Citrus Sinensis ID: 044343

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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-
Protein Sequence
VPWNFSVASGDSEKGQSSRNENSFDFLESSASQLPTSWHQTSHSLDTDVDDFSDATEISEGMERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPKLGMGSGIGTGMVDVLFSWSSRDIIGSLGQSASFISS
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHEEccEEccccHHHccccccccEEcc
Coil and Loop (DISEMBL)
vpwnfsvasgdsekgqssrnensFDFLEssasqlptswhqtshsldtdvddfsdateisegmerkpdnrpkrthsaevhnqserRRRDRINKRLKSLKElvpncnksdrasvLDDAVNYVKALRHQLEMMSaqggaifqspfmspsghqstevpqispnvpispklgmgsgigtGMVDVLFSwssrdiigslgqsasfiss
Flexible Loop (DISEMBL)
vpwnfsvasgdsekgqssrNENSFDFLESSASQLPTSWHQTSHSLDTDVDDFSDATEisegmerkpdnrpkrthsaevhnqserrrrdriNKRLKslkelvpncnksdrasvlDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPKLGMGSGIGTGMVDVLFSWSSRDIIgslgqsasfiss
Low Complexity Region (SEG)
VPWNFSVASGDSEKGQSSRNENSFDFLESSASQLPTSWHQTSHSLDTDVDDFSDATEISEGMERKPDNRPKRTHSAEVHNQSErrrrdrINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPKLGMGSGIGTGMVDVLFSWSSRDIIGSLGQSASFISS
Disordered region (IsUnstruct)
***************************************************************************************************************VLDDAVNYVKALRHQLE***************************************MGSGIGTGMVDVLFSWSSRDIIGS**********
Disordered Region (DISOPRED)
*PWNF**********************************************************************************DRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLE*************************************************************************
Disordered Region (DISEMBL)
*********************NSFDFLESSASQLPTSWHQTSHSLDTDVDDFSDATEISE**************************RDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFM***********QISPNVPISPKLGMGSGIGTGMVDVLFSWSSRDIIGSLGQSASFISS
Disordered Region (DISPRO)
************************************************************************************RRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPKLGMGSGIGTGMVDVLFSWSSRDIIGSLGQ*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
VPWNFSVASGDSEKGQSSRNENSFDFLESSASQLPTSWHQTSHSLDTDVDDFSDATEISEGMERKPDNRPKRTHSAEVHxxxxxxxxxxxxxxxxxxxxxVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPKLGMGSGIGTGMVDVLFSWSSRDIIGSLGQSASFISS
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	201	2.2.26 [Sep-21-2011]
O80536	524	Transcription factor PIF3	yes	no	0.572	0.219	0.439	3e-20
Q8GZM7	478	Transcription factor PIF1	no	no	0.303	0.127	0.639	8e-19
Q8L5W8	416	Transcription factor PIL1	no	no	0.487	0.235	0.435	1e-17
Q9SVU7	445	Putative transcription fa	no	no	0.497	0.224	0.398	1e-15
Q8GZ38	399	Transcription factor UNE1	no	no	0.303	0.152	0.557	1e-15
Q9SVU6	413	Transcription factor bHLH	no	no	0.502	0.244	0.372	2e-15
Q9FUA4	373	Transcription factor SPAT	no	no	0.417	0.225	0.416	2e-14
Q7XHI7	307	Transcription factor bHLH	no	no	0.398	0.260	0.432	3e-14
Q8S3D5	310	Transcription factor bHLH	no	no	0.368	0.238	0.486	1e-13
Q84LH8	444	Transcription factor PIF5	no	no	0.432	0.195	0.467	3e-13

>sp|O80536|PIF3_ARATH Transcription factor PIF3 OS=Arabidopsis thaliana GN=PIF3 PE=1 SV=1

 Score = 98.2 bits (243), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 54/123 (43%), Positives = 78/123 (63%), Gaps = 8/123 (6%)

Query: 32  SQLPTSWHQTSHSLDTDVDDFSDATEISEGMERKPDNRP-------KRTHSAEVHNQSER 84
           S+ P+   +  HS   D+D  S+  E   G  RK +  P       KR+ SAEVHN SER
Sbjct: 295 SESPSLSLKRKHSNIQDIDCHSEDVEEESGDGRK-EAGPSRTGLGSKRSRSAEVHNLSER 353

Query: 85  RRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMS 144
           RRRDRIN+++++L+EL+PNCNK D+AS+LD+A+ Y+K+L+ Q+++MS   G       M 
Sbjct: 354 RRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKSLQLQVQIMSMASGYYLPPAVMF 413

Query: 145 PSG 147
           P G
Sbjct: 414 PPG 416

Transcription factor acting positively in the phytochrome signaling pathway. Activates transcription by binding to the G box (5'-CACGTG-3').
Arabidopsis thaliana (taxid: 3702)

>sp|Q8GZM7|PIF1_ARATH Transcription factor PIF1 OS=Arabidopsis thaliana GN=PIF1 PE=1 SV=1

 Score = 93.6 bits (231), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 39/61 (63%), Positives = 56/61 (91%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMM 130
           KR+ +AEVHN SER+RRDRIN+R+K+L+EL+P CNKSD+AS+LD+A+ Y+K+L+ Q++MM
Sbjct: 281 KRSRAAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQLQIQMM 340

Query: 131 S 131
           S
Sbjct: 341 S 341

Transcription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA).

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L5W8|PIL1_ARATH Transcription factor PIL1 OS=Arabidopsis thaliana GN=PIL1 PE=1 SV=1

 Score = 89.7 bits (221), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/101 (43%), Positives = 64/101 (63%), Gaps = 3/101 (2%)

Query: 50  DDFSDATEISEGMERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDR 109
           D+  DA        RKP    KR  S EVH   ER+RRD  NK++++L++L+PNC K D+
Sbjct: 207 DESDDAKTQVHARTRKPVT--KRKRSTEVHKLYERKRRDEFNKKMRALQDLLPNCYKDDK 264

Query: 110 ASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQS 150
           AS+LD+A+ Y++ L+ Q++MMS  G  + + P M P GH S
Sbjct: 265 ASLLDEAIKYMRTLQLQVQMMS-MGNGLIRPPTMLPMGHYS 304

Transcription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVU7|BH056_ARATH Putative transcription factor bHLH056 OS=Arabidopsis thaliana GN=BHLH56 PE=4 SV=2

 Score = 83.2 bits (204), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 43/108 (39%), Positives = 69/108 (63%), Gaps = 8/108 (7%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLE-M 129
           KR+ +AE+HN +ERRRR++IN+++K+L++L+P CNKS + S LDDA+ YVK+L+ Q++ M
Sbjct: 252 KRSRTAEMHNLAERRRREKINEKMKTLQQLIPRCNKSTKVSTLDDAIEYVKSLQSQIQGM 311

Query: 130 MSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPIS----PKLGMGSGIG 173
           MS    A     FM    H + ++ +  P +P      P     +G+G
Sbjct: 312 MSPMMNAGNTQQFMP---HMAMDMNRPPPFIPFPGTSFPMPAQMAGVG 356

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GZ38|UNE10_ARATH Transcription factor UNE10 OS=Arabidopsis thaliana GN=UNE10 PE=2 SV=1

 Score = 82.8 bits (203), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 34/61 (55%), Positives = 53/61 (86%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMM 130
           KR+ +A +HNQSER+RRD+IN+R+K+L++LVPN +K+D+AS+LD+ + Y+K L+ Q+ MM
Sbjct: 210 KRSRAAAIHNQSERKRRDKINQRMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVSMM 269

Query: 131 S 131
           S
Sbjct: 270 S 270

Required during the fertilization of ovules by pollen.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SVU6|BH023_ARATH Transcription factor bHLH23 OS=Arabidopsis thaliana GN=BHLH23 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 41/110 (37%), Positives = 65/110 (59%), Gaps = 9/110 (8%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMM 130
           KR+ +A +H  SERRRR +IN+ +K+L+EL+P C K+DR+S+LDD + YVK+L+ Q++M 
Sbjct: 274 KRSRAAIMHKLSERRRRQKINEMMKALQELLPRCTKTDRSSMLDDVIEYVKSLQSQIQMF 333

Query: 131 SAQGGAIFQSPFMSPSGHQSTEVPQISPN-------VPISPKLGMGSGIG 173
           S   G +   P M     Q   +P ++         +P   +  M  G+G
Sbjct: 334 SM--GHVMIPPMMYAGNIQQQYMPHMAMGMNRPPAFIPFPRQAHMAEGVG 381

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FUA4|SPT_ARATH Transcription factor SPATULA OS=Arabidopsis thaliana GN=SPT PE=1 SV=1

 Score = 79.3 bits (194), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 59/84 (70%)

Query: 75  SAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQG 134
           +AEVHN SE+RRR RIN+++K+L+ L+PN NK+D+AS+LD+A+ Y+K L+ Q++M++ + 
Sbjct: 198 AAEVHNLSEKRRRSRINEKMKALQSLIPNSNKTDKASMLDEAIEYLKQLQLQVQMLTMRN 257

Query: 135 GAIFQSPFMSPSGHQSTEVPQISP 158
           G       +  +     ++ QI P
Sbjct: 258 GINLHPLCLPGTTLHPLQLSQIRP 281

Transcription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7XHI7|BH127_ARATH Transcription factor bHLH127 OS=Arabidopsis thaliana GN=BHLH127 PE=2 SV=1

 Score = 78.2 bits (191), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 56/81 (69%), Gaps = 1/81 (1%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQL-EM 129
           KR+ +AE+HN +ERRRR++IN+R+K+L++L+P CNKS + S+L+D + YVK+L  Q+ + 
Sbjct: 147 KRSRAAEMHNLAERRRREKINERMKTLQQLIPRCNKSTKVSMLEDVIEYVKSLEMQINQF 206

Query: 130 MSAQGGAIFQSPFMSPSGHQS 150
           M      + Q P   P   Q+
Sbjct: 207 MPHMAMGMNQPPAYIPFPSQA 227

Arabidopsis thaliana (taxid: 3702)

>sp|Q8S3D5|BH069_ARATH Transcription factor bHLH69 OS=Arabidopsis thaliana GN=BHLH69 PE=2 SV=2

