Citrus Sinensis ID: 020172

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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
Protein Sequence
MADQSQVANKAVGVSTTTCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHLFQGGGFKLISENPPKAKKPRLDKRPSSANINFQLQASNNSSVSSSIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQNPNHIHRP
Secondary Structure (PSIPRED)
cccHHHHccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHccccccccccccccccHHHHHEccccccccccccccccEEEEEcccccccEcccccccEEEccccccccccccccccccccccccccccccccccHHHcccccEEcccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
madqsqvaNKAVGVSTTTCSLESLDCLLsatnsnsaetsaedddgisILFSSDcrnlwnfgsnssavssgesennapnnfarnnngpvnneldhetishcssvqyvnngrivhqeelrpgstkrkniddhqSEQFHlfqgggfklisenppkakkprldkrpssaninfqlqasnnssvsssieepdpEAIAHMKEMIYRAAafrpvnlglevvekpkrknvristdpQTVAARQRRERISERIRVLQRlvpggskmdtASMLDEAANYLKFLRSQVKAlenpghqkpdhhhsmnypptnlafsslpfnnnsfpvqthfslqnpnhihrp
Flexible Loop (DISEMBL)
madqsqvankavgvsTTTCSLESLDCLLSATNSnsaetsaedddGISILFSSDCRNLWNFGSNSSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHLFQGGGFKLISENPPKAKKPRLDKRPSSANINfqlqasnnssvsssIEEPDPEAIAHMKEMIYRAAAFRPVNlglevvekpkrknvristdpqtvaarqrreriserirvlqrlvpggskmdTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHfslqnpnhihrp
Low Complexity Region (SEG)
MADQSQVANKAVGVSTTTCSLESLDCLLsatnsnsaetsaeDDDGISILFSSDCRNLWNFgsnssavssgesennapnnfarnnngpvnnELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHLFQGGGFKLISENPPKAKKPRLDKRPSSANINFQLQAsnnssvsssIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAArqrreriserirVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQNPNHIHRP
Disordered region (IsUnstruct)
***************TTTCSLESLDCLL*****************ISILFSSDCRNLWNF**************************************HCSSVQYVNNGRIV************************LFQG**F*************************************************HMKEMIYRAAAFRPVNLGLEVV*******************************VL******************AANYLKFL*********************************************************
Disordered Region (DISOPRED)
*************************************************************************************************************************************************************************************************************************************************ERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKA***************************************************
Disordered Region (DISEMBL)
**************STTTCSLESLDCLLSATN*********DDDGISILFSSDCRNLWNFGSN************APNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHLFQGGGFKLISENP***********PSSANINFQLQA************PDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRIST***********ERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQNPNHIHRP
Disordered Region (DISPRO)
********************LESLDCLLSAT*******SAEDDDGISILFSSDCRNLWNFGSN**************************************SV**VNNGRIVHQEELRPGS************QFHLF*G***K****************************************EPDPEAIAHMKEMIYRAAAFRPVNLG*******************T****QRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQN*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MADQSQVANKAVGVSTTTCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHLFQGGGFKLISENPPKAKKPRLDKRPSSANINFQLQASNNSSVSSSIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQNPNHIHRP
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	330	2.2.26 [Sep-21-2011]
Q8S3D2	373	Transcription factor bHLH	yes	no	0.884	0.782	0.529	7e-73
O81313	198	Transcription factor IND	no	no	0.293	0.489	0.554	1e-27
Q9FHA7	241	Transcription factor HEC1	no	no	0.275	0.377	0.681	5e-24
Q9SND4	231	Transcription factor HEC2	no	no	0.275	0.393	0.692	6e-24
Q9LXD8	224	Transcription factor HEC3	no	no	0.278	0.410	0.663	9e-23
Q9M041	912	Transcription factor bHLH	no	no	0.330	0.119	0.424	9e-17
Q7XAQ6	215	Transcription factor LAX	no	no	0.166	0.255	0.690	1e-16
Q84WK0	352	Transcription factor bHLH	no	no	0.169	0.159	0.589	2e-14
Q7XHI9	328	Transcription factor bHLH	no	no	0.169	0.170	0.589	3e-14
Q9C707	298	Transcription factor bHLH	no	no	0.206	0.228	0.529	5e-14

>sp|Q8S3D2|BH087_ARATH Transcription factor bHLH87 OS=Arabidopsis thaliana GN=BHLH87 PE=2 SV=1

 Score =  274 bits (700), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 180/340 (52%), Positives = 207/340 (60%), Gaps = 48/340 (14%)

Query: 1   MADQSQVANKAVGVSTTTCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNF 60
           +  Q  V N+A  +  +     SLDCLLSAT SNS  TS EDD+GIS+LFS DC+ LW+F
Sbjct: 70  IQQQQHVGNRASSIDPS-----SLDCLLSAT-SNSNNTSTEDDEGISVLFS-DCQTLWSF 122

Query: 61  GSNSSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPG 120
           G     VSS ESEN            P   + +       +                +P 
Sbjct: 123 G----GVSSAESENREITTETTTTIKPKPLKRNRGGDGGTTETTTTTT---------KPK 169

Query: 121 STKRKNIDDHQSEQFHLF------QGGGFKLI-SENPPKAKKPRLDK-RPSSANINFQLQ 172
           S KR N  D     F L       + GGFKLI  EN  K+KKPR +K R  S+NI+FQ  
Sbjct: 170 SLKR-NRGDETGSHFSLVHPQDDSEKGGFKLIYDENQSKSKKPRTEKERGGSSNISFQ-- 226

Query: 173 ASNNSSVSSSIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVA 232
              +S+  S   EPD EAIA MKEMIYRAAAFRPVN GLE+VEKPKRKNV+ISTDPQTVA
Sbjct: 227 ---HSTCLSDNVEPDAEAIAQMKEMIYRAAAFRPVNFGLEIVEKPKRKNVKISTDPQTVA 283

Query: 233 ARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHH 292
           ARQRRERISE+IRVLQ LVPGG+KMDTASMLDEAANYLKFLR+QVKALEN    K D   
Sbjct: 284 ARQRRERISEKIRVLQTLVPGGTKMDTASMLDEAANYLKFLRAQVKALENL-RPKLDQ-- 340

Query: 293 SMNYPPTNLAFSSLPFNNNSFPV--QTHFSLQNPNHIHRP 330
                 TNL+FSS P    SFP+   +   LQNPN IH P
Sbjct: 341 ------TNLSFSSAP---TSFPLFHPSFLPLQNPNQIHHP 371

Arabidopsis thaliana (taxid: 3702)

>sp|O81313|IND_ARATH Transcription factor IND OS=Arabidopsis thaliana GN=IND PE=1 SV=3

 Score =  123 bits (309), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 61/110 (55%), Positives = 76/110 (69%), Gaps = 13/110 (11%)

Query: 185 EPDPEAIAH-------------MKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTV 231
           +P PE + H             MKEM Y  A  +PV++    V KP R+NVRIS DPQTV
Sbjct: 66  DPPPETLIHLDEDEEYDEDMDAMKEMQYMIAVMQPVDIDPATVPKPNRRNVRISDDPQTV 125

Query: 232 AARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALE 281
            AR+RRERISE+IR+L+R+VPGG+KMDTASMLDEA  Y KFL+ QV+ L+
Sbjct: 126 VARRRRERISEKIRILKRIVPGGAKMDTASMLDEAIRYTKFLKRQVRILQ 175

Transcription regulator required for seed dispersal. Involved in the differentiation of all three cell types required for fruit dehiscence. Acts as the key regulator in a network including SHP and ALC that controls specification of the valve margin. Works with ALC, SHP, and FUL to allow differentiation of the lignified valve layer, the spring-loaded mechanism of fruit that promotes opening. Regulates the expression of the YJ80 marker.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHA7|HEC1_ARATH Transcription factor HEC1 OS=Arabidopsis thaliana GN=HEC1 PE=1 SV=1

 Score =  112 bits (279), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 62/91 (68%), Positives = 79/91 (86%)

Query: 191 IAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRL 250
           +A M+EMI+R A  +P+++  E V+ PKR+NVRIS DPQ+VAAR RRERISERIR+LQRL
Sbjct: 95  MAAMREMIFRIAVMQPIHIDPEAVKPPKRRNVRISKDPQSVAARHRRERISERIRILQRL 154

Query: 251 VPGGSKMDTASMLDEAANYLKFLRSQVKALE 281
           VPGG+KMDTASMLDEA +Y+KFL+ QV++LE
Sbjct: 155 VPGGTKMDTASMLDEAIHYVKFLKKQVQSLE 185

Required for the female reproductive tract development and fertility.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SND4|HEC2_ARATH Transcription factor HEC2 OS=Arabidopsis thaliana GN=HEC2 PE=1 SV=1

 Score =  112 bits (279), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 63/91 (69%), Positives = 79/91 (86%)

Query: 191 IAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRL 250
           +A M+EMI+R A  +P+++  E V+ PKRKNVRIS DPQ+VAAR RRERISERIR+LQRL
Sbjct: 92  MAAMREMIFRIAVMQPIHIDPESVKPPKRKNVRISKDPQSVAARHRRERISERIRILQRL 151

Query: 251 VPGGSKMDTASMLDEAANYLKFLRSQVKALE 281
           VPGG+KMDTASMLDEA +Y+KFL+ QV++LE
Sbjct: 152 VPGGTKMDTASMLDEAIHYVKFLKKQVQSLE 182

Required for the female reproductive tract development and fertility.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LXD8|HEC3_ARATH Transcription factor HEC3 OS=Arabidopsis thaliana GN=HEC3 PE=1 SV=1

 Score =  107 bits (268), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 61/92 (66%), Positives = 76/92 (82%)

Query: 191 IAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRL 250
           +  MKEM+Y+ AA + V++    V+KPKR+NVRIS DPQ+VAAR RRERISERIR+LQRL
Sbjct: 92  LGAMKEMMYKIAAMQSVDIDPATVKKPKRRNVRISDDPQSVAARHRRERISERIRILQRL 151

Query: 251 VPGGSKMDTASMLDEAANYLKFLRSQVKALEN 282
           VPGG+KMDTASMLDEA  Y+KFL+ Q++ L N
Sbjct: 152 VPGGTKMDTASMLDEAIRYVKFLKRQIRLLNN 183

Required for the female reproductive tract development and fertility.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M041|BH140_ARATH Transcription factor bHLH140 OS=Arabidopsis thaliana GN=BHLH140 PE=4 SV=1

 Score = 87.8 bits (216), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 48/113 (42%), Positives = 67/113 (59%), Gaps = 4/113 (3%)

Query: 216 KPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRS 275
           K  R    +STDPQ+VAAR RR RIS+R ++LQ +VPGG+KMDT SMLDEA +Y+KFL++
Sbjct: 35  KRSRSTSTLSTDPQSVAARDRRHRISDRFKILQSMVPGGAKMDTVSMLDEAISYVKFLKA 94

