Citrus Sinensis ID: 042908

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240--
Protein Sequence
MALENRNTSDDQPAGVMGFFSNGSFFDHHQQPQLCMSFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccHHHHHHHHHHHHHHHHHHHHHccccccHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccHHHHcccccHHHHHHHHHHHHccccccccccccccc
Coil and Loop (DISEMBL)
malenrntsddqpagvmgffsngsffdhhqqpqlcmsfadnniqsealvvPSIGliadfshdtsngkKAAAHTVESFmnlsptpasgsgllsvnnkgtgmqglsgrkrkrnnervvekpKEVIHVRAkrgqatdshsLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYdfnseldttetmpgtnecdaQDMERMVregyggpsyfhsawsl
Flexible Loop (DISEMBL)
malenrntsddqpagVMGFFSNGSFFDHHQQPQLCMSFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGtgmqglsgrkrkrnnervvekpkevihvrakrgqatdshslaervrrekINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL
Low Complexity Region (SEG)
MALENRNTSDDQPAGVMGFFSNGSFFDHHQQPQLCMSFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL
Disordered region (IsUnstruct)
***************VMGFFSNGSFFDHHQQPQLCMSFADNNIQSEALVVPSIGLIADFS**************************************************************************************INERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNS***************************************
Disordered Region (DISOPRED)
***************************************************************************************************************************************************NERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSM****************************************************
Disordered Region (DISEMBL)
**********DQPAGVMGFFSNGSFFDHHQQPQLCMSFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGT***************RVVEKPKEVIH*************LAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL
Disordered Region (DISPRO)
**LENRNTS*DQPAGVMGFFSNGSFFDHHQQP**************************************************************************************PKEVIHVRAKRGQ*T*SHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTN*****D*ERMVREGYGGPSYFHS***L
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MALENRNTSDDQPAGVMGFFSNGSFFDHHQQPQLCMSFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL
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	242	2.2.26 [Sep-21-2011]
A4D998	223	Transcription factor bHLH	yes	no	0.524	0.569	0.705	2e-45
Q8GWK7	261	Transcription factor BEE	no	no	0.640	0.593	0.596	2e-43
Q8GZ13	260	Transcription factor BEE	no	no	0.491	0.457	0.677	5e-43
Q93W88	286	Transcription factor bHLH	no	no	0.681	0.576	0.450	2e-34
Q9FJL4	498	Transcription factor bHLH	no	no	0.388	0.188	0.694	7e-32
Q9SRT2	456	Transcription factor bHLH	no	no	0.454	0.241	0.584	8e-31
Q9LK48	371	Transcription factor bHLH	no	no	0.475	0.309	0.555	1e-30
Q9CAA9	486	Transcription factor bHLH	no	no	0.396	0.197	0.649	9e-30
Q9C670	390	Transcription factor bHLH	no	no	0.338	0.210	0.756	4e-29
Q6NKN9	366	Transcription factor bHLH	no	no	0.363	0.240	0.681	1e-27

>sp|A4D998|BH075_ARATH Transcription factor bHLH75 OS=Arabidopsis thaliana GN=BHLH75 PE=2 SV=1

 Score =  182 bits (461), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 91/129 (70%), Positives = 103/129 (79%), Gaps = 2/129 (1%)

Query: 116 VEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVII 175
            +KPK+V+HVRAKRGQATDSHSLAERVRREKINERL+CLQDLVPGCYK MGMAVMLDVII
Sbjct: 95  TQKPKDVVHVRAKRGQATDSHSLAERVRREKINERLKCLQDLVPGCYKAMGMAVMLDVII 154

Query: 176 NYVRSLQNQIEFLSMKLSAASMYYDFNS-ELDTTETMPGTNECDAQDMERMVREGYGG-P 233
           +YVRSLQNQIEFLSMKLSAAS  YD NS +++ T+   G N   A +MER++RE  G  P
Sbjct: 155 DYVRSLQNQIEFLSMKLSAASACYDLNSLDIEPTDIFQGGNIHSAAEMERILRESVGTQP 214

Query: 234 SYFHSAWSL 242
             F S    
Sbjct: 215 PNFSSTLPF 223

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GWK7|BEE3_ARATH Transcription factor BEE 3 OS=Arabidopsis thaliana GN=BEE3 PE=2 SV=1

 Score =  176 bits (445), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 96/161 (59%), Positives = 118/161 (73%), Gaps = 6/161 (3%)

Query: 83  TPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERV 142
           T ++ S  +S+N      +  S R+ KR+  R  EK +EV+HVRA+RGQATDSHS+AERV
Sbjct: 106 TLSTSSAQVSING-NISTKNNSSRRGKRSKNREEEKEREVVHVRARRGQATDSHSIAERV 164

Query: 143 RREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFN 202
           RR KINERL+CLQD+VPGCYKTMGMA MLD IINYV+SLQNQ+EFLSMKL+AAS YYDFN
Sbjct: 165 RRGKINERLKCLQDIVPGCYKTMGMATMLDEIINYVQSLQNQVEFLSMKLTAASSYYDFN 224

Query: 203 SELDTTETMPGTNECDAQDMERMVREGYGGPSYFH-SAWSL 242
           SE D  E+M      +A +M     +G  G S FH S+W+L
Sbjct: 225 SETDAVESMQKAKAREAVEMG----QGRDGSSVFHSSSWTL 261

Positive regulator of brassinosteroid signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8GZ13|BEE1_ARATH Transcription factor BEE 1 OS=Arabidopsis thaliana GN=BEE1 PE=2 SV=1

 Score =  174 bits (441), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 82/121 (67%), Positives = 95/121 (78%), Gaps = 2/121 (1%)

Query: 122 VIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSL 181
           V+HVRA+RGQATDSHSLAERVRR KINERLRCLQD+VPGCYK MGMA MLD IINYV+SL
Sbjct: 142 VVHVRARRGQATDSHSLAERVRRGKINERLRCLQDMVPGCYKAMGMATMLDEIINYVQSL 201

Query: 182 QNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWS 241
           QNQ+EFLSMKL+AAS +YDFNSE D  ++M      +  +M R  R+  G P +  S WS
Sbjct: 202 QNQVEFLSMKLTAASSFYDFNSETDAVDSMQRAKARETVEMGRQTRD--GSPVFHLSTWS 259

Query: 242 L 242
           L
Sbjct: 260 L 260

Positive regulator of brassinosteroid signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q93W88|BH137_ARATH Transcription factor bHLH137 OS=Arabidopsis thaliana GN=BHLH137 PE=2 SV=1

 Score =  145 bits (367), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 87/193 (45%), Positives = 114/193 (59%), Gaps = 28/193 (14%)

Query: 37  SFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGS-------- 88
           SF D   Q+    +P+I  + D S    N  K      E   N + T  +GS        
Sbjct: 31  SFID---QNHLYPLPNISTVEDISFLEYNVDKTENSGSEKLANTTKTATTGSSSCDQLSH 87

Query: 89  GLLSVNNKGT--------------GMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATD 134
           G  ++ N G               G++G   +K+KR ++   E P + IHVRA+RGQATD
Sbjct: 88  GPSAITNTGKTRGRKARNSNNSKEGVEGRKSKKQKRGSKE--EPPTDYIHVRARRGQATD 145

Query: 135 SHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSA 194
           SHSLAERVRREKI+ER+R LQ+LVPGC K  G A+MLD IINYV++LQ Q+EFLSMKL++
Sbjct: 146 SHSLAERVRREKISERMRTLQNLVPGCDKVTGKALMLDEIINYVQTLQTQVEFLSMKLTS 205

Query: 195 AS-MYYDFNSELD 206
            S + YDF S+LD
Sbjct: 206 ISPVVYDFGSDLD 218

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJL4|BH078_ARATH Transcription factor bHLH78 OS=Arabidopsis thaliana GN=BHLH78 PE=2 SV=1

 Score =  137 bits (345), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 66/95 (69%), Positives = 76/95 (80%), Gaps = 1/95 (1%)

Query: 109 KRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMA 168
           K NN +  E PK+ IHVRA+RGQATDSHSLAERVRREKI ER++ LQDLVPGC K  G A
Sbjct: 285 KSNNTKPPEPPKDYIHVRARRGQATDSHSLAERVRREKIGERMKLLQDLVPGCNKVTGKA 344

Query: 169 VMLDVIINYVRSLQNQIEFLSMKLSAAS-MYYDFN 202
           +MLD IINYV+SLQ Q+EFLSMKLS+ +    DFN
Sbjct: 345 LMLDEIINYVQSLQRQVEFLSMKLSSVNDTRLDFN 379

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SRT2|BH062_ARATH Transcription factor bHLH62 OS=Arabidopsis thaliana GN=BHLH62 PE=2 SV=1

 Score =  134 bits (336), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 66/113 (58%), Positives = 86/113 (76%), Gaps = 3/113 (2%)

Query: 106 RKRKRNNERV--VEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYK 163
           +K + N ++   ++  K+ IHVRA+RGQATDSHSLAERVRREKI+ER++ LQDLVPGC K
Sbjct: 237 KKSEENGDKTKSIDPYKDYIHVRARRGQATDSHSLAERVRREKISERMKLLQDLVPGCNK 296

Query: 164 TMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSE-LDTTETMPGTN 215
             G A+MLD IINYV+SLQ Q+EFLSMKLS+ +   DFN + L + +  P +N
Sbjct: 297 VTGKALMLDEIINYVQSLQRQVEFLSMKLSSVNTRLDFNMDALLSKDIFPSSN 349

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LK48|BH077_ARATH Transcription factor bHLH77 OS=Arabidopsis thaliana GN=BHLH77 PE=2 SV=1

 Score =  133 bits (335), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 65/117 (55%), Positives = 84/117 (71%), Gaps = 2/117 (1%)

Query: 99  GMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLV 158
           G++    +   +++ +  E PK+ IHVRA+RGQATDSHSLAER RREKI+ER+  LQDLV
Sbjct: 165 GVEKCDSKGDNKDDAKPPEAPKDYIHVRARRGQATDSHSLAERARREKISERMTLLQDLV 224