 Score = 76.6 bits (187), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 37/76 (48%), Positives = 57/76 (75%), Gaps = 2/76 (2%)

Query: 63  ERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKA 122
           + KP  R +R  + + H+ +ER RR+RI +R+KSL+ELVPN NK+D+AS+LD+ ++YVK 
Sbjct: 125 QTKPKVRARRGQATDPHSIAERLRRERIAERMKSLQELVPNGNKTDKASMLDEIIDYVKF 184

Query: 123 LRHQLEM--MSAQGGA 136
           L+ Q+++  MS  GGA
Sbjct: 185 LQLQVKVLSMSRLGGA 200

Arabidopsis thaliana (taxid: 3702)

>sp|Q84LH8|PIF5_ARATH Transcription factor PIF5 OS=Arabidopsis thaliana GN=PIF5 PE=1 SV=1

 Score = 75.1 bits (183), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 43/92 (46%), Positives = 68/92 (73%), Gaps = 5/92 (5%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMM 130
           +R+ +AEVHN SERRRRDRIN+R+K+L+EL+P+C+++D+AS+LD+A++Y+K+L+ QL++M
Sbjct: 253 RRSRAAEVHNLSERRRRDRINERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQLQVM 312

Query: 131 SAQGG-----AIFQSPFMSPSGHQSTEVPQIS 157
               G     A   SP M P    S  + Q++
Sbjct: 313 WMGSGMAAAAAAAASPMMFPGVQSSPYINQMA 344

Transcription factor acting negatively in the phytochrome B signaling pathway to promote the shade-avoidance response. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. Promotes ethylene activity in the dark. May regulate the expression of a subset of genes by binding to the G-box motif. Might be involved in the integration of light-signals to control both circadian and photomorphogenic processes.

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	201
168023762	1015	predicted protein [Physcomitrella patens	0.527	0.104	0.504	3e-23
356575289	633	PREDICTED: transcription factor PIF3-lik	0.447	0.142	0.505	2e-21
356534971	665	PREDICTED: transcription factor PIF3-lik	0.562	0.169	0.434	7e-21
238015240	435	unknown [Zea mays]	0.592	0.273	0.436	1e-20
238008194	638	unknown [Zea mays] gi|413946840|gb|AFW79	0.572	0.180	0.442	2e-20
56784181	565	putative BP-5 protein [Oryza sativa Japo	0.547	0.194	0.445	2e-20
297606720	447	Os07g0143200 [Oryza sativa Japonica Grou	0.502	0.225	0.435	3e-20
297596562	637	Os01g0286100 [Oryza sativa Japonica Grou	0.547	0.172	0.445	3e-20
23495742	417	transcription factor BHLH9-like protein	0.502	0.242	0.435	3e-20
222618221	705	hypothetical protein OsJ_01348 [Oryza sa	0.547	0.156	0.445	3e-20

>gi|168023762|ref|XP_001764406.1| predicted protein [Physcomitrella patens subsp. patens] gi|162684270|gb|EDQ70673.1| predicted protein [Physcomitrella patens subsp. patens]

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 55/109 (50%), Positives = 82/109 (75%), Gaps = 3/109 (2%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMM 130
           KR+ +AEVHNQSERRRRDRIN+++++L+EL+PN NK+D+AS+LD+A++Y+K L+ QL+MM
Sbjct: 731 KRSRAAEVHNQSERRRRDRINEKMRALQELIPNSNKTDKASMLDEAIDYLKILQLQLQMM 790

Query: 131 SAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPKLGMGS-GIGTGMVD 178
           S + G     P + P G Q  ++PQ+ P V   P +GM   G+G GM++
Sbjct: 791 SIRTGMTL-PPMVMPPGLQHMQMPQM-PQVAAMPSMGMVQMGLGMGMME 837

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356575289|ref|XP_003555774.1| PREDICTED: transcription factor PIF3-like [Glycine max]

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 46/91 (50%), Positives = 69/91 (75%), Gaps = 1/91 (1%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMM 130
           KR+ +AEVHN SERRRRDRIN+++++L+EL+PNCNK D+AS+LD+A+ Y+K L+ Q+++M
Sbjct: 368 KRSRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKTLQLQVQIM 427

Query: 131 SAQGGAIFQSPFMSPSGHQSTEVPQISPNVP 161
           S  G  ++  P M P+G Q    P ++P  P
Sbjct: 428 S-MGAGLYMPPMMLPAGMQHMHAPHMAPFSP 457

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356534971|ref|XP_003536024.1| PREDICTED: transcription factor PIF3-like [Glycine max]

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 53/122 (43%), Positives = 79/122 (64%), Gaps = 9/122 (7%)

Query: 48  DVDDFS----DATEISEGMERKPDNR----PKRTHSAEVHNQSERRRRDRINKRLKSLKE 99
           D DD      D  E S G ++    R     KR+ +AEVHN SER+RRDRIN+++++L+E
Sbjct: 401 DTDDSECHSEDVEEESAGAKKTAGGRGGAGSKRSRAAEVHNLSERKRRDRINEKMRALQE 460

Query: 100 LVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPN 159
           L+PNCNK D+AS+LD+A+ Y+K L+ Q+++MS  G  ++  P M P+G Q    P ++P 
Sbjct: 461 LIPNCNKVDKASMLDEAIEYLKTLQLQVQIMS-MGAGLYMPPMMLPAGMQHMHAPHMAPF 519

Query: 160 VP 161
            P
Sbjct: 520 SP 521

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|238015240|gb|ACR38655.1| unknown [Zea mays]

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 55/126 (43%), Positives = 79/126 (62%), Gaps = 7/126 (5%)

Query: 36  TSWHQTSHSLDTDVDDFSDATEISEGMERKPDNRPKRTHSAEVHNQSERRRRDRINKRLK 95
           T   + S S D D DD S       GM R      KR+ +AEVHN SERRRRDRIN++++
Sbjct: 149 TLQAECSASQDDDPDDESG------GMRRSCSRGAKRSRTAEVHNLSERRRRDRINEKMR 202

Query: 96  SLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQ 155
           +L+EL+PNCNK D+AS+LD+A+ Y+K L+ Q++MMS  G  +   P + P   Q  ++P 
Sbjct: 203 ALQELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMS-MGSGLCIPPMLLPPAMQHLQIPP 261

Query: 156 ISPNVP 161
            + + P
Sbjct: 262 AAAHFP 267

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|238008194|gb|ACR35132.1| unknown [Zea mays] gi|413946840|gb|AFW79489.1| putative HLH DNA-binding domain superfamily protein [Zea mays]

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 54/122 (44%), Positives = 78/122 (63%), Gaps = 7/122 (5%)

Query: 40  QTSHSLDTDVDDFSDATEISEGMERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKE 99
           + S S D D DD S       GM R      KR+ +AEVHN SERRRRDRIN+++++L+E
Sbjct: 356 ECSASQDDDPDDESG------GMRRSCSRGAKRSRTAEVHNLSERRRRDRINEKMRALQE 409

Query: 100 LVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPN 159
           L+PNCNK D+AS+LD+A+ Y+K L+ Q++MMS  G  +   P + P   Q  ++P  + +
Sbjct: 410 LIPNCNKIDKASMLDEAIEYLKTLQLQVQMMS-MGSGLCIPPMLLPPAMQHLQIPPAAAH 468

Query: 160 VP 161
            P
Sbjct: 469 FP 470

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|56784181|dbj|BAD81566.1| putative BP-5 protein [Oryza sativa Japonica Group]

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 53/119 (44%), Positives = 80/119 (67%), Gaps = 9/119 (7%)

Query: 40  QTSHSLDTDVDDFSDATEISEGMERKPDNR-PKRTHSAEVHNQSERRRRDRINKRLKSLK 98
           + S S D D+DD         G+ RK   R  KR+ +AEVHN SERRRRDRIN+++++L+
Sbjct: 284 ECSASQDDDLDD-------EPGVLRKSGTRSTKRSRTAEVHNLSERRRRDRINEKMRALQ 336

Query: 99  ELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQIS 157
           EL+PNCNK D+AS+LD+A+ Y+K L+ Q++MMS  G  +   P + P+  Q  ++P ++
Sbjct: 337 ELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMS-MGTGLCIPPMLLPTAMQHLQIPPMA 394

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297606720|ref|NP_001058876.2| Os07g0143200 [Oryza sativa Japonica Group] gi|255677508|dbj|BAF20790.2| Os07g0143200 [Oryza sativa Japonica Group]

 Score =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 54/124 (43%), Positives = 79/124 (63%), Gaps = 23/124 (18%)

Query: 49  VDDFSDATEISEGMERKPDNRP---KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN 105
           VD  S+  +     E +P  RP   +RT +AEVHN SERRRRDRIN++L++L+ELVP+CN
Sbjct: 206 VDSLSEVAD-----ETRPSKRPAAKRRTRAAEVHNLSERRRRDRINEKLRALQELVPHCN 260

Query: 106 KSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPK 165
           K+D+AS+LD+A+ Y+K+L+ Q+++M    G +   P M P  HQ            + P 
Sbjct: 261 KTDKASILDEAIEYLKSLQMQVQIMWMTTGIV---PMMFPGTHQ------------LMPP 305

Query: 166 LGMG 169
           +GMG
Sbjct: 306 MGMG 309

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297596562|ref|NP_001042775.2| Os01g0286100 [Oryza sativa Japonica Group] gi|215717101|dbj|BAG95464.1| unnamed protein product [Oryza sativa Japonica Group] gi|255673123|dbj|BAF04689.2| Os01g0286100 [Oryza sativa Japonica Group]

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 53/119 (44%), Positives = 80/119 (67%), Gaps = 9/119 (7%)

Query: 40  QTSHSLDTDVDDFSDATEISEGMERKPDNR-PKRTHSAEVHNQSERRRRDRINKRLKSLK 98
           + S S D D+DD         G+ RK   R  KR+ +AEVHN SERRRRDRIN+++++L+
Sbjct: 356 ECSASQDDDLDD-------EPGVLRKSGTRSTKRSRTAEVHNLSERRRRDRINEKMRALQ 408

Query: 99  ELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQIS 157
           EL+PNCNK D+AS+LD+A+ Y+K L+ Q++MMS  G  +   P + P+  Q  ++P ++
Sbjct: 409 ELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMS-MGTGLCIPPMLLPTAMQHLQIPPMA 466