Query: 276 QVKALENPGHQKPDHH--HSMNYPPTNLAFSS--LPFNNNSFPVQTHFSLQNP 324
           Q+   +N      DH    S  Y P    F      ++++  P+   +S   P
Sbjct: 95  QIWYHQNMLLFINDHETTSSCTYSPGAGEFGPKLFGYDDDYAPIMDTYSQGVP 147

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XAQ6|LAX_ORYSJ Transcription factor LAX PANICLE OS=Oryza sativa subsp. japonica GN=LAX PE=1 SV=1

 Score = 87.4 bits (215), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 38/55 (69%), Positives = 50/55 (90%)

Query: 223 RISTDPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQV 277
           ++STDPQ+VAAR+RR RIS+R RVL+ LVPGGSKMDT SML++A +Y+KFL++QV
Sbjct: 39  KLSTDPQSVAARERRHRISDRFRVLRSLVPGGSKMDTVSMLEQAIHYVKFLKAQV 93

Transcription factor that seems to regulate organogenesis in postembryonic development. Involved in regulating shoot branching by controlling axillary meristem initiation.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q84WK0|BH085_ARATH Transcription factor bHLH85 OS=Arabidopsis thaliana GN=BHLH85 PE=2 SV=1

 Score = 80.1 bits (196), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 49/56 (87%)

Query: 225 STDPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKAL 280
           +TDPQ++ AR+RRERI+ER+R+LQ LVP G+K+D ++ML+EA +Y+KFL+ Q+K L
Sbjct: 273 ATDPQSLYARKRRERINERLRILQNLVPNGTKVDISTMLEEAVHYVKFLQLQIKLL 328

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XHI9|BH084_ARATH Transcription factor bHLH84 OS=Arabidopsis thaliana GN=BHLH84 PE=2 SV=1

 Score = 79.7 bits (195), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 33/56 (58%), Positives = 48/56 (85%)

Query: 225 STDPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKAL 280
           +TDPQ++ AR+RRERI+ER+R+LQ LVP G+K+D ++ML+EA  Y+KFL+ Q+K L
Sbjct: 244 ATDPQSLYARKRRERINERLRILQHLVPNGTKVDISTMLEEAVQYVKFLQLQIKLL 299

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C707|BH083_ARATH Transcription factor bHLH83 OS=Arabidopsis thaliana GN=BHLH83 PE=2 SV=1

 Score = 79.0 bits (193), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 36/68 (52%), Positives = 50/68 (73%)

Query: 213 VVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKF 272
           V  K K K      DPQ++AA+ RRERISER+++LQ LVP G+K+D  +ML++A +Y+KF
Sbjct: 190 VTGKTKPKPTTSPKDPQSLAAKNRRERISERLKILQELVPNGTKVDLVTMLEKAISYVKF 249

Query: 273 LRSQVKAL 280
           L+ QVK L
Sbjct: 250 LQVQVKVL 257

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	330
224059166	304	predicted protein [Populus trichocarpa]	0.872	0.947	0.680	9e-99
255549698	395	DNA binding protein, putative [Ricinus c	0.866	0.724	0.677	6e-91
359482873	471	PREDICTED: transcription factor bHLH87-l	0.930	0.651	0.639	2e-89
356522216	431	PREDICTED: transcription factor bHLH87-l	0.866	0.663	0.609	1e-80
356528881	443	PREDICTED: transcription factor bHLH87-l	0.830	0.618	0.599	5e-76
147797615	447	hypothetical protein VITISV_023488 [Viti	0.857	0.633	0.584	8e-76
223702408	495	putative basic helix-loop-helix protein	0.821	0.547	0.583	3e-75
449448090	393	PREDICTED: transcription factor bHLH87-l	0.821	0.689	0.573	2e-74
357454723	392	Transcription factor bHLH87 [Medicago tr	0.845	0.711	0.568	1e-72
297830832	374	basic helix-loop-helix family protein [A	0.884	0.780	0.526	2e-71

>gi|224059166|ref|XP_002299748.1| predicted protein [Populus trichocarpa] gi|222847006|gb|EEE84553.1| predicted protein [Populus trichocarpa]

 Score =  366 bits (939), Expect = 9e-99,   Method: Compositional matrix adjust.
 Identities = 219/322 (68%), Positives = 244/322 (75%), Gaps = 34/322 (10%)

Query: 23  SLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSA-VSSGESENNAPNNFA 81
           SLDCLLSATNSN+ +TS EDD GIS++FS DCRNLWNF  NSSA VSSGESENN  N   
Sbjct: 1   SLDCLLSATNSNT-DTSVEDD-GISMIFS-DCRNLWNFAPNSSAAVSSGESENNTCNPGN 57

Query: 82  RNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQ------- 134
           +  + PV+ ELD ET+SHCSS QY   G+     + +P STKR N  DH SE        
Sbjct: 58  KEMHCPVS-ELD-ETVSHCSSDQY---GKNRDCSQTKPVSTKRSN--DHCSELKMGLKHP 110

Query: 135 -FHLFQG------GGFKLISENPPKAKKPRLDKRPSSANINFQLQASNNSSVSSSIEEPD 187
            F + Q       GGF+LIS+NPPK+KKPR DKRPSS+NINFQ  +S+ SS        D
Sbjct: 111 FFDILQSECSNQEGGFRLISDNPPKSKKPRSDKRPSSSNINFQQPSSSISSSIEEP---D 167

Query: 188 PEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVL 247
           PEAIA MKEMIYRAAAFRPVNLGLEV EKPKRKNVRISTDPQTVAARQRRERIS+RIRVL
Sbjct: 168 PEAIAQMKEMIYRAAAFRPVNLGLEVAEKPKRKNVRISTDPQTVAARQRRERISDRIRVL 227

Query: 248 QRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYP-PTNLAFSSL 306
           Q +VPGGSKMDTASMLDEAANYLKFLRSQVKALEN GH+      S+N P PTN+AFSSL
Sbjct: 228 QGMVPGGSKMDTASMLDEAANYLKFLRSQVKALENLGHKL----DSVNCPQPTNIAFSSL 283

Query: 307 PFNNNSFPVQTHFSLQNPNHIH 328
           PF N+SFP+Q HF  QNPNHIH
Sbjct: 284 PF-NHSFPLQNHFPFQNPNHIH 304

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255549698|ref|XP_002515900.1| DNA binding protein, putative [Ricinus communis] gi|223544805|gb|EEF46320.1| DNA binding protein, putative [Ricinus communis]

 Score =  340 bits (872), Expect = 6e-91,   Method: Compositional matrix adjust.
 Identities = 221/326 (67%), Positives = 247/326 (75%), Gaps = 40/326 (12%)

Query: 18  TCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSAVSSGESENNAP 77
           T SLESLDCLLSATNSN+ +TS EDD GIS++FS DCRNLWNF +NS+A SSGESENN  
Sbjct: 95  TGSLESLDCLLSATNSNT-DTSVEDD-GISMIFS-DCRNLWNFSANSAA-SSGESENNTS 150

Query: 78  NNFARNNNGPVNNELDHETIS---HCSSVQYVNNGRIVHQEELRPGSTKRKNID-DHQSE 133
           N  ARN      +E   ++IS    CS                +P STKR N   + +++
Sbjct: 151 N--ARNKEMHCPDETVSQSISSDKKCSQTS-------------KPVSTKRSNDQTELKAD 195

Query: 134 QFHLFQG------GGFKLISENPPKAKKPRLD-KRPSSANINFQLQASNNSSVSSSIEEP 186
            F L Q       GGF+LISENP K+K+ R D K+PSS+NINFQ  +S   SVSSSIEEP
Sbjct: 196 IFDLLQTNSCTTQGGFRLISENPSKSKRLRSDNKKPSSSNINFQQPSS---SVSSSIEEP 252

Query: 187 DPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRV 246
           DPEAIA MKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRV
Sbjct: 253 DPEAIAQMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRV 312

Query: 247 LQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSL 306
           LQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALEN GH+       +N PPTN+AFSSL
Sbjct: 313 LQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENLGHK-----LEVNSPPTNIAFSSL 367

Query: 307 PFNNNSF-PVQTHF-SLQNPNHIHRP 330
           PFN++ F P+QTHF SLQNPNHIH P
Sbjct: 368 PFNSHPFHPMQTHFSSLQNPNHIHHP 393

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482873|ref|XP_003632856.1| PREDICTED: transcription factor bHLH87-like [Vitis vinifera]

 Score =  335 bits (859), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 220/344 (63%), Positives = 249/344 (72%), Gaps = 37/344 (10%)

Query: 4   QSQVANK----AVGVSTTTCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWN 59
           Q QV N       GVS T  SLESLDCLLSATNSN+ ETS EDD GIS++FS DCRNLWN
Sbjct: 146 QFQVVNGFQDGTAGVSATG-SLESLDCLLSATNSNT-ETSIEDD-GISVIFS-DCRNLWN 201

Query: 60  FGSNSSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRP 119
           FGS S AVSSG+SENN  N   +     VN ELD ET+S  +S +  N G      E +P
Sbjct: 202 FGSGS-AVSSGDSENNGFNTRKKEMRCAVN-ELD-ETVSQGASDRLANPGIC---SETKP 255

Query: 120 GSTKRKNIDDHQ---SEQFHLFQ---------GGGFKLISENPPKAKKPRLDKRP-SSAN 166
            STKR + D ++   S  +H F           GGF+LISEN PK KKPR +KRP SS+N
Sbjct: 256 NSTKR-SCDQNELKVSPNYHCFDLLQSDACTPDGGFRLISENSPKPKKPRAEKRPPSSSN 314

Query: 167 INFQLQASNNSSVSSSIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRIST 226
           INFQ      SS +SS+EEPD EAIA MKE+IYRAAAFRPVN G++ VEKPKRKNVRIST
Sbjct: 315 INFQ----QPSSSASSVEEPDSEAIAQMKEIIYRAAAFRPVNFGMDAVEKPKRKNVRIST 370

Query: 227 DPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQ 286
           DPQTVAARQRRERISERIRVLQRLVPGG+KMDTASMLDEAANYLKFLRSQVKALE  GH+
Sbjct: 371 DPQTVAARQRRERISERIRVLQRLVPGGNKMDTASMLDEAANYLKFLRSQVKALETLGHK 430

Query: 287 KPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQNPNHIHRP 330
                 S+N   TNL FS+LPF N+SFP+QTH  LQNP+ IH+P
Sbjct: 431 ----LDSVNCVHTNLPFSALPF-NHSFPMQTHLPLQNPSPIHQP 469

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356522216|ref|XP_003529743.1| PREDICTED: transcription factor bHLH87-like [Glycine max]

 Score =  306 bits (783), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 189/310 (60%), Positives = 221/310 (71%), Gaps = 24/310 (7%)

Query: 19  CSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSAVSSGESENNAPN 78
           CSLE  DCL+SATNSN+ +TS EDDDGIS++ S DC NLWN  S  S  S+GESE+NA N
Sbjct: 144 CSLEPFDCLISATNSNT-DTSVEDDDGISMILS-DCGNLWNNFSYGSVASTGESESNASN 201

