Citrus Sinensis ID: 038097

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------27
Protein Sequence
LDAGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQPLPMSMLRTPLGLMHKTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNVEINKRNVEHHKIRPSA
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHcHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccHHcEEEcccccccccccccc
Coil and Loop (DISEMBL)
ldagkcieppvpssslcslgasnnnpacntfnlkrryedtegsacpcdqyekKLERKAVTvrgsksnrkkrtpevHKRYERKRRDKINKKMRALQELIpncnkvdkASMLEEAIDYLKTLQFQVMMMSMgtgvcmpsmmlptgIIGMQQMhavapqmshfppmgigmdgrmqmgagcnpaqflmppipgatavpgiqmpgfpgqplpmsmlrtplglmhktnpvagVSRAAAsmevkdsapltnpgdsnqnveinkrnvehhkirpsa
Flexible Loop (DISEMBL)
ldagkcieppvpssslcslgasnNNPACNTFNLKRRYEDtegsacpcdqyekklerkavtvrgsksnrkkrtpevhkryerkrrdkinkkmralqelipncnkvdkasMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQPLPMSMLRTPLGLMHKTNPVAGVSRAAASMEVKdsapltnpgdsnqnveinkrnvehhkirpsa
Low Complexity Region (SEG)
LDAGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQPLPMSMLRTPLGLMHKTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNVEINKRNVEHHKIRPSA
Disordered region (IsUnstruct)
**********************************************************************************************QELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAP*********I********GAGCNPAQFLMPPIPGATAV***************************************************************************
Disordered Region (DISOPRED)
************************************************************************************DKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVM***********************************************************************************************************************************************
Disordered Region (DISEMBL)
LDAGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLERKA*********************ERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQPLPMSMLRTPLGLMHKTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNVEINKRNVEHHKIRPSA
Disordered Region (DISPRO)
***********************************************************************************RDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQPLPMSMLRTPLGLMHKT*****************************NVE***R*VEH*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LDAGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQPLPMSMLRTPLGLMHKTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNVEINKRNVEHHKIRPSA
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	268	2.2.26 [Sep-21-2011]
Q8L5W8	416	Transcription factor PIL1	yes	no	0.701	0.451	0.415	6e-32
O80536	524	Transcription factor PIF3	no	no	0.645	0.330	0.382	3e-25
Q8GZM7	478	Transcription factor PIF1	no	no	0.369	0.207	0.495	3e-21
Q8L5W7	363	Transcription factor PIF6	no	no	0.410	0.303	0.426	2e-18
Q9FUA4	373	Transcription factor SPAT	no	no	0.317	0.227	0.505	1e-17
Q9SVU6	413	Transcription factor bHLH	no	no	0.447	0.290	0.422	4e-17
Q8GZ38	399	Transcription factor UNE1	no	no	0.294	0.197	0.537	7e-17
Q9FHA2	210	Transcription factor ALC	no	no	0.343	0.438	0.468	5e-16
Q84LH8	444	Transcription factor PIF5	no	no	0.261	0.157	0.6	1e-15
Q9SVU7	445	Putative transcription fa	no	no	0.335	0.202	0.445	2e-15

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

 Score =  137 bits (346), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 96/231 (41%), Positives = 118/231 (51%), Gaps = 43/231 (18%)

Query: 3   AGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPC----DQYEKKLERKA 58
            G+  E    SSS  S G S +   C+   LKR+Y D E             E    +  
Sbjct: 159 VGRSTELYFASSSKFSRGTSRDLSCCS---LKRKYGDIEEEESTYLSNNSDDESDDAKTQ 215

Query: 59  VTVRGSK-SNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYL 117
           V  R  K   ++KR+ EVHK YERKRRD+ NKKMRALQ+L+PNC K DKAS+L+EAI Y+
Sbjct: 216 VHARTRKPVTKRKRSTEVHKLYERKRRDEFNKKMRALQDLLPNCYKDDKASLLDEAIKYM 275

Query: 118 KTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGC 177
           +TLQ QV MMSMG G+  P  MLP G               H+ PMG+G    M MGA  
Sbjct: 276 RTLQLQVQMMSMGNGLIRPPTMLPMG---------------HYSPMGLG----MHMGAAA 316

Query: 178 NPA---QFLMPPIPGATAVPGIQMPGFPGQ----PLPMSMLRTPLGLMHKT 221
            P    QFL  P+        +Q  GFPG     P  +S L  P GL+  T
Sbjct: 317 TPTSIPQFL--PM-------NVQATGFPGMNNAPPQMLSFLNHPSGLIPNT 358

Transcription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  115 bits (289), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 73/191 (38%), Positives = 107/191 (56%), Gaps = 18/191 (9%)

Query: 30  TFNLKRRYEDTEGSACPCDQYEKKL---ERKAVTVRGSKSNRKKRTPEVHKRYERKRRDK 86
           + +LKR++ + +   C  +  E++     ++A   R    +++ R+ EVH   ER+RRD+
Sbjct: 299 SLSLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDR 358

Query: 87  INKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCM-PSMMLPTGII 145
           IN+KMRALQELIPNCNKVDKASML+EAI+YLK+LQ QV +MSM +G  + P++M P G +
Sbjct: 359 INEKMRALQELIPNCNKVDKASMLDEAIEYLKSLQLQVQIMSMASGYYLPPAVMFPPG-M 417

Query: 146 GMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQP 205
           G     A A  M    P  +G+    + G+  N               P  Q+ G   QP
Sbjct: 418 GHYPAAAAAMAMGMGMPYAMGLPDLSRGGSSVNHG-------------PQFQVSGMQQQP 464

Query: 206 LPMSMLRTPLG 216
           + M + R   G
Sbjct: 465 VAMGIPRVSGG 475

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  102 bits (254), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 51/103 (49%), Positives = 67/103 (65%), Gaps = 4/103 (3%)

Query: 28  CNTFNLKRRYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKI 87
            N  + KR+    E  A   D+ E + E        + S ++ R  EVH   ERKRRD+I
Sbjct: 245 TNVDDRKRK----EREATTTDETESRSEETKQARVSTTSTKRSRAAEVHNLSERKRRDRI 300

Query: 88  NKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMG 130
           N++M+ALQELIP CNK DKASML+EAI+Y+K+LQ Q+ MMSMG
Sbjct: 301 NERMKALQELIPRCNKSDKASMLDEAIEYMKSLQLQIQMMSMG 343

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q8L5W7|PIF6_ARATH Transcription factor PIF6 OS=Arabidopsis thaliana GN=PIF6 PE=1 SV=1

 Score = 93.2 bits (230), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 55/129 (42%), Positives = 72/129 (55%), Gaps = 19/129 (14%)

Query: 68  RKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMM 127
           ++KR  E +   ER +R+ INKKMR LQ L+PN +K D  SML+EAI+Y+  LQ QV MM
Sbjct: 185 KRKRNAEAYNSPERNQRNDINKKMRTLQNLLPNSHKDDNESMLDEAINYMTNLQLQVQMM 244

Query: 128 SMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPAQFLMPPI 187
           +MG     PSMM+P G               ++  MG+ M   MQMG      QFL   +
Sbjct: 245 TMGNRFVTPSMMMPLG--------------PNYSQMGLAMGVGMQMGE----QQFLPAHV 286

Query: 188 PGATAVPGI 196
            GA  +PGI
Sbjct: 287 LGA-GLPGI 294

Arabidopsis thaliana (taxid: 3702)

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

 Score = 90.5 bits (223), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 43/85 (50%), Positives = 58/85 (68%)

Query: 71  RTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMG 130
           R  EVH   E++RR +IN+KM+ALQ LIPN NK DKASML+EAI+YLK LQ QV M++M 
Sbjct: 197 RAAEVHNLSEKRRRSRINEKMKALQSLIPNSNKTDKASMLDEAIEYLKQLQLQVQMLTMR 256

Query: 131 TGVCMPSMMLPTGIIGMQQMHAVAP 155
            G+ +  + LP   +   Q+  + P
Sbjct: 257 NGINLHPLCLPGTTLHPLQLSQIRP 281

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 88.6 bits (218), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 52/123 (42%), Positives = 72/123 (58%), Gaps = 3/123 (2%)

Query: 61  VRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTL 120
            R S S+++ R   +HK  ER+RR KIN+ M+ALQEL+P C K D++SML++ I+Y+K+L
Sbjct: 267 ARDSTSSKRSRAAIMHKLSERRRRQKINEMMKALQELLPRCTKTDRSSMLDDVIEYVKSL 326