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|23495742|dbj|BAC19953.1| transcription factor BHLH9-like protein [Oryza sativa Japonica Group] gi|24059945|dbj|BAC21408.1| transcription factor BHLH9-like protein [Oryza sativa Japonica Group]

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 54/124 (43%), Positives = 79/124 (63%), Gaps = 23/124 (18%)

Query: 49  VDDFSDATEISEGMERKPDNRP---KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN 105
           VD  S+  +     E +P  RP   +RT +AEVHN SERRRRDRIN++L++L+ELVP+CN
Sbjct: 205 VDSLSEVAD-----ETRPSKRPAAKRRTRAAEVHNLSERRRRDRINEKLRALQELVPHCN 259

Query: 106 KSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPK 165
           K+D+AS+LD+A+ Y+K+L+ Q+++M    G +   P M P  HQ            + P 
Sbjct: 260 KTDKASILDEAIEYLKSLQMQVQIMWMTTGIV---PMMFPGTHQ------------LMPP 304

Query: 166 LGMG 169
           +GMG
Sbjct: 305 MGMG 308

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222618221|gb|EEE54353.1| hypothetical protein OsJ_01348 [Oryza sativa Japonica Group]

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 53/119 (44%), Positives = 80/119 (67%), Gaps = 9/119 (7%)

Query: 40  QTSHSLDTDVDDFSDATEISEGMERKPDNR-PKRTHSAEVHNQSERRRRDRINKRLKSLK 98
           + S S D D+DD         G+ RK   R  KR+ +AEVHN SERRRRDRIN+++++L+
Sbjct: 424 ECSASQDDDLDD-------EPGVLRKSGTRSTKRSRTAEVHNLSERRRRDRINEKMRALQ 476

Query: 99  ELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQIS 157
           EL+PNCNK D+AS+LD+A+ Y+K L+ Q++MMS  G  +   P + P+  Q  ++P ++
Sbjct: 477 ELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMS-MGTGLCIPPMLLPTAMQHLQIPPMA 534

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	201
UNIPROTKB|Q5NAE0	565	P0498A12.33 "Putative BP-5 pro	0.636	0.226	0.397	1.2e-19
TAIR|locus:2012345	524	PIF3 "AT1G09530" [Arabidopsis	0.835	0.320	0.337	8.5e-17
UNIPROTKB|Q8GRJ1	417	OJ1343_B12.103 "Transcription	0.442	0.213	0.432	4.5e-16
TAIR|locus:2053733	430	PIF4 "AT2G43010" [Arabidopsis	0.761	0.355	0.345	1e-15
UNIPROTKB|Q7FA23	181	OSJNBa0058K23.6 "Os04g0618600	0.517	0.574	0.405	5.4e-15
TAIR|locus:2061634	478	PIL5 "phytochrome interacting	0.567	0.238	0.391	6.2e-15
UNIPROTKB|Q948F6	298	OSJNBa0049O12.18 "Putative SPA	0.487	0.328	0.393	8.5e-15
TAIR|locus:2041369	416	PIL1 "phytochrome interacting	0.537	0.259	0.383	9.4e-15
TAIR|locus:2126876	399	UNE10 "AT4G00050" [Arabidopsis	0.681	0.343	0.346	1.1e-14
TAIR|locus:2077680	444	PIL6 "AT3G59060" [Arabidopsis	0.731	0.331	0.318	3e-14

UNIPROTKB|Q5NAE0 P0498A12.33 "Putative BP-5 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 242 (90.2 bits), Expect = 1.2e-19, P = 1.2e-19
 Identities = 56/141 (39%), Positives = 85/141 (60%)

Query:    40 QTSHSLDTDVDDFSDATEISEGMERKPDNRP-KRTHSAEVHNQSEXXXXXXINKRLKSLK 98
             + S S D D+DD         G+ RK   R  KR+ +AEVHN SE      IN+++++L+
Sbjct:   284 ECSASQDDDLDD-------EPGVLRKSGTRSTKRSRTAEVHNLSERRRRDRINEKMRALQ 336

Query:    99 ELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISP 158
             EL+PNCNK D+AS+LD+A+ Y+K L+ Q++MMS  G  +   P + P+  Q  ++P ++ 
Sbjct:   337 ELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMS-MGTGLCIPPMLLPTAMQHLQIPPMAH 395

Query:   159 NVPISPKLGMGSGIGTGMVDV 179
                  P LGMG G G G+ D+
Sbjct:   396 ----FPHLGMGLGYGMGVFDM 412

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2012345 PIF3 "AT1G09530" [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 8.5e-17, P = 8.5e-17
 Identities = 61/181 (33%), Positives = 92/181 (50%)

Query:    11 DSEKGQSSRNENSFDFLESSASQLPTSWHQTSHSLDTDVDDFSDATEISEGMERK---PD 67
             +SEK     +  S + L+   S+ P+   +  HS   D+D  S+  E   G  RK   P 
Sbjct:   275 ESEKAVVCSSVGSGNSLDGP-SESPSLSLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPS 333

Query:    68 NR---PKRTHSAEVHNQSEXXXXXXINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALR 124
                   KR+ SAEVHN SE      IN+++++L+EL+PNCNK D+AS+LD+A+ Y+K+L+
Sbjct:   334 RTGLGSKRSRSAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKSLQ 393

Query:   125 HQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQISPNVPISPKLGMGSGIGTGMVDVLFSWS 184
              Q+++MS   G       M P G          P    +  +GMG     G+ D+    S
Sbjct:   394 LQVQIMSMASGYYLPPAVMFPPGMGHY------PAAAAAMAMGMGMPYAMGLPDLSRGGS 447

Query:   185 S 185
             S
Sbjct:   448 S 448

GO:0003677 "DNA binding" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0009639 "response to red or far red light" evidence=IMP

GO:0010017 "red or far-red light signaling pathway" evidence=RCA;IMP

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0042802 "identical protein binding" evidence=IPI

GO:0031539 "positive regulation of anthocyanin metabolic process" evidence=IMP

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=IMP

GO:0009704 "de-etiolation" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0007165 "signal transduction" evidence=TAS

UNIPROTKB|Q8GRJ1 OJ1343_B12.103 "Transcription factor BHLH9-like protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 206 (77.6 bits), Expect = 4.5e-16, P = 4.5e-16
 Identities = 42/97 (43%), Positives = 67/97 (69%)

Query:    56 TEISEGMERKPDNRP---KRTHSAEVHNQSEXXXXXXINKRLKSLKELVPNCNKSDRASV 112
             +E+++  E +P  RP   +RT +AEVHN SE      IN++L++L+ELVP+CNK+D+AS+
Sbjct:   209 SEVAD--ETRPSKRPAAKRRTRAAEVHNLSERRRRDRINEKLRALQELVPHCNKTDKASI 266

Query:   113 LDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQ 149
             LD+A+ Y+K+L+ Q+++M    G +   P M P  HQ
Sbjct:   267 LDEAIEYLKSLQMQVQIMWMTTGIV---PMMFPGTHQ 300

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2053733 PIF4 "AT2G43010" [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 1.0e-15, P = 1.0e-15
 Identities = 56/162 (34%), Positives = 88/162 (54%)

Query:     9 SGDSEKGQSSRNENSFDFLESSASQLPTSWHQTSHSLDTDVD-DFSDATEISEGMERKPD 67
             +  S  G SS      D  E ++ +  T+  +      TD     SDA   ++  +R   
Sbjct:   194 NASSSSGGSSGCSFGKDIKEMASGRCITTDRKRKRINHTDESVSLSDAIG-NKSNQRSGS 252

Query:    68 NRPKRTHSAEVHNQSEXXXXXXINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQL 127
             NR  R+ +AEVHN SE      IN+R+K+L+EL+P+C+K+D+AS+LD+A++Y+K+L+ QL
Sbjct:   253 NR--RSRAAEVHNLSERRRRDRINERMKALQELIPHCSKTDKASILDEAIDYLKSLQLQL 310

Query:   128 EMM---SAQGGAIFQSPFMSPSGHQSTEVPQI-SP-NVPISP 164
             ++M   S    A   +P M P       + QI SP  +P  P
Sbjct:   311 QVMWMGSGMAAAAASAPMMFPGVQPQQFIRQIQSPVQLPRFP 352

GO:0003677 "DNA binding" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0010017 "red or far-red light signaling pathway" evidence=RCA;IMP

GO:0010161 "red light signaling pathway" evidence=IGI

GO:0009704 "de-etiolation" evidence=IMP

GO:0010600 "regulation of auxin biosynthetic process" evidence=IDA

GO:0010928 "regulation of auxin mediated signaling pathway" evidence=IDA

GO:0000165 "MAPK cascade" evidence=RCA

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

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0007623 "circadian rhythm" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0009867 "jasmonic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

GO:0030003 "cellular cation homeostasis" evidence=RCA

GO:0031348 "negative regulation of defense response" evidence=RCA

GO:0035304 "regulation of protein dephosphorylation" evidence=RCA

UNIPROTKB|Q7FA23 OSJNBa0058K23.6 "Os04g0618600 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 190 (71.9 bits), Expect = 5.4e-15, P = 5.4e-15
 Identities = 43/106 (40%), Positives = 65/106 (61%)

Query:    62 MERKPDNRPKRTHSAEVHNQSEXXXXXXINKRLKSLKELVPNCNKSDRASVLDDAVNYVK 121
             ME +     +R+ SAE HN SE      IN++LK+L+EL+PNC K+D+ S+LD+A++Y+K
Sbjct:     1 MEARRPTPTRRSRSAEFHNFSERRRRDRINEKLKALQELLPNCTKTDKVSMLDEAIDYLK 60

Query:   122 ALRHQLEMM-SAQGGAIFQSPFMSPSGHQSTEVP-QISPNVPISPK 165
             +L+ QL+M+   +G A    P +    H  T  P QI P  P  P+
Sbjct:    61 SLQLQLQMLVMGKGMAPVVPPELQQYMHYITADPSQIPPIRPSEPR 106