Query: 79  NFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHLF 138
              ++   PVN E+D ET+S     +   + R   Q ++        +I  + S      
Sbjct: 202 GRNKDMQCPVN-EVD-ETVSQTVESEANCSKRSHDQSKMIQVGDSCFSIVQNSSP----I 255

Query: 139 QGGGFKLISENPPKAKKPRLDKRPSSANINFQLQASNNSSVSSSIEEPDPEAIAHMKEMI 198
           + GGF+LIS+NPP+ KKPR D   SS NINFQ     NSS+SSSIEEPDPEAIA MKEMI
Sbjct: 256 EEGGFRLISDNPPECKKPRWDMSSSSNNINFQ---QPNSSISSSIEEPDPEAIAQMKEMI 312

Query: 199 YRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPGGSKMD 258
           YRAAAFRPVN GLEVVEK KRKNV+ISTDPQTVAAR RRERISE+IRVLQ+LVPGGSKMD
Sbjct: 313 YRAAAFRPVNFGLEVVEKLKRKNVKISTDPQTVAARHRRERISEKIRVLQKLVPGGSKMD 372

Query: 259 TASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTH 318
           TASMLDEAANYLKFLRSQVKALE+ G++      +MN PPT++AFS  P    SFP+QT 
Sbjct: 373 TASMLDEAANYLKFLRSQVKALESLGNKV----DAMNCPPTSIAFSFNP----SFPMQTP 424

Query: 319 FSLQNPNHIH 328
            S     HIH
Sbjct: 425 LS-----HIH 429

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356528881|ref|XP_003533026.1| PREDICTED: transcription factor bHLH87-like [Glycine max]

 Score =  290 bits (743), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 184/307 (59%), Positives = 216/307 (70%), Gaps = 33/307 (10%)

Query: 21  LESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSAVSSGESENNAPNNF 80
           LES DCL+SATNSN+  TS EDDDGIS++ S DC NLW+  S  SA S+GESE+NA N  
Sbjct: 142 LESFDCLISATNSNTDITSVEDDDGISMILS-DCGNLWSNFSYGSAASTGESESNASN-- 198

Query: 81  ARNNN---GPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHL 137
            RN +    PVN E+D ET+S     +  N  +  H  +     +K   + D     F +
Sbjct: 199 GRNKDMQCSPVNIEVD-ETVSQTVESE-ANCSKRSHAHD----QSKMIKVGD---SCFSI 249

Query: 138 FQG------GGFKLISE-NPPKAKKPRLDKRPSSANINFQLQASNNSSVSSSIEEPDPEA 190
            Q       GGF+L+S+ N P+ KK R D   SS NINFQ     NSS+SSSIEEPDPEA
Sbjct: 250 VQNSSPIEEGGFRLVSDINQPECKKSRWDMSSSSNNINFQ---QPNSSISSSIEEPDPEA 306

Query: 191 IAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRL 250
           IA MKEMIYRAAAFRPVN GLEV EKPKRKNV+ISTDPQTVAAR RRERI+E+IRVLQ+L
Sbjct: 307 IAQMKEMIYRAAAFRPVNFGLEVAEKPKRKNVKISTDPQTVAARHRRERINEKIRVLQKL 366

Query: 251 VPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNN 310
           VPGGSKMDTASMLDEAANYLKFLRSQVKALE+ G++      +MN PPT++AFS  P   
Sbjct: 367 VPGGSKMDTASMLDEAANYLKFLRSQVKALESLGNKV----DAMNCPPTSIAFSFNP--- 419

Query: 311 NSFPVQT 317
            SFP+QT
Sbjct: 420 -SFPMQT 425

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147797615|emb|CAN65002.1| hypothetical protein VITISV_023488 [Vitis vinifera]

 Score =  290 bits (741), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 201/344 (58%), Positives = 225/344 (65%), Gaps = 61/344 (17%)

Query: 4   QSQVANK----AVGVSTTTCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWN 59
           Q QV N       GVS T  SLESLDCLL                           NLWN
Sbjct: 146 QFQVVNGFQDGTAGVSATG-SLESLDCLL---------------------------NLWN 177

Query: 60  FGSNSSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRP 119
           FGS S AVSSG+SENN  N   +     VN ELD ETIS  SS +  N G      E +P
Sbjct: 178 FGSGS-AVSSGDSENNGFNTRKKEMRCAVN-ELD-ETISQGSSDRLANPGIC---PETKP 231

Query: 120 GSTKRKNIDDHQ---SEQFHLFQ---------GGGFKLISENPPKAKKPRLDKRP-SSAN 166
            S KR + D ++   S  +H F           GGF+LISEN PK KKPR +KRP SS+N
Sbjct: 232 NSMKR-SCDQNELKVSPNYHCFDLLQSDACTPDGGFRLISENSPKPKKPRSEKRPPSSSN 290

Query: 167 INFQLQASNNSSVSSSIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRIST 226
           INFQ      SS +SS+EEPD EAIA MKE+IYRAAAFRPVN G++ VEKPKRKNVRIST
Sbjct: 291 INFQ----QPSSSASSVEEPDSEAIAQMKEIIYRAAAFRPVNFGMDAVEKPKRKNVRIST 346

Query: 227 DPQTVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQ 286
           DPQTVAARQRRERISERIRVLQRLVPGG+KMDTASMLDEAANYLKFLRSQVKALE  GH+
Sbjct: 347 DPQTVAARQRRERISERIRVLQRLVPGGNKMDTASMLDEAANYLKFLRSQVKALETLGHK 406

Query: 287 KPDHHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQNPNHIHRP 330
                 S+N   TNL FS+LPF N+SFP+QTH  LQNP+ IH+P
Sbjct: 407 L----DSVNCVHTNLPFSALPF-NHSFPMQTHLPLQNPSPIHQP 445

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|223702408|gb|ACN21635.1| putative basic helix-loop-helix protein BHLH11 [Lotus japonicus]

 Score =  288 bits (736), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 181/310 (58%), Positives = 215/310 (69%), Gaps = 39/310 (12%)

Query: 23  SLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSAVSSGESENNAPNNFAR 82
           SLDCLLSATNSN+ +TS EDD GIS++   DC NLWNF   S+A SSGESE NA N   +
Sbjct: 207 SLDCLLSATNSNT-DTSVEDD-GISMILP-DCGNLWNFSHGSAAASSGESETNASNG-TK 262

Query: 83  NNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQFHLFQG-- 140
           N +         +T+S  SS            ++L+P   KR+N      + F + +   
Sbjct: 263 NKHMEFQVNEPVQTVSQSSS------------DQLKP---KRRNNQSSDDQYFTMLENSP 307

Query: 141 --GGFKLISENPPKAKKPRLDK-RPSSANINFQLQASNNSSVSSSIEEPDPEAIAHMKEM 197
             GGF+LISENPPK KKPR +K   SS+NINFQ   S     SSSIEEPDPEAIA MKEM
Sbjct: 308 IEGGFRLISENPPKCKKPRWEKGSCSSSNINFQQPNS-----SSSIEEPDPEAIAQMKEM 362

Query: 198 IYRAAAFRPVNL-GLE-VVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPGGS 255
           IYRAAAFRPV+L GLE V EKPKRKNV+IS+DPQTVAARQRRERIS+RIRVLQ++VPGGS
Sbjct: 363 IYRAAAFRPVSLLGLEEVAEKPKRKNVKISSDPQTVAARQRRERISDRIRVLQKIVPGGS 422

Query: 256 KMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNY-PPTNLAFSSLPFNNNSFP 314
           KMDTASMLDEAANYLKFLRSQVKALE+ G++      +M+Y  P+++AFS  P    SFP
Sbjct: 423 KMDTASMLDEAANYLKFLRSQVKALESLGNKVST---AMDYCSPSSIAFSFNP----SFP 475

Query: 315 VQTHFSLQNP 324
           +Q     Q P
Sbjct: 476 MQMKDDYQLP 485

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449448090|ref|XP_004141799.1| PREDICTED: transcription factor bHLH87-like [Cucumis sativus]

 Score =  285 bits (730), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 183/319 (57%), Positives = 222/319 (69%), Gaps = 48/319 (15%)

Query: 15  STTTCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNFGSNSSAVSSGESEN 74
           + TTCSLESLDCLLSATNSN+ +TS EDD  +S++ + D  NLWNFG N+ AVSS ESE 
Sbjct: 110 TVTTCSLESLDCLLSATNSNT-DTSVEDDGSVSMMLT-DYTNLWNFGGNA-AVSSKESEK 166

Query: 75  NAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTKRKNIDDHQSEQ 134
           N  N+  R+          HE     ++   + +  I+             N+ D  S+ 
Sbjct: 167 NGSNSTKRS----------HEQTQFKAADYSIFSNNII-------------NLSDSTSD- 202

Query: 135 FHLFQGGGFKLISE-NPPKAKKPRLDKRPSSANINFQLQASNNSSVSSSIEEPDPEAIAH 193
                 GGF++I++ + PK KKPR +K PSS+NINFQ   S+ SS     +EPDPEAIA 
Sbjct: 203 -----SGGFRIITDHDLPKQKKPRSEKPPSSSNINFQQSCSSGSSCID--QEPDPEAIAQ 255

Query: 194 MKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPG 253
           MKEMIYRAAAFRPVNLGLE++EKPKRKNVRIS+DPQTVAARQRRERISERIRVLQRLVPG
Sbjct: 256 MKEMIYRAAAFRPVNLGLEMIEKPKRKNVRISSDPQTVAARQRRERISERIRVLQRLVPG 315

Query: 254 GSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAFSSLPFNNNSF 313
           GSKMDTASMLDEAANYLKFL+SQ+KALEN G +      S+N PPT++AFS  P    SF
Sbjct: 316 GSKMDTASMLDEAANYLKFLKSQIKALENLGQK----LESLNCPPTSIAFSFNP----SF 367

Query: 314 PVQT-----HFSLQNPNHI 327
           P+QT     +F+L NPNH+
Sbjct: 368 PIQTSSSHNNFTLLNPNHL 386

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357454723|ref|XP_003597642.1| Transcription factor bHLH87 [Medicago truncatula] gi|355486690|gb|AES67893.1| Transcription factor bHLH87 [Medicago truncatula]

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 191/336 (56%), Positives = 226/336 (67%), Gaps = 57/336 (16%)

Query: 7   VANKAVGVSTTTCSLES-LDCLLSATNSNSAETSAEDDDGISILFSSDC--RNLWNFGSN 63
           +A++ +  STTTCSLES LDCLLSAT +++ +T++  DDGIS++FS DC  RNLWNF + 
Sbjct: 89  MAHQPISKSTTTCSLESSLDCLLSATTNSNTDTNSVQDDGISMIFS-DCKNRNLWNFSAV 147

Query: 64  SSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPGSTK 123
           SSA S   +  N    +          ELD ET+S  SS Q    G+I+   ++   STK
Sbjct: 148 SSAESESTNARNKDMQYGFK-------ELDQETVSPASSDQ----GKIIDNSKVH--STK 194