Query: 121 QFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPA 180
           Q Q+ M SMG  V +P MM   G I  Q M  +A  M+  PP  I    +  M  G  P 
Sbjct: 327 QSQIQMFSMG-HVMIPPMMY-AGNIQQQYMPHMAMGMNR-PPAFIPFPRQAHMAEGVGPV 383

Query: 181 QFL 183
              
Sbjct: 384 DLF 386

Arabidopsis thaliana (taxid: 3702)

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

 Score = 87.8 bits (216), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 43/80 (53%), Positives = 58/80 (72%), Gaps = 1/80 (1%)

Query: 49  QYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKAS 108
           Q E + E+KA   + S S ++ R   +H + ERKRRDKIN++M+ LQ+L+PN +K DKAS
Sbjct: 192 QMEDEEEKKAGG-KSSVSTKRSRAAAIHNQSERKRRDKINQRMKTLQKLVPNSSKTDKAS 250

Query: 109 MLEEAIDYLKTLQFQVMMMS 128
           ML+E I+YLK LQ QV MMS
Sbjct: 251 MLDEVIEYLKQLQAQVSMMS 270

Required during the fertilization of ovules by pollen.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHA2|ALC_ARATH Transcription factor ALC OS=Arabidopsis thaliana GN=ALC PE=2 SV=1

 Score = 84.7 bits (208), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 44/94 (46%), Positives = 61/94 (64%), Gaps = 2/94 (2%)

Query: 48  DQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKA 107
           D+Y  + +R     R S   ++    + H   E+KRR KIN+KM+ALQ+LIPN NK DKA
Sbjct: 72  DKYAFEHKRSGAKQRNSL--KRNIDAQFHNLSEKKRRSKINEKMKALQKLIPNSNKTDKA 129

Query: 108 SMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLP 141
           SML+EAI+YLK LQ QV  +++  G+ +  M LP
Sbjct: 130 SMLDEAIEYLKQLQLQVQTLAVMNGLGLNPMRLP 163

Required for the dehiscence of fruit, especially for the separation of the valve cells from the replum. Promotes the differentiation of a strip of labile nonlignified cells sandwiched between layers of lignified cells.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 83.6 bits (205), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 42/70 (60%), Positives = 58/70 (82%)

Query: 64  SKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQ 123
           S S R+ R  EVH   ER+RRD+IN++M+ALQELIP+C++ DKAS+L+EAIDYLK+LQ Q
Sbjct: 249 SGSTRRSRAAEVHNLSERRRRDRINERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQ 308

Query: 124 VMMMSMGTGV 133
           + +M MG+G+
Sbjct: 309 LQVMWMGSGM 318

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 83.2 bits (204), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 45/101 (44%), Positives = 63/101 (62%), Gaps = 11/101 (10%)

Query: 51  EKKLERKAVT-----VRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVD 105
           E KL+ +  T      RGS S ++ RT E+H   ER+RR+KIN+KM+ LQ+LIP CNK  
Sbjct: 230 ESKLKAREETHGTEEARGSTSRKRSRTAEMHNLAERRRREKINEKMKTLQQLIPRCNKST 289

Query: 106 KASMLEEAIDYLKTLQFQV------MMMSMGTGVCMPSMML 140
           K S L++AI+Y+K+LQ Q+      MM +  T   MP M +
Sbjct: 290 KVSTLDDAIEYVKSLQSQIQGMMSPMMNAGNTQQFMPHMAM 330

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	268
224130812	555	predicted protein [Populus trichocarpa]	0.712	0.344	0.550	1e-51
118486519	561	unknown [Populus trichocarpa]	0.712	0.340	0.550	1e-51
359487706	752	PREDICTED: transcription factor PIF3-lik	0.906	0.323	0.447	1e-47
296089857	573	unnamed protein product [Vitis vinifera]	0.906	0.424	0.447	3e-47
147770956	627	hypothetical protein VITISV_023382 [Viti	0.570	0.244	0.560	1e-40
339778387	589	phytochrome-interacting factor 3.1 [Popu	0.929	0.422	0.428	4e-39
339778389	589	phytochrome-interacting factor 3.1 [Popu	0.914	0.415	0.432	4e-39
339778391	589	phytochrome-interacting factor 3.1 [Popu	0.902	0.410	0.434	8e-39
225437758	569	PREDICTED: uncharacterized protein LOC10	0.873	0.411	0.427	1e-38
339778403	589	phytochrome-interacting factor 3.1 [Popu	0.902	0.410	0.434	1e-38

>gi|224130812|ref|XP_002320931.1| predicted protein [Populus trichocarpa] gi|222861704|gb|EEE99246.1| predicted protein [Populus trichocarpa]

 Score =  209 bits (532), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 119/216 (55%), Positives = 144/216 (66%), Gaps = 25/216 (11%)

Query: 2   DAGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLERKAVTV 61
           D GK I+    +SS+CS GASN+     T +L+R+YEDTEG+A   D  E   E + V  
Sbjct: 313 DRGKSIDQLTATSSICSRGASNDP----TSSLERQYEDTEGTAYSSDDLE---EEEQVPA 365

Query: 62  RGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQ 121
           RGS  ++++R  E+H   ERKRRD+INKKMRALQ+LIPN NKVDKASML EAIDYLK+LQ
Sbjct: 366 RGSAGSKRRRATEIHNLSERKRRDRINKKMRALQDLIPNSNKVDKASMLGEAIDYLKSLQ 425

Query: 122 FQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGR-MQMGAGCNPA 180
            QV MMSMGT +CMP MMLPT   GMQ +H  AP ++ F PMG+GMD R MQMG GC+PA
Sbjct: 426 LQVQMMSMGTRLCMPLMMLPT---GMQHIH--APLLAQFSPMGVGMDTRLMQMGVGCSPA 480

Query: 181 QFLMPPIPGATAVPGIQMPGFP-GQPLPMSMLRTPL 215
            F           P   M G P GQ LPMS+ + P 
Sbjct: 481 TF-----------PASGMFGLPAGQMLPMSVSQAPF 505

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118486519|gb|ABK95099.1| unknown [Populus trichocarpa]

 Score =  209 bits (531), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 119/216 (55%), Positives = 144/216 (66%), Gaps = 25/216 (11%)

Query: 2   DAGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLERKAVTV 61
           D GK I+    +SS+CS GASN+     T +L+R+YEDTEG+A   D  E   E + V  
Sbjct: 319 DRGKSIDQLTATSSICSRGASNDP----TSSLERQYEDTEGTAYSSDDLE---EEEQVPA 371

Query: 62  RGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQ 121
           RGS  ++++R  E+H   ERKRRD+INKKMRALQ+LIPN NKVDKASML EAIDYLK+LQ
Sbjct: 372 RGSAGSKRRRATEIHNLSERKRRDRINKKMRALQDLIPNSNKVDKASMLGEAIDYLKSLQ 431

Query: 122 FQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGR-MQMGAGCNPA 180
            QV MMSMGT +CMP MMLPT   GMQ +H  AP ++ F PMG+GMD R MQMG GC+PA
Sbjct: 432 LQVQMMSMGTRLCMPLMMLPT---GMQHIH--APLLAQFSPMGVGMDTRLMQMGVGCSPA 486

Query: 181 QFLMPPIPGATAVPGIQMPGFP-GQPLPMSMLRTPL 215
            F           P   M G P GQ LPMS+ + P 
Sbjct: 487 TF-----------PASGMFGLPAGQMLPMSVSQAPF 511

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359487706|ref|XP_002276198.2| PREDICTED: transcription factor PIF3-like [Vitis vinifera]

 Score =  195 bits (496), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 128/286 (44%), Positives = 160/286 (55%), Gaps = 43/286 (15%)

Query: 2   DAGKCIEPPVPSSSLCS---LGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLE--R 56
           D  K IEP V  SS+CS   +  ++N+P     NLKR+  DTE S CP +  E++    R
Sbjct: 391 DGEKTIEPAVACSSVCSGNSVERASNDP---KHNLKRKCRDTEESECPSEDVEEESVGVR 447

Query: 57  KAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDY 116
           K+   +G   +++ R  EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+Y
Sbjct: 448 KSAPAKGGTGSKRSRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEY 507