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2061634 PIL5 "phytochrome interacting factor 3-like 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 197 (74.4 bits), Expect = 6.2e-15, P = 6.2e-15
 Identities = 47/120 (39%), Positives = 69/120 (57%)

Query:    47 TDVDDFSDATEISEGMERKPDNRPKRTHSAEVHNQSEXXXXXXINKRLKSLKELVPNCNK 106
             T  D+    +E ++   R      KR+ +AEVHN SE      IN+R+K+L+EL+P CNK
Sbjct:   258 TTTDETESRSEETK-QARVSTTSTKRSRAAEVHNLSERKRRDRINERMKALQELIPRCNK 316

Query:   107 SDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTE--VPQISPNVPISP 164
             SD+AS+LD+A+ Y+K+L+ Q++MMS   G +   P M P   Q        +  N PI P
Sbjct:   317 SDKASMLDEAIEYMKSLQLQIQMMSMGCGMM---PMMYPGMQQYMPHMAMGMGMNQPIPP 373

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0015995 "chlorophyll biosynthetic process" evidence=IMP

GO:0010187 "negative regulation of seed germination" evidence=IGI;IMP

GO:0010313 "phytochrome binding" evidence=IDA

GO:0009959 "negative gravitropism" evidence=IMP;TAS

GO:0010029 "regulation of seed germination" evidence=TAS

GO:0010099 "regulation of photomorphogenesis" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

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

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=RCA;IMP

GO:0010100 "negative regulation of photomorphogenesis" evidence=IMP

GO:0010161 "red light signaling pathway" evidence=IDA

GO:0006783 "heme biosynthetic process" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0009686 "gibberellin biosynthetic process" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0048608 "reproductive structure development" evidence=RCA

UNIPROTKB|Q948F6 OSJNBa0049O12.18 "Putative SPATULA" [Oryza sativa (taxid:4530)]

 Score = 189 (71.6 bits), Expect = 8.5e-15, P = 8.5e-15
 Identities = 39/99 (39%), Positives = 63/99 (63%)

Query:    59 SEGMERKPDNRPKRTHSAEVHNQSEXXXXXXINKRLKSLKELVPNCNKSDRASVLDDAVN 118
             SE   R    R KR+ +AEVHN SE      IN+++K+L+ L+PN +K+D+AS+LDDA+ 
Sbjct:    17 SEQPTRPARPRGKRSRAAEVHNLSEKRRRSRINEKMKALQSLIPNSSKTDKASMLDDAIE 76

Query:   119 YVKALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQIS 157
             Y+K L+ Q++M+S + G ++  P       +   +PQ+S
Sbjct:    77 YLKQLQLQVQMLSMRNG-LYLPPVNLSGAPEHLPIPQMS 114

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2041369 PIL1 "phytochrome interacting factor 3-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 194 (73.4 bits), Expect = 9.4e-15, P = 9.4e-15
 Identities = 43/112 (38%), Positives = 65/112 (58%)

Query:    40 QTSHSLDTDVDDFSDATEIS-EGMERKPDNRPKRTHSAEVHNQSEXXXXXXINKRLKSLK 98
             + S  L  + DD SD  +       RKP  + KR  S EVH   E       NK++++L+
Sbjct:   196 EESTYLSNNSDDESDDAKTQVHARTRKPVTKRKR--STEVHKLYERKRRDEFNKKMRALQ 253

Query:    99 ELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQS 150
             +L+PNC K D+AS+LD+A+ Y++ L+ Q++MMS  G  + + P M P GH S
Sbjct:   254 DLLPNCYKDDKASLLDEAIKYMRTLQLQVQMMS-MGNGLIRPPTMLPMGHYS 304

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0009641 "shade avoidance" evidence=IEP

GO:0010017 "red or far-red light signaling pathway" evidence=IEP;IMP

TAIR|locus:2126876 UNE10 "AT4G00050" [Arabidopsis thaliana (taxid:3702)]

 Score = 193 (73.0 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 53/153 (34%), Positives = 83/153 (54%)

Query:    36 TSWHQTSHSLDTDVDDFSDATEISEGMERKPDNRP--------KRTHSAEVHNQSEXXXX 87
             TS    SH  D  +DD          ME + + +         KR+ +A +HNQSE    
Sbjct:   169 TSTSMGSH--DNTIDDHDSVCHSRPQMEDEEEKKAGGKSSVSTKRSRAAAIHNQSERKRR 226

Query:    88 XXINKRLKSLKELVPNCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSG 147
               IN+R+K+L++LVPN +K+D+AS+LD+ + Y+K L+ Q+ MMS         P M+   
Sbjct:   227 DKINQRMKTLQKLVPNSSKTDKASMLDEVIEYLKQLQAQVSMMSRMNMPSMMLP-MAMQQ 285

Query:   148 HQSTEVPQISPNVPISPKLGMGSGI-GTGMVDV 179
              Q  ++  +S N P+   LGMG G+ G G++D+
Sbjct:   286 QQQLQMSLMS-N-PMG--LGMGMGMPGLGLLDL 314

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009567 "double fertilization forming a zygote and endosperm" evidence=IMP

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2077680 PIL6 "AT3G59060" [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 3.0e-14, P = 3.0e-14
 Identities = 51/160 (31%), Positives = 85/160 (53%)

Query:    11 DSEKGQSSRNENSFDFLESSASQLPTSWHQTSHSLDTDVDDFSDA----TEISEG-MERK 65
             D+  G SS      +  E+ +    T   +  H +D D +  S +    T   +  M  K
Sbjct:   185 DTSSGGSSGCSYGRNNKETVSGTSVTIDRKRKHVMDADQESVSQSDIGLTSTDDQTMGNK 244

Query:    66 PDNRP---KRTHSAEVHNQSEXXXXXXINKRLKSLKELVPNCNKSDRASVLDDAVNYVKA 122
                R    +R+ +AEVHN SE      IN+R+K+L+EL+P+C+++D+AS+LD+A++Y+K+
Sbjct:   245 SSQRSGSTRRSRAAEVHNLSERRRRDRINERMKALQELIPHCSRTDKASILDEAIDYLKS 304

Query:   123 LRHQLEMM-----SAQGGAIFQSPFMSPSGHQSTEVPQIS 157
             L+ QL++M      A   A   SP M P    S  + Q++
Sbjct:   305 LQMQLQVMWMGSGMAAAAAAAASPMMFPGVQSSPYINQMA 344

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

GO:0009585 "red, far-red light phototransduction" evidence=IMP

GO:0009693 "ethylene biosynthetic process" evidence=IMP

GO:0010600 "regulation of auxin biosynthetic process" evidence=IDA

GO:0010928 "regulation of auxin mediated signaling pathway" evidence=IDA

GO:0000096 "sulfur amino acid metabolic process" evidence=RCA

GO:0006546 "glycine catabolic process" evidence=RCA

GO:0006636 "unsaturated fatty acid biosynthetic process" evidence=RCA

GO:0006733 "oxidoreduction coenzyme metabolic process" evidence=RCA

GO:0006766 "vitamin metabolic process" evidence=RCA

GO:0007623 "circadian rhythm" evidence=RCA

GO:0008652 "cellular amino acid biosynthetic process" evidence=RCA

GO:0009072 "aromatic amino acid family metabolic process" evidence=RCA

GO:0009073 "aromatic amino acid family biosynthetic process" evidence=RCA

GO:0009106 "lipoate metabolic process" evidence=RCA

GO:0009108 "coenzyme biosynthetic process" evidence=RCA

GO:0009117 "nucleotide metabolic process" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0009684 "indoleacetic acid biosynthetic process" evidence=RCA

GO:0009695 "jasmonic acid biosynthetic process" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010017 "red or far-red light signaling pathway" evidence=RCA

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0019344 "cysteine biosynthetic process" evidence=RCA

GO:0019748 "secondary metabolic process" evidence=RCA

GO:0019761 "glucosinolate biosynthetic process" evidence=RCA

GO:0030003 "cellular cation homeostasis" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0044272 "sulfur compound biosynthetic process" evidence=RCA

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

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	201
smart00353	53	smart00353, HLH, helix loop helix domain	1e-14
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	2e-14
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-13

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

 Score = 65.3 bits (160), Expect = 1e-14
 Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 3/52 (5%)

Query: 80  NQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALRHQLE 128
           N  ERRRR +IN+    L+ L+P      K  +A +L  A+ Y+K+L+ +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 = 64.5 bits (158), Expect = 2e-14
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 77  EVHNQSERRRRDRINKRLKSLKELVPNC---NKSDRASVLDDAVNYVKALRHQLE 128
           E HN  ERRRR+RIN     L+ L+P      K  +A +L  AV+Y+K+L+  L+
Sbjct: 6   EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 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 = 61.7 bits (151), Expect = 2e-13
 Identities = 22/50 (44%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 77  EVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDAVNYVKALR 124
           + HN+ ERRRRDRIN   + L+EL+P     K  +A +L  A+ Y+K L+
Sbjct: 3   KAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	201
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.59
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.57
smart00353	53	HLH helix loop helix domain.	99.5
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	99.45
KOG1318	411	consensus Helix loop helix transcription factor EB	99.41
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.28
KOG4304	250	consensus Transcriptional repressors of the hairy/	99.15
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.83
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.63
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.53
KOG0561	373	consensus bHLH transcription factor [Transcription	98.34
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.3
PLN03217	93	transcription factor ATBS1; Provisional	98.17
KOG3910	632	consensus Helix loop helix transcription factor [T	97.71
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.79
KOG3898	254	consensus Transcription factor NeuroD and related	95.8
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	95.03
KOG4395	285	consensus Transcription factor Atonal, contains HT	95.02
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	92.31
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	91.35

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

Probab=99.59  E-value=2.2e-15  Score=101.45  Aligned_cols=49  Identities=49%  Similarity=0.899  Sum_probs=46.6

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhhcCCC-----CCcchHhHHHHHHHHHHHHH
Q 044343           76 AEVHNQSERRRRDRINKRLKSLKELVPNC-----NKSDRASVLDDAVNYVKALR  124 (201)
Q Consensus        76 ~~~H~~~ER~RR~~in~~~~~Lr~lvP~~-----~K~dKasiL~~AI~YIk~Lq  124 (201)
                      |..|+..||+||++||++|.+|+.+||.+     .|++|++||+.||+||++||
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            67899999999999999999999999987     38999999999999999997

; 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 ....