Query: 124 RKNIDDHQ------------SEQFHLFQGGGFKLISENPPKAKKPRLD-KRPSSANINFQ 170
           R NID +             S +F      GFKLISE PPK+KKPR D K P S+NINFQ
Sbjct: 195 RTNIDQYDPCFSITAQNSSSSTEF------GFKLISEKPPKSKKPRWDNKCPGSSNINFQ 248

Query: 171 LQASNNSSVSSSIEEPDPEAIAHMKEMIYRAAAFRPV-NLGLEVVEKPKRKNVRISTDPQ 229
                    +SS EEPDPEAIA MKEMIYRAAAFRPV NLGLEV+EKPKRKNV+IS DPQ
Sbjct: 249 -------QPNSSFEEPDPEAIAQMKEMIYRAAAFRPVTNLGLEVMEKPKRKNVKISKDPQ 301

Query: 230 TVAARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPD 289
           TVAARQRRERISERIRVLQ++VPGG+KMDTASMLDEAANYLKFLR+QVK LEN G+ K D
Sbjct: 302 TVAARQRRERISERIRVLQKIVPGGTKMDTASMLDEAANYLKFLRAQVKELENIGN-KID 360

Query: 290 HHHSMNYPPTNLAFSSLPFNNNSFPVQTHFSLQNPN 325
             +  N PPTN+AFS  P            S+QNPN
Sbjct: 361 TVN--NCPPTNIAFSFNP----------SISMQNPN 384

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297830832|ref|XP_002883298.1| basic helix-loop-helix family protein [Arabidopsis lyrata subsp. lyrata] gi|297329138|gb|EFH59557.1| basic helix-loop-helix family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  275 bits (704), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 179/340 (52%), Positives = 208/340 (61%), Gaps = 48/340 (14%)

Query: 1   MADQSQVANKAVGVSTTTCSLESLDCLLSATNSNSAETSAEDDDGISILFSSDCRNLWNF 60
           +  Q  V N+A  +  +     SLDCLLSAT SNS  TS EDD+GIS+LFS DC+ LW+F
Sbjct: 71  IQQQQHVGNRASSIDPS-----SLDCLLSAT-SNSNNTSTEDDEGISVLFS-DCQTLWSF 123

Query: 61  GSNSSAVSSGESENNAPNNFARNNNGPVNNELDHETISHCSSVQYVNNGRIVHQEELRPG 120
           G     VSS ESEN    N       P + + +       +                +P 
Sbjct: 124 G----GVSSAESENREVTNETTTTIKPKSLKRNRGGDGGTTETT--------TTTTTKPK 171

Query: 121 STKRKNIDDHQSEQFHLF------QGGGFKLI-SENPPKAKKPRLDK-RPSSANINFQLQ 172
             KR N  D     F L       + GGFKLI  EN  K+KKPR +K R  S+NI+FQ  
Sbjct: 172 YVKR-NRGDETGSHFSLLHPQDDSEKGGFKLIYDENQSKSKKPRTEKERGGSSNISFQ-- 228

Query: 173 ASNNSSVSSSIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVA 232
              +S+  S   EPD EAIA MKEMIYRAAAFRPVN GLE+VEKPKRKNV+ISTDPQTVA
Sbjct: 229 ---HSTCLSDNVEPDAEAIAQMKEMIYRAAAFRPVNFGLEIVEKPKRKNVKISTDPQTVA 285

Query: 233 ARQRRERISERIRVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHH 292
           ARQRRERISE+IRVLQ LVPGG+KMDTASMLDEAANYLKFLR+QVKALEN    +P    
Sbjct: 286 ARQRRERISEKIRVLQTLVPGGTKMDTASMLDEAANYLKFLRAQVKALEN---LRP---- 338

Query: 293 SMNYPPTNLAFSSLPFNNNSFPV--QTHFSLQNPNHIHRP 330
                 TNL+FSS P    SFP+   +   LQNPN IH P
Sbjct: 339 --KLDQTNLSFSSAP----SFPLFHPSFLPLQNPNQIHHP 372

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	330
TAIR|locus:2089418	373	AT3G21330 "AT3G21330" [Arabido	0.590	0.522	0.565	9.9e-56
UNIPROTKB|Q657D1	484	P0697C12.40 "BHLH transcriptio	0.521	0.355	0.466	9e-34
UNIPROTKB|Q8S0N2	393	P0692C11.41-1 "BHLH transcript	0.554	0.465	0.461	6.9e-31
UNIPROTKB|Q5TKP7	416	OJ1362_G11.11 "Putative unchar	0.387	0.307	0.496	8.4e-26
UNIPROTKB|Q6Z9R3	246	P0461F06.33 "BHLH protein fami	0.293	0.394	0.564	8.7e-24
TAIR|locus:2144791	224	HEC3 "AT5G09750" [Arabidopsis	0.318	0.468	0.514	1e-22
TAIR|locus:2074865	231	HEC2 "AT3G50330" [Arabidopsis	0.287	0.411	0.557	2.1e-22
TAIR|locus:2155543	241	HEC1 "HECATE 1" [Arabidopsis t	0.275	0.377	0.560	3.4e-22
UNIPROTKB|Q67TR8	236	B1342C04.6 "Basic helix-loop-h	0.266	0.372	0.590	4.3e-22
TAIR|locus:2126856	198	IND "AT4G00120" [Arabidopsis t	0.363	0.606	0.450	9.2e-20

TAIR|locus:2089418 AT3G21330 "AT3G21330" [Arabidopsis thaliana (taxid:3702)]

 Score = 495 (179.3 bits), Expect = 9.9e-56, Sum P(2) = 9.9e-56
 Identities = 126/223 (56%), Positives = 139/223 (62%)

Query:   118 RPGSTKRKNIDDHQSEQFHLF------QGGGFKLI-SENPPKAKKPRLDK-RPSSANINF 169
             +P S KR N  D     F L       + GGFKLI  EN  K+KKPR +K R  S+NI+F
Sbjct:   167 KPKSLKR-NRGDETGSHFSLVHPQDDSEKGGFKLIYDENQSKSKKPRTEKERGGSSNISF 225

Query:   170 QLQAXXXXXXXXXIEEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQ 229
             Q              EPD EAIA MKEMIYRAAAFRPVN GLE+VEKPKRKNV+ISTDPQ
Sbjct:   226 QHSTCLSDNV-----EPDAEAIAQMKEMIYRAAAFRPVNFGLEIVEKPKRKNVKISTDPQ 280

Query:   230 TVAAXXXXXXXXXXXXVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPD 289
             TVAA            VLQ LVPGG+KMDTASMLDEAANYLKFLR+QVKALEN    K D
Sbjct:   281 TVAARQRRERISEKIRVLQTLVPGGTKMDTASMLDEAANYLKFLRAQVKALENL-RPKLD 339

Query:   290 HHHSMNYPPTNLAFSSLPFNNNSFPV--QTHFSLQNPNHIHRP 330
                      TNL+FSS P    SFP+   +   LQNPN IH P
Sbjct:   340 Q--------TNLSFSSAP---TSFPLFHPSFLPLQNPNQIHHP 371

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

UNIPROTKB|Q657D1 P0697C12.40 "BHLH transcription-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 346 (126.9 bits), Expect = 9.0e-34, Sum P(2) = 9.0e-34
 Identities = 84/180 (46%), Positives = 112/180 (62%)

Query:   141 GGFKL-ISENPPKAKKPRLDKRPSSANINFQLQAXXXXXXXXX----IEEPDPEAIAHMK 195
             GG ++  S + P +K+ +     SS++I+F  +              + EPD EA+A +K
Sbjct:   281 GGIQIAFSTSAPASKRAKPSLSSSSSSISFDGRGPGGNCGGGGGDDPLYEPDTEALAQVK 340

Query:   196 EMIYRAAAFRPVNLGLEVV-EKPKRKNVRISTDPQTVAAXXXXXXXXXXXXVLQRLVPGG 254
             EMIYRAAA RPV LG E   E+P+R+NVRIS+DPQTVAA            VLQ+LVPGG
Sbjct:   341 EMIYRAAAMRPVTLGAEDAGERPRRRNVRISSDPQTVAARQRRERISERLRVLQKLVPGG 400

Query:   255 SKMDTASMLDEAANYLKFLRSQVKALENPGHQK-PDHHHSMNYPP-TNLAFSSLPFNNNS 312
             +KMDTASMLDEAANYL+FL+SQ++ L+    +  P+   S+N    T +A SS P  NNS
Sbjct:   401 AKMDTASMLDEAANYLRFLKSQIRELQTLDRRNYPNAAMSINTAAATTMATSSSPTYNNS 460

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q8S0N2 P0692C11.41-1 "BHLH transcription factor-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 96/208 (46%), Positives = 115/208 (55%)

Query:   123 KRKNIDDHQSEQFHLFQGGGFKLISENPPKAKKPR------LDKR---PSSANINFQLQA 173
             KRK  DDH     H     G    +  PP A  PR        KR    S+ +I F  Q 
Sbjct:   176 KRKLYDDHH----H---PAGIAAAAAAPPLAPCPRPTTGAVAAKRRASTSATSITFGHQP 228

Query:   174 XXXXXXXXXIE-EPDPEAIAHMKEMIYRAAAFRPVNLGLEVV-EKPKRKNVRISTDPQTV 231
                         EPD EA+A +KEMIYRAAA RPV+LG E   +KP+RKNVRIS+DPQTV
Sbjct:   229 HHHHAGATTAGYEPDMEAMAQVKEMIYRAAAMRPVHLGTEAAADKPRRKNVRISSDPQTV 288

Query:   232 AAXXXXXXXXXXXXVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPG-----HQ 286
             AA            VLQ+LVPGG+KMDTASMLDEAA+YLKFL+SQV+ LE  G      +
Sbjct:   289 AARLRRERVSDRLRVLQKLVPGGNKMDTASMLDEAASYLKFLKSQVQKLETLGTTTTTSK 348

Query:   287 KPDHHHSMNYPPTNLAFSSLPF--NNNS 312
              P  ++S N   +N     L F  NNN+
Sbjct:   349 LPQQYYSGNINSSNNHHGFLGFAANNNT 376

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q5TKP7 OJ1362_G11.11 "Putative uncharacterized protein OJ1362_G11.11" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 71/143 (49%), Positives = 88/143 (61%)

Query:   185 EPDPEAIAHMKEMIYRAAAFRPVNLGLEVV------------EKPKRKNVRISTDPQTVA 232
             EPD EAIA +KEM+YRAA  RPV LG                ++P+RKNVRIS+DPQTVA
Sbjct:   252 EPDTEAIAQVKEMVYRAAPMRPVTLGGPASASDPSSRPPPPPQRPRRKNVRISSDPQTVA 311

Query:   233 AXXXXXXXXXXXXVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDH-- 290
             A            VLQRLVPGGSKMDTA+MLDEAA+YLKFL+SQ++ALE  G+   +   
Sbjct:   312 ARLRRERVSERLRVLQRLVPGGSKMDTATMLDEAASYLKFLKSQLEALETLGNGNGNGNL 371