Query: 117 LKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPP---------MGIGM 167
           LKTLQ QV +MSMGTG+CMP MMLPT   GMQ +HA    M HFPP              
Sbjct: 508 LKTLQLQVQIMSMGTGLCMPPMMLPT---GMQHIHAA--HMGHFPPMGVGMGMGMGMGYG 562

Query: 168 DGRMQMGAGCNPAQFLMPPIPGATAVPG----------------IQMPGFPGQPLPMSML 211
            G + M  G     F+  P    T  PG                +Q+ G PGQ +P+SM 
Sbjct: 563 MGMLDMNGGSPSCPFIQAPPMQGTHFPGRPISVPPNLHGMVGSNLQVFGLPGQGIPLSMP 622

Query: 212 RTPLGLMH-----KTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNV 252
             PL  M      K++     S AA SMEV DSAP ++  D  QNV
Sbjct: 623 HAPLIPMSGSPLMKSSMALNDSGAAGSMEVPDSAPASSSKDLIQNV 668

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296089857|emb|CBI39676.3| unnamed protein product [Vitis vinifera]

 Score =  194 bits (494), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 128/286 (44%), Positives = 160/286 (55%), Gaps = 43/286 (15%)

Query: 2   DAGKCIEPPVPSSSLCS---LGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLE--R 56
           D  K IEP V  SS+CS   +  ++N+P     NLKR+  DTE S CP +  E++    R
Sbjct: 255 DGEKTIEPAVACSSVCSGNSVERASNDP---KHNLKRKCRDTEESECPSEDVEEESVGVR 311

Query: 57  KAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDY 116
           K+   +G   +++ R  EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+Y
Sbjct: 312 KSAPAKGGTGSKRSRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEY 371

Query: 117 LKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPP---------MGIGM 167
           LKTLQ QV +MSMGTG+CMP MMLPT   GMQ +HA    M HFPP              
Sbjct: 372 LKTLQLQVQIMSMGTGLCMPPMMLPT---GMQHIHAA--HMGHFPPMGVGMGMGMGMGYG 426

Query: 168 DGRMQMGAGCNPAQFLMPPIPGATAVPG----------------IQMPGFPGQPLPMSML 211
            G + M  G     F+  P    T  PG                +Q+ G PGQ +P+SM 
Sbjct: 427 MGMLDMNGGSPSCPFIQAPPMQGTHFPGRPISVPPNLHGMVGSNLQVFGLPGQGIPLSMP 486

Query: 212 RTPLGLMH-----KTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNV 252
             PL  M      K++     S AA SMEV DSAP ++  D  QNV
Sbjct: 487 HAPLIPMSGSPLMKSSMALNDSGAAGSMEVPDSAPASSSKDLIQNV 532

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147770956|emb|CAN76246.1| hypothetical protein VITISV_023382 [Vitis vinifera]

 Score =  172 bits (436), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 93/166 (56%), Positives = 115/166 (69%), Gaps = 13/166 (7%)

Query: 2   DAGKCIEPPVPSSSLCS---LGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLE--R 56
           D  K IEP V  SS+CS   +  ++N+P     NLKR+  DTE S CP +  E++    R
Sbjct: 376 DGEKSIEPAVACSSVCSGNSVERASNDP---KHNLKRKCRDTEESECPSEDVEEESVGVR 432

Query: 57  KAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDY 116
           K+   +G   +++ R  EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+Y
Sbjct: 433 KSAPAKGGTGSKRSRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEY 492

Query: 117 LKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPP 162
           LKTLQ QV +MSMGTG+CMP MMLPT   GMQ +HA    M HFPP
Sbjct: 493 LKTLQLQVQIMSMGTGLCMPPMMLPT---GMQHIHAA--HMGHFPP 533

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|339778387|gb|AEK06075.1| phytochrome-interacting factor 3.1 [Populus balsamifera]

 Score =  167 bits (424), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 125/292 (42%), Positives = 161/292 (55%), Gaps = 43/292 (14%)

Query: 2   DAGKCIEPPVPSSSLCSLGASNNNPACN-TFNLKRRYEDTEGSACPCDQYEKKL--ERKA 58
           D  K  EP V SSS+ S G S   P+ + T NLKR++ DTE S  P +  E++    +K 
Sbjct: 250 DVEKTTEPLVASSSVGS-GNSAERPSDDPTENLKRKHRDTEESEGPSEDAEEESVGAKKP 308

Query: 59  VTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLK 118
            + R    +++ R  EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+YLK
Sbjct: 309 ASARAGNGSKRGRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLK 368

Query: 119 TLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGI-----------GM 167
           TLQ QV +MSMG G+ MPSMMLP    GM  MHA    M  F PMG+            M
Sbjct: 369 TLQLQVQIMSMGAGIYMPSMMLPP---GMPHMHAA--HMGQFLPMGVGMGMGFRMGMPDM 423

Query: 168 DGRMQMGAGC--------NPAQFLMPPIPGATAV-----PGIQMPGFPGQPLPMSMLRTP 214
           +G     +GC        + A F   P+ G +A+     P +QM G  GQ LPMS  R P
Sbjct: 424 NGGY---SGCPMYQVPPMHGAHFPGSPMSGPSALHGMGGPSLQMFGLSGQGLPMSFPRAP 480

Query: 215 LGLMH-----KTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNV--EINKRNV 259
           L  M      KTN           M+  DSA  ++  D+ QN+  ++ + NV
Sbjct: 481 LMPMSGGPPPKTNREPNACGVVGPMDNLDSATASSSKDAIQNINSQVMRNNV 532

Source: Populus balsamifera

Species: Populus balsamifera

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|339778389|gb|AEK06076.1| phytochrome-interacting factor 3.1 [Populus balsamifera]

 Score =  167 bits (423), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 121/280 (43%), Positives = 152/280 (54%), Gaps = 35/280 (12%)

Query: 2   DAGKCIEPPVPSSSLCSLGASNNNPACN-TFNLKRRYEDTEGSACPCDQYEKKL--ERKA 58
           D  K  EP V SSS+ S G S   P+ + T NLKR++ DTE S  P +  E++    +K 
Sbjct: 250 DVEKTTEPLVASSSVGS-GNSAERPSDDPTENLKRKHRDTEESEGPSEDAEEESVGAKKP 308

Query: 59  VTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLK 118
            + R    +++ R  EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+YLK
Sbjct: 309 ASARAGNGSKRGRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLK 368

Query: 119 TLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHF---------------PPM 163
           TLQ QV +MSMG G+ MPSMMLP    GM  MHA    M  F               P M
Sbjct: 369 TLQLQVQIMSMGAGMYMPSMMLPP---GMPHMHAA--HMGQFLPMGVGMGMGFRMGMPDM 423

Query: 164 GIGMDG-RMQMGAGCNPAQFLMPPIPGATAV-----PGIQMPGFPGQPLPMSMLRTPLGL 217
             G  G  M   +  + A F   P+ G +A+     P +QM G  GQ LPMS  R PL  
Sbjct: 424 NGGYSGCPMYQVSPMHGAHFPGSPMSGPSALHGMGGPSLQMFGLSGQGLPMSFPRAPLMP 483

Query: 218 MH-----KTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNV 252
           M      KTN           M+  DSA  ++  D+ QN+
Sbjct: 484 MSGGPPPKTNREPNACGVVGPMDNLDSATASSSKDAIQNI 523

Source: Populus balsamifera

Species: Populus balsamifera

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|339778391|gb|AEK06077.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778393|gb|AEK06078.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778395|gb|AEK06079.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778399|gb|AEK06081.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778401|gb|AEK06082.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778405|gb|AEK06084.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778407|gb|AEK06085.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778409|gb|AEK06086.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778411|gb|AEK06087.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778413|gb|AEK06088.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778415|gb|AEK06089.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778417|gb|AEK06090.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778419|gb|AEK06091.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778421|gb|AEK06092.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778423|gb|AEK06093.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778425|gb|AEK06094.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778427|gb|AEK06095.1| phytochrome-interacting factor 3.1 [Populus balsamifera] gi|339778429|gb|AEK06096.1| phytochrome-interacting factor 3.1 [Populus balsamifera]

 Score =  166 bits (421), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 123/283 (43%), Positives = 156/283 (55%), Gaps = 41/283 (14%)

Query: 2   DAGKCIEPPVPSSSLCSLGASNNNPACN-TFNLKRRYEDTEGSACPCDQYEKKL--ERKA 58
           D  K  EP V SSS+ S G S   P+ + T NLKR++ DTE S  P +  E++    +K 
Sbjct: 250 DVEKTTEPLVASSSVGS-GNSAERPSDDPTENLKRKHRDTEESEGPSEDAEEESVGAKKP 308