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

Probab=99.57  E-value=5.4e-15  Score=100.20  Aligned_cols=53  Identities=43%  Similarity=0.735  Sum_probs=50.1

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCC---CCcchHhHHHHHHHHHHHHHHHH
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNC---NKSDRASVLDDAVNYVKALRHQL  127 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~---~K~dKasiL~~AI~YIk~Lq~~v  127 (201)
                      .+..|+..||+||++||++|.+|+.+||..   .|++|++||+.||+||++|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            467899999999999999999999999998   69999999999999999999876

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=99.50  E-value=6.9e-14  Score=92.95  Aligned_cols=49  Identities=39%  Similarity=0.706  Sum_probs=45.5

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCC---CCCcchHhHHHHHHHHHHHHHHHHH
Q 044343           80 NQSERRRRDRINKRLKSLKELVPN---CNKSDRASVLDDAVNYVKALRHQLE  128 (201)
Q Consensus        80 ~~~ER~RR~~in~~~~~Lr~lvP~---~~K~dKasiL~~AI~YIk~Lq~~v~  128 (201)
                      |..||+||++||++|..|+.+||.   ..|++|++||..||+||++|+.+++
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            578999999999999999999996   4599999999999999999999875

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

Probab=99.45  E-value=3.7e-14  Score=138.51  Aligned_cols=86  Identities=24%  Similarity=0.366  Sum_probs=77.2

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhhcCCCC----CcchHhHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCCccCCCc
Q 044343           76 AEVHNQSERRRRDRINKRLKSLKELVPNCN----KSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPSGHQST  151 (201)
Q Consensus        76 ~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~----K~dKasiL~~AI~YIk~Lq~~v~~l~~~~~~~~~~~~~~~~~~~~l  151 (201)
                      |+.|+.+|||||+++|..|.+|.+|||.|.    |+||.+||++||.+||.++..- .....+...|+|.|+...++.||
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~~-~~~~~~~~d~KpSflS~~eL~~L   99 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQE-SENSSIDQDYKPSFLSNDELTHL   99 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhhh-cccccccccccccccchHHHHHH
Confidence            788999999999999999999999999875    9999999999999999998875 23344557899999999999999


Q ss_pred             ccCCCCCCCCC
Q 044343          152 EVPQISPNVPI  162 (201)
Q Consensus       152 ~~~~~~~f~p~  162 (201)
                      +++++++|+-+
T Consensus       100 mLeAlDGF~fv  110 (803)
T KOG3561|consen  100 ILEALDGFLFV  110 (803)
T ss_pred             HHHHhcCeEEE
Confidence            99999998643

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

Probab=99.41  E-value=2.4e-13  Score=124.42  Aligned_cols=59  Identities=37%  Similarity=0.800  Sum_probs=52.6

Q ss_pred             CCCccchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC----CcchHhHHHHHHHHHHHHHHHHH
Q 044343           70 PKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN----KSDRASVLDDAVNYVKALRHQLE  128 (201)
Q Consensus        70 ~~~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~----K~dKasiL~~AI~YIk~Lq~~v~  128 (201)
                      .+.+++|..||++|||||++||++|++|..|||.|.    |..|..||..+++||+.||+..+
T Consensus       228 ~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q  290 (411)
T KOG1318|consen  228 ERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ  290 (411)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence            344567889999999999999999999999999985    78999999999999999976655

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.28  E-value=4.4e-12  Score=105.15  Aligned_cols=66  Identities=26%  Similarity=0.534  Sum_probs=57.0

Q ss_pred             CCCCccchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC-------CcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           69 RPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN-------KSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        69 ~~~~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~-------K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      ...+.++|..|...||+||+.||..+..|+.|||.|.       |+.||.||.++|+||.+|++++..-+.+.
T Consensus        56 ~syk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~  128 (229)
T KOG1319|consen   56 ESYKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEV  128 (229)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445667889999999999999999999999999764       88999999999999999988876655444

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

Probab=99.15  E-value=2.4e-11  Score=105.53  Aligned_cols=56  Identities=30%  Similarity=0.498  Sum_probs=49.2

Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHHHhhcCCC--------CCcchHhHHHHHHHHHHHHHHHHH
Q 044343           73 THSAEVHNQSERRRRDRINKRLKSLKELVPNC--------NKSDRASVLDDAVNYVKALRHQLE  128 (201)
Q Consensus        73 ~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~--------~K~dKasiL~~AI~YIk~Lq~~v~  128 (201)
                      ..++..|-++|||||+|||+++.+|+.||+.+        .|++||.||+.||+|+|.||...+
T Consensus        30 ~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~   93 (250)
T KOG4304|consen   30 QYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ   93 (250)
T ss_pred             HHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence            33566789999999999999999999999953        388999999999999999987654

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

Probab=98.83  E-value=7.7e-09  Score=88.92  Aligned_cols=59  Identities=31%  Similarity=0.447  Sum_probs=49.9

Q ss_pred             CCccchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC--Ccc-hHhHHHHHHHHHHHHHHHHHH
Q 044343           71 KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSD-RASVLDDAVNYVKALRHQLEM  129 (201)
Q Consensus        71 ~~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~--K~d-KasiL~~AI~YIk~Lq~~v~~  129 (201)
                      ....+|..||+.||+||+.|+++|..|+.+||...  +.. .++||++|++||+.|+.+...
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~  116 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSAT  116 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHH
Confidence            34556889999999999999999999999999865  433 699999999999998765533

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.63  E-value=1.5e-08  Score=100.28  Aligned_cols=62  Identities=29%  Similarity=0.523  Sum_probs=56.0

Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC-CcchHhHHHHHHHHHHHHHHHHHHHhhccC
Q 044343           74 HSAEVHNQSERRRRDRINKRLKSLKELVPNCN-KSDRASVLDDAVNYVKALRHQLEMMSAQGG  135 (201)
Q Consensus        74 ~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~-K~dKasiL~~AI~YIk~Lq~~v~~l~~~~~  135 (201)
                      .+|.+||++|||.|..||++|.+|+.+||+.. |+.|..+|..||+||++|+...+.+..++.
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~  337 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENA  337 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhh
Confidence            45889999999999999999999999999987 999999999999999999988877765543

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

Probab=98.53  E-value=2.6e-07  Score=79.96  Aligned_cols=62  Identities=21%  Similarity=0.392  Sum_probs=53.5

Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHH-HhhcCCCC-CcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           73 THSAEVHNQSERRRRDRINKRLKSL-KELVPNCN-KSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        73 ~~~~~~H~~~ER~RR~~in~~~~~L-r~lvP~~~-K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      .-+|+.-.+.||||-.++|+.|++| |.-+++.+ .+-|.+||..||+||..||.-++++....
T Consensus       116 vDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~  179 (284)
T KOG3960|consen  116 VDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAE  179 (284)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence            3457778899999999999999999 55667765 88999999999999999999998887544

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.34  E-value=3.2e-07  Score=81.30  Aligned_cols=59  Identities=29%  Similarity=0.497  Sum_probs=51.8

Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC--CcchHhHHHHHHHHHHHHHHHHHHHhh
Q 044343           74 HSAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDAVNYVKALRHQLEMMSA  132 (201)
Q Consensus        74 ~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~--K~dKasiL~~AI~YIk~Lq~~v~~l~~  132 (201)
                      -+|+.-|.-||||-.-||..|..||.|||...  |++||.||+.+.+||.+|..+.-+|--
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~  119 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLP  119 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccccc
Confidence            45788899999999999999999999999765  999999999999999999776554443

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

Probab=98.30  E-value=1.3e-06  Score=74.66  Aligned_cols=60  Identities=25%  Similarity=0.413  Sum_probs=52.3

Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHhhcCC----CCCcchHhHHHHHHHHHHHHHHHHHHHhhc
Q 044343           74 HSAEVHNQSERRRRDRINKRLKSLKELVPN----CNKSDRASVLDDAVNYVKALRHQLEMMSAQ  133 (201)
Q Consensus        74 ~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~----~~K~dKasiL~~AI~YIk~Lq~~v~~l~~~  133 (201)
                      ..+..+|.+||+|-..+|..|.+||.+||.    ..|++|..+|..||.||++|+.-++.-+..
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            346678999999999999999999999995    348999999999999999999888766543

>PLN03217 transcription factor ATBS1; Provisional

Probab=98.17  E-value=3.6e-06  Score=61.83  Aligned_cols=51  Identities=29%  Similarity=0.533  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHHhhcCCC------CCcchHhHHHHHHHHHHHHHHHHHHHhhccCC
Q 044343           86 RRDRINKRLKSLKELVPNC------NKSDRASVLDDAVNYVKALRHQLEMMSAQGGA  136 (201)
Q Consensus        86 RR~~in~~~~~Lr~lvP~~------~K~dKasiL~~AI~YIk~Lq~~v~~l~~~~~~  136 (201)
                      --++||+.+..|+.|+|..      .|...+-||+++|.||+.|++++..|++....
T Consensus        18 sddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~   74 (93)
T PLN03217         18 SEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSE   74 (93)
T ss_pred             CHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3478999999999999963      27788899999999999999999999876543

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.71  E-value=2.6e-05  Score=73.25  Aligned_cols=58  Identities=24%  Similarity=0.296  Sum_probs=49.2

Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHHHhhcCCCCC----cchHhHHHHHHHHHHHHHHHHHHH
Q 044343           73 THSAEVHNQSERRRRDRINKRLKSLKELVPNCNK----SDRASVLDDAVNYVKALRHQLEMM  130 (201)
Q Consensus        73 ~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~K----~dKasiL~~AI~YIk~Lq~~v~~l  130 (201)
                      +.+|...|.+||.|-..||+.|++|..++-..-|    ..|.-||..||..|-.|++||.+-
T Consensus       524 kERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  524 KERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            4456778999999999999999999998764332    378999999999999999999764

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.79  E-value=0.00072  Score=54.89  Aligned_cols=54  Identities=24%  Similarity=0.425  Sum_probs=48.7