Query: 159 PGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAAS--MYYDFNSELDTTETMPG 213
           PGC +  G AVMLD IINYV+SLQ Q+EFLSMKL+  +  M ++ N+ L T    PG
Sbjct: 225 PGCNRITGKAVMLDEIINYVQSLQRQVEFLSMKLATVNPRMEFNANASLSTEMIQPG 281

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAA9|BH049_ARATH Transcription factor bHLH49 OS=Arabidopsis thaliana GN=BHLH49 PE=2 SV=1

 Score =  130 bits (327), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 63/97 (64%), Positives = 77/97 (79%), Gaps = 1/97 (1%)

Query: 109 KRNNERVVEKPKE-VIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGM 167
           K+  ++  + PK+  IHVRA+RGQAT+SHSLAERVRREKI+ER++ LQDLVPGC K  G 
Sbjct: 286 KQQGKQSSDPPKDGYIHVRARRGQATNSHSLAERVRREKISERMKFLQDLVPGCNKVTGK 345

Query: 168 AVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSE 204
           AVMLD IINYV+SLQ Q+EFLSMKL+  +   DFN E
Sbjct: 346 AVMLDEIINYVQSLQRQVEFLSMKLATVNPQMDFNLE 382

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C670|BH076_ARATH Transcription factor bHLH76 OS=Arabidopsis thaliana GN=BHLH76 PE=2 SV=1

 Score =  128 bits (321), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 62/82 (75%), Positives = 70/82 (85%)

Query: 123 IHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQ 182
           IH+RA+RGQAT+SHSLAERVRREKI+ER++ LQDLVPGC K  G AVMLD IINYV+SLQ
Sbjct: 221 IHMRARRGQATNSHSLAERVRREKISERMKFLQDLVPGCDKVTGKAVMLDEIINYVQSLQ 280

Query: 183 NQIEFLSMKLSAASMYYDFNSE 204
            QIEFLSMKLSA +   DFN E
Sbjct: 281 CQIEFLSMKLSAVNPVLDFNLE 302

Arabidopsis thaliana (taxid: 3702)

>sp|Q6NKN9|BH074_ARATH Transcription factor bHLH74 OS=Arabidopsis thaliana GN=BHLH74 PE=2 SV=1

 Score =  123 bits (309), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 62/91 (68%), Positives = 75/91 (82%), Gaps = 3/91 (3%)

Query: 117 EKPKE-VIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVII 175
           E PKE  IH+RA+RGQAT+SHSLAERVRREKI+ER+R LQ+LVPGC K  G AVMLD II
Sbjct: 197 EAPKENYIHMRARRGQATNSHSLAERVRREKISERMRLLQELVPGCNKITGKAVMLDEII 256

Query: 176 NYVRSLQNQIEFLSMKLSAASMYYDFNSELD 206
           NYV+SLQ Q+EFLSMKL  A++  + N ++D
Sbjct: 257 NYVQSLQQQVEFLSMKL--ATVNPEINIDID 285

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	242
225424017	258	PREDICTED: transcription factor bHLH75 [	0.917	0.860	0.568	3e-64
297737801	241	unnamed protein product [Vitis vinifera]	0.925	0.929	0.564	3e-64
147773703	237	hypothetical protein VITISV_010828 [Viti	0.925	0.945	0.564	4e-64
255582765	190	DNA binding protein, putative [Ricinus c	0.615	0.784	0.657	5e-52
356529573	273	PREDICTED: transcription factor BEE 3-li	0.665	0.589	0.604	6e-50
356520601	272	PREDICTED: transcription factor BEE 3-li	0.665	0.591	0.604	7e-50
224118802	273	predicted protein [Populus trichocarpa]	0.516	0.457	0.728	2e-49
224127674	265	predicted protein [Populus trichocarpa]	0.834	0.762	0.479	2e-48
449439537	265	PREDICTED: transcription factor BEE 3-li	0.723	0.660	0.565	7e-48
356513103	246	PREDICTED: transcription factor BEE 3-li	0.797	0.784	0.514	8e-47

>gi|225424017|ref|XP_002279412.1| PREDICTED: transcription factor bHLH75 [Vitis vinifera]

 Score =  250 bits (639), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 141/248 (56%), Positives = 163/248 (65%), Gaps = 26/248 (10%)

Query: 3   LENRNTSDDQPAGVMGF--FSNGSFFDHHQQPQLCMSFADNNIQ-------SEALVVPSI 53
           + NR+  ++      GF  FSN  F  HHQQ +  ++F DN          S   V+   
Sbjct: 25  MNNRSAPENSHMNGHGFMAFSNVGFSIHHQQ-EFPVNFRDNTQSPVHAGGLSAVQVLQFS 83

Query: 54  GLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNE 113
               DF  +T  GK            +S  PASGS  L  N      + L GRKRKR+NE
Sbjct: 84  SQPGDFGQETKTGKVNF---------VSSPPASGSEFLGDN------KNLGGRKRKRSNE 128

Query: 114 RVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDV 173
           R   KP+EVIHVRAKRGQATDSHSLAERVRREKINE+LRCLQDLVPGCYKTMGMAVMLDV
Sbjct: 129 RENNKPREVIHVRAKRGQATDSHSLAERVRREKINEKLRCLQDLVPGCYKTMGMAVMLDV 188

Query: 174 IINYVRSLQNQIEFLSMKLSAASMYYDFN-SELDTTETMPGTNECDAQDMERMVREGYGG 232
           IINYV+SLQNQIEFLSMKLSAAS +YDFN SE +  ETM GTN  +  ++ER V+EGYGG
Sbjct: 189 IINYVQSLQNQIEFLSMKLSAASTFYDFNSSEAEALETMQGTNAYEVHEVERSVKEGYGG 248

Query: 233 PSYFHSAW 240
           PS+ HS W
Sbjct: 249 PSHLHSTW 256

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297737801|emb|CBI27002.3| unnamed protein product [Vitis vinifera]

 Score =  250 bits (639), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 141/250 (56%), Positives = 163/250 (65%), Gaps = 26/250 (10%)

Query: 3   LENRNTSDDQPAGVMGF--FSNGSFFDHHQQPQLCMSFADNNIQ-------SEALVVPSI 53
           + NR+  ++      GF  FSN  F  HHQQ +  ++F DN          S   V+   
Sbjct: 8   MNNRSAPENSHMNGHGFMAFSNVGFSIHHQQ-EFPVNFRDNTQSPVHAGGLSAVQVLQFS 66

Query: 54  GLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNE 113
               DF  +T  GK            +S  PASGS  L  N      + L GRKRKR+NE
Sbjct: 67  SQPGDFGQETKTGKVNF---------VSSPPASGSEFLGDN------KNLGGRKRKRSNE 111

Query: 114 RVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDV 173
           R   KP+EVIHVRAKRGQATDSHSLAERVRREKINE+LRCLQDLVPGCYKTMGMAVMLDV
Sbjct: 112 RENNKPREVIHVRAKRGQATDSHSLAERVRREKINEKLRCLQDLVPGCYKTMGMAVMLDV 171

Query: 174 IINYVRSLQNQIEFLSMKLSAASMYYDFN-SELDTTETMPGTNECDAQDMERMVREGYGG 232
           IINYV+SLQNQIEFLSMKLSAAS +YDFN SE +  ETM GTN  +  ++ER V+EGYGG
Sbjct: 172 IINYVQSLQNQIEFLSMKLSAASTFYDFNSSEAEALETMQGTNAYEVHEVERSVKEGYGG 231

Query: 233 PSYFHSAWSL 242
           PS+ HS W  
Sbjct: 232 PSHLHSTWPF 241

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147773703|emb|CAN76460.1| hypothetical protein VITISV_010828 [Vitis vinifera]

 Score =  250 bits (638), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 141/250 (56%), Positives = 163/250 (65%), Gaps = 26/250 (10%)

Query: 3   LENRNTSDDQPAGVMGF--FSNGSFFDHHQQPQLCMSFADNNIQ-------SEALVVPSI 53
           + NR+  ++      GF  FSN  F  HHQQ +  ++F DN          S   V+   
Sbjct: 4   MNNRSAPENSHMNGHGFMAFSNVGFSIHHQQ-EFPVNFRDNTQSPVHAGGLSAVQVLQFS 62

Query: 54  GLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNE 113
               DF  +T  GK            +S  PASGS  L  N      + L GRKRKR+NE
Sbjct: 63  SQPGDFGQETKTGKVNF---------VSSPPASGSEFLGDN------KNLGGRKRKRSNE 107

Query: 114 RVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDV 173
           R   KP+EVIHVRAKRGQATDSHSLAERVRREKINE+LRCLQDLVPGCYKTMGMAVMLDV
Sbjct: 108 RENNKPREVIHVRAKRGQATDSHSLAERVRREKINEKLRCLQDLVPGCYKTMGMAVMLDV 167

Query: 174 IINYVRSLQNQIEFLSMKLSAASMYYDFN-SELDTTETMPGTNECDAQDMERMVREGYGG 232
           IINYV+SLQNQIEFLSMKLSAAS +YDFN SE +  ETM GTN  +  ++ER V+EGYGG
Sbjct: 168 IINYVQSLQNQIEFLSMKLSAASTFYDFNSSEAEALETMQGTNAYEVHEVERSVKEGYGG 227

Query: 233 PSYFHSAWSL 242
           PS+ HS W  
Sbjct: 228 PSHLHSTWPF 237

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255582765|ref|XP_002532159.1| DNA binding protein, putative [Ricinus communis] gi|223528169|gb|EEF30233.1| DNA binding protein, putative [Ricinus communis]

 Score =  210 bits (534), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 100/152 (65%), Positives = 120/152 (78%), Gaps = 3/152 (1%)

Query: 91  LSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINER 150
           +S N KG        R + + ++   EKPKEV+HVRA+RGQATDSHSLAERVRR KINER
Sbjct: 42  VSENGKGKNNSRRGKRTKSKEDD---EKPKEVVHVRARRGQATDSHSLAERVRRGKINER 98