Query: 59  VTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLK 118
            + R    +++ R  EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+YLK
Sbjct: 309 ASARAGNGSKRGRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLK 368

Query: 119 TLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGI-----------GM 167
           TLQ QV +MSMG G+ MPSMMLP    GM  MHA    M  F PMG+            M
Sbjct: 369 TLQLQVQIMSMGAGMYMPSMMLPP---GMPHMHAA--HMGQFLPMGVGMGMGFRMGMPDM 423

Query: 168 DGRMQMGAGC--------NPAQFLMPPIPGATAV-----PGIQMPGFPGQPLPMSMLRTP 214
           +G     +GC        + A F   P+ G +A+     P +QM G  GQ LPMS  R P
Sbjct: 424 NGGY---SGCPMYQVPPMHGAHFPGSPMSGPSALHGMGGPSLQMFGLSGQGLPMSFPRAP 480

Query: 215 LGLMH-----KTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNV 252
           L  M      KTN           M+  DSA  ++  D+ QN+
Sbjct: 481 LMPMSGGPPPKTNREPNACGVVGPMDNLDSATASSSKDAIQNI 523

Source: Populus balsamifera

Species: Populus balsamifera

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225437758|ref|XP_002273729.1| PREDICTED: uncharacterized protein LOC100253874 [Vitis vinifera]

 Score =  166 bits (419), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 112/262 (42%), Positives = 155/262 (59%), Gaps = 28/262 (10%)

Query: 3   AGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLERK--AVT 60
           A K +EP + SSS CS  ASN      +++LK + +++E S  P   +E++  R   A++
Sbjct: 316 AEKSVEPLLASSSTCSREASN----YPSYSLKSKCQESEESEHPSQSFEEEPRRAEGAMS 371

Query: 61  VRG-SKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKT 119
            RG S  +++ R+ E H   E++RRD+INKKMR+LQELIPNC KVDK S+L+EAIDYLKT
Sbjct: 372 TRGGSAGSKRNRSAEGHSLSEKRRRDRINKKMRSLQELIPNCKKVDKISILDEAIDYLKT 431

Query: 120 LQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPP--------MGIGMDGRM 171
           LQ QV +MSMG G+CM  +M+P  +  +Q  H     + HF P        MG+G+   +
Sbjct: 432 LQLQVQVMSMGAGMCMAPVMIPAVLQQIQAAH-----LPHFSPMGMGMGMGMGMGLGLGL 486

Query: 172 QMGAGCNPAQFLMPPIPGATAVPGI-----QMPGFPGQPLPMSMLRTPLGLMHKTNPVAG 226
            +G GC+P QF  PPI GA A+ GI     QM G PGQ LPMS+   P   +H  +    
Sbjct: 487 GLGLGCSPEQFPSPPILGAAALSGIAGTAPQMLGHPGQVLPMSLSSAPFIPLHAGSLTQS 546

Query: 227 VSRAAASMEVKDSAPLTNPGDS 248
           V   +     KD  P+ +PG S
Sbjct: 547 VLVPSVP---KDIHPVEHPGSS 565

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|339778403|gb|AEK06083.1| phytochrome-interacting factor 3.1 [Populus balsamifera]

 Score =  165 bits (418), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 123/283 (43%), Positives = 156/283 (55%), Gaps = 41/283 (14%)

Query: 2   DAGKCIEPPVPSSSLCSLGASNNNPACN-TFNLKRRYEDTEGSACPCDQYEKKL--ERKA 58
           D  K  EP V SSS+ S G S   P+ + T NLKR++ DTE S  P +  E++    +K 
Sbjct: 250 DVEKTTEPLVASSSVGS-GNSAERPSDDPTENLKRKHRDTEESEGPSEDAEEESVGAKKP 308

Query: 59  VTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLK 118
            + R    +++ R  EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+YLK
Sbjct: 309 ASARAGNGSKRGRAAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLK 368

Query: 119 TLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGI-----------GM 167
           TLQ QV +MSMG G+ MPSMMLP    GM  MHA    M  F PMG+            M
Sbjct: 369 TLQLQVQIMSMGAGMYMPSMMLPP---GMPHMHAA--HMGQFLPMGVGMGMGFRMGMPDM 423

Query: 168 DGRMQMGAGC--------NPAQFLMPPIPGATAVPG-----IQMPGFPGQPLPMSMLRTP 214
           +G     +GC        + A F   P+ G +A+ G     +QM G  GQ LPMS  R P
Sbjct: 424 NGGY---SGCPMYQVPPMHGAHFPGSPMSGPSALHGMGGSSLQMFGLSGQGLPMSFPRAP 480

Query: 215 LGLMH-----KTNPVAGVSRAAASMEVKDSAPLTNPGDSNQNV 252
           L  M      KTN           M+  DSA  ++  D+ QN+
Sbjct: 481 LMPMSGGPPPKTNREPNACGVVGPMDNLDSATASSSKDAIQNI 523

Source: Populus balsamifera

Species: Populus balsamifera

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	268
UNIPROTKB|Q5NAE0	565	P0498A12.33 "Putative BP-5 pro	0.917	0.435	0.404	7.8e-39
TAIR|locus:2041369	416	PIL1 "phytochrome interacting	0.608	0.391	0.440	2.8e-27
TAIR|locus:2012345	524	PIF3 "AT1G09530" [Arabidopsis	0.723	0.370	0.398	1.2e-26
TAIR|locus:2053733	430	PIF4 "AT2G43010" [Arabidopsis	0.723	0.451	0.382	2.6e-23
TAIR|locus:2061634	478	PIL5 "phytochrome interacting	0.533	0.299	0.460	4.7e-23
TAIR|locus:2126876	399	UNE10 "AT4G00050" [Arabidopsis	0.589	0.395	0.427	5.5e-23
UNIPROTKB|Q8GRJ1	417	OJ1343_B12.103 "Transcription	0.522	0.335	0.413	7.2e-21
TAIR|locus:4010713915	544	AT4G28811 [Arabidopsis thalian	0.522	0.257	0.384	3.1e-20
UNIPROTKB|Q7FA23	181	OSJNBa0058K23.6 "Os04g0618600	0.339	0.502	0.5	5.7e-20
TAIR|locus:2115080	373	SPT "AT4G36930" [Arabidopsis t	0.757	0.544	0.331	6.7e-20

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

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 114/282 (40%), Positives = 155/282 (54%)

Query:     2 DAGKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRYE-DTEGSACPCDQYEKKLERKAVT 60
             +A K  E  V +SS+CS   + ++        KR+ +   E SA   D  +   E   + 
Sbjct:   246 EARKAPEATVATSSVCSGNGAGSDELWR--QQKRKCQAQAECSASQDDDLDD--EPGVLR 301

Query:    61 VRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTL 120
               G++S ++ RT EVH   ER+RRD+IN+KMRALQELIPNCNK+DKASML+EAI+YLKTL
Sbjct:   302 KSGTRSTKRSRTAEVHNLSERRRRDRINEKMRALQELIPNCNKIDKASMLDEAIEYLKTL 361

Query:   121 QFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPA 180
             Q QV MMSMGTG+C+P M+LPT    MQ  H   P M+HFP +G+G+   M +    N  
Sbjct:   362 QLQVQMMSMGTGLCIPPMLLPTA---MQ--HLQIPPMAHFPHLGMGLGYGMGVFDMSNTG 416

Query:   181 QFLMPPIPGA--------------TAVPGIQ-MP--GFPGQPLPMSMLRTPLGLMHKTNP 223
                MPP+PGA                +PG   MP  G PGQ +P S    P        P
Sbjct:   417 ALQMPPMPGAHFPCPMIPGASPQGLGIPGTSTMPMFGVPGQTIPSSASSVPPFASLAGLP 476

Query:   224 V--AGVSRAAASME--VKDSAPLTNPGDSNQNVE-INKRNVE 260
             V  +GV + + +M   V+D       G +NQ  + +NK  ++
Sbjct:   477 VRPSGVPQVSGAMANMVQDQ----QQGIANQQQQCLNKEAIQ 514

GO:0005634 "nucleus" evidence=IC

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

 Score = 306 (112.8 bits), Expect = 2.8e-27, P = 2.8e-27
 Identities = 78/177 (44%), Positives = 102/177 (57%)