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCCC--CcchHhHHHHHHHHHHHHHHHHH
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDAVNYVKALRHQLE  128 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~--K~dKasiL~~AI~YIk~Lq~~v~  128 (201)
                      .+.-||+.||+|-..+|+.|..||.++|...  |++|.-.|+-|..||-+|-+-.+
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl~  133 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQ  133 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhccc
Confidence            3668999999999999999999999999754  99999999999999999976553

>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]

Probab=95.80  E-value=0.03  Score=48.94  Aligned_cols=53  Identities=32%  Similarity=0.441  Sum_probs=46.1

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCC---CCCcchHhHHHHHHHHHHHHHHHH
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPN---CNKSDRASVLDDAVNYVKALRHQL  127 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~---~~K~dKasiL~~AI~YIk~Lq~~v  127 (201)
                      +|..=|..||+|-..+|+.|..||++||.   ..|+.|...|..|-+||..|+.-.
T Consensus        72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~  127 (254)
T KOG3898|consen   72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVL  127 (254)
T ss_pred             hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcccc
Confidence            35566889999999999999999999995   339999999999999999998543

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=95.03  E-value=0.028  Score=53.93  Aligned_cols=45  Identities=36%  Similarity=0.578  Sum_probs=38.6

Q ss_pred             hhhHHHHHHHHHHHHHHHHHHhhcCCCC----CcchHhHHHHHHHHHHH
Q 044343           78 VHNQSERRRRDRINKRLKSLKELVPNCN----KSDRASVLDDAVNYVKA  122 (201)
Q Consensus        78 ~H~~~ER~RR~~in~~~~~Lr~lvP~~~----K~dKasiL~~AI~YIk~  122 (201)
                      .+.---||-|+|+|.-++.|..|+|-..    |+||.+||.-+|-|++-
T Consensus        28 tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~   76 (712)
T KOG3560|consen   28 TKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV   76 (712)
T ss_pred             ccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence            3444567889999999999999999653    99999999999999863

>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]

Probab=95.02  E-value=0.042  Score=48.12  Aligned_cols=55  Identities=31%  Similarity=0.445  Sum_probs=48.6

Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC---CcchHhHHHHHHHHHHHHHHHHH
Q 044343           74 HSAEVHNQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALRHQLE  128 (201)
Q Consensus        74 ~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~---K~dKasiL~~AI~YIk~Lq~~v~  128 (201)
                      .+|..-|..||+|-..+|..|..||..||...   |++|-..|+.|-.||--|-...+
T Consensus       173 ~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  173 HRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             hhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            34567789999999999999999999999765   88999999999999999877664

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

Probab=92.31  E-value=0.13  Score=50.72  Aligned_cols=46  Identities=26%  Similarity=0.461  Sum_probs=39.0

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHhhcCCCC----CcchHhHHHHHHHHHHH
Q 044343           77 EVHNQSERRRRDRINKRLKSLKELVPNCN----KSDRASVLDDAVNYVKA  122 (201)
Q Consensus        77 ~~H~~~ER~RR~~in~~~~~Lr~lvP~~~----K~dKasiL~~AI~YIk~  122 (201)
                      +.-.-+.|-||-+=|+-|-+|..+||-..    .+|||+|+.-||-|+|-
T Consensus        48 EkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   48 EKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            33446788999999999999999999533    78999999999999874

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=91.35  E-value=0.22  Score=46.67  Aligned_cols=43  Identities=28%  Similarity=0.478  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHHHHHHHhhcCCCC----CcchHhHHHHHHHHHHHH
Q 044343           81 QSERRRRDRINKRLKSLKELVPNCN----KSDRASVLDDAVNYVKAL  123 (201)
Q Consensus        81 ~~ER~RR~~in~~~~~Lr~lvP~~~----K~dKasiL~~AI~YIk~L  123 (201)
                      -..|.||++=|.-|.+|..++|-..    ..||++|+.-|..|||--
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            4568899999999999999999654    689999999999999854

---

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	201
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	5e-18
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	1e-14
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	5e-14
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	6e-14
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	1e-13
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	4e-10
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	5e-08
4f3l_A	361	Mclock, circadian locomoter output cycles protein	5e-08
1a0a_A	63	BHLH, protein (phosphate system positive regulator	1e-07
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	2e-04
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	4e-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 = 74.0 bits (182), Expect = 5e-18
 Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN-KSDRASVLDDAVNYVKALRHQLEM 129
            R      HN  E+R R  IN ++  LK+LV     K ++++VL  A++Y++ L+H  + 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 130 MSAQ 133
           +  +
Sbjct: 62  LKQE 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 = 65.1 bits (159), Expect = 1e-14
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 6/65 (9%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDAVNYVKALRHQLE 128
           KR H    HN  ER+RRD I     SL++ VP+    K+ RA +LD A  Y++ +R +  
Sbjct: 2   KRAH----HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNH 57

Query: 129 MMSAQ 133
                
Sbjct: 58  THQQD 62

>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 = 63.5 bits (155), Expect = 5e-14
 Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 7/77 (9%)

Query: 59  SEGMERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDA 116
           ++ +E + D   KR H    HN  ER+RRD I     SL++ VP+    K+ RA +LD A
Sbjct: 1   NDDIEVESDAD-KRAH----HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKA 55

Query: 117 VNYVKALRHQLEMMSAQ 133
             Y++ +R +       
Sbjct: 56  TEYIQYMRRKNHTHQQD 72

>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 = 63.5 bits (155), Expect = 6e-14
 Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 7/69 (10%)

Query: 68  NRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALR 124
              KR      HN  ER+RR+ + +   +L++ +P      K+ +  +L  A  Y+ +++
Sbjct: 3   MNVKRRT----HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQ 58

Query: 125 HQLEMMSAQ 133
            + + + ++
Sbjct: 59  AEEQKLISE 67

>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 = 62.0 bits (151), Expect = 1e-13
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 10/64 (15%)

Query: 69  RPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN------KSDRASVLDDAVNYVKA 122
             +R      HN+ ERRRRD+IN  +  L +++P+ +         +  +L  A +Y++ 
Sbjct: 3   EKRRAQ----HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQE 58

Query: 123 LRHQ 126
           LR  
Sbjct: 59  LRQS 62

>1nlw_A MAD protein, MAX dimerizer; transcription factor, DNA, BHLHZ, transcription/DNA complex; 2.00A {Homo sapiens} SCOP: a.38.1.1 Length = 80

 Score = 53.3 bits (128), Expect = 4e-10
 Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 77  EVHNQSERRRRDRINKRLKSLKELVPNCNKSDRAS---VLDDAVNYVKALRHQLEMMSAQ 133
             HN+ E+ RR  +   L+ LK LVP    S R +   +L  A  ++K L         Q
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62

>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins, transcription-activato; 2.27A {Mus musculus} Length = 387

 Score = 51.2 bits (122), Expect = 5e-08
 Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 5/67 (7%)

Query: 62  MERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN----KSDRASVLDDAV 117
           ME   +++ +  ++ E H+Q E+RRRD++N  +  L  LVP CN    K D+ +VL  AV
Sbjct: 1   MEYA-EHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAV 59

Query: 118 NYVKALR 124
            ++K LR
Sbjct: 60  QHMKTLR 66

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

 Score = 50.7 bits (121), Expect = 5e-08
 Identities = 20/95 (21%), Positives = 44/95 (46%), Gaps = 5/95 (5%)

Query: 62  MERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVP-NCNKSDRASVLDDAVNYV 120
           +E    ++ KR       N+SE++RRD+ N  +K L  ++P N  K D+++VL  +++++
Sbjct: 3   VEEDDKDKAKR----VSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFL 58

Query: 121 KALRHQLEMMSAQGGAIFQSPFMSPSGHQSTEVPQ 155
           +  +       A        P    +   +  + +
Sbjct: 59  RKHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLE 93

>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 Length = 63

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 11/65 (16%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSD-------RASVLDDAVNYVKAL 123
           KR      H  +E+ RR+R+   L  L  L+P   K         +A+ ++ A  Y++ L
Sbjct: 2   KRE----SHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHL 57

Query: 124 RHQLE 128
           +    
Sbjct: 58  QQNGS 62

>3u5v_A Protein MAX, transcription factor E2-alpha chimer; basic helix-loop-helix (BHLH); 1.70A {Mus musculus} PDB: 2ql2_A* Length = 76

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 4/53 (7%)

Query: 79  HNQSERRRRDRINKRLKSLK-ELVPNCNKSDRAS---VLDDAVNYVKALRHQL 127
           HN  ER+RR  IN+  + L      +       +   +L  AV  +  L  Q+
Sbjct: 9   HNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQV 61

>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* Length = 68

 Score = 36.6 bits (85), Expect = 4e-04
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 62  MERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCNKSDRAS---VLDDAVN 118
           ++RK  N  +R          ERRR  ++N+  ++LK      N + R     +L +A+ 
Sbjct: 3   LKRKTTNADRRK----AATMRERRRLSKVNEAFETLKRSTS-SNPNQRLPKVEILRNAIR 57

Query: 119 YVKALRHQLE 128
           Y++ L+  L 
Sbjct: 58  YIEGLQALLR 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	201
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.75
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.72
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.69
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.68
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.67
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.67
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.66
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.65
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.62
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.61
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.6
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.48
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.43
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.38
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.37
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.08
4ath_A	83	MITF, microphthalmia-associated transcription fact	99.04
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.69

>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=99.75  E-value=1.6e-18  Score=125.64  Aligned_cols=63  Identities=29%  Similarity=0.488  Sum_probs=58.3

Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHHHhhcCCC-CCcchHhHHHHHHHHHHHHHHHHHHHhhccC
Q 044343           73 THSAEVHNQSERRRRDRINKRLKSLKELVPNC-NKSDRASVLDDAVNYVKALRHQLEMMSAQGG  135 (201)
Q Consensus        73 ~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~-~K~dKasiL~~AI~YIk~Lq~~v~~l~~~~~  135 (201)
                      ..++..|+.+||+||++||++|.+|+.+||++ .|++|++||.+||+||++||.+++.|+.++.
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~   67 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENL   67 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34678999999999999999999999999998 6999999999999999999999999987653

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

Probab=99.72  E-value=8.3e-18  Score=118.85  Aligned_cols=60  Identities=23%  Similarity=0.474  Sum_probs=54.5