Query:   291 -HHSMNYPPTNLAFSSLPFNNNS 312
              HH       N   ++   ++NS
Sbjct:   372 LHHGYYTGSRNATATAATGSSNS 394

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q6Z9R3 P0461F06.33 "BHLH protein family-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 273 (101.2 bits), Expect = 8.7e-24, P = 8.7e-24
 Identities = 57/101 (56%), Positives = 72/101 (71%)

Query:   192 AHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAAXXXXXXXXXXXXVLQRLV 251
             A M+EMI+  AA +PVN+  E V  PKR+NVRISTDPQ+VAA            +LQRLV
Sbjct:   125 AAMREMIFHIAALQPVNIDPETVRPPKRRNVRISTDPQSVAARMRRERISERIRILQRLV 184

Query:   252 PGGSKMDTASMLDEAANYLKFLRSQVKALENP----GHQKP 288
             PGG+KMDTASMLDEA +Y+KFL++QV++LE      GH+ P
Sbjct:   185 PGGTKMDTASMLDEAIHYVKFLKTQVQSLERAAAANGHRPP 225

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2144791 HEC3 "AT5G09750" [Arabidopsis thaliana (taxid:3702)]

 Score = 263 (97.6 bits), Expect = 1.0e-22, P = 1.0e-22
 Identities = 55/107 (51%), Positives = 73/107 (68%)

Query:   184 EEPDP-EAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAAXXXXXXXXX 242
             +E +P E +  MKEM+Y+ AA + V++    V+KPKR+NVRIS DPQ+VAA         
Sbjct:    84 DEEEPLEELGAMKEMMYKIAAMQSVDIDPATVKKPKRRNVRISDDPQSVAARHRRERISE 143

Query:   243 XXXVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALEN-PGHQKP 288
                +LQRLVPGG+KMDTASMLDEA  Y+KFL+ Q++ L N  G+  P
Sbjct:   144 RIRILQRLVPGGTKMDTASMLDEAIRYVKFLKRQIRLLNNNTGYTPP 190

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

TAIR|locus:2074865 HEC2 "AT3G50330" [Arabidopsis thaliana (taxid:3702)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 53/95 (55%), Positives = 69/95 (72%)

Query:   187 DPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAAXXXXXXXXXXXXV 246
             D   +A M+EMI+R A  +P+++  E V+ PKRKNVRIS DPQ+VAA            +
Sbjct:    88 DNANMAAMREMIFRIAVMQPIHIDPESVKPPKRKNVRISKDPQSVAARHRRERISERIRI 147

Query:   247 LQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALE 281
             LQRLVPGG+KMDTASMLDEA +Y+KFL+ QV++LE
Sbjct:   148 LQRLVPGGTKMDTASMLDEAIHYVKFLKKQVQSLE 182

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

GO:0080126 "ovary septum development" evidence=IGI

TAIR|locus:2155543 HEC1 "HECATE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 51/91 (56%), Positives = 68/91 (74%)

Query:   191 IAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAAXXXXXXXXXXXXVLQRL 250
             +A M+EMI+R A  +P+++  E V+ PKR+NVRIS DPQ+VAA            +LQRL
Sbjct:    95 MAAMREMIFRIAVMQPIHIDPEAVKPPKRRNVRISKDPQSVAARHRRERISERIRILQRL 154

Query:   251 VPGGSKMDTASMLDEAANYLKFLRSQVKALE 281
             VPGG+KMDTASMLDEA +Y+KFL+ QV++LE
Sbjct:   155 VPGGTKMDTASMLDEAIHYVKFLKKQVQSLE 185

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010500 "transmitting tissue development" evidence=IGI

GO:0048462 "carpel formation" evidence=IMP

GO:0048445 "carpel morphogenesis" evidence=RCA

UNIPROTKB|Q67TR8 B1342C04.6 "Basic helix-loop-helix (BHLH)-like protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 52/88 (59%), Positives = 65/88 (73%)

Query:   194 MKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAAXXXXXXXXXXXXVLQRLVPG 253
             M+EMI+  AA +PV +  E V  PKR+NVRIS DPQ+VAA            +LQRLVPG
Sbjct:   117 MREMIFHIAALQPVEIDPEAVRPPKRRNVRISKDPQSVAARLRRERISERIRILQRLVPG 176

Query:   254 GSKMDTASMLDEAANYLKFLRSQVKALE 281
             G+KMDTASMLDEA +Y+KFL+SQV++LE
Sbjct:   177 GTKMDTASMLDEAIHYVKFLKSQVQSLE 204

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2126856 IND "AT4G00120" [Arabidopsis thaliana (taxid:3702)]

 Score = 235 (87.8 bits), Expect = 9.2e-20, P = 9.2e-20
 Identities = 59/131 (45%), Positives = 76/131 (58%)

Query:   184 EEPDPEAIAHMKEMIYRAAAFRPVNLGLEVVEKPKRKNVRISTDPQTVAAXXXXXXXXXX 243
             EE D +  A MKEM Y  A  +PV++    V KP R+NVRIS DPQTV A          
Sbjct:    79 EEYDEDMDA-MKEMQYMIAVMQPVDIDPATVPKPNRRNVRISDDPQTVVARRRRERISEK 137

Query:   244 XXVLQRLVPGGSKMDTASMLDEAANYLKFLRSQVKALENPGHQKPDHHHSMNYPPTNLAF 303
               +L+R+VPGG+KMDTASMLDEA  Y KFL+ QV+ L+ P       H  +  P  N ++
Sbjct:   138 IRILKRIVPGGAKMDTASMLDEAIRYTKFLKRQVRILQ-P-------HSQIGAPMANPSY 189

Query:   304 SSLPFNNNSFP 314
               L + +NS P
Sbjct:   190 --LCYYHNSQP 198

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0010197 "polar nucleus fusion" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8S3D2	BH087_ARATH	No assigned EC number	0.5294	0.8848	0.7828	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	330
smart00353	53	smart00353, HLH, helix loop helix domain	2e-10
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	9e-10
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	3e-06

>gnl|CDD|197674 smart00353, HLH, helix loop helix domain

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 3/52 (5%)

Query: 230 TVAARQRRERISERIRVLQRLVPG---GSKMDTASMLDEAANYLKFLRSQVK 278
               R+RR +I+E    L+ L+P      K+  A +L  A  Y+K L+ +++
Sbjct: 1   NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

Length = 53

>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 230 TVAARQRRERISERIRVLQRLVPG---GSKMDTASMLDEAANYLKFLRSQVK 278
            +  R+RRERI++    L+ L+P      K+  A +L +A +Y+K L+  ++
Sbjct: 9   NLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and have a PAS domain which allows the dimerization between PAS proteins, the binding of small molecules (e.g., dioxin), and interactions with non-PAS proteins. Length = 60

>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain

 Score = 43.6 bits (104), Expect = 3e-06
 Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 234 RQRRERISERIRVLQRLVP--GGSKMDTASMLDEAANYLKFLR 274
           R+RR+RI++    L+ L+P     K+  A +L  A  Y+K L+
Sbjct: 10  RRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	330
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.33
smart00353	53	HLH helix loop helix domain.	99.31
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.25
KOG1318	411	consensus Helix loop helix transcription factor EB	98.81
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.62
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.56
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.06
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.83
KOG0561	373	consensus bHLH transcription factor [Transcription	97.6
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	97.53
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.52
PLN03217	93	transcription factor ATBS1; Provisional	96.98
KOG4029	228	consensus Transcription factor HAND2/Transcription	96.84
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	95.49
KOG3910	632	consensus Helix loop helix transcription factor [T	93.07
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	88.27
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	85.55
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	85.43

>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long

Probab=99.33  E-value=2e-12  Score=93.87  Aligned_cols=52  Identities=31%  Similarity=0.569  Sum_probs=48.9

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHH
Q 020172          227 DPQTVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVK  278 (330)
Q Consensus       227 ~~Hs~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq  278 (330)
                      ..|+.+||+||++||+.|..|+.|||..   .|+||++||+.||+||++|+.+++
T Consensus         6 ~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083           6 EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            3689999999999999999999999988   899999999999999999998863

A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and

>smart00353 HLH helix loop helix domain

Probab=99.31  E-value=4e-12  Score=90.93  Aligned_cols=49  Identities=31%  Similarity=0.547  Sum_probs=45.6

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCC---CCCCChhchHHHHHHHHHHHHHHHH
Q 020172          230 TVAARQRRERISERIRVLQRLVPG---GSKMDTASMLDEAANYLKFLRSQVK  278 (330)
Q Consensus       230 s~aER~RRerINer~~~LrsLVPg---~~KmDKASILeeAIdYIK~LQ~QVq  278 (330)
                      +.+||+||++||++|..|+.|||.   ..|+||++||.+||+||+.|+.+++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            368999999999999999999994   6799999999999999999999886

>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt)

Probab=99.25  E-value=9.3e-12  Score=90.55  Aligned_cols=47  Identities=34%  Similarity=0.593  Sum_probs=44.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC-----CCCChhchHHHHHHHHHHHH
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG-----SKMDTASMLDEAANYLKFLR  274 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~-----~KmDKASILeeAIdYIK~LQ  274 (330)
                      .|+..||+||++||+.|..|+.+||.+     .|++|++||+.||+||+.||
T Consensus         4 ~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    4 KHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            588999999999999999999999986     68999999999999999997

; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....

>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]

Probab=98.81  E-value=3.1e-09  Score=106.38  Aligned_cols=56  Identities=29%  Similarity=0.551  Sum_probs=50.0

Q ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHHHHHHH
Q 020172          223 RISTDPQTVAARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFLRSQVK  278 (330)
Q Consensus       223 r~ss~~Hs~aER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~LQ~QVq  278 (330)
                      |.+++.|+..|||||++||++|++|..|||.+    .|..|..||..++|||+.||+..+
T Consensus       231 r~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q  290 (411)
T KOG1318|consen  231 RRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ  290 (411)
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence            45567999999999999999999999999998    356799999999999999998654

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.62  E-value=1.4e-08  Score=93.47  Aligned_cols=61  Identities=30%  Similarity=0.427  Sum_probs=54.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC-------CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG-------SKMDTASMLDEAANYLKFLRSQVKALENPGHQKP  288 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~-------~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L~  288 (330)
                      .|..+||+||+.|+..+..|+.|||.|       .|+.||.||..+|+||.+|+.++.+-+.++..|.
T Consensus        65 aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~  132 (229)
T KOG1319|consen   65 AHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLR  132 (229)
T ss_pred             HHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999999999999965       3788999999999999999999888877766553

>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]

Probab=98.56  E-value=3.5e-08  Score=93.28  Aligned_cols=51  Identities=27%  Similarity=0.492  Sum_probs=45.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC--------CCCChhchHHHHHHHHHHHHHHHH
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG--------SKMDTASMLDEAANYLKFLRSQVK  278 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~--------~KmDKASILeeAIdYIK~LQ~QVq  278 (330)
                      .+-+.||+||+|||+.|..|+.|||..        .|++||.||+-||+|++.|+.+..
T Consensus        35 ~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   35 RKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             cchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            456899999999999999999999943        678999999999999999998653