Query:     4 GKCIEPPVPSSSLCSLGASNNNPACNTFNLKRRY---EDTEGSACPCDQYEKKLERKA-V 59
             G+  E    SSS  S G S +   C+   LKR+Y   E+ E +    +  ++  + K  V
Sbjct:   160 GRSTELYFASSSKFSRGTSRDLSCCS---LKRKYGDIEEEESTYLSNNSDDESDDAKTQV 216

Query:    60 TVRGSKS-NRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLK 118
               R  K   ++KR+ EVHK YERKRRD+ NKKMRALQ+L+PNC K DKAS+L+EAI Y++
Sbjct:   217 HARTRKPVTKRKRSTEVHKLYERKRRDEFNKKMRALQDLLPNCYKDDKASLLDEAIKYMR 276

Query:   119 TLQFQVMMMSMGTGVCMPSMMLPTGI-----IGMQQMHAVAP-QMSHFPPMGIGMDG 169
             TLQ QV MMSMG G+  P  MLP G      +GM    A  P  +  F PM +   G
Sbjct:   277 TLQLQVQMMSMGNGLIRPPTMLPMGHYSPMGLGMHMGAAATPTSIPQFLPMNVQATG 333

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0009641 "shade avoidance" evidence=IEP

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

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

 Score = 305 (112.4 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 82/206 (39%), Positives = 119/206 (57%)

Query:     8 EPPVPSSSLCSLGASNNNPACN-TFNLKRRYEDTEGSACPCDQYEKKL---ERKAVTVRG 63
             E  V  SS+ S G S + P+ + + +LKR++ + +   C  +  E++     ++A   R 
Sbjct:   277 EKAVVCSSVGS-GNSLDGPSESPSLSLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPSRT 335

Query:    64 SKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQ 123
                +++ R+ EVH   ER+RRD+IN+KMRALQELIPNCNKVDKASML+EAI+YLK+LQ Q
Sbjct:   336 GLGSKRSRSAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKSLQLQ 395

Query:   124 VMMMSMGTGVCMP-SMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCNPA-Q 181
             V +MSM +G  +P ++M P G+ G     A A  M    P  +G+    + G+  N   Q
Sbjct:   396 VQIMSMASGYYLPPAVMFPPGM-GHYPAAAAAMAMGMGMPYAMGLPDLSRGGSSVNHGPQ 454

Query:   182 FL---MPPIPGATAVPGIQMPG-FPG 203
             F    M   P A  +P +   G F G
Sbjct:   455 FQVSGMQQQPVAMGIPRVSGGGIFAG 480

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0042802 "identical protein binding" evidence=IPI

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

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

GO:0009704 "de-etiolation" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0007165 "signal transduction" evidence=TAS

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

 Score = 271 (100.5 bits), Expect = 2.6e-23, P = 2.6e-23
 Identities = 83/217 (38%), Positives = 111/217 (51%)

Query:    14 SSLCSLGASNNNPA---CNTFNLKR-RYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRK 69
             SS CS G      A   C T + KR R   T+ S    D    K  ++      S SNR+
Sbjct:   202 SSGCSFGKDIKEMASGRCITTDRKRKRINHTDESVSLSDAIGNKSNQR------SGSNRR 255

Query:    70 KRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMMSM 129
              R  EVH   ER+RRD+IN++M+ALQELIP+C+K DKAS+L+EAIDYLK+LQ Q+ +M M
Sbjct:   256 SRAAEVHNLSERRRRDRINERMKALQELIPHCSKTDKASILDEAIDYLKSLQLQLQVMWM 315

Query:   130 GTGVCMPSMMLPTGIIGMQQMHAV----AP-QMSHFPPMGIGMDGRMQMGAG--C-NPAQ 181
             G+G+   +   P    G+Q    +    +P Q+  FP M       +Q   G  C NP Q
Sbjct:   316 GSGMAAAAASAPMMFPGVQPQQFIRQIQSPVQLPRFPVMD---QSAIQNNPGLVCQNPVQ 372

Query:   182 FLMPPIPGATAVPGIQMPGFPGQPLPMSMLR--TPLG 216
               +     A  + G        Q  PM MLR  +P G
Sbjct:   373 NQIISDRFARYIGGFPHMQAATQMQPMEMLRFSSPAG 409

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0009704 "de-etiolation" evidence=IMP

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

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

GO:0000165 "MAPK cascade" evidence=RCA

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

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

GO:0007623 "circadian rhythm" evidence=RCA

GO:0009617 "response to bacterium" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

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

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

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

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

GO:0030003 "cellular cation homeostasis" evidence=RCA

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

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

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

 Score = 271 (100.5 bits), Expect = 4.7e-23, P = 4.7e-23
 Identities = 75/163 (46%), Positives = 96/163 (58%)

Query:     7 IEPPVPSSSLCSLGASNNNPA-CNTFNLKRRYEDTEGSACPCDQYEKKLERKAVTVRGSK 65
             IE    SSS+ S   S   P   N  + KR+    E  A   D+ E + E        + 
Sbjct:   225 IEITGTSSSVVS--KSEIEPEKTNVDDRKRK----EREATTTDETESRSEETKQARVSTT 278

Query:    66 SNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVM 125
             S ++ R  EVH   ERKRRD+IN++M+ALQELIP CNK DKASML+EAI+Y+K+LQ Q+ 
Sbjct:   279 STKRSRAAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQLQIQ 338

Query:   126 MMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMD 168
             MMSMG G+ MP MM P    GMQQ     P M+    MG+GM+
Sbjct:   339 MMSMGCGM-MP-MMYP----GMQQY---MPHMA----MGMGMN 368

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0015995 "chlorophyll biosynthetic process" evidence=IMP

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

GO:0010313 "phytochrome binding" evidence=IDA

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

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

GO:0010099 "regulation of photomorphogenesis" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

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

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

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

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

GO:0006783 "heme biosynthetic process" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0009686 "gibberellin biosynthetic process" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0048608 "reproductive structure development" evidence=RCA

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

 Score = 266 (98.7 bits), Expect = 5.5e-23, P = 5.5e-23
 Identities = 74/173 (42%), Positives = 96/173 (55%)

Query:    39 DTEGSACPC-DQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQEL 97
             D   S C    Q E + E+KA   + S S ++ R   +H + ERKRRDKIN++M+ LQ+L
Sbjct:   181 DDHDSVCHSRPQMEDEEEKKAGG-KSSVSTKRSRAAAIHNQSERKRRDKINQRMKTLQKL 239

Query:    98 IPNCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQM 157
             +PN +K DKASML+E I+YLK LQ QV MMS    + MPSMMLP   + MQQ   +  QM
Sbjct:   240 VPNSSKTDKASMLDEVIEYLKQLQAQVSMMSR---MNMPSMMLP---MAMQQQQQL--QM 291

Query:   158 SHFP-PMGIGMDGRMQMGAGCNPAQFLMPPIPGATAVPGIQMPGFPGQPLPMS 209
             S    PMG+GM G    G G      +      A + P I     P   LPM+
Sbjct:   292 SLMSNPMGLGM-GMGMPGLGLLDLNSMNR---AAASAPNIHANMMPNPFLPMN 340

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

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

GO:0009506 "plasmodesma" evidence=IDA

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

 Score = 249 (92.7 bits), Expect = 7.2e-21, P = 7.2e-21
 Identities = 69/167 (41%), Positives = 93/167 (55%)

Query:    54 LERKAVTVRGSK---SNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASML 110
             L   A   R SK   + R+ R  EVH   ER+RRD+IN+K+RALQEL+P+CNK DKAS+L
Sbjct:   208 LSEVADETRPSKRPAAKRRTRAAEVHNLSERRRRDRINEKLRALQELVPHCNKTDKASIL 267

Query:   111 EEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGR 170
             +EAI+YLK+LQ QV +M M TG+ +P MM P    G  Q+          PPMG+G++  
Sbjct:   268 DEAIEYLKSLQMQVQIMWMTTGI-VP-MMFP----GTHQL---------MPPMGMGLNTA 312

Query:   171 MQMGA---GCNPAQ----FLMPPIPGATAVPGIQMPGFPGQPLPMSM 210
                GA   G N  Q    ++   +P    +P I  P      +P  M
Sbjct:   313 CMPGAQAQGLNQMQRTTYYMNNSLPNQ--MPQIPSPAMNAPSVPDDM 357