Query: 151 LRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTET 210
           LRCLQD+VPGCYKTMGMAVMLD IINYV+SLQNQ+EFLSMKL+AAS +YDFNSE D  ET
Sbjct: 99  LRCLQDIVPGCYKTMGMAVMLDEIINYVQSLQNQVEFLSMKLTAASTFYDFNSETDAIET 158

Query: 211 MPGTNECDAQDMERMVREGYGGPSYFHSAWSL 242
           M      +A+++ER+++EGYGG + FH  WSL
Sbjct: 159 MQRAKAQEAKEIERVMKEGYGGLTNFHPTWSL 190

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356529573|ref|XP_003533364.1| PREDICTED: transcription factor BEE 3-like [Glycine max]

 Score =  203 bits (516), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 98/162 (60%), Positives = 125/162 (77%), Gaps = 1/162 (0%)

Query: 82  PTPASGSGLLSVNNKGTGMQGLSGR-KRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAE 140
           P  +S +   +V+  G+ ++  SGR KR ++N    EK KEV+HVRA+RGQATDSHSLAE
Sbjct: 112 PETSSANSTPAVSESGSKIKHSSGRGKRVKSNVTEEEKAKEVVHVRARRGQATDSHSLAE 171

Query: 141 RVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYD 200
           RVRR KINE+LRCLQ++VPGCYKTMGMAVMLD IINYV+SLQ+Q+EFLS+KL+AAS +YD
Sbjct: 172 RVRRGKINEKLRCLQNIVPGCYKTMGMAVMLDEIINYVQSLQHQVEFLSLKLTAASTFYD 231

Query: 201 FNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL 242
           FNSE D  ETM      +A+++ +  +EGYGG S+F  AW L
Sbjct: 232 FNSETDALETMQRARASEAKELGKYKKEGYGGVSFFQPAWPL 273

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356520601|ref|XP_003528950.1| PREDICTED: transcription factor BEE 3-like [Glycine max]

 Score =  202 bits (515), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 98/162 (60%), Positives = 125/162 (77%), Gaps = 1/162 (0%)

Query: 82  PTPASGSGLLSVNNKGTGMQGLSGR-KRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAE 140
           P  +S +   +V+  G+ ++  SGR KR ++N    EK KEV+HVRA+RGQATDSHSLAE
Sbjct: 111 PETSSANSTPAVSESGSKIKHSSGRGKRVKSNVTEEEKAKEVVHVRARRGQATDSHSLAE 170

Query: 141 RVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYD 200
           RVRR KINE+LRCLQ++VPGCYKTMGMAVMLD IINYV+SLQ+Q+EFLS+KL+AAS +YD
Sbjct: 171 RVRRGKINEKLRCLQNIVPGCYKTMGMAVMLDEIINYVQSLQHQVEFLSLKLTAASTFYD 230

Query: 201 FNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL 242
           FNSE D  ETM      +A+++ +  +EGYGG S+F  AW L
Sbjct: 231 FNSETDALETMQRARASEAKELGKYKKEGYGGVSFFQPAWPL 272

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118802|ref|XP_002317910.1| predicted protein [Populus trichocarpa] gi|222858583|gb|EEE96130.1| predicted protein [Populus trichocarpa]

 Score =  201 bits (511), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 91/125 (72%), Positives = 108/125 (86%)

Query: 118 KPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINY 177
           KPK+V+HVRA+RGQATDSHSLAERVRR KINERLRCLQD+VPGCYKTMGMAVMLD IINY
Sbjct: 149 KPKDVVHVRARRGQATDSHSLAERVRRGKINERLRCLQDIVPGCYKTMGMAVMLDEIINY 208

Query: 178 VRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFH 237
           V+SLQNQ+EFLSMKL+AAS +YDFN+E D  ETM      +A++++R +REG GG ++ H
Sbjct: 209 VQSLQNQVEFLSMKLTAASTFYDFNAETDAIETMQRAKAQEAKELQRAMREGSGGFAHIH 268

Query: 238 SAWSL 242
           S WSL
Sbjct: 269 STWSL 273

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224127674|ref|XP_002329336.1| predicted protein [Populus trichocarpa] gi|222870790|gb|EEF07921.1| predicted protein [Populus trichocarpa]

 Score =  198 bits (503), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 106/221 (47%), Positives = 145/221 (65%), Gaps = 19/221 (8%)

Query: 30  QQPQLCMSFADNN--------IQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLS 81
           QQP+   ++   N        I S A VV ++ L  + SHD S  +K+   +  S+  +S
Sbjct: 56  QQPEFTATYDHKNLSSTFHPDILSTATVVHTVTLNQNDSHD-SKKRKSMEQSTSSY--IS 112

Query: 82  PTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAER 141
           PT ++        N+      L G K+  N E+  +K +EVIHVRAKRGQATDSHS+AER
Sbjct: 113 PTAST--------NETKKKNNLGGSKKGENKEKEGDKAEEVIHVRAKRGQATDSHSIAER 164

Query: 142 VRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDF 201
           VRREKIN +LRCLQDLVPGC+++MGMAVML+ IINYV SLQNQ+EFLSM+L+AAS   D 
Sbjct: 165 VRREKINNKLRCLQDLVPGCHRSMGMAVMLEEIINYVHSLQNQVEFLSMELAAASSSNDL 224

Query: 202 NSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL 242
           N+  ++++   GT+  +AQ  ++ +RE YG  + FHSAWS+
Sbjct: 225 NNLTESSKRAQGTDSTEAQKTQKWLRERYGEITCFHSAWSI 265

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439537|ref|XP_004137542.1| PREDICTED: transcription factor BEE 3-like [Cucumis sativus] gi|449532109|ref|XP_004173026.1| PREDICTED: transcription factor BEE 3-like [Cucumis sativus]

 Score =  196 bits (498), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 104/184 (56%), Positives = 131/184 (71%), Gaps = 9/184 (4%)

Query: 61  HDTSNGKKAAAHTV-ESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEK- 118
           HD +N +K+    V ES   +S    S SG  +  + G G       KR ++ E+  EK 
Sbjct: 89  HDINNKRKSMPMDVSESTSGISTPQVSESGFNTKYSSGKG-------KRLKSLEKEEEKS 141

Query: 119 PKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYV 178
            +EV+HVRA+RGQATDSHSLAERVRR KINERLRCL+D+VPGCYKTMGMAVMLD IINYV
Sbjct: 142 TREVVHVRARRGQATDSHSLAERVRRGKINERLRCLKDIVPGCYKTMGMAVMLDEIINYV 201

Query: 179 RSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHS 238
           +SLQNQ+EFLSMKL+AAS +YDFNSE D    +      +A+++ER+++EGYGG + FHS
Sbjct: 202 QSLQNQVEFLSMKLAAASSFYDFNSEADAISKLQRAKAHEAKELERLMKEGYGGIACFHS 261

Query: 239 AWSL 242
              L
Sbjct: 262 NLPL 265

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513103|ref|XP_003525253.1| PREDICTED: transcription factor BEE 3-like [Glycine max]

 Score =  192 bits (489), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 106/206 (51%), Positives = 136/206 (66%), Gaps = 13/206 (6%)

Query: 37  SFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNK 96
           +F D+N     ++VP I  + +  H+   G+K  A  +         P+S +   +V   
Sbjct: 50  NFPDHN--EVPVLVPIINSVKNEIHE---GQKRKATDIWE-------PSSANSTPAVFES 97

Query: 97  GTGMQGLSGR-KRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQ 155
           G+  +   GR KR + N    +KP EV+HVRAKRGQATDSHSLAERVRR KINE+LRCLQ
Sbjct: 98  GSKTKNSCGRGKRVKRNMIEDKKPNEVVHVRAKRGQATDSHSLAERVRRGKINEKLRCLQ 157

Query: 156 DLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSELDTTETMPGTN 215
           ++VPGCYKTMGMA+MLD IINYV+SLQ+Q+EFLSMKL+AAS YYDFNSE D  ETM    
Sbjct: 158 NIVPGCYKTMGMAIMLDEIINYVQSLQHQVEFLSMKLNAASTYYDFNSESDVLETMQRAR 217

Query: 216 ECDAQDMERMVREGYGGPSYFHSAWS 241
             + ++++R VRE   G S F   WS
Sbjct: 218 ASEVKELDRYVREECEGVSCFEPTWS 243

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	242
TAIR|locus:2027809	261	BEE3 "AT1G73830" [Arabidopsis	0.876	0.812	0.5	1.2e-44
TAIR|locus:2014144	260	BEE1 "BR enhanced expression 1	0.871	0.811	0.495	1.9e-44
TAIR|locus:2032990	223	CES "AT1G25330" [Arabidopsis t	0.607	0.659	0.638	1.7e-43
TAIR|locus:505006688	286	AT5G50915 "AT5G50915" [Arabido	0.545	0.461	0.547	3.7e-32
UNIPROTKB|Q5N802	481	P0004D12.24 "BHLH transcriptio	0.557	0.280	0.531	2e-31
TAIR|locus:2205420	486	AT1G68920 [Arabidopsis thalian	0.425	0.211	0.615	4.1e-31
TAIR|locus:2028804	390	CIB5 "AT1G26260" [Arabidopsis	0.429	0.266	0.632	3.3e-30
UNIPROTKB|Q84QW1	405	OJ1191_A10.109 "BHLH transcrip	0.570	0.340	0.513	6.2e-30
TAIR|locus:2152551	498	AT5G48560 "AT5G48560" [Arabido	0.458	0.222	0.622	6.8e-30
TAIR|locus:2095198	371	AT3G23690 "AT3G23690" [Arabido	0.719	0.469	0.437	2.1e-29

TAIR|locus:2027809 BEE3 "AT1G73830" [Arabidopsis thaliana (taxid:3702)]

 Score = 470 (170.5 bits), Expect = 1.2e-44, P = 1.2e-44
 Identities = 113/226 (50%), Positives = 144/226 (63%)

Query:    24 SFFDHHQQPQLCMSFA-DNNIQSEALVVPS-IGLIADFSH--DTSNGKKA--AAHTVESF 77
             S F H+Q P      + +NN   + +  PS I    + S   DT   K    A  T E+ 
Sbjct:    43 SLFFHNQFPDHFPGKSLENNFH-QGIFFPSNIQNNEESSSQFDTKKRKSLMEAVSTSENS 101