Q ss_pred             CccchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC-CcchHhHHHHHHHHHHHHHHHHHHHh
Q 044343           72 RTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN-KSDRASVLDDAVNYVKALRHQLEMMS  131 (201)
Q Consensus        72 ~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~-K~dKasiL~~AI~YIk~Lq~~v~~l~  131 (201)
                      ....|.+|+.+||+||++||++|.+|+.|||.+. |+||++||++||+||++||.++.-|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            3456889999999999999999999999999754 99999999999999999999987664

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

Probab=99.69  E-value=3.2e-17  Score=126.28  Aligned_cols=66  Identities=30%  Similarity=0.533  Sum_probs=52.3

Q ss_pred             CCCCccchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC----CcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           69 RPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN----KSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        69 ~~~~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~----K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      ..++..++..|+.+||+||++||++|.+|+.|||.+.    |++|++||++||+||++||.+++.|....
T Consensus        21 ~~k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           21 LAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445556788999999999999999999999999875    78999999999999999999999998654

>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=99.68  E-value=7.1e-18  Score=116.82  Aligned_cols=54  Identities=31%  Similarity=0.638  Sum_probs=49.8

Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC------CcchHhHHHHHHHHHHHHHHHH
Q 044343           74 HSAEVHNQSERRRRDRINKRLKSLKELVPNCN------KSDRASVLDDAVNYVKALRHQL  127 (201)
Q Consensus        74 ~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~------K~dKasiL~~AI~YIk~Lq~~v  127 (201)
                      .++..|+.+||+||++||++|.+|+.|||.+.      |++|++||++||+||++||+++
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            35678999999999999999999999999876      7899999999999999999865

>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=99.67  E-value=9.1e-18  Score=116.11  Aligned_cols=53  Identities=26%  Similarity=0.515  Sum_probs=48.2

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCC-------CCcchHhHHHHHHHHHHHHHHHH
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNC-------NKSDRASVLDDAVNYVKALRHQL  127 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~-------~K~dKasiL~~AI~YIk~Lq~~v  127 (201)
                      ++.+|+.+||+||++||.+|.+|+.|||.+       .|.+||+||++||+||++||+++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            367899999999999999999999999965       36789999999999999999865

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

Probab=99.67  E-value=2e-17  Score=117.51  Aligned_cols=55  Identities=42%  Similarity=0.661  Sum_probs=50.5

Q ss_pred             CCccchhhhhHHHHHHHHHHHHHHHHHHhhcCCC----CCcchHhHHHHHHHHHHHHHH
Q 044343           71 KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNC----NKSDRASVLDDAVNYVKALRH  125 (201)
Q Consensus        71 ~~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~----~K~dKasiL~~AI~YIk~Lq~  125 (201)
                      +..+++..|+.+||+||++||++|.+|+.|||.|    .|+||++||+.||+|||.|+.
T Consensus         5 k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            5 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            4456788999999999999999999999999976    599999999999999999974

>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=99.66  E-value=7.7e-17  Score=116.00  Aligned_cols=62  Identities=32%  Similarity=0.533  Sum_probs=57.5

Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHhhcCCC--CCcchHhHHHHHHHHHHHHHHHHHHHhhccC
Q 044343           74 HSAEVHNQSERRRRDRINKRLKSLKELVPNC--NKSDRASVLDDAVNYVKALRHQLEMMSAQGG  135 (201)
Q Consensus        74 ~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~--~K~dKasiL~~AI~YIk~Lq~~v~~l~~~~~  135 (201)
                      ..+..|+.+||+||..||++|..|+.+||.+  .|++|++||..||+||++|+.+++.|..+..
T Consensus        11 ~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~   74 (80)
T 1hlo_A           11 DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDID   74 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999986  4999999999999999999999999987654

>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=99.65  E-value=2e-16  Score=114.42  Aligned_cols=60  Identities=33%  Similarity=0.548  Sum_probs=55.1

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCC--CCcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNC--NKSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~--~K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      +|..||.+||+||++||++|.+|+.+||.+  .|++|++||..||+||++|+.+++.|+.+.
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~   63 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI   63 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999985  599999999999999999999988887654

>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=99.62  E-value=4.5e-16  Score=114.16  Aligned_cols=59  Identities=20%  Similarity=0.473  Sum_probs=54.1

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCC---CCcchHhHHHHHHHHHHHHHHHHHHHhhc
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNC---NKSDRASVLDDAVNYVKALRHQLEMMSAQ  133 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~---~K~dKasiL~~AI~YIk~Lq~~v~~l~~~  133 (201)
                      .|..||.+||+||+.||++|..|+.+||..   .|++|++||.+||+||++|+.+++.+..+
T Consensus         6 ~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~   67 (88)
T 1nkp_A            6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISE   67 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578899999999999999999999999975   49999999999999999999998877643

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

Probab=99.61  E-value=4.2e-16  Score=111.50  Aligned_cols=58  Identities=26%  Similarity=0.404  Sum_probs=49.8

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCC---CCCc-chHhHHHHHHHHHHHHHHHHHHHhh
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPN---CNKS-DRASVLDDAVNYVKALRHQLEMMSA  132 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~---~~K~-dKasiL~~AI~YIk~Lq~~v~~l~~  132 (201)
                      +|..||.+||+||+.||++|.+|+.+||.   ..|. +|++||..||+||++||+++++++.
T Consensus         5 rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            57789999999999999999999999995   3365 7999999999999999999998874

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

Probab=99.60  E-value=2e-15  Score=108.87  Aligned_cols=59  Identities=29%  Similarity=0.318  Sum_probs=54.2

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhhcCCC---CCcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           76 AEVHNQSERRRRDRINKRLKSLKELVPNC---NKSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        76 ~~~H~~~ER~RR~~in~~~~~Lr~lvP~~---~K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      |..||.+||+||+.||++|..|+++||..   .|.+|+.||.+|++||+.|+.+.+.|..+.
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~   63 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQI   63 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999965   488999999999999999999998887654

>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=99.48  E-value=2.9e-14  Score=99.88  Aligned_cols=55  Identities=22%  Similarity=0.450  Sum_probs=50.0

Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHHHhhcCCC--CCcchHhHHHHHHHHHHHHHHHH
Q 044343           73 THSAEVHNQSERRRRDRINKRLKSLKELVPNC--NKSDRASVLDDAVNYVKALRHQL  127 (201)
Q Consensus        73 ~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~--~K~dKasiL~~AI~YIk~Lq~~v  127 (201)
                      ...|..||..||+|+..||+.|..|+.+||..  .|++|+.||..||+||++|++.+
T Consensus        10 ~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            34577899999999999999999999999975  49999999999999999999765

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

Probab=99.43  E-value=2.1e-13  Score=93.25  Aligned_cols=54  Identities=31%  Similarity=0.395  Sum_probs=49.1

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCCC---CcchHhHHHHHHHHHHHHHHHHH
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALRHQLE  128 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~---K~dKasiL~~AI~YIk~Lq~~v~  128 (201)
                      +|..||..||+|+..||+.|..|+.+||...   |++|..||..||+||++|++.++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            3667999999999999999999999999753   99999999999999999998653

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

Probab=99.38  E-value=6.8e-14  Score=123.94  Aligned_cols=89  Identities=19%  Similarity=0.359  Sum_probs=63.2

Q ss_pred             CccchhhhhHHHHHHHHHHHHHHHHHHhhcC-CCCCcchHhHHHHHHHHHHHHHHHHHHHh-hccCCCCCCCCCCCccCC
Q 044343           72 RTHSAEVHNQSERRRRDRINKRLKSLKELVP-NCNKSDRASVLDDAVNYVKALRHQLEMMS-AQGGAIFQSPFMSPSGHQ  149 (201)
Q Consensus        72 ~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP-~~~K~dKasiL~~AI~YIk~Lq~~v~~l~-~~~~~~~~~~~~~~~~~~  149 (201)
                      ...++..|+.+||+||++||..|.+|+.||| ...|+||++||+.||+|||.|+....... .+....++|+++...++.
T Consensus         9 ~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (361)
T 4f3l_A            9 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFT   88 (361)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHHTSCSCGGGTSCCSCTTSCHHHHH
T ss_pred             cchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhcccccccccccccCcccccHHHHH
Confidence            3445778999999999999999999999999 45599999999999999999986543211 223356788888877777


Q ss_pred             CcccCCCCCCC
Q 044343          150 STEVPQISPNV  160 (201)
Q Consensus       150 ~l~~~~~~~f~  160 (201)
                      ++.+.++++|+
T Consensus        89 ~~~l~a~~~~i   99 (361)
T 4f3l_A           89 QLMLEALDGFF   99 (361)
T ss_dssp             HHHHHHTTEEE
T ss_pred             HHHHHhcCceE
Confidence            77767776664

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

Probab=99.37  E-value=1e-13  Score=124.16  Aligned_cols=88  Identities=28%  Similarity=0.377  Sum_probs=69.5

Q ss_pred             CCccchhhhhHHHHHHHHHHHHHHHHHHhhcC----CCCCcchHhHHHHHHHHHHHHHHHHHHHhhccCCCCCCCCCCCc
Q 044343           71 KRTHSAEVHNQSERRRRDRINKRLKSLKELVP----NCNKSDRASVLDDAVNYVKALRHQLEMMSAQGGAIFQSPFMSPS  146 (201)
Q Consensus        71 ~~~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP----~~~K~dKasiL~~AI~YIk~Lq~~v~~l~~~~~~~~~~~~~~~~  146 (201)
                      |...++.+|+.+||+||++||+.|.+|+.|||    ...|+||++||+.||+|||.|+.......   ...+.|.++...
T Consensus         9 ~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~~~~~~---~~~~~~~~~~~~   85 (387)
T 4f3l_B            9 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYT---EANYKPTFLSDD   85 (387)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC---------CCSSCTTSCHH
T ss_pred             hhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhccccccc---ccccCcccCCHH
Confidence            34556889999999999999999999999999    45699999999999999999985433222   245678888888


Q ss_pred             cCCCcccCCCCCCCC
Q 044343          147 GHQSTEVPQISPNVP  161 (201)
Q Consensus       147 ~~~~l~~~~~~~f~p  161 (201)
                      ++.++.+.++++|+-
T Consensus        86 ~~~~~ll~~~~gfi~  100 (387)
T 4f3l_B           86 ELKHLILRAADGFLF  100 (387)
T ss_dssp             HHHHHHHHTCCSEEE
T ss_pred             HHHHHHHhcCCCEEE
Confidence            888888888887753