>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]

Probab=98.06  E-value=4e-06  Score=90.13  Aligned_cols=51  Identities=24%  Similarity=0.475  Sum_probs=47.6

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCCC----CCChhchHHHHHHHHHHHHHH
Q 020172          226 TDPQTVAARQRRERISERIRVLQRLVPGGS----KMDTASMLDEAANYLKFLRSQ  276 (330)
Q Consensus       226 s~~Hs~aER~RRerINer~~~LrsLVPg~~----KmDKASILeeAIdYIK~LQ~Q  276 (330)
                      ...|+.+||+||+++|..|.+|.+|||.+.    |+||-+||.+||++||.++.+
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            457899999999999999999999999884    999999999999999999985

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.83  E-value=1.1e-05  Score=87.72  Aligned_cols=62  Identities=23%  Similarity=0.424  Sum_probs=55.5

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCC
Q 020172          226 TDPQTVAARQRRERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALENPGHQK  287 (330)
Q Consensus       226 s~~Hs~aER~RRerINer~~~LrsLVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L  287 (330)
                      +..|+++||+.|-.||++|.+|+.+||+. .|+.|..+|..||+||++|+...+.+..+++.+
T Consensus       277 RtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l  339 (953)
T KOG2588|consen  277 RTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASL  339 (953)
T ss_pred             cchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhh
Confidence            56799999999999999999999999987 799999999999999999999887776655543

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.60  E-value=2.7e-05  Score=76.25  Aligned_cols=55  Identities=25%  Similarity=0.458  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCC--CCCCChhchHHHHHHHHHHHHHHHHHHhCCCC
Q 020172          231 VAARQRRERISERIRVLQRLVPG--GSKMDTASMLDEAANYLKFLRSQVKALENPGH  285 (330)
Q Consensus       231 ~aER~RRerINer~~~LrsLVPg--~~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~  285 (330)
                      .-||+|=.-||-.|..||.|+|.  +.|+.||.||+.+.+||..|..+.-+|-.++.
T Consensus        66 sNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~  122 (373)
T KOG0561|consen   66 SNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNG  122 (373)
T ss_pred             chHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccc
Confidence            34999999999999999999995  68999999999999999999887654444333

>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]

Probab=97.53  E-value=8.6e-05  Score=70.04  Aligned_cols=54  Identities=22%  Similarity=0.272  Sum_probs=46.0

Q ss_pred             CCCCcccHHHHHHHHHHHHHHHHHHhcCCCC--CCCC-hhchHHHHHHHHHHHHHHH
Q 020172          224 ISTDPQTVAARQRRERISERIRVLQRLVPGG--SKMD-TASMLDEAANYLKFLRSQV  277 (330)
Q Consensus       224 ~ss~~Hs~aER~RRerINer~~~LrsLVPg~--~KmD-KASILeeAIdYIK~LQ~QV  277 (330)
                      .+...|+.-||+||..|.++|..|+.+||.+  .+.. .++||..|+.||+.|+.+.
T Consensus        58 ~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~  114 (232)
T KOG2483|consen   58 SSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKS  114 (232)
T ss_pred             cchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHH
Confidence            3445689999999999999999999999976  2333 6999999999999998765

>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]

Probab=97.52  E-value=0.00038  Score=66.86  Aligned_cols=59  Identities=17%  Similarity=0.345  Sum_probs=49.5

Q ss_pred             ccHHHHHHHHHHHHHHHHHHh-cCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCC
Q 020172          229 QTVAARQRRERISERIRVLQR-LVPGG-SKMDTASMLDEAANYLKFLRSQVKALENPGHQK  287 (330)
Q Consensus       229 Hs~aER~RRerINer~~~Lrs-LVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L  287 (330)
                      -++.||+|=.||||.|.+|++ -+++. .++-|..||..||+||..||.-++++..+..-+
T Consensus       122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            467899999999999999985 34554 678999999999999999999998887665544

>PLN03217 transcription factor ATBS1; Provisional

Probab=96.98  E-value=0.00061  Score=56.16  Aligned_cols=52  Identities=27%  Similarity=0.423  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHHhcCCCC------CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCCC
Q 020172          237 RERISERIRVLQRLVPGG------SKMDTASMLDEAANYLKFLRSQVKALENPGHQKP  288 (330)
Q Consensus       237 RerINer~~~LrsLVPg~------~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L~  288 (330)
                      -+.|++-+..||.|+|..      .|...+-||+||..||+.|+.+|..|.+....|-
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL   76 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL   76 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999953      5677888999999999999999999988766653

>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]

Probab=96.84  E-value=0.0011  Score=61.11  Aligned_cols=56  Identities=23%  Similarity=0.427  Sum_probs=48.4

Q ss_pred             ccHHHHHHHHHHHHHHHHHHhcCCC----CCCCChhchHHHHHHHHHHHHHHHHHHhCCC
Q 020172          229 QTVAARQRRERISERIRVLQRLVPG----GSKMDTASMLDEAANYLKFLRSQVKALENPG  284 (330)
Q Consensus       229 Hs~aER~RRerINer~~~LrsLVPg----~~KmDKASILeeAIdYIK~LQ~QVq~Le~~~  284 (330)
                      ++..||.|=+.+|..|..||.+||.    ..|+.|..+|..||.||++|+.-++.-+...
T Consensus       113 ~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~  172 (228)
T KOG4029|consen  113 RNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL  172 (228)
T ss_pred             hhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence            4566999999999999999999994    4689999999999999999999777666443

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=95.49  E-value=0.027  Score=51.10  Aligned_cols=73  Identities=29%  Similarity=0.452  Sum_probs=58.3

Q ss_pred             CCCCCCcccccCcccCCCCCCCCc-------------ccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhchHHHHHHH
Q 020172          205 RPVNLGLEVVEKPKRKNVRISTDP-------------QTVAARQRRERISERIRVLQRLVPGG--SKMDTASMLDEAANY  269 (330)
Q Consensus       205 rP~s~g~~ss~K~rrkr~r~ss~~-------------Hs~aER~RRerINer~~~LrsLVPg~--~KmDKASILeeAIdY  269 (330)
                      +....|.++..|++++.-++.++.             |++.||+|-..+|+.|..||.++|..  .|+.|.--|.-|..|
T Consensus        45 g~l~pgspa~gk~~~ktlr~~~~~~~~~dE~q~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ry  124 (173)
T KOG4447|consen   45 GKLEPGSPADGKRGKKTLRIGTDSIQSLDELQKQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARY  124 (173)
T ss_pred             cccCCCCCCcccccccccccCCCchhhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccC
Confidence            444556666677766655555543             78889999999999999999999954  899999999999999


Q ss_pred             HHHHHHHH
Q 020172          270 LKFLRSQV  277 (330)
Q Consensus       270 IK~LQ~QV  277 (330)
                      |.+|=.-.
T Consensus       125 idfl~~vl  132 (173)
T KOG4447|consen  125 IDFLYQVL  132 (173)
T ss_pred             Cchhhhcc
Confidence            99996543

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=93.07  E-value=0.053  Score=56.71  Aligned_cols=52  Identities=23%  Similarity=0.257  Sum_probs=41.2

Q ss_pred             ccHHHHHHHHHHHHHHHHHHhcCCCCCCC----ChhchHHHHHHHHHHHHHHHHHH
Q 020172          229 QTVAARQRRERISERIRVLQRLVPGGSKM----DTASMLDEAANYLKFLRSQVKAL  280 (330)
Q Consensus       229 Hs~aER~RRerINer~~~LrsLVPg~~Km----DKASILeeAIdYIK~LQ~QVq~L  280 (330)
                      .+..||.|=..|||.|++|.++.----|.    -|--||..||.-|-.|++||++-
T Consensus       530 NNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  530 NNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             hhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            34557777677999999999987543333    37789999999999999999863

>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]

Probab=88.27  E-value=0.25  Score=53.47  Aligned_cols=45  Identities=33%  Similarity=0.499  Sum_probs=39.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHHH
Q 020172          230 TVAARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFLR  274 (330)
Q Consensus       230 s~aER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~LQ  274 (330)
                      .-|.|.||.|-|+-|.+|..+||-.    .-+|||+|+.-||-|+|-=+
T Consensus        51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlrk   99 (768)
T KOG3558|consen   51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLRK   99 (768)
T ss_pred             hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHHH
Confidence            4579999999999999999999933    56999999999999997433

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=85.55  E-value=0.89  Score=48.49  Aligned_cols=39  Identities=31%  Similarity=0.564  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHH
Q 020172          233 ARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLK  271 (330)
Q Consensus       233 ER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK  271 (330)
                      -|+-|+|+|..|+.|-+|+|=.    .|+||-+||.-+|-|++
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            4567999999999999999943    89999999999999986

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=85.43  E-value=0.94  Score=47.02  Aligned_cols=44  Identities=36%  Similarity=0.508  Sum_probs=39.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHH
Q 020172          230 TVAARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFL  273 (330)
Q Consensus       230 s~aER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~L  273 (330)
                      .-+.|.||++-|-.|.+|-.|+|-.    ..+||++|+.-|..|||.-
T Consensus         6 KnaA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    6 KNAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             hhHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            3578999999999999999999954    5699999999999999863

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	330
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	1e-09
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	2e-06
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-06
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-06
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-05
4f3l_A	361	Mclock, circadian locomoter output cycles protein	3e-04

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C Length = 82

 Score = 53.2 bits (128), Expect = 1e-09
 Identities = 14/49 (28%), Positives = 33/49 (67%), Gaps = 1/49 (2%)

Query: 234 RQRRERISERIRVLQRLVPG-GSKMDTASMLDEAANYLKFLRSQVKALE 281
           ++ R  I+++I  L+ LV G  +K++ +++L +A +Y++FL+   + L+
Sbjct: 15  KRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLK 63

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 Length = 88

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 3/51 (5%)

Query: 234 RQRRERISERIRVLQRLVPG---GSKMDTASMLDEAANYLKFLRSQVKALE 281
           RQRR  +      L+  +P      K     +L +A  Y+  ++++ + L 
Sbjct: 15  RQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLI 65

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B Length = 83

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 234 RQRRERISERIRVLQRLVPG--GSKMDTASMLDEAANYLKFLRSQVKALE 281
           R+RR+ I +    L+  VP   G K   A +LD+A  Y++++R +    +
Sbjct: 11  RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQ 60

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 43.1 bits (102), Expect = 4e-06
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 234 RQRRERISERIRVLQRLVPG--GSKMDTASMLDEAANYLKFLRSQVKALE 281
           R+RR+ I +    L+  VP   G K   A +LD+A  Y++++R +    +
Sbjct: 21  RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQ 70

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1 Length = 65

 Score = 41.2 bits (97), Expect = 2e-05
 Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 234 RQRRERISERIRVLQRLVPGGSKMDT------ASMLDEAANYLKFLRSQVK 278
           R+RR++I+  I  L +++P  S   T        +L +A++Y++ LR    
Sbjct: 14  RRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 361