Query:    78 MNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHS 137
             ++   T ++ S  +S+N      +  S R+ KR+  R  EK +EV+HVRA+RGQATDSHS
Sbjct:   102 VS-DQTLSTSSAQVSINGN-ISTKNNSSRRGKRSKNREEEKEREVVHVRARRGQATDSHS 159

Query:   138 LAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASM 197
             +AERVRR KINERL+CLQD+VPGCYKTMGMA MLD IINYV+SLQNQ+EFLSMKL+AAS 
Sbjct:   160 IAERVRRGKINERLKCLQDIVPGCYKTMGMATMLDEIINYVQSLQNQVEFLSMKLTAASS 219

Query:   198 YYDFNSELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSA-WSL 242
             YYDFNSE D  E+M      +A +M     +G  G S FHS+ W+L
Sbjct:   220 YYDFNSETDAVESMQKAKAREAVEMG----QGRDGSSVFHSSSWTL 261

GO:0003677 "DNA binding" evidence=ISS

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

TAIR|locus:2014144 BEE1 "BR enhanced expression 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 109/220 (49%), Positives = 132/220 (60%)

Query:    24 SFFDHHQQPQLCMSFADNNIQSEALVVPSIGLIADFSHDTSNGKKAAAHTVESFMNLSPT 83
             S F HH Q QL + F  N+  S      +    + F H   N              LS +
Sbjct:    49 SLFLHHHQQQL-LHFPGNSPDSSN----NFSSTSSFLHSDHNIVDETKKRKALLPTLSSS 103

Query:    84 PASG-SGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERV 142
               SG S   +V    TG     G++ K+  E   EK +EV+HVRA+RGQATDSHSLAERV
Sbjct:   104 ETSGVSDNTNVIATETGSLR-RGKRLKKKKEEEDEKEREVVHVRARRGQATDSHSLAERV 162

Query:   143 RREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFN 202
             RR KINERLRCLQD+VPGCYK MGMA MLD IINYV+SLQNQ+EFLSMKL+AAS +YDFN
Sbjct:   163 RRGKINERLRCLQDMVPGCYKAMGMATMLDEIINYVQSLQNQVEFLSMKLTAASSFYDFN 222

Query:   203 SELDTTETMPGTNECDAQDMERMVREGYGGPSYFHSAWSL 242
             SE D  ++M      +  +M R  R+G   P +  S WSL
Sbjct:   223 SETDAVDSMQRAKARETVEMGRQTRDG--SPVFHLSTWSL 260

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

TAIR|locus:2032990 CES "AT1G25330" [Arabidopsis thaliana (taxid:3702)]

 Score = 459 (166.6 bits), Expect = 1.7e-43, P = 1.7e-43
 Identities = 99/155 (63%), Positives = 115/155 (74%)

Query:    92 SVNNKGTGMQGLSGRKRKRNNERVV------EKPKEVIHVRAKRGQATDSHSLAERVRRE 145
             +   KG   +  S R+RKR+ E         +KPK+V+HVRAKRGQATDSHSLAERVRRE
Sbjct:    65 NTRRKGNKEESGSKRRRKRSEEEEAMNGDETQKPKDVVHVRAKRGQATDSHSLAERVRRE 124

Query:   146 KINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNS-E 204
             KINERL+CLQDLVPGCYK MGMAVMLDVII+YVRSLQNQIEFLSMKLSAAS  YD NS +
Sbjct:   125 KINERLKCLQDLVPGCYKAMGMAVMLDVIIDYVRSLQNQIEFLSMKLSAASACYDLNSLD 184

Query:   205 LDTTETMPGTNECDAQDMERMVREGYGG-PSYFHS 238
             ++ T+   G N   A +MER++RE  G  P  F S
Sbjct:   185 IEPTDIFQGGNIHSAAEMERILRESVGTQPPNFSS 219

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:2000488 "positive regulation of brassinosteroid biosynthetic process" evidence=IMP

GO:0048441 "petal development" evidence=RCA

GO:0048443 "stamen development" evidence=RCA

TAIR|locus:505006688 AT5G50915 "AT5G50915" [Arabidopsis thaliana (taxid:3702)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 75/137 (54%), Positives = 97/137 (70%)

Query:    71 AHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVIHVRAKRG 130
             +H   +  N   T   G    + NN   G++G   +K+KR ++   E P + IHVRA+RG
Sbjct:    86 SHGPSAITNTGKT--RGRKARNSNNSKEGVEGRKSKKQKRGSKE--EPPTDYIHVRARRG 141

Query:   131 QATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSM 190
             QATDSHSLAERVRREKI+ER+R LQ+LVPGC K  G A+MLD IINYV++LQ Q+EFLSM
Sbjct:   142 QATDSHSLAERVRREKISERMRTLQNLVPGCDKVTGKALMLDEIINYVQTLQTQVEFLSM 201

Query:   191 KLSAAS-MYYDFNSELD 206
             KL++ S + YDF S+LD
Sbjct:   202 KLTSISPVVYDFGSDLD 218

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

GO:0009739 "response to gibberellin stimulus" evidence=IEP

UNIPROTKB|Q5N802 P0004D12.24 "BHLH transcription factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 345 (126.5 bits), Expect = 2.0e-31, P = 2.0e-31
 Identities = 76/143 (53%), Positives = 101/143 (70%)

Query:    62 DTSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKR-KRNNERVVEKPK 120
             + S+GK+  + T ES  N +    SG G  + +N   G     G+K+ K ++ +  E PK
Sbjct:   220 EDSSGKRCKS-TEES--NAAAEENSGKGKAAQSNSENG----GGKKQGKDSSSKPPEPPK 272

Query:   121 EVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRS 180
             + IHVRA+RG+ATDSHSLAERVRREKI++R++ LQDLVPGC K +G AVMLD IINYV+S
Sbjct:   273 DYIHVRARRGEATDSHSLAERVRREKISQRMKLLQDLVPGCNKVVGKAVMLDEIINYVQS 332

Query:   181 LQNQIEFLSMKLSAASMYYDFNS 203
             LQ Q+EFLSMKL+  +   DFN+
Sbjct:   333 LQRQVEFLSMKLATVNPQLDFNN 355

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2205420 AT1G68920 [Arabidopsis thaliana (taxid:3702)]

 Score = 311 (114.5 bits), Expect = 4.1e-31, Sum P(2) = 4.1e-31
 Identities = 64/104 (61%), Positives = 78/104 (75%)

Query:   102 GLSGRKRKRNNERVVEKPKE-VIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPG 160
             G      K+  ++  + PK+  IHVRA+RGQAT+SHSLAERVRREKI+ER++ LQDLVPG
Sbjct:   279 GKKSNSGKQQGKQSSDPPKDGYIHVRARRGQATNSHSLAERVRREKISERMKFLQDLVPG 338

Query:   161 CYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSE 204
             C K  G AVMLD IINYV+SLQ Q+EFLSMKL+  +   DFN E
Sbjct:   339 CNKVTGKAVMLDEIINYVQSLQRQVEFLSMKLATVNPQMDFNLE 382

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

TAIR|locus:2028804 CIB5 "AT1G26260" [Arabidopsis thaliana (taxid:3702)]

 Score = 304 (112.1 bits), Expect = 3.3e-30, Sum P(2) = 3.3e-30
 Identities = 67/106 (63%), Positives = 80/106 (75%)

Query:   101 QGLSGRKRKRNNERVV-EKPKE-VIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLV 158
             Q  +    K N+E+   +  K+  IH+RA+RGQAT+SHSLAERVRREKI+ER++ LQDLV
Sbjct:   197 QSPTSNANKTNSEKQPSDSLKDGYIHMRARRGQATNSHSLAERVRREKISERMKFLQDLV 256

Query:   159 PGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNSE 204
             PGC K  G AVMLD IINYV+SLQ QIEFLSMKLSA +   DFN E
Sbjct:   257 PGCDKVTGKAVMLDEIINYVQSLQCQIEFLSMKLSAVNPVLDFNLE 302

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009911 "positive regulation of flower development" evidence=IGI

GO:0048513 "organ development" evidence=RCA

UNIPROTKB|Q84QW1 OJ1191_A10.109 "BHLH transcription factor(GBOF-1)-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 331 (121.6 bits), Expect = 6.2e-30, P = 6.2e-30
 Identities = 74/144 (51%), Positives = 96/144 (66%)

Query:    64 SNGKKAAAHTVESFMNLSPTPASGSGLLSVNNKGTGMQGLSGRKRKRNNERVVEKPKEVI 123
             S+GK+      E   ++ P         SV + G G Q    ++ K  N + VE PK+ +
Sbjct:   147 SDGKRCKTGNGEKESSVKPKAEQAGSDSSVEDGGGGGQ----KQGKGKNAKPVEPPKDYV 202

Query:   124 HVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQN 183
             HVRA+RGQATDSHSLAERVRRE+I++R++ LQDLVPGC K +G A+MLD IINYV+SLQ 
Sbjct:   203 HVRARRGQATDSHSLAERVRRERISQRMKVLQDLVPGCNKVIGKALMLDEIINYVQSLQR 262

Query:   184 QIEFLSMKLSAASMYYDFNSELDT 207
             Q+EFLSMKL+  +   DF S L T
Sbjct:   263 QVEFLSMKLATVNPL-DF-SNLPT 284

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2152551 AT5G48560 "AT5G48560" [Arabidopsis thaliana (taxid:3702)]

 Score = 332 (121.9 bits), Expect = 6.8e-30, P = 6.8e-30
 Identities = 71/114 (62%), Positives = 85/114 (74%)

Query:   105 GRKRKRNNERVVEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKT 164
             G   K NN +  E PK+ IHVRA+RGQATDSHSLAERVRREKI ER++ LQDLVPGC K 
Sbjct:   281 GEGNKSNNTKPPEPPKDYIHVRARRGQATDSHSLAERVRREKIGERMKLLQDLVPGCNKV 340