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

Probab=99.08  E-value=2.2e-11  Score=84.89  Aligned_cols=46  Identities=22%  Similarity=0.409  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHhhcCCC---CCcchHhHHHHHHHHHHHHHH
Q 044343           80 NQSERRRRDRINKRLKSLKELVPNC---NKSDRASVLDDAVNYVKALRH  125 (201)
Q Consensus        80 ~~~ER~RR~~in~~~~~Lr~lvP~~---~K~dKasiL~~AI~YIk~Lq~  125 (201)
                      +..||+|+..||++|..||.+||..   .|++|..||+.||+||+.||.
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            4778999999999999999999975   399999999999999999984

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

Probab=99.04  E-value=3.3e-10  Score=81.82  Aligned_cols=46  Identities=28%  Similarity=0.585  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHhhcCCCC----CcchHhHHHHHHHHHHHHHHHHHHHhh
Q 044343           87 RDRINKRLKSLKELVPNCN----KSDRASVLDDAVNYVKALRHQLEMMSA  132 (201)
Q Consensus        87 R~~in~~~~~Lr~lvP~~~----K~dKasiL~~AI~YIk~Lq~~v~~l~~  132 (201)
                      |..||++|.+|..|||.+.    |.+|++||.+||+||++||+.++.+..
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e   53 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKD   53 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999999999753    889999999999999999987776654

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

Probab=98.69  E-value=3.5e-08  Score=73.19  Aligned_cols=50  Identities=24%  Similarity=0.365  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhcCCC---CCcchHhHHHHHHHHHHHHHHHHHHHh
Q 044343           82 SERRRRDRINKRLKSLKELVPNC---NKSDRASVLDDAVNYVKALRHQLEMMS  131 (201)
Q Consensus        82 ~ER~RR~~in~~~~~Lr~lvP~~---~K~dKasiL~~AI~YIk~Lq~~v~~l~  131 (201)
                      .||.|-..||+.|..||.+||..   .|++|..+|..||+||++|+..++.-.
T Consensus        32 ~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~   84 (97)
T 4aya_A           32 DPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHL   84 (97)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             cHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            45778889999999999999964   389999999999999999998876543

---

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	201
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	6e-16
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-15
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	1e-14
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-14
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	4e-14
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	8e-14
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-13
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	2e-13

>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 = 67.6 bits (165), Expect = 6e-16
 Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 6/65 (9%)

Query: 71  KRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDAVNYVKALRHQLE 128
           KR H    HN  ER+RRD I     SL++ VP+    K+ RA +LD A  Y++ +R +  
Sbjct: 2   KRAH----HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNH 57

Query: 129 MMSAQ 133
                
Sbjct: 58  THQQD 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 = 66.5 bits (162), Expect = 2e-15
 Identities = 12/60 (20%), Positives = 32/60 (53%), Gaps = 3/60 (5%)

Query: 77  EVHNQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALRHQLEMMSAQ 133
             HN  ER+RR+ + +   +L++ +P      K+ +  +L  A  Y+ +++ + + + ++
Sbjct: 8   RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISE 67

>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 = 63.7 bits (155), Expect = 1e-14
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 4/69 (5%)

Query: 62  MERKPDNRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDAVNY 119
           ME K          A      ERRR  ++N+  ++LK    +    +  +  +L +A+ Y
Sbjct: 1   MELKRKTTNADRRKA--ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRY 58

Query: 120 VKALRHQLE 128
           ++ L+  L 
Sbjct: 59  IEGLQALLR 67

>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 = 63.4 bits (154), Expect = 1e-14
 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 7/59 (11%)

Query: 77  EVHNQSERRRRDRINKRLKSLKELVPNCN-------KSDRASVLDDAVNYVKALRHQLE 128
           E H  +E+ RR+R+   L  L  L+P             +A+ ++ A  Y++ L+    
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>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 = 63.0 bits (153), Expect = 4e-14
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 75  SAEVHNQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALRHQLEMMS 131
           S   HN+ E+ RR  +   L+ LK LVP      +    S+L  A  ++K L        
Sbjct: 1   SRSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAV 60

Query: 132 AQ 133
            Q
Sbjct: 61  HQ 62

>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 = 61.9 bits (150), Expect = 8e-14
 Identities = 18/56 (32%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 79  HNQSERRRRDRINKRLKSLKELVPNCN-KSDRASVLDDAVNYVKALRHQLEMMSAQ 133
           HN  E+R R  IN ++  LK+LV     K ++++VL  A++Y++ L+H  + +  +
Sbjct: 10  HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE 65

>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 = 60.9 bits (148), Expect = 1e-13
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 10/65 (15%)

Query: 68  NRPKRTHSAEVHNQSERRRRDRINKRLKSLKELVPNCN------KSDRASVLDDAVNYVK 121
           +  +R      HN+ ERRRRD+IN  +  L +++P+ +         +  +L  A +Y++
Sbjct: 2   DEKRRAQ----HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQ 57

Query: 122 ALRHQ 126
            LR  
Sbjct: 58  ELRQS 62

>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 = 60.1 bits (146), Expect = 2e-13
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 87  RDRINKRLKSLKELVPNCN-KSDRASVLDDAVNYVKALRHQLEMMSAQ 133
           R  IN ++  LK+LV   + K  ++ VL  A++Y+K L+     +  +
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQE 48

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	201
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.67
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.67
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.67
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.63
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.62
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.6
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.49

>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=99.69  E-value=1.2e-17  Score=118.50  Aligned_cols=61  Identities=30%  Similarity=0.540  Sum_probs=56.6

Q ss_pred             cchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC-CcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           74 HSAEVHNQSERRRRDRINKRLKSLKELVPNCN-KSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        74 ~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~-K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      .+|..|+.+||+||++||++|.+|+.|||++. |++|++||..||+||++|+.+++.|..++
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~   66 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN   66 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35778999999999999999999999999865 99999999999999999999999998765

>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=99.67  E-value=1.1e-17  Score=115.64  Aligned_cols=56  Identities=21%  Similarity=0.434  Sum_probs=51.1

Q ss_pred             ccchhhhhHHHHHHHHHHHHHHHHHHhhcCCCC--CcchHhHHHHHHHHHHHHHHHHH
Q 044343           73 THSAEVHNQSERRRRDRINKRLKSLKELVPNCN--KSDRASVLDDAVNYVKALRHQLE  128 (201)
Q Consensus        73 ~~~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~--K~dKasiL~~AI~YIk~Lq~~v~  128 (201)
                      ..++..||..||+||++||++|.+|+.+||.+.  |++|++||+.||+||++||+.++
T Consensus        10 ~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          10 ADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            345778999999999999999999999999865  88999999999999999998764

>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=99.67  E-value=1.6e-17  Score=112.94  Aligned_cols=53  Identities=26%  Similarity=0.534  Sum_probs=48.3

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCC-------CCCcchHhHHHHHHHHHHHHHHHH
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPN-------CNKSDRASVLDDAVNYVKALRHQL  127 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~-------~~K~dKasiL~~AI~YIk~Lq~~v  127 (201)
                      +|..|+.+||+||++||++|.+|+.|||.       ..|++|++||+.||+||++||+++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            36779999999999999999999999995       348999999999999999999765

>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=99.67  E-value=6.3e-17  Score=114.27  Aligned_cols=59  Identities=29%  Similarity=0.308  Sum_probs=54.5

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHhhcCCCC---CcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           76 AEVHNQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        76 ~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~---K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      |..||.+||+||++||++|.+|+.+||++.   |++|++||..||+||++|+.+++.+..+.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~   63 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQI   63 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999754   89999999999999999999999887654

>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=99.63  E-value=1.6e-16  Score=113.14  Aligned_cols=60  Identities=33%  Similarity=0.548  Sum_probs=54.7

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCC--CCcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNC--NKSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~--~K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      +|..|+.+||+||++||++|.+|+++||++  .|++|++||..||+||++|+.+++.|..+.
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~   63 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI   63 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999975  489999999999999999999998887654

>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=99.62  E-value=2.5e-16  Score=113.31  Aligned_cols=60  Identities=20%  Similarity=0.461  Sum_probs=54.7

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCCC---CcchHhHHHHHHHHHHHHHHHHHHHhhcc
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNCN---KSDRASVLDDAVNYVKALRHQLEMMSAQG  134 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~---K~dKasiL~~AI~YIk~Lq~~v~~l~~~~  134 (201)
                      +|..||.+||+||++||++|..|+++||++.   |.+|++||..||+||++|+.+++.|..+.
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~   68 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEE   68 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999753   89999999999999999999998887644

>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=99.60  E-value=8.9e-17  Score=109.86  Aligned_cols=53  Identities=32%  Similarity=0.646  Sum_probs=48.3

Q ss_pred             chhhhhHHHHHHHHHHHHHHHHHHhhcCCCC------CcchHhHHHHHHHHHHHHHHHH
Q 044343           75 SAEVHNQSERRRRDRINKRLKSLKELVPNCN------KSDRASVLDDAVNYVKALRHQL  127 (201)
Q Consensus        75 ~~~~H~~~ER~RR~~in~~~~~Lr~lvP~~~------K~dKasiL~~AI~YIk~Lq~~v  127 (201)
                      ++..|+.+||+||++||++|.+|+.+||.+.      |++|++||..||+||++||++.
T Consensus         5 rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            4567999999999999999999999999753      8899999999999999999764

>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=99.49  E-value=5.4e-15  Score=99.70  Aligned_cols=49  Identities=29%  Similarity=0.475  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHhhcCCCC-CcchHhHHHHHHHHHHHHHHHHHHHhhccC
Q 044343           87 RDRINKRLKSLKELVPNCN-KSDRASVLDDAVNYVKALRHQLEMMSAQGG  135 (201)
Q Consensus        87 R~~in~~~~~Lr~lvP~~~-K~dKasiL~~AI~YIk~Lq~~v~~l~~~~~  135 (201)
                      |++||++|.+|+.+||++. |+|||+||.+||+||++||.+++.|+.++.
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~   50 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENM   50 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999876 999999999999999999999999987663