 Score = 41.1 bits (96), Expect = 3e-04
 Identities = 18/82 (21%), Positives = 41/82 (50%), Gaps = 5/82 (6%)

Query: 215 EKPKRKNVRISTDPQTVAARQRRERISERIRVLQRLVPG-GSKMDTASMLDEAANYLKFL 273
           E  K K  R+S +    + ++RR++ +  I+ L  ++PG   KMD +++L ++ ++L+  
Sbjct: 5   EDDKDKAKRVSRNK---SEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR-K 60

Query: 274 RSQVKALENPGHQKPDHHHSMN 295
             +  A  +    + D   +  
Sbjct: 61  HKETTAQSDASEIRQDWKPTFL 82

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	330
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.56
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.53
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.46
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.45
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.45
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.39
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.39
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.36
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.3
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.24
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.16
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.9
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	98.86
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	98.82
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.77
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.44
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.39
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	97.86

>1am9_A Srebp-1A, protein (sterol regulatory element binding protein 1A); basic-helix-loop- helix-leucine zipper, transcription factor; HET: DNA; 2.30A {Homo sapiens} SCOP: a.38.1.1 PDB: 1ukl_C

Probab=99.56  E-value=1e-15  Score=120.38  Aligned_cols=62  Identities=23%  Similarity=0.444  Sum_probs=57.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCCC
Q 020172          227 DPQTVAARQRRERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALENPGHQKP  288 (330)
Q Consensus       227 ~~Hs~aER~RRerINer~~~LrsLVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L~  288 (330)
                      ..|+.+||+||++||++|..|+.|||++ .|+||++||++||+||++||.+++.|+.+...|.
T Consensus         8 ~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~   70 (82)
T 1am9_A            8 TAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3799999999999999999999999997 8999999999999999999999999998765543

>4ati_A MITF, microphthalmia-associated transcription factor; DNA-binding protein-DNA complex, melanoma; 2.60A {Mus musculus} PDB: 4atk_A

Probab=99.53  E-value=8.4e-15  Score=122.42  Aligned_cols=63  Identities=22%  Similarity=0.474  Sum_probs=52.4

Q ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHhcCCCCC----CCChhchHHHHHHHHHHHHHHHHHHhCCCC
Q 020172          223 RISTDPQTVAARQRRERISERIRVLQRLVPGGS----KMDTASMLDEAANYLKFLRSQVKALENPGH  285 (330)
Q Consensus       223 r~ss~~Hs~aER~RRerINer~~~LrsLVPg~~----KmDKASILeeAIdYIK~LQ~QVq~Le~~~~  285 (330)
                      +..+.+|+++||+||++||++|..|+.|||++.    |++|++||+.||+||++||.+++.|+++..
T Consensus        25 ~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~   91 (118)
T 4ati_A           25 RQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN   91 (118)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445679999999999999999999999999873    688999999999999999999999986543

>4h10_B Circadian locomoter output cycles protein kaput; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.46  E-value=5.7e-14  Score=108.98  Aligned_cols=56  Identities=23%  Similarity=0.469  Sum_probs=51.9

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhC
Q 020172          227 DPQTVAARQRRERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALEN  282 (330)
Q Consensus       227 ~~Hs~aER~RRerINer~~~LrsLVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~  282 (330)
                      ..|+.+||+||++||++|.+|+.|||+. .|+||++||+.||+||++||.++.=|+.
T Consensus        10 ~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~~   66 (71)
T 4h10_B           10 VSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLEH   66 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             hhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHHh
Confidence            4799999999999999999999999975 6999999999999999999999887763

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1

Probab=99.45  E-value=1.1e-14  Score=109.99  Aligned_cols=53  Identities=21%  Similarity=0.429  Sum_probs=48.0

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCC-------CCCChhchHHHHHHHHHHHHHHHH
Q 020172          226 TDPQTVAARQRRERISERIRVLQRLVPGG-------SKMDTASMLDEAANYLKFLRSQVK  278 (330)
Q Consensus       226 s~~Hs~aER~RRerINer~~~LrsLVPg~-------~KmDKASILeeAIdYIK~LQ~QVq  278 (330)
                      ...|.++||+||++||..|..|+.|||++       .|++||+||+.||+||++||.+|+
T Consensus         3 r~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            45899999999999999999999999954       577899999999999999998763

>1an4_A Protein (upstream stimulatory factor); protein-DNA complex, double helix, overhanging base, transcription/DNA complex; HET: DNA; 2.90A {Homo sapiens} SCOP: a.38.1.1

Probab=99.45  E-value=2.5e-14  Score=107.20  Aligned_cols=52  Identities=25%  Similarity=0.491  Sum_probs=48.3

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCCCCC------CCChhchHHHHHHHHHHHHHHH
Q 020172          226 TDPQTVAARQRRERISERIRVLQRLVPGGS------KMDTASMLDEAANYLKFLRSQV  277 (330)
Q Consensus       226 s~~Hs~aER~RRerINer~~~LrsLVPg~~------KmDKASILeeAIdYIK~LQ~QV  277 (330)
                      ...|+.+||+||++||+.|..|+.|||++.      |+||++||++||+||++||.++
T Consensus         6 r~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            458999999999999999999999999875      7899999999999999999865

>1hlo_A Protein (transcription factor MAX); transcriptional regulation, DNA binding, complex (transcription factor MAX/DNA), transcription/DNA complex; HET: DNA; 2.80A {Homo sapiens} SCOP: a.38.1.1

Probab=99.39  E-value=1.2e-13  Score=107.49  Aligned_cols=60  Identities=23%  Similarity=0.429  Sum_probs=55.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG--SKMDTASMLDEAANYLKFLRSQVKALENPGHQK  287 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~--~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L  287 (330)
                      .|+.+||+||..||+.|..|+.|||..  .|++|++||..||+||+.|+.+++.|+.+...|
T Consensus        15 ~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L   76 (80)
T 1hlo_A           15 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            799999999999999999999999976  699999999999999999999999998766554

>4h10_A ARYL hydrocarbon receptor nuclear translocator-LI 1; BHLH, circadian transcription, transcription-DNA complex; 2.40A {Homo sapiens}

Probab=99.39  E-value=3.5e-14  Score=110.33  Aligned_cols=49  Identities=29%  Similarity=0.465  Sum_probs=46.1

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHHHH
Q 020172          227 DPQTVAARQRRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFLRS  275 (330)
Q Consensus       227 ~~Hs~aER~RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~LQ~  275 (330)
                      ..|+.+||+||++||+.|.+|+.|||.+    .|+|||+||+.||+||+.|+.
T Consensus        11 ~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A           11 EAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            4799999999999999999999999976    799999999999999999974

>1nkp_B MAX protein, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1 PDB: 1an2_A* 1r05_A 1nlw_B

Probab=99.36  E-value=8.5e-13  Score=103.09  Aligned_cols=58  Identities=24%  Similarity=0.451  Sum_probs=53.0

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhchHHHHHHHHHHHHHHHHHHhCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG--SKMDTASMLDEAANYLKFLRSQVKALENPGH  285 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~--~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~  285 (330)
                      .|+.+||+||+.||+.|..|+.+||.+  .|++|++||..||+||+.|+.+++.|+.+..
T Consensus         5 ~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~   64 (83)
T 1nkp_B            5 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID   64 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999974  8999999999999999999998888776543

>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ, heterodimer, transcription/DNA complex; 1.80A {Homo sapiens} SCOP: a.38.1.1

Probab=99.30  E-value=2.1e-12  Score=102.93  Aligned_cols=56  Identities=21%  Similarity=0.341  Sum_probs=51.6

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHHHHhCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVKALENP  283 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq~Le~~  283 (330)
                      .|+.+||+||+.||++|..|+.+||..   .|++|++||..||+||++|+.+.+.|..+
T Consensus         9 ~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~   67 (88)
T 1nkp_A            9 THNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISE   67 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999999999999975   69999999999999999999998876543

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A*

Probab=99.24  E-value=4.9e-12  Score=98.84  Aligned_cols=56  Identities=25%  Similarity=0.296  Sum_probs=49.5

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC---CCCC-ChhchHHHHHHHHHHHHHHHHHHhC
Q 020172          227 DPQTVAARQRRERISERIRVLQRLVPG---GSKM-DTASMLDEAANYLKFLRSQVKALEN  282 (330)
Q Consensus       227 ~~Hs~aER~RRerINer~~~LrsLVPg---~~Km-DKASILeeAIdYIK~LQ~QVq~Le~  282 (330)
                      ..|+..||+||+.||++|..|+.+||.   +.|. .|..||..||+||++||.++++++.
T Consensus         7 ~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            7 AHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             hhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            378999999999999999999999995   3555 6889999999999999999999865

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1

Probab=99.16  E-value=3.7e-11  Score=94.46  Aligned_cols=59  Identities=25%  Similarity=0.290  Sum_probs=53.3

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHHHHhCCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVKALENPGHQ  286 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~  286 (330)
                      .|+..||+||..|++.|..|+++||..   .|++|+.||..|++||+.|+.+.+.|..+...
T Consensus         4 ~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~   65 (80)
T 1nlw_A            4 THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQ   65 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999999965   68899999999999999999999888765443

>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.90  E-value=1e-09  Score=103.29  Aligned_cols=52  Identities=19%  Similarity=0.446  Sum_probs=42.9

Q ss_pred             CCcccHHHHHHHHHHHHHHHHHHhcCC-CCCCCChhchHHHHHHHHHHHHHHH
Q 020172          226 TDPQTVAARQRRERISERIRVLQRLVP-GGSKMDTASMLDEAANYLKFLRSQV  277 (330)
Q Consensus       226 s~~Hs~aER~RRerINer~~~LrsLVP-g~~KmDKASILeeAIdYIK~LQ~QV  277 (330)
                      ..+|+.+||+||++||+.|.+|++||| ...|+||++||..||+|||.|+...
T Consensus        13 ~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~   65 (361)
T 4f3l_A           13 RVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETT   65 (361)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhc
Confidence            347889999999999999999999999 4579999999999999999998653

>1mdy_A Protein (MYOD BHLH domain); protein-DNA complex, transcription/DNA complex; HET: DNA; 2.80A {Mus musculus} SCOP: a.38.1.1 PDB: 1mdy_B*

Probab=98.86  E-value=1.8e-09  Score=82.84  Aligned_cols=50  Identities=20%  Similarity=0.406  Sum_probs=46.3

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhchHHHHHHHHHHHHHHH
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG--SKMDTASMLDEAANYLKFLRSQV  277 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~--~KmDKASILeeAIdYIK~LQ~QV  277 (330)
                      .|+..||+|+..||+.|..|+.+||..  .|++|+.+|..||+||.+|+..+
T Consensus        15 ~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           15 AATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999964  78999999999999999999865

>2ql2_B Neurod1, neurogenic differentiation factor 1; basic-helix-loop-helix; HET: DNA; 2.50A {Mus musculus}

Probab=98.82  E-value=4.4e-09  Score=78.73  Aligned_cols=51  Identities=22%  Similarity=0.322  Sum_probs=46.2