Query:   165 MGMAVMLDVIINYVRSLQNQIEFLSMKLSAAS-MYYDFNSE-LDTTETM-PGTN 215
              G A+MLD IINYV+SLQ Q+EFLSMKLS+ +    DFN + L + + M P +N
Sbjct:   341 TGKALMLDEIINYVQSLQRQVEFLSMKLSSVNDTRLDFNVDALVSKDVMIPSSN 394

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0016132 "brassinosteroid biosynthetic process" evidence=RCA

TAIR|locus:2095198 AT3G23690 "AT3G23690" [Arabidopsis thaliana (taxid:3702)]

 Score = 326 (119.8 bits), Expect = 2.1e-29, P = 2.1e-29
 Identities = 81/185 (43%), Positives = 109/185 (58%)

Query:    63 TSNGKKAAAHTVESFMNLSPTPASGSGLLSVNNK----GTGMQGLSGRKRKRNNE---RV 115
             + NGK++ A +  +  N   +  +G       +K    G+   G+     K +N+   + 
Sbjct:   122 SGNGKESPASSSLTASNSKVSGENGGSKGGKRSKQDVAGSSKNGVEKCDSKGDNKDDAKP 181

Query:   116 VEKPKEVIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVII 175
              E PK+ IHVRA+RGQATDSHSLAER RREKI+ER+  LQDLVPGC +  G AVMLD II
Sbjct:   182 PEAPKDYIHVRARRGQATDSHSLAERARREKISERMTLLQDLVPGCNRITGKAVMLDEII 241

Query:   176 NYVRSLQNQIEFLSMKLSAAS--MYYDFNSELDTTETMPGTNECDAQDMERMVREGYGGP 233
             NYV+SLQ Q+EFLSMKL+  +  M ++ N+ L T    PG  E   Q +  M       P
Sbjct:   242 NYVQSLQRQVEFLSMKLATVNPRMEFNANASLSTEMIQPG--ESLTQSLYAMACSEQRLP 299

Query:   234 SYFHS 238
             S ++S
Sbjct:   300 SAYYS 304

GO:0003677 "DNA binding" evidence=ISS

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
A4D998	BH075_ARATH	No assigned EC number	0.7054	0.5247	0.5695	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	242
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	3e-10
smart00353	53	smart00353, HLH, helix loop helix domain	5e-10
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	4e-06

>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 = 54.5 bits (132), Expect = 3e-10
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 129 RGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGM--AVMLDVIINYVRSLQNQIE 186
           R    ++H+L ER RRE+IN+    L+ L+P    +  +  A +L   ++Y++SLQ  ++
Sbjct: 1   RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 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|197674 smart00353, HLH, helix loop helix domain

 Score = 53.4 bits (129), Expect = 5e-10
 Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 137 SLAERVRREKINERLRCLQDLVPGCYKTMGM--AVMLDVIINYVRSLQNQIE 186
           +  ER RR KINE    L+ L+P   K   +  A +L + I Y++SLQ +++
Sbjct: 1   NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

Length = 53

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

 Score = 42.4 bits (101), Expect = 4e-06
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 135 SHSLAERVRREKINERLRCLQDLVPGCYKT-MGMAVMLDVIINYVRSLQ 182
           +H+  ER RR++IN+    L++L+P      +  A +L + I Y++ LQ
Sbjct: 4   AHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	242
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.47
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.41
smart00353	53	HLH helix loop helix domain.	99.39
KOG1318	411	consensus Helix loop helix transcription factor EB	99.28
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.95
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.7
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.59
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.47
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.09
PLN03217	93	transcription factor ATBS1; Provisional	97.92
KOG0561	373	consensus bHLH transcription factor [Transcription	97.47
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.26
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.19
KOG3910	632	consensus Helix loop helix transcription factor [T	96.46
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	89.54
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	87.01
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	81.04

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

Probab=99.47  E-value=5.1e-14  Score=98.60  Aligned_cols=55  Identities=35%  Similarity=0.605  Sum_probs=49.9

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCC--ccCCChhhhHHHHHHHHHHHHHHHH
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGC--YKTMGMAVMLDVIINYVRSLQNQIE  186 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~--~k~~dKasIL~eAI~YIK~Lq~qvq  186 (242)
                      .+..|+..||+||++||+.|..|+.|||.+  ..++||++||+.||+||++|+.+++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            455799999999999999999999999999  3558999999999999999998863

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

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

Probab=99.41  E-value=3e-13  Score=94.66  Aligned_cols=49  Identities=35%  Similarity=0.693  Sum_probs=45.2

Q ss_pred             CCcchHHHHHHHHHHHHHHHhhhhcCCC----ccCCChhhhHHHHHHHHHHHH
Q 042908          134 DSHSLAERVRREKINERLRCLQDLVPGC----YKTMGMAVMLDVIINYVRSLQ  182 (242)
Q Consensus       134 ~~Hs~aERrRR~kIne~~~~LrsLVP~~----~k~~dKasIL~eAI~YIK~Lq  182 (242)
                      ..|+..||+||++||+.|..|+.|||.+    ..+++|++||+.||+||++||
T Consensus         3 ~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    3 QKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            3599999999999999999999999997    345899999999999999997

; 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 ....

>smart00353 HLH helix loop helix domain

Probab=99.39  E-value=9.3e-13  Score=90.74  Aligned_cols=50  Identities=38%  Similarity=0.604  Sum_probs=45.0

Q ss_pred             chHHHHHHHHHHHHHHHhhhhcCCC--ccCCChhhhHHHHHHHHHHHHHHHH
Q 042908          137 SLAERVRREKINERLRCLQDLVPGC--YKTMGMAVMLDVIINYVRSLQNQIE  186 (242)
Q Consensus       137 s~aERrRR~kIne~~~~LrsLVP~~--~k~~dKasIL~eAI~YIK~Lq~qvq  186 (242)
                      +..||+||++||+.|..|+.|||.+  ..+++|++||..||+||++|+.+++
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            4689999999999999999999964  2347999999999999999999886

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

Probab=99.28  E-value=3.5e-12  Score=122.19  Aligned_cols=61  Identities=31%  Similarity=0.584  Sum_probs=53.0

Q ss_pred             cccCCCCCCcchHHHHHHHHHHHHHHHhhhhcCCCcc---CCChhhhHHHHHHHHHHHHHHHHH
Q 042908          127 AKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYK---TMGMAVMLDVIINYVRSLQNQIEF  187 (242)
Q Consensus       127 akr~~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k---~~dKasIL~eAI~YIK~Lq~qvq~  187 (242)
                      .|.+++++.|+.+|||||++||++|.+|..|||.|..   +++|++||..+++||+.||+..+.
T Consensus       228 ~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~  291 (411)
T KOG1318|consen  228 ERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQR  291 (411)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHH
Confidence            3445678899999999999999999999999999942   367999999999999999986663

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.95  E-value=1.5e-09  Score=95.51  Aligned_cols=64  Identities=28%  Similarity=0.464  Sum_probs=53.7

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCCcc------CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGCYK------TMGMAVMLDVIINYVRSLQNQIEFLSMKLSAA  195 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k------~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~  195 (242)
                      ++..|..+||+||+-||.....|+.|||.|..      ++.||.||.++|+||.+|.+++..-+++++++
T Consensus        62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L  131 (229)
T KOG1319|consen   62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTL  131 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44569999999999999999999999998843      25799999999999999988776666555443

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

Probab=98.70  E-value=6.9e-09  Score=94.12  Aligned_cols=55  Identities=33%  Similarity=0.478  Sum_probs=47.7

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCCcc-------CCChhhhHHHHHHHHHHHHHHHHH
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGCYK-------TMGMAVMLDVIINYVRSLQNQIEF  187 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k-------~~dKasIL~eAI~YIK~Lq~qvq~  187 (242)
                      +..|-+.||+||.|||+.|.+|++|||.+.+       +++||.||+-|++|++.||...+.
T Consensus        33 k~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   33 KVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             hhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            4457899999999999999999999997743       378999999999999999886544

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.59  E-value=1.2e-07  Score=98.45  Aligned_cols=66  Identities=27%  Similarity=0.481  Sum_probs=59.3

Q ss_pred             CCCCCCcchHHHHHHHHHHHHHHHhhhhcCCCccCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042908          130 GQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAA  195 (242)
Q Consensus       130 ~~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~  195 (242)
                      +.++.+|+++|||.|..|||+|.+|++|||+..-++.|..+|..||+||++|+...+.+....+..
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l  339 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASL  339 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhh
Confidence            567899999999999999999999999999998779999999999999999999888776554444

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

Probab=98.47  E-value=1.7e-07  Score=96.42  Aligned_cols=52  Identities=21%  Similarity=0.395  Sum_probs=48.8

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCCc---cCCChhhhHHHHHHHHHHHHHH
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGCY---KTMGMAVMLDVIINYVRSLQNQ  184 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~~---k~~dKasIL~eAI~YIK~Lq~q  184 (242)
                      +.+|+.+|||||+++|..|.+|.+|||.|.   -++||.+||.+||.+||.++..
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            678999999999999999999999999997   5689999999999999999885

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

Probab=98.09  E-value=6.2e-06  Score=74.47  Aligned_cols=57  Identities=21%  Similarity=0.299  Sum_probs=47.1

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCCccCC--ChhhhHHHHHHHHHHHHHHHHHH
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGCYKTM--GMAVMLDVIINYVRSLQNQIEFL  188 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k~~--dKasIL~eAI~YIK~Lq~qvq~L  188 (242)
                      ++..|+.-||+||..|.++|..|+.+||......  +.++||+.|+.||+.|+......
T Consensus        59 ~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~  117 (232)
T KOG2483|consen   59 SRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQ  117 (232)
T ss_pred             chhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHH
Confidence            4556999999999999999999999999764432  25899999999999998754433