GO:0005634 "nucleus" evidence=IC

TAIR|locus:4010713915 AT4G28811 [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 3.1e-20, P = 3.1e-20
 Identities = 60/156 (38%), Positives = 87/156 (55%)

Query:    63 GSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQF 122
             GS S ++ R  ++H   ER+RR++IN++M+ LQEL+P C K DK SMLE+ I+Y+K+LQ 
Sbjct:   349 GSTSRKRSRAADMHNLSERRRRERINERMKTLQELLPRCRKTDKVSMLEDVIEYVKSLQL 408

Query:   123 QVMMMSMGTGVCMPSMM--------LPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMG 174
             Q+ MMSMG G+ MP MM        +P   +GM+ M+   P +  FP       G M   
Sbjct:   409 QIQMMSMGHGM-MPPMMHEGNTQQFMPHMAMGMKGMNRPPPFVP-FPGKTFPRPGHM--- 463

Query:   175 AGCNPAQ-FLMPPIPGATA--VPGIQMPGFPGQPLP 207
             AG  P+   L  P P   A  +  + +P     P+P
Sbjct:   464 AGVGPSYPALRYPFPDTQASDLSRVHVPSLHSNPVP 499

GO:0005634 "nucleus" evidence=ISM

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

 Score = 237 (88.5 bits), Expect = 5.7e-20, P = 5.7e-20
 Identities = 48/96 (50%), Positives = 66/96 (68%)

Query:    68 RKKRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLKTLQFQVMMM 127
             R+ R+ E H   ER+RRD+IN+K++ALQEL+PNC K DK SML+EAIDYLK+LQ Q+ M+
Sbjct:    10 RRSRSAEFHNFSERRRRDRINEKLKALQELLPNCTKTDKVSMLDEAIDYLKSLQLQLQML 69

Query:   128 SMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPM 163
              MG G+  P  ++P  +   Q MH +    S  PP+
Sbjct:    70 VMGKGMA-P--VVPPEL--QQYMHYITADPSQIPPI 100

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2115080 SPT "AT4G36930" [Arabidopsis thaliana (taxid:3702)]

 Score = 238 (88.8 bits), Expect = 6.7e-20, P = 6.7e-20
 Identities = 74/223 (33%), Positives = 110/223 (49%)

Query:    13 SSSLC---SLGASNNNPACNTFNLKRRYEDTEGSACPCDQYEKKLER--KAVTVRG---- 63
             S++ C   S G +NNN   N+   +        S    D+Y+ + E   +AV        
Sbjct:   125 SAAACFGFSGGGNNNNVQGNSSGTRVSSSSVGASGNETDEYDCESEEGGEAVVDEAPSSK 184

Query:    64 ----SKSNRKK-RTPEVHKRYERKRRDKINKKMRALQELIPNCNKVDKASMLEEAIDYLK 118
                 S+S+ K+ R  EVH   E++RR +IN+KM+ALQ LIPN NK DKASML+EAI+YLK
Sbjct:   185 SGPSSRSSSKRCRAAEVHNLSEKRRRSRINEKMKALQSLIPNSNKTDKASMLDEAIEYLK 244

Query:   119 TLQFQVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRMQMGAGCN 178
              LQ QV M++M  G+ +  + LP   +   Q+  + P  +   P+   ++   Q  +  N
Sbjct:   245 QLQLQVQMLTMRNGINLHPLCLPGTTLHPLQLSQIRPPEATNDPL---LNHTNQFASTSN 301

Query:   179 PAQFLMPPIPGATAVPGIQMP-G-FPGQPLPMSMLRTPLGLMH 219
               + +          P I+   G FP    P+ M R   GL H
Sbjct:   302 APEMINTVASSYALEPSIRSHFGPFPLLTSPVEMSREG-GLTH 343

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009908 "flower development" evidence=NAS

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

GO:0009409 "response to cold" evidence=IMP

GO:0010114 "response to red light" evidence=IMP

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

GO:0010154 "fruit development" evidence=IMP

GO:0048440 "carpel development" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0007623 "circadian rhythm" evidence=IEP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	268
smart00353	53	smart00353, HLH, helix loop helix domain	5e-14
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	6e-14
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	4e-12

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

 Score = 64.5 bits (158), Expect = 5e-14
 Identities = 20/48 (41%), Positives = 31/48 (64%), Gaps = 3/48 (6%)

Query: 80  ERKRRDKINKKMRALQELIPNCN---KVDKASMLEEAIDYLKTLQFQV 124
           ER+RR KIN+    L+ L+P      K+ KA +L  AI+Y+K+LQ ++
Sbjct: 4   ERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEEL 51

Length = 53

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

 Score = 64.5 bits (158), Expect = 6e-14
 Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 7/63 (11%)

Query: 65  KSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQ 121
           + +R++         ER+RR++IN     L+ L+P      K+ KA +L +A+DY+K+LQ
Sbjct: 1   RKSRREAHNLR----ERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQ 56

Query: 122 FQV 124
             +
Sbjct: 57  ELL 59

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

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

 Score = 59.4 bits (145), Expect = 4e-12
 Identities = 21/44 (47%), Positives = 29/44 (65%), Gaps = 2/44 (4%)

Query: 80  ERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQ 121
           ER+RRD+IN     L+EL+P     K+ KA +L  AI+Y+K LQ
Sbjct: 9   ERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	268
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.52
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.49
smart00353	53	HLH helix loop helix domain.	99.42
KOG1318	411	consensus Helix loop helix transcription factor EB	99.34
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.34
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	99.17
KOG4304	250	consensus Transcriptional repressors of the hairy/	99.07
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.54
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.32
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.16
KOG0561	373	consensus bHLH transcription factor [Transcription	98.1
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.03
PLN03217	93	transcription factor ATBS1; Provisional	98.03
KOG3910	632	consensus Helix loop helix transcription factor [T	97.96
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.43
KOG3898	254	consensus Transcription factor NeuroD and related	95.74
KOG3582	856	consensus Mlx interactors and related transcriptio	95.45
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	94.94
KOG4395	285	consensus Transcription factor Atonal, contains HT	93.69
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	93.53
KOG1924	1102	consensus RhoA GTPase effector DIA/Diaphanous [Sig	91.93
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	90.03
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	88.94

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

Probab=99.52  E-value=1.4e-14  Score=102.64  Aligned_cols=49  Identities=51%  Similarity=0.881  Sum_probs=46.6

Q ss_pred             cchhhhHHHHHHHHHHHHHHHHHhhCCCC-----CCCchhhHHHHHHHHHHHHH
Q 038097           73 PEVHKRYERKRRDKINKKMRALQELIPNC-----NKVDKASMLEEAIDYLKTLQ  121 (268)
Q Consensus        73 r~~H~~~ERrRR~~In~~~~~L~~LVP~~-----~K~dKasIL~~AI~YIk~Lq  121 (268)
                      |..|+..||+||++||++|.+|+++||.+     .|++|++||+.||+||++||
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            56899999999999999999999999998     49999999999999999997

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

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

Probab=99.49  E-value=4.9e-14  Score=100.35  Aligned_cols=53  Identities=40%  Similarity=0.681  Sum_probs=50.0

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHH
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQFQV  124 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~---~K~dKasIL~~AI~YIk~Lq~qv  124 (268)
                      .+..|+..||+||++||++|..|+.+||..   .|+||++||+.||+||++|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            456899999999999999999999999999   69999999999999999999876

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

>smart00353 HLH helix loop helix domain

Probab=99.42  E-value=4.7e-13  Score=93.49  Aligned_cols=49  Identities=41%  Similarity=0.655  Sum_probs=45.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHhhCCC---CCCCchhhHHHHHHHHHHHHHHHHH
Q 038097           77 KRYERKRRDKINKKMRALQELIPN---CNKVDKASMLEEAIDYLKTLQFQVM  125 (268)
Q Consensus        77 ~~~ERrRR~~In~~~~~L~~LVP~---~~K~dKasIL~~AI~YIk~Lq~qv~  125 (268)
                      +..||+||++||++|..|+.+||.   ..|.+|++||.+||+||++|+.+++
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            468999999999999999999996   4599999999999999999999875

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

Probab=99.34  E-value=8.6e-13  Score=127.33  Aligned_cols=63  Identities=35%  Similarity=0.694  Sum_probs=56.4