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHH
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVK  278 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq  278 (330)
                      .++..||+|+..||+.|..||.+||..   .|+.|..+|..||+||.+|+..++
T Consensus         5 ~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            5 KANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            367889999999999999999999964   589999999999999999998753

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus}

Probab=98.77  E-value=1.9e-09  Score=102.90  Aligned_cols=51  Identities=27%  Similarity=0.453  Sum_probs=47.2

Q ss_pred             CCCcccHHHHHHHHHHHHHHHHHHhcCC----CCCCCChhchHHHHHHHHHHHHH
Q 020172          225 STDPQTVAARQRRERISERIRVLQRLVP----GGSKMDTASMLDEAANYLKFLRS  275 (330)
Q Consensus       225 ss~~Hs~aER~RRerINer~~~LrsLVP----g~~KmDKASILeeAIdYIK~LQ~  275 (330)
                      ++.+|+.+||+||++||+.|.+|+.|||    ...|+||++||..||+|||.|+.
T Consensus        13 ~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            3458999999999999999999999999    56899999999999999999984

>4ath_A MITF, microphthalmia-associated transcription factor; DNA binding protein, melanoma; HET: MSE; 1.95A {Mus musculus}

Probab=98.44  E-value=1.8e-07  Score=74.73  Aligned_cols=48  Identities=21%  Similarity=0.450  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHhcCCCC----CCCChhchHHHHHHHHHHHHHHHHHHhCC
Q 020172          236 RRERISERIRVLQRLVPGG----SKMDTASMLDEAANYLKFLRSQVKALENP  283 (330)
Q Consensus       236 RRerINer~~~LrsLVPg~----~KmDKASILeeAIdYIK~LQ~QVq~Le~~  283 (330)
                      -|..||++|.+|..|||.+    .|.+|++||..||+||++||.+++.+.++
T Consensus         3 ~R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~   54 (83)
T 4ath_A            3 MRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   54 (83)
T ss_dssp             CHHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHH
T ss_pred             chhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3889999999999999975    47899999999999999999987766543

>2lfh_A DNA-binding protein inhibitor ID-3; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=98.39  E-value=7.3e-08  Score=74.45  Aligned_cols=45  Identities=18%  Similarity=0.310  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHH
Q 020172          231 VAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRS  275 (330)
Q Consensus       231 ~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~  275 (330)
                      ..||+|+..||+.|..||.+||..   .|++|..+|..||+||..||.
T Consensus        20 erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           20 EEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            448888999999999999999965   689999999999999999984

>4aya_A DNA-binding protein inhibitor ID-2; cell cycle; 2.10A {Homo sapiens}

Probab=97.86  E-value=2.6e-05  Score=63.81  Aligned_cols=50  Identities=16%  Similarity=0.211  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHHHHhC
Q 020172          233 ARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVKALEN  282 (330)
Q Consensus       233 ER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq~Le~  282 (330)
                      ||.|=..||+.|..||.+||..   .|+.|..+|..||+||..|+..++.-..
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~~   85 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLK   85 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            5667788999999999999964   6899999999999999999998776544

---

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	330
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	4e-13
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-09
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-09
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	2e-09
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-08
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	3e-08
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	7e-08
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	9e-08

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.3 bits (149), Expect = 4e-13
 Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 1/46 (2%)

Query: 237 RERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALE 281
           R  I+++I  L+ LV G  +KM  + +L +A +Y+K+L+     L 
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLR 46

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 51.4 bits (123), Expect = 1e-09
 Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 7/55 (12%)

Query: 231 VAARQRRERISERIRVLQRLVPG-------GSKMDTASMLDEAANYLKFLRSQVK 278
            A + RR R++  +  L  L+P         +    A+ ++ A  Y++ L+    
Sbjct: 8   HAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (123), Expect = 2e-09
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 3/51 (5%)

Query: 234 RQRRERISERIRVLQRLVP---GGSKMDTASMLDEAANYLKFLRSQVKALE 281
           RQRR  +      L+  +P      K     +L +A  Y+  ++++ + L 
Sbjct: 15  RQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLI 65

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.4 bits (123), Expect = 2e-09
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 2/50 (4%)

Query: 234 RQRRERISERIRVLQRLVPG--GSKMDTASMLDEAANYLKFLRSQVKALE 281
           R+RR+ I +    L+  VP   G K   A +LD+A  Y++++R +    +
Sbjct: 11  RKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQ 60

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.2 bits (117), Expect = 1e-08
 Identities = 14/49 (28%), Positives = 33/49 (67%), Gaps = 1/49 (2%)

Query: 234 RQRRERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALE 281
           ++ R  I+++I  L+ LV G  +K++ +++L +A +Y++FL+   + L+
Sbjct: 15  KRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLK 63

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.4 bits (115), Expect = 3e-08
 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 3/51 (5%)

Query: 234 RQRRERISERIRVLQRLVPGGS---KMDTASMLDEAANYLKFLRSQVKALE 281
           + RR  +   +  L+ LVP G    +  T S+L +A  ++K L    +   
Sbjct: 10  KNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAV 60

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 68

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.8 bits (111), Expect = 7e-08
 Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 3/66 (4%)

Query: 216 KPKRKNVRIST-DPQTVAARQRRERISERIRVLQRLVPG--GSKMDTASMLDEAANYLKF 272
           + KRK          T+  R+R  +++E    L+R        ++    +L  A  Y++ 
Sbjct: 2   ELKRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEG 61

Query: 273 LRSQVK 278
           L++ ++
Sbjct: 62  LQALLR 67

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (110), Expect = 9e-08
 Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 6/51 (11%)

Query: 234 RQRRERISERIRVLQRLVP------GGSKMDTASMLDEAANYLKFLRSQVK 278
           R+RR++I+  I  L +++P        S      +L +A++Y++ LR    
Sbjct: 14  RRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	330
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.42
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.42
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.38
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.33
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.32
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.29

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.42  E-value=3.4e-14  Score=104.68  Aligned_cols=51  Identities=22%  Similarity=0.455  Sum_probs=47.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCC-------CCCCChhchHHHHHHHHHHHHHHH
Q 020172          227 DPQTVAARQRRERISERIRVLQRLVPG-------GSKMDTASMLDEAANYLKFLRSQV  277 (330)
Q Consensus       227 ~~Hs~aER~RRerINer~~~LrsLVPg-------~~KmDKASILeeAIdYIK~LQ~QV  277 (330)
                      ..|+.+||+||++||+.|..|+.|||+       ..|++|+.||+.||+||++||.+|
T Consensus         4 ~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           4 ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            479999999999999999999999994       478999999999999999999865

>d1am9a_ a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-1a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=5.9e-14  Score=107.43  Aligned_cols=60  Identities=23%  Similarity=0.464  Sum_probs=55.0

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALENPGHQK  287 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L  287 (330)
                      .|+.+||+||++||+.|..|++|||+. .|++|++||..||+||++|+.+++.|+.+...|
T Consensus         9 ~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~l   69 (80)
T d1am9a_           9 AHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999999999999986 699999999999999999999999998765433

>d1mdya_ a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myod B/HLH domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=1e-13  Score=103.81  Aligned_cols=51  Identities=20%  Similarity=0.416  Sum_probs=47.7

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC--CCCChhchHHHHHHHHHHHHHHHH
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG--SKMDTASMLDEAANYLKFLRSQVK  278 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~--~KmDKASILeeAIdYIK~LQ~QVq  278 (330)
                      .|+..||+||++||+.|..|+.|||.+  .|+||++||..||+||++||.+|+
T Consensus        15 ~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          15 AATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            689999999999999999999999985  689999999999999999998764

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Mad protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.37  E-value=4.1e-13  Score=102.02  Aligned_cols=58  Identities=24%  Similarity=0.279  Sum_probs=52.9

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHHHHhCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVKALENPGH  285 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~  285 (330)
                      .|+.+||+||++||++|..|+.|||++   .|++|++||..||+||++|+.+++.|+.+..
T Consensus         4 ~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~   64 (79)
T d1nlwa_           4 THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQID   64 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999975   5899999999999999999999998876543

>d1nkpb_ a.38.1.1 (B:) Max protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Max protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=7.5e-13  Score=101.39  Aligned_cols=58  Identities=26%  Similarity=0.514  Sum_probs=52.8

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCC--CCCCChhchHHHHHHHHHHHHHHHHHHhCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPG--GSKMDTASMLDEAANYLKFLRSQVKALENPGH  285 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg--~~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~  285 (330)
                      .|+.+||+||++||+.|..|++|||+  ..|++|++||..||+||++|+.+++.|+.+..
T Consensus         5 ~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~   64 (83)
T d1nkpb_           5 HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID   64 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            68999999999999999999999996  47899999999999999999999988876443

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=6.2e-14  Score=102.90  Aligned_cols=51  Identities=29%  Similarity=0.475  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHHhcCCCC-CCCChhchHHHHHHHHHHHHHHHHHHhCCCCCC
Q 020172          237 RERISERIRVLQRLVPGG-SKMDTASMLDEAANYLKFLRSQVKALENPGHQK  287 (330)
Q Consensus       237 RerINer~~~LrsLVPg~-~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~~L  287 (330)
                      |++||++|..|++|||++ .|+||++||.+||+||++||.+++.|+.+...|
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L   52 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVL   52 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999987 599999999999999999999999998776544

>d1nkpa_ a.38.1.1 (A:) Myc proto-oncogene protein {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Myc proto-oncogene protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=8e-13  Score=102.23  Aligned_cols=58  Identities=21%  Similarity=0.327  Sum_probs=52.9

Q ss_pred             cccHHHHHHHHHHHHHHHHHHhcCCCC---CCCChhchHHHHHHHHHHHHHHHHHHhCCCC
Q 020172          228 PQTVAARQRRERISERIRVLQRLVPGG---SKMDTASMLDEAANYLKFLRSQVKALENPGH  285 (330)
Q Consensus       228 ~Hs~aER~RRerINer~~~LrsLVPg~---~KmDKASILeeAIdYIK~LQ~QVq~Le~~~~  285 (330)
                      .|+.+||+||++||+.|..|++|||+.   .|++|++||..||+||+.|+.+++.|+.+..
T Consensus         9 ~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~   69 (88)
T d1nkpa_           9 THNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEED   69 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            699999999999999999999999965   6799999999999999999999988876443

>d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Usf B/HLH domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=7.2e-13  Score=97.98  Aligned_cols=51  Identities=25%  Similarity=0.502  Sum_probs=46.7

Q ss_pred             CcccHHHHHHHHHHHHHHHHHHhcCCCC------CCCChhchHHHHHHHHHHHHHHH
Q 020172          227 DPQTVAARQRRERISERIRVLQRLVPGG------SKMDTASMLDEAANYLKFLRSQV  277 (330)
Q Consensus       227 ~~Hs~aER~RRerINer~~~LrsLVPg~------~KmDKASILeeAIdYIK~LQ~QV  277 (330)
                      ..|+.+||+||++||+.|..|+.|||..      .|++|++||..||+||++||.+.
T Consensus         7 ~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           7 AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            3799999999999999999999999964      48999999999999999998753