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.92  E-value=1.7e-05  Score=62.06  Aligned_cols=52  Identities=31%  Similarity=0.464  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHhhhhcCCCcc-----CCChhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042908          144 REKINERLRCLQDLVPGCYK-----TMGMAVMLDVIINYVRSLQNQIEFLSMKLSAA  195 (242)
Q Consensus       144 R~kIne~~~~LrsLVP~~~k-----~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~  195 (242)
                      -+.|++.+..||+|+|....     +..-+-||+||+.||+.|+.+|..|+++|...
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~L   75 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSEL   75 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999996532     23567799999999999999999999998665

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.47  E-value=7.8e-05  Score=70.04  Aligned_cols=55  Identities=24%  Similarity=0.366  Sum_probs=46.5

Q ss_pred             CCcchHHHHHHHHHHHHHHHhhhhcCCC-ccCCChhhhHHHHHHHHHHHHHHHHHH
Q 042908          134 DSHSLAERVRREKINERLRCLQDLVPGC-YKTMGMAVMLDVIINYVRSLQNQIEFL  188 (242)
Q Consensus       134 ~~Hs~aERrRR~kIne~~~~LrsLVP~~-~k~~dKasIL~eAI~YIK~Lq~qvq~L  188 (242)
                      +.-+..||||=.-||-.|..|++|+|-. +.++.||.||+.+.+||..|+.+.-+|
T Consensus        62 eIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   62 EIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             HhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence            3456789999999999999999999954 334899999999999999998865444

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

Probab=97.26  E-value=0.00053  Score=63.06  Aligned_cols=55  Identities=22%  Similarity=0.304  Sum_probs=48.1

Q ss_pred             chHHHHHHHHHHHHHHHhhh-hcCCCccCCChhhhHHHHHHHHHHHHHHHHHHHHH
Q 042908          137 SLAERVRREKINERLRCLQD-LVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMK  191 (242)
Q Consensus       137 s~aERrRR~kIne~~~~Lrs-LVP~~~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~  191 (242)
                      .+-||||=.|+||.|.+|+. -+++.+..+-|.-||..||+||..||.-++++...
T Consensus       123 TMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~  178 (284)
T KOG3960|consen  123 TMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQA  178 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            47899999999999999976 45677777899999999999999999998888654

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

Probab=97.19  E-value=0.00032  Score=62.13  Aligned_cols=59  Identities=22%  Similarity=0.323  Sum_probs=50.7

Q ss_pred             CCcchHHHHHHHHHHHHHHHhhhhcCCC---ccCCChhhhHHHHHHHHHHHHHHHHHHHHHH
Q 042908          134 DSHSLAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRSLQNQIEFLSMKL  192 (242)
Q Consensus       134 ~~Hs~aERrRR~kIne~~~~LrsLVP~~---~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l  192 (242)
                      ..++..||.|=..+|..|..|+.+||..   .|++.|..+|..||.||++|++-++.-+..+
T Consensus       111 ~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~  172 (228)
T KOG4029|consen  111 QARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL  172 (228)
T ss_pred             hhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence            3466779999999999999999999944   5568999999999999999999888776544

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.46  E-value=0.0037  Score=62.26  Aligned_cols=65  Identities=22%  Similarity=0.217  Sum_probs=51.9

Q ss_pred             CCCCCcchHHHHHHHHHHHHHHHhhhhcCCC---ccCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042908          131 QATDSHSLAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAA  195 (242)
Q Consensus       131 ~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~---~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~  195 (242)
                      .++...++-||.|=.-||+.|++|-.+.--.   .|.--|..||-.||.-|-.|++||.+-..--.++
T Consensus       525 ERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERNLNPKaa  592 (632)
T KOG3910|consen  525 ERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERNLNPKAA  592 (632)
T ss_pred             HHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHccCChhhh
Confidence            3556678899999999999999999986522   3334699999999999999999999865443343

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=89.54  E-value=0.2  Score=43.43  Aligned_cols=53  Identities=19%  Similarity=0.327  Sum_probs=44.1

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCCc-cCCChhhhHHHHHHHHHHHHHHH
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGCY-KTMGMAVMLDVIINYVRSLQNQI  185 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~~-k~~dKasIL~eAI~YIK~Lq~qv  185 (242)
                      +-.|++-||+|-..+|+.|.+||.+||... .+..|.-.|.-|-.||-+|=+-+
T Consensus        79 rv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   79 RVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            345999999999999999999999999653 22578888999999999886543

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

Probab=87.01  E-value=0.41  Score=49.73  Aligned_cols=44  Identities=32%  Similarity=0.390  Sum_probs=37.6

Q ss_pred             chHHHHHHHHHHHHHHHhhhhcCCC---ccCCChhhhHHHHHHHHHH
Q 042908          137 SLAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRS  180 (242)
Q Consensus       137 s~aERrRR~kIne~~~~LrsLVP~~---~k~~dKasIL~eAI~YIK~  180 (242)
                      .-+.|.||.|=|+-|.+|..+||--   .-.+|||+|+.-||.|++-
T Consensus        51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            3588999999999999999999933   2237999999999999873

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=81.04  E-value=1.6  Score=43.42  Aligned_cols=44  Identities=27%  Similarity=0.353  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCCC---ccCCChhhhHHHHHHHHHHH
Q 042908          138 LAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRSL  181 (242)
Q Consensus       138 ~aERrRR~kIne~~~~LrsLVP~~---~k~~dKasIL~eAI~YIK~L  181 (242)
                      -+.|.||++=|..|.+|..|+|-.   +...||++|+.-|-.|||--
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            467999999999999999999944   23379999999999999853

---

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	242
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	4e-17
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	3e-08
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	6e-07
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	2e-06
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	4e-06
1a0a_A	63	BHLH, protein (phosphate system positive regulator	5e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

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

 Score = 72.8 bits (179), Expect = 4e-17
 Identities = 19/67 (28%), Positives = 36/67 (53%)

Query: 128 KRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEF 187
            RG+   +H+  E+  R  IN+++  L+DLV G    +  + +L   I+Y+R LQ+  + 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 188 LSMKLSA 194
           L  +  +
Sbjct: 62  LKQENLS 68

>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 = 48.1 bits (115), Expect = 3e-08
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 5/56 (8%)

Query: 134 DSHSLAERVRREKINERLRCLQDLVPGCYKTMGM-----AVMLDVIINYVRSLQNQ 184
             H+  ER RR+KIN  +  L  ++P               +L    +Y++ L+  
Sbjct: 7   AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS 62

>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 = 45.1 bits (107), Expect = 6e-07
 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 1/56 (1%)

Query: 134 DSHSLAERVRREKINERLRCLQDLVPGCYKT-MGMAVMLDVIINYVRSLQNQIEFL 188
             H+  ER RR+ I +    L+D VP         A +LD    Y++ ++ +    
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTH 59

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

 Score = 43.9 bits (104), Expect = 2e-06
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 134 DSHSLAERVRREKINERLRCLQDLVPGCYKTMGM--AVMLDVIINYVRSLQNQIEFLSMK 191
             H+  ER RR+ I +    L+D VP   +      A +LD    Y++ ++ +       
Sbjct: 14  AHHNALERKRRDHIKDSFHSLRDSVPSL-QGEKASRAQILDKATEYIQYMRRKNHTHQQD 72

Query: 192 L 192
           +
Sbjct: 73  I 73

>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 = 43.1 bits (102), Expect = 4e-06
 Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 135 SHSLAERVRREKINERLRCLQDLVPGCYKTMGM--AVMLDVIINYVRSLQNQIE 186
           +H++ ER RR ++      L+D +P           V+L     Y+ S+Q + +
Sbjct: 9   THNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQ 62

>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 = 42.1 bits (99), Expect = 5e-06
 Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 6/58 (10%)

Query: 135 SHSLAERVRREKINERLRCLQDLVPGCYKTMGM------AVMLDVIINYVRSLQNQIE 186
           SH  AE+ RR ++   L  L  L+P  +K   +      A  ++    Y+R LQ    
Sbjct: 5   SHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 40.6 bits (94), Expect = 3e-04
 Identities = 39/246 (15%), Positives = 85/246 (34%), Gaps = 48/246 (19%)

Query: 28  HHQQPQLCMSFADNNIQ---SEALVVPSIGLIADFS-HDTSNGKKAAAHT--VESFMNLS 81
           HH      M F     Q    + L V     + +F   D  +  K+      ++  +  S
Sbjct: 3   HHHH----MDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIM-S 57

Query: 82  PTPASGSGLL--SVNNKGT-GMQGLSGRKRKRN----NERVVEKPKE-----VIHVRAKR 129
               SG+  L  ++ +K    +Q       + N       +  + ++      +++  + 
Sbjct: 58  KDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117

Query: 130 GQATDSHSLAER-VRREKINERLR-CLQDLVPGCYKTM-GMA-----VM-LDVIINY--V 178
               D+   A+  V R +   +LR  L +L P     + G+       + LDV ++Y   
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQ 177

Query: 179 RSLQNQIEFLSMKLSA---------ASMYY----DFNSELDTTETMP-GTNECDAQDMER 224
             +  +I +L++K              + Y    ++ S  D +  +    +   A+    
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237

Query: 225 MVREGY 230
           +  + Y
Sbjct: 238 LKSKPY 243

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	242
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.72
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.7
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.64
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.63
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.62
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.56
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.54
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.54
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.49
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.46
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.36
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.1
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.09
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.01
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.96
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.89
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.59
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.05

>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=99.72  E-value=2.7e-18  Score=129.80  Aligned_cols=64  Identities=27%  Similarity=0.366  Sum_probs=59.0

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCCccCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAA  195 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~  195 (242)
                      .+.+|+++||+||++||++|.+|++|||++..++||++||.+||+||++||.+++.|+.+..+.
T Consensus         6 rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L   69 (82)
T 1am9_A            6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567999999999999999999999999996668999999999999999999999999887654

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

Probab=99.70  E-value=2.3e-17  Score=132.64  Aligned_cols=71  Identities=30%  Similarity=0.404  Sum_probs=52.2