Q ss_pred             CCcccCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHHhhh
Q 038097           66 SNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQFQVMMMS  128 (268)
Q Consensus        66 ~~kr~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~----K~dKasIL~~AI~YIk~Lq~qv~~L~  128 (268)
                      ..|.+++|..||.+|||||++||++|++|..|||.|.    |..|.+||..++|||+.||+..++..
T Consensus       227 ~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~  293 (411)
T KOG1318|consen  227 LERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR  293 (411)
T ss_pred             hHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence            3456667899999999999999999999999999995    88899999999999999998877444

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.34  E-value=1e-12  Score=114.84  Aligned_cols=63  Identities=35%  Similarity=0.573  Sum_probs=55.4

Q ss_pred             CcccCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC-------CCchhhHHHHHHHHHHHHHHHHHhhhc
Q 038097           67 NRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN-------KVDKASMLEEAIDYLKTLQFQVMMMSM  129 (268)
Q Consensus        67 ~kr~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~-------K~dKasIL~~AI~YIk~Lq~qv~~L~~  129 (268)
                      +-+.|+|..|...||+||+.||.++..|+.|||.|.       |++||.||.++||||.+|+.++..-+.
T Consensus        57 syk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~  126 (229)
T KOG1319|consen   57 SYKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEE  126 (229)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344566788999999999999999999999999885       899999999999999999887765554

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

Probab=99.17  E-value=3e-11  Score=124.77  Aligned_cols=83  Identities=27%  Similarity=0.304  Sum_probs=73.7

Q ss_pred             cchhhhHHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcCCCCcccchh
Q 038097           73 PEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGIIGMQ  148 (268)
Q Consensus        73 r~~H~~~ERrRR~~In~~~~~L~~LVP~~~----K~dKasIL~~AI~YIk~Lq~qv~~L~~~~~~~~p~~~l~~~i~~l~  148 (268)
                      |+.|+.+||||||++|..|.+|.+|||.|.    |+||.+||++||++||.+++.-.+-......|+|.|+-..   +|.
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~~~~~~~~~~d~KpSflS~~---eL~   97 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQESENSSIDQDYKPSFLSND---ELT   97 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhhhcccccccccccccccchH---HHH
Confidence            778999999999999999999999999986    9999999999999999999876445555578999999987   999


Q ss_pred             hhhhhcCCCC
Q 038097          149 QMHAVAPQMS  158 (268)
Q Consensus       149 ~~~~~a~~~~  158 (268)
                      |++.+|+.-.
T Consensus        98 ~LmLeAlDGF  107 (803)
T KOG3561|consen   98 HLILEALDGF  107 (803)
T ss_pred             HHHHHHhcCe
Confidence            9999886443

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

Probab=99.07  E-value=5.1e-11  Score=109.07  Aligned_cols=60  Identities=30%  Similarity=0.454  Sum_probs=51.3

Q ss_pred             ccCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC--------CCchhhHHHHHHHHHHHHHHHHHhhh
Q 038097           69 KKRTPEVHKRYERKRRDKINKKMRALQELIPNCN--------KVDKASMLEEAIDYLKTLQFQVMMMS  128 (268)
Q Consensus        69 r~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~--------K~dKasIL~~AI~YIk~Lq~qv~~L~  128 (268)
                      +..++..|-++|||||+|||+++.+|++||+.+.        |++||.||+.||+|++.||...+.-.
T Consensus        29 ~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~~~   96 (250)
T KOG4304|consen   29 RQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQAAA   96 (250)
T ss_pred             HHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccccc
Confidence            3345667899999999999999999999999653        88999999999999999988655433

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

Probab=98.54  E-value=2.1e-07  Score=84.52  Aligned_cols=58  Identities=19%  Similarity=0.379  Sum_probs=49.4

Q ss_pred             cCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC--CCc-hhhHHHHHHHHHHHHHHHHHhh
Q 038097           70 KRTPEVHKRYERKRRDKINKKMRALQELIPNCN--KVD-KASMLEEAIDYLKTLQFQVMMM  127 (268)
Q Consensus        70 ~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~--K~d-KasIL~~AI~YIk~Lq~qv~~L  127 (268)
                      ..+|..||..||+||+.|+++|..|+.+||...  +.. .++||++|++||+.|+.+....
T Consensus        57 ~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~  117 (232)
T KOG2483|consen   57 ASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQ  117 (232)
T ss_pred             CcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHH
Confidence            345788999999999999999999999999876  333 7999999999999997665443

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.32  E-value=2.9e-07  Score=96.18  Aligned_cols=61  Identities=30%  Similarity=0.517  Sum_probs=55.9

Q ss_pred             CCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC-CCchhhHHHHHHHHHHHHHHHHHhhhcCC
Q 038097           71 RTPEVHKRYERKRRDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQFQVMMMSMGT  131 (268)
Q Consensus        71 ~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~-K~dKasIL~~AI~YIk~Lq~qv~~L~~~~  131 (268)
                      .+|..||++|||.|..||++|.+|+++||+.. |+.|..+|.+||+||++|+...+.+...+
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~  336 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLEN  336 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhh
Confidence            45778999999999999999999999999886 99999999999999999999888877554

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

Probab=98.16  E-value=4.4e-06  Score=76.38  Aligned_cols=58  Identities=26%  Similarity=0.366  Sum_probs=50.1

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHh-hCCCCC-CCchhhHHHHHHHHHHHHHHHHHhhhc
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQE-LIPNCN-KVDKASMLEEAIDYLKTLQFQVMMMSM  129 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~-LVP~~~-K~dKasIL~~AI~YIk~Lq~qv~~L~~  129 (268)
                      +|..-.+.||||-.++||.|.+|+. -+++-+ ++-|+.||..||+||..||.-++++..
T Consensus       118 RRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~  177 (284)
T KOG3960|consen  118 RRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQ  177 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3455688999999999999999997 556654 899999999999999999999888764

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.10  E-value=2.4e-06  Score=79.87  Aligned_cols=58  Identities=28%  Similarity=0.472  Sum_probs=50.5

Q ss_pred             CCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC--CCchhhHHHHHHHHHHHHHHHHHhhh
Q 038097           71 RTPEVHKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQFQVMMMS  128 (268)
Q Consensus        71 ~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~--K~dKasIL~~AI~YIk~Lq~qv~~L~  128 (268)
                      -+|+.-|.-||||-.-||.+|..||.|+|...  |++||.||+.+.+||..|..+.-+|-
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll  118 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELL  118 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccc
Confidence            35677788999999999999999999999765  99999999999999999976654444

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

Probab=98.03  E-value=4.5e-06  Score=75.13  Aligned_cols=59  Identities=22%  Similarity=0.343  Sum_probs=51.8

Q ss_pred             CCcchhhhHHHHHHHHHHHHHHHHHhhCCCC----CCCchhhHHHHHHHHHHHHHHHHHhhhc
Q 038097           71 RTPEVHKRYERKRRDKINKKMRALQELIPNC----NKVDKASMLEEAIDYLKTLQFQVMMMSM  129 (268)
Q Consensus        71 ~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~----~K~dKasIL~~AI~YIk~Lq~qv~~L~~  129 (268)
                      ..+..+|..||.|-..+|..|.+||.+||..    .|++|..+|..||.||++|+.-++.-+.
T Consensus       108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~  170 (228)
T KOG4029|consen  108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA  170 (228)
T ss_pred             hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence            3466788889999999999999999999964    4899999999999999999988776554

>PLN03217 transcription factor ATBS1; Provisional

Probab=98.03  E-value=6.2e-06  Score=64.05  Aligned_cols=49  Identities=31%  Similarity=0.488  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHhhCCCCC------CCchhhHHHHHHHHHHHHHHHHHhhhcCCC
Q 038097           84 RDKINKKMRALQELIPNCN------KVDKASMLEEAIDYLKTLQFQVMMMSMGTG  132 (268)
Q Consensus        84 R~~In~~~~~L~~LVP~~~------K~dKasIL~~AI~YIk~Lq~qv~~L~~~~~  132 (268)
                      -|.|++.+..|+.|+|...      |.+-+-||++|+.||+.|+++|..|+++..
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs   73 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLS   73 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999743      778899999999999999999999997654

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.96  E-value=9.5e-06  Score=80.16  Aligned_cols=59  Identities=24%  Similarity=0.254  Sum_probs=49.7

