~C~k~F~~~~~L~~H~--r~Ht~~   33 (35)
T d1srka_           8 FVCRICLSAFTTKANCARHL--KVHTDT   33 (35)
T ss_dssp             EECSSSCCEESSHHHHHHHH--GGGTSC
T ss_pred             ccCCCCCCcccChHHHHHHc--cccCCc
Confidence            35999999999999999998  677654

>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=90.38  E-value=0.14  Score=39.35  Aligned_cols=38  Identities=32%  Similarity=0.592  Sum_probs=33.6

Q ss_pred             chHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990           3 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK   40 (382)
Q Consensus         3 KiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~   40 (382)
                      +.+...|++|..+||-+|.++|.+|.++|++++.+.+.
T Consensus        35 kaMeatW~~meKkEki~wikkaaedqkryerel~emr~   72 (84)
T d1l8ya_          35 KAMEMTWNNMEKKEKLMWIKKAAEDQKRYERELSEMRA   72 (84)
T ss_dssp             HHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHTTSC
T ss_pred             HHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence            34566899999999999999999999999999988753

>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=89.18  E-value=0.029  Score=35.00  Aligned_cols=21  Identities=24%  Similarity=0.640  Sum_probs=18.7

Q ss_pred             hhhhhhhhhhhhhhhhhhhch
Q psy1990         167 YCRVCDQWFTTLHNKREHLNG  187 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~~  187 (382)
                      -|.+|+.+||+.-+++-||-.
T Consensus         3 kc~~c~kcfsrkdklk~hmr~   23 (26)
T d2dmda2           3 KCEVCGKCFSRKDKLKTHMRC   23 (26)
T ss_dssp             CBTTTTBCCCCHHHHHHHGGG
T ss_pred             ccchhhhHhcchhHHHHHhhc
Confidence            399999999999999999853

>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=87.27  E-value=0.04  Score=34.81  Aligned_cols=19  Identities=26%  Similarity=0.667  Sum_probs=17.9

Q ss_pred             hhhhhhhhhhhhhhhhhhh
Q psy1990         167 YCRVCDQWFTTLHNKREHL  185 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~  185 (382)
                      -|.+|+..|+...+++.||
T Consensus         4 ~C~~C~k~F~~~~~L~~H~   22 (29)
T d2adra1           4 VCEVCTRAFARQEHLKRHY   22 (29)
T ss_dssp             CCTTTCCCBSCHHHHHHHH
T ss_pred             CCCCCCCCCCCchHccccc
Confidence            3999999999999999998

>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=86.97  E-value=0.04  Score=36.27  Aligned_cols=24  Identities=25%  Similarity=0.510  Sum_probs=20.8

Q ss_pred             hhhhhhhhhhhhhhhhhhhchhhhHH
Q psy1990         167 YCRVCDQWFTTLHNKREHLNGRQHFQ  192 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~~~~h~~  192 (382)
                      -|..|+..|++..+++.||  |-|+.
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            5999999999999999998  56653

>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=86.75  E-value=0.041  Score=34.69  Aligned_cols=19  Identities=26%  Similarity=0.670  Sum_probs=17.8

Q ss_pred             hhhhhhhhhhhhhhhhhhh
Q psy1990         167 YCRVCDQWFTTLHNKREHL  185 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~  185 (382)
                      -|.+|+..|+...|+..||
T Consensus         5 ~C~~C~k~F~~~~~L~~H~   23 (28)
T d1a1ia2           5 QCRICMRNFSRSDHLTTHI   23 (28)
T ss_dssp             ECTTTCCEESCHHHHHHHH
T ss_pred             cCCCCcCEecccccccccC
Confidence            3999999999999999997

>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=84.49  E-value=0.1  Score=36.93  Aligned_cols=32  Identities=22%  Similarity=0.504  Sum_probs=29.2

Q ss_pred             hhhhhhhhhhhhhhhhhhhchhhhHHhhhhcc
Q psy1990         167 YCRVCDQWFTTLHNKREHLNGRQHFQAVEQSG  198 (382)
Q Consensus       167 ~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~  198 (382)
                      -|..|+-.+|..-..|.|++.+||+..|....
T Consensus         8 eC~lC~vKYs~~~SvrdHiFskqHI~~Vk~~v   39 (48)
T d2yrka1           8 ECTLCGVKYSARLSIRDHIFSKQHISKVRETV   39 (48)
T ss_dssp             CCTTTTCCCCSSSCHHHHHTSHHHHHHHHHTT
T ss_pred             cCcccceeeeeecchHhhhhhHHHHHHHHHHH
Confidence            39999999999999999999999999998765

>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=82.30  E-value=0.094  Score=39.74  Aligned_cols=36  Identities=22%  Similarity=0.394  Sum_probs=32.4

Q ss_pred             cchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhcc
Q psy1990         163 NEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSG  198 (382)
Q Consensus       163 ~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~  198 (382)
                      =-+.||.+|+.-.-+-.-+--|..|+.|-++|.-+|
T Consensus        30 Ftd~~CkvC~a~L~seSQriaHYeskkHa~kvr~yf   65 (72)
T d1zu1a1          30 FSDTQCKVCSAVLISESQKLAHYQSRKHANKVRRYM   65 (72)
T ss_dssp             BCSSEETTTTEECCSHHHHHHHHHCHHHHHHHHHHH
T ss_pred             cchhhHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346799999999999999999999999999998776