Q ss_pred             chhhhcccCCCCCCcchHHHHHHHHHHHHHHHhhhhcCCCcc---CCChhhhHHHHHHHHHHHHHHHHHHHHHH
Q 042908          122 VIHVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYK---TMGMAVMLDVIINYVRSLQNQIEFLSMKL  192 (242)
Q Consensus       122 ~~~~rakr~~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k---~~dKasIL~eAI~YIK~Lq~qvq~L~~~l  192 (242)
                      ..+..+++.+++.+|+++||+||++||++|.+|++|||+|.+   +++|++||++||+||++||.+++.|+...
T Consensus        17 ~~~~~~k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           17 EARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345567778889999999999999999999999999999853   47899999999999999999999998653

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

Probab=99.64  E-value=4.9e-17  Score=120.94  Aligned_cols=58  Identities=22%  Similarity=0.418  Sum_probs=53.2

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCCccCCChhhhHHHHHHHHHHHHHHHHHHH
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLS  189 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k~~dKasIL~eAI~YIK~Lq~qvq~L~  189 (242)
                      .+.+|+++||+||++||++|.+|++|||++..++||++||+.||+||+.||.++.-|+
T Consensus         8 kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            8 KRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            4567999999999999999999999999876568999999999999999999988764

>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=99.63  E-value=7.6e-17  Score=116.87  Aligned_cols=55  Identities=29%  Similarity=0.460  Sum_probs=48.9

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCCcc------CCChhhhHHHHHHHHHHHHHHHH
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGCYK------TMGMAVMLDVIINYVRSLQNQIE  186 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k------~~dKasIL~eAI~YIK~Lq~qvq  186 (242)
                      .+.+|+++||+||++||+.|.+|+.|||.+.+      +++||+||+.||+||+.||++|+
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            35789999999999999999999999997743      35799999999999999998764

>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=99.62  E-value=1.3e-16  Score=115.14  Aligned_cols=56  Identities=23%  Similarity=0.374  Sum_probs=50.7

Q ss_pred             CCCCCcchHHHHHHHHHHHHHHHhhhhcCCCcc-----CCChhhhHHHHHHHHHHHHHHHH
Q 042908          131 QATDSHSLAERVRREKINERLRCLQDLVPGCYK-----TMGMAVMLDVIINYVRSLQNQIE  186 (242)
Q Consensus       131 ~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k-----~~dKasIL~eAI~YIK~Lq~qvq  186 (242)
                      ..+.+|+++||+||++||+.|.+|++|||.|..     +++|++||+.||+||++||++++
T Consensus         4 ~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            457789999999999999999999999999863     47999999999999999998753

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

Probab=99.56  E-value=3.2e-16  Score=116.82  Aligned_cols=54  Identities=28%  Similarity=0.528  Sum_probs=48.4

Q ss_pred             CCCCCcchHHHHHHHHHHHHHHHhhhhcCCCc---cCCChhhhHHHHHHHHHHHHHH
Q 042908          131 QATDSHSLAERVRREKINERLRCLQDLVPGCY---KTMGMAVMLDVIINYVRSLQNQ  184 (242)
Q Consensus       131 ~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~---k~~dKasIL~eAI~YIK~Lq~q  184 (242)
                      +++.+|+++||+||++||+.|.+|+.|||.|.   .++|||+||+.||+||+.|+.-
T Consensus         8 ~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~~   64 (73)
T 4h10_A            8 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   64 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhcC
Confidence            45678999999999999999999999999883   3489999999999999999753

>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=99.54  E-value=6.8e-15  Score=110.21  Aligned_cols=64  Identities=22%  Similarity=0.365  Sum_probs=57.6

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCCc-cCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGCY-KTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAA  195 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~-k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~  195 (242)
                      .+..|+..||+||..||+.|..|++|||.+. .+++|++||..||+||+.|+.+++.|+.++..+
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L   76 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDL   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467999999999999999999999999873 348999999999999999999999999887654

>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=99.54  E-value=8.1e-15  Score=110.23  Aligned_cols=62  Identities=23%  Similarity=0.373  Sum_probs=54.9

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCC-ccCCChhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGC-YKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSA  194 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~-~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a  194 (242)
                      +..|+..||+||..||+.|..|+++||.+ ..+++|++||..||+||+.|+.+++.|+.++..
T Consensus         3 R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~   65 (83)
T 1nkp_B            3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD   65 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35699999999999999999999999986 234899999999999999999999998876544

>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=99.49  E-value=2.6e-14  Score=109.51  Aligned_cols=60  Identities=23%  Similarity=0.338  Sum_probs=53.4

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCCc--cCCChhhhHHHHHHHHHHHHHHHHHHHHHH
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGCY--KTMGMAVMLDVIINYVRSLQNQIEFLSMKL  192 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~~--k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l  192 (242)
                      +..|+..||+||..||++|..|+.+||.+.  .+++|++||..||+||++|+.+.+.|....
T Consensus         7 R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~   68 (88)
T 1nkp_A            7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEE   68 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346999999999999999999999999873  348999999999999999999988876554

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

Probab=99.46  E-value=3.3e-14  Score=106.60  Aligned_cols=58  Identities=24%  Similarity=0.288  Sum_probs=48.6

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCC---ccCCChhhhHHHHHHHHHHHHHHHHHHH
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRSLQNQIEFLS  189 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~---~k~~dKasIL~eAI~YIK~Lq~qvq~L~  189 (242)
                      .+..|+..||+||..||+.|..|+.+||.+   .+..+|+.||..||+||++||+++++++
T Consensus         5 rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            456799999999999999999999999953   3333688999999999999999999874

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

Probab=99.36  E-value=1.2e-12  Score=98.80  Aligned_cols=61  Identities=18%  Similarity=0.179  Sum_probs=53.8

Q ss_pred             CCcchHHHHHHHHHHHHHHHhhhhcCCCc--cCCChhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 042908          134 DSHSLAERVRREKINERLRCLQDLVPGCY--KTMGMAVMLDVIINYVRSLQNQIEFLSMKLSA  194 (242)
Q Consensus       134 ~~Hs~aERrRR~kIne~~~~LrsLVP~~~--k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a  194 (242)
                      ..|+..||+||..||++|..|+++||.+.  .+++|++||..||+||+.|+.+.+.|..+...
T Consensus         3 ~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~   65 (80)
T 1nlw_A            3 STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQ   65 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            35999999999999999999999999653  34789999999999999999999988876543

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

Probab=99.10  E-value=6.2e-11  Score=107.72  Aligned_cols=54  Identities=22%  Similarity=0.415  Sum_probs=42.5

Q ss_pred             CCCCCcchHHHHHHHHHHHHHHHhhhhcCCCccCCChhhhHHHHHHHHHHHHHH
Q 042908          131 QATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQ  184 (242)
Q Consensus       131 ~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k~~dKasIL~eAI~YIK~Lq~q  184 (242)
                      ..+.+|+.+||+||++||+.|.+|+.|||....++||++||..||+|||.|+..
T Consensus        11 ~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           11 AKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            456789999999999999999999999995555589999999999999999864

>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=99.09  E-value=1.8e-11  Score=89.98  Aligned_cols=54  Identities=22%  Similarity=0.344  Sum_probs=47.9

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCC-ccCCChhhhHHHHHHHHHHHHHHHH
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGC-YKTMGMAVMLDVIINYVRSLQNQIE  186 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~-~k~~dKasIL~eAI~YIK~Lq~qvq  186 (242)
                      +..|+..||+|+..||+.|..|+.+||.. +++++|..||..||+||.+||+.++
T Consensus        13 R~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             hhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            34599999999999999999999999965 3568999999999999999998653

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

Probab=99.01  E-value=3.5e-10  Score=81.18  Aligned_cols=52  Identities=23%  Similarity=0.337  Sum_probs=47.1

Q ss_pred             CcchHHHHHHHHHHHHHHHhhhhcCCC--ccCCChhhhHHHHHHHHHHHHHHHH
Q 042908          135 SHSLAERVRREKINERLRCLQDLVPGC--YKTMGMAVMLDVIINYVRSLQNQIE  186 (242)
Q Consensus       135 ~Hs~aERrRR~kIne~~~~LrsLVP~~--~k~~dKasIL~eAI~YIK~Lq~qvq  186 (242)
                      .|+.-||+|+..||+.|..|+.+||..  +++++|..||..||+||..|++.++
T Consensus         5 ~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            5 KANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            478999999999999999999999965  4568999999999999999998764

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

Probab=98.96  E-value=2e-10  Score=105.75  Aligned_cols=54  Identities=28%  Similarity=0.520  Sum_probs=47.5

Q ss_pred             CCCCCCcchHHHHHHHHHHHHHHHhhhhcCCC---ccCCChhhhHHHHHHHHHHHHH
Q 042908          130 GQATDSHSLAERVRREKINERLRCLQDLVPGC---YKTMGMAVMLDVIINYVRSLQN  183 (242)
Q Consensus       130 ~~~~~~Hs~aERrRR~kIne~~~~LrsLVP~~---~k~~dKasIL~eAI~YIK~Lq~  183 (242)
                      ..++.+|+.+||+||++||+.|.+|+.|||.+   ..++||++||..||+|||.|+.
T Consensus        11 ~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           11 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            44567899999999999999999999999953   2338999999999999999984

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

Probab=98.89  E-value=2.7e-09  Score=81.44  Aligned_cols=50  Identities=24%  Similarity=0.363  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHhhhhcCCCcc---CCChhhhHHHHHHHHHHHHHHHHHHHHHH
Q 042908          143 RREKINERLRCLQDLVPGCYK---TMGMAVMLDVIINYVRSLQNQIEFLSMKL  192 (242)
Q Consensus       143 RR~kIne~~~~LrsLVP~~~k---~~dKasIL~eAI~YIK~Lq~qvq~L~~~l  192 (242)
                      -|..||++|.+|..|||.+..   +++|++||..||+||++||+.++.+.+..
T Consensus         3 ~R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e   55 (83)
T 4ath_A            3 MRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   55 (83)
T ss_dssp             CHHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHH
T ss_pred             chhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            389999999999999998643   37999999999999999999888776543

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

Probab=98.59  E-value=1.6e-08  Score=74.61  Aligned_cols=46  Identities=24%  Similarity=0.357  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHHHHHHhhhhcCCC--ccCCChhhhHHHHHHHHHHHHH
Q 042908          138 LAERVRREKINERLRCLQDLVPGC--YKTMGMAVMLDVIINYVRSLQN  183 (242)
Q Consensus       138 ~aERrRR~kIne~~~~LrsLVP~~--~k~~dKasIL~eAI~YIK~Lq~  183 (242)
                      .-||+|...||+.|..|+.+||..  +++++|..+|.-||+||..||.
T Consensus        20 erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           20 EEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            358899999999999999999966  4468999999999999999984

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

Probab=98.05  E-value=7.8e-06  Score=63.95  Aligned_cols=48  Identities=23%  Similarity=0.328  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHHHhhhhcCCC--ccCCChhhhHHHHHHHHHHHHHHHHH
Q 042908          140 ERVRREKINERLRCLQDLVPGC--YKTMGMAVMLDVIINYVRSLQNQIEF  187 (242)
Q Consensus       140 ERrRR~kIne~~~~LrsLVP~~--~k~~dKasIL~eAI~YIK~Lq~qvq~  187 (242)
                      ||.|=..||+.|..|+.+||..  .+++.|.-+|.-||+||..|+..++.
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~   82 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDS   82 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhc
Confidence            5778888999999999999965  45689999999999999999988765

---

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	242
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	5e-15
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-14
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-13
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	2e-13
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	1e-11
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	1e-10
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	2e-10
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-09

>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 = 65.1 bits (159), Expect = 5e-15
 Identities = 16/60 (26%), Positives = 27/60 (45%)

Query: 144 REKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAASMYYDFNS 203
           R  IN+++  L+DLV G    M  + +L   I+Y++ LQ     L  +     +    N 
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKLANQKNK 60

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

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

 Score = 65.0 bits (158), Expect = 1e-14
 Identities = 19/67 (28%), Positives = 36/67 (53%)

Query: 128 KRGQATDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEF 187
            RG+   +H+  E+  R  IN+++  L+DLV G    +  + +L   I+Y+R LQ+  + 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 188 LSMKLSA 194
           L  +  +
Sbjct: 62  LKQENLS 68

>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 = 62.2 bits (151), Expect = 2e-13
 Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 6/71 (8%)

Query: 124 HVRAKRGQATDSHSLAERVRREKINERLRCLQDLVPGCYK--TMGMAVMLDVIINYVRSL 181
           H+  KR     +H++ ER RR ++      L+D +P           V+L     Y+ S+
Sbjct: 2   HMNVKR----RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV 57

Query: 182 QNQIEFLSMKL 192
           Q + + L  + 
Sbjct: 58  QAEEQKLISEE 68

>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 = 61.4 bits (149), Expect = 2e-13
 Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 6/59 (10%)

Query: 134 DSHSLAERVRREKINERLRCLQDLVPGCYKT------MGMAVMLDVIINYVRSLQNQIE 186
           +SH  AE+ RR ++   L  L  L+P  +K          A  ++    Y+R LQ    
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>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 = 56.4 bits (136), Expect = 1e-11
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 135 SHSLAERVRREKINERLRCLQDLVPGCY-KTMGMAVMLDVIINYVRSLQNQIE 186
           + ++ ER R  K+NE    L+        + +    +L   I Y+  LQ  + 
Sbjct: 15  AATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR 67

>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 = 54.5 bits (131), Expect = 1e-10
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 135 SHSLAERVRREKINERLRCLQDLVPGCYKT-MGMAVMLDVIINYVRSLQNQIEFLSMKL 192
            H+  ER RR+ I +    L+D VP         A +LD    Y++ ++ +       +
Sbjct: 5   HHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 63

>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 = 53.2 bits (128), Expect = 2e-10
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 5/56 (8%)

Query: 134 DSHSLAERVRREKINERLRCLQDLVPGCYKT-----MGMAVMLDVIINYVRSLQNQ 184
             H+  ER RR+KIN  +  L  ++P               +L    +Y++ L+  
Sbjct: 7   AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS 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 = 51.1 bits (122), Expect = 1e-09
 Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 135 SHSLAERVRREKINERLRCLQDLVPGCYKTMGM--AVMLDVIINYVRSLQNQIEFLSMKL 192
           +H+  E+ RR  +   L  L+ LVP    +       +L     +++ L++       ++
Sbjct: 4   THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQI 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	242
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.64
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.57
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.53
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.52
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.49
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.48

>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=99.64  E-value=4e-17  Score=120.58  Aligned_cols=63  Identities=27%  Similarity=0.374  Sum_probs=57.9

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCCccCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAA  195 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~  195 (242)
                      +..|+.+||+||++||+.|..|++|||++..+++|++||..||+||+.|+.+++.|.++....
T Consensus         7 R~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~l   69 (80)
T d1am9a_           7 RTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSL   69 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457999999999999999999999999988778999999999999999999999998776543

>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=99.57  E-value=6.7e-16  Score=109.46  Aligned_cols=53  Identities=28%  Similarity=0.418  Sum_probs=47.7

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCC------ccCCChhhhHHHHHHHHHHHHHHH
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGC------YKTMGMAVMLDVIINYVRSLQNQI  185 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~------~k~~dKasIL~eAI~YIK~Lq~qv  185 (242)
                      +..|+++||+||++||+.|..|++|||++      ..+++|+.||+.||+||++||++|
T Consensus         3 R~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            46799999999999999999999999954      334799999999999999999875

>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=99.54  E-value=2.7e-15  Score=109.96  Aligned_cols=61  Identities=18%  Similarity=0.179  Sum_probs=54.6

Q ss_pred             CCcchHHHHHHHHHHHHHHHhhhhcCCCc--cCCChhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 042908          134 DSHSLAERVRREKINERLRCLQDLVPGCY--KTMGMAVMLDVIINYVRSLQNQIEFLSMKLSA  194 (242)
Q Consensus       134 ~~Hs~aERrRR~kIne~~~~LrsLVP~~~--k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a  194 (242)
                      ..|+.+||+||++||+.|.+|++|||.+.  .+++|++||..||+||+.|+.+++.|..+...
T Consensus         3 ~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~   65 (79)
T d1nlwa_           3 STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQ   65 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999999999999999999763  24799999999999999999999999877644

>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=99.53  E-value=3e-15  Score=110.70  Aligned_cols=62  Identities=23%  Similarity=0.385  Sum_probs=55.3

Q ss_pred             CCCcchHHHHHHHHHHHHHHHhhhhcCCCc-cCCChhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 042908          133 TDSHSLAERVRREKINERLRCLQDLVPGCY-KTMGMAVMLDVIINYVRSLQNQIEFLSMKLSA  194 (242)
Q Consensus       133 ~~~Hs~aERrRR~kIne~~~~LrsLVP~~~-k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a  194 (242)
                      +..|+.+||+||++||+.|..|++|||++. ++++|++||..||+||++|+.+++.|..++..
T Consensus         3 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~   65 (83)
T d1nkpb_           3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDD   65 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356999999999999999999999999763 45899999999999999999999999876543

>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=99.52  E-value=2.1e-15  Score=108.66  Aligned_cols=53  Identities=23%  Similarity=0.341  Sum_probs=48.5

Q ss_pred             CCcchHHHHHHHHHHHHHHHhhhhcCCCc-cCCChhhhHHHHHHHHHHHHHHHH
Q 042908          134 DSHSLAERVRREKINERLRCLQDLVPGCY-KTMGMAVMLDVIINYVRSLQNQIE  186 (242)
Q Consensus       134 ~~Hs~aERrRR~kIne~~~~LrsLVP~~~-k~~dKasIL~eAI~YIK~Lq~qvq  186 (242)
                      ..|+..||+||.+||+.|..|++|||.+. ++++|++||..||+||++||++|+
T Consensus        14 ~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          14 KAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            46999999999999999999999999874 457999999999999999998764

>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=99.52  E-value=2e-15  Score=106.60  Aligned_cols=53  Identities=28%  Similarity=0.332  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHhhhhcCCCccCCChhhhHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 042908          144 REKINERLRCLQDLVPGCYKTMGMAVMLDVIINYVRSLQNQIEFLSMKLSAAS  196 (242)
Q Consensus       144 R~kIne~~~~LrsLVP~~~k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a~~  196 (242)
                      |++||++|.+|++|||++.+++|||+||.+||+||++||.+++.|+++.....
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~   53 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK   53 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999986789999999999999999999999998876654

>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=99.49  E-value=1.5e-14  Score=107.84  Aligned_cols=61  Identities=23%  Similarity=0.330  Sum_probs=54.8

Q ss_pred             CCcchHHHHHHHHHHHHHHHhhhhcCCCc--cCCChhhhHHHHHHHHHHHHHHHHHHHHHHhh
Q 042908          134 DSHSLAERVRREKINERLRCLQDLVPGCY--KTMGMAVMLDVIINYVRSLQNQIEFLSMKLSA  194 (242)
Q Consensus       134 ~~Hs~aERrRR~kIne~~~~LrsLVP~~~--k~~dKasIL~eAI~YIK~Lq~qvq~L~~~l~a  194 (242)
                      ..|+.+||+||++||+.|..|++|||++.  .+++|++||..||+||++|+.+++.|..+...
T Consensus         8 ~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~   70 (88)
T d1nkpa_           8 RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDL   70 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46999999999999999999999999763  34799999999999999999999999876654

>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=99.48  E-value=5e-15  Score=105.46  Aligned_cols=54  Identities=24%  Similarity=0.385  Sum_probs=48.1

Q ss_pred             CCCCcchHHHHHHHHHHHHHHHhhhhcCCCc-----cCCChhhhHHHHHHHHHHHHHHH
Q 042908          132 ATDSHSLAERVRREKINERLRCLQDLVPGCY-----KTMGMAVMLDVIINYVRSLQNQI  185 (242)
Q Consensus       132 ~~~~Hs~aERrRR~kIne~~~~LrsLVP~~~-----k~~dKasIL~eAI~YIK~Lq~qv  185 (242)
                      .+..|+.+||+||++||+.|.+|++|||.+.     .+++|++||..||+||+.||++.
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            4567999999999999999999999999763     24799999999999999999764