Q ss_pred             ccCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCCC----CchhhHHHHHHHHHHHHHHHHHhh
Q 038097           69 KKRTPEVHKRYERKRRDKINKKMRALQELIPNCNK----VDKASMLEEAIDYLKTLQFQVMMM  127 (268)
Q Consensus        69 r~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~K----~dKasIL~~AI~YIk~Lq~qv~~L  127 (268)
                      .+.+|...|.+||.|-..||+.|++|.++.-..-|    ..|..||..||..|-.|++||.+-
T Consensus       523 EkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  523 EKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            34456778999999999999999999998765443    369999999999999999999753

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.43  E-value=0.0016  Score=55.84  Aligned_cols=53  Identities=26%  Similarity=0.381  Sum_probs=48.1

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCCC--CCchhhHHHHHHHHHHHHHHHH
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQFQV  124 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~--K~dKasIL~~AI~YIk~Lq~qv  124 (268)
                      .+.-||+.||+|-..+|+.|..||.++|...  |++|.-.|+-|..||-+|-+-.
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            4678999999999999999999999999875  9999999999999999986533

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

Probab=95.74  E-value=0.019  Score=52.92  Aligned_cols=52  Identities=29%  Similarity=0.381  Sum_probs=45.6

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHH
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQFQ  123 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~---~K~dKasIL~~AI~YIk~Lq~q  123 (268)
                      +|..=|..||+|--.+|+.|+.||++||..   .|+.|..+|..|-.||..|++-
T Consensus        72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~  126 (254)
T KOG3898|consen   72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV  126 (254)
T ss_pred             hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence            455668899999999999999999999943   3999999999999999999763

>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]

Probab=95.45  E-value=0.0038  Score=64.30  Aligned_cols=81  Identities=20%  Similarity=0.263  Sum_probs=66.7

Q ss_pred             CCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC-----CCchhhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcCCCCccc
Q 038097           71 RTPEVHKRYERKRRDKINKKMRALQELIPNCN-----KVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTGII  145 (268)
Q Consensus        71 ~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~-----K~dKasIL~~AI~YIk~Lq~qv~~L~~~~~~~~p~~~l~~~i~  145 (268)
                      .+...|..+|++||.+|+-+|..|.+++.+..     |+.++.-|+.++.||-.++.+...+.++..      .|..+|.
T Consensus       650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~------~lr~~~s  723 (856)
T KOG3582|consen  650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAH------SLRKEIS  723 (856)
T ss_pred             CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhh------hhhhhhH
Confidence            35677999999999999999999999998865     778888999999999999998888876643      5667777


Q ss_pred             chhhhhhhcCCCCC
Q 038097          146 GMQQMHAVAPQMSH  159 (268)
Q Consensus       146 ~l~~~~~~a~~~~~  159 (268)
                      +++.++.  +|...
T Consensus       724 ~~~A~~~--~~~q~  735 (856)
T KOG3582|consen  724 ELNAVIS--ACQQP  735 (856)
T ss_pred             HHHHHHH--HhhcC
Confidence            8887775  44443

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=94.94  E-value=0.28  Score=51.81  Aligned_cols=9  Identities=22%  Similarity=0.298  Sum_probs=4.7

Q ss_pred             HHHHHHHHH
Q 038097          112 EAIDYLKTL  120 (268)
Q Consensus       112 ~AI~YIk~L  120 (268)
                      +|++|=|.+
T Consensus       475 kA~e~~kk~  483 (1102)
T KOG1924|consen  475 KAAELEKKF  483 (1102)
T ss_pred             HHHHHHHHH
Confidence            555555444

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

Probab=93.69  E-value=0.094  Score=48.55  Aligned_cols=56  Identities=21%  Similarity=0.318  Sum_probs=48.5

Q ss_pred             cCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC---CCchhhHHHHHHHHHHHHHHHHH
Q 038097           70 KRTPEVHKRYERKRRDKINKKMRALQELIPNCN---KVDKASMLEEAIDYLKTLQFQVM  125 (268)
Q Consensus        70 ~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~---K~dKasIL~~AI~YIk~Lq~qv~  125 (268)
                      +++|..-|..||+|-..+|..|+.|+..||...   |++|-..|+.|-.||--|-..++
T Consensus       172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            345566789999999999999999999999875   89999999999999998865543

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=93.53  E-value=0.067  Score=54.25  Aligned_cols=38  Identities=34%  Similarity=0.670  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHH
Q 038097           81 RKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLK  118 (268)
Q Consensus        81 RrRR~~In~~~~~L~~LVP~~~----K~dKasIL~~AI~YIk  118 (268)
                      ||-|||+|.-++.|..|+|--.    |+||.+||.-+|-|++
T Consensus        34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            6889999999999999999764    9999999999999976

>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]

Probab=91.93  E-value=1.1  Score=47.67  Aligned_cols=13  Identities=15%  Similarity=0.539  Sum_probs=7.5

Q ss_pred             CchhhHHHHHHHH
Q 038097          104 VDKASMLEEAIDY  116 (268)
Q Consensus       104 ~dKasIL~~AI~Y  116 (268)
                      +|-+.+++.-||-
T Consensus       454 id~~~liD~~vdk  466 (1102)
T KOG1924|consen  454 IDLTELIDKMVDK  466 (1102)
T ss_pred             CcHHHHHHHHHHH
Confidence            3555666666654

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

Probab=90.03  E-value=0.25  Score=51.36  Aligned_cols=43  Identities=35%  Similarity=0.547  Sum_probs=37.1

Q ss_pred             hhHHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHH
Q 038097           77 KRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKT  119 (268)
Q Consensus        77 ~~~ERrRR~~In~~~~~L~~LVP~~~----K~dKasIL~~AI~YIk~  119 (268)
                      .-+.|-||-+-|+-|.+|..+||--.    -+|||+|+.-||-|++-
T Consensus        51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            34668899999999999999999432    78999999999999874

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=88.94  E-value=0.43  Score=47.18  Aligned_cols=42  Identities=36%  Similarity=0.533  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHH
Q 038097           79 YERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTL  120 (268)
Q Consensus        79 ~ERrRR~~In~~~~~L~~LVP~~~----K~dKasIL~~AI~YIk~L  120 (268)
                      ..|.||++-|--|-+|..++|-..    .+||++|+.-|..|||--
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            458899999999999999999764    689999999999999854

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	268
4f3l_B	387	Crystal Structure Of The Heterodimeric Clock:bmal1		2e-05
4h10_A	73	Intermolecular Recognition Revealed By The Complex		3e-05

>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1 Transcriptional Activator Complex Length = 387

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 68  RKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQ 121
           R K   E H + E++RRDK+N  +  L  L+P CN    K+DK ++L  A+ ++KTL+
Sbjct: 9   RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66

>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex Structure Of Human Clock-bmal1 Basic Helix-loop-helix Domains With E-box Dna Length = 73

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 68  RKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQ 121
           R K   E H + E++RRDK+N  +  L  L+P CN    K+DK ++L  A+ ++KTL+
Sbjct: 5   RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	268
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	2e-16
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	2e-14
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	6e-13
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	5e-12
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-11
4f3l_A	361	Mclock, circadian locomoter output cycles protein	1e-08
1a0a_A	63	BHLH, protein (phosphate system positive regulator	2e-08
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	1e-07
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	4e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-06

>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 = 71.6 bits (176), Expect = 2e-16
 Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 3/66 (4%)

Query: 65  KSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQFQ 123
           +S  +KRT   H   E++ R  IN K+  L++L+     K++K+++L +AIDY++ LQ  
Sbjct: 1   QSRGEKRTA--HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHS 58

Query: 124 VMMMSM 129
              +  
Sbjct: 59  NQKLKQ 64

>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 = 65.4 bits (160), Expect = 2e-14
 Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 8/60 (13%)

Query: 68  RKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN------KVDKASMLEEAIDYLKTLQ 121
            K+R    H   ER+RRDKIN  +  L ++IP+ +         K  +L +A DY++ L+
Sbjct: 3   EKRR--AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

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

 Score = 62.0 bits (151), Expect = 6e-13
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 63  GSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTL 120
             +          H   ERKRRD I     +L++ +P+    K  +A +L++A +Y++ +
Sbjct: 3   DIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYM 62

Query: 121 Q 121
           +
Sbjct: 63  R 63

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

 Score = 59.7 bits (145), Expect = 5e-12
 Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 7/62 (11%)

Query: 63  GSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN---KVDKASMLEEAIDYLKT 119
           G  + ++      H   ER+RR+++ +   AL++ IP      K  K  +L++A  Y+ +
Sbjct: 1   GHMNVKR----RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILS 56

Query: 120 LQ 121
           +Q
Sbjct: 57  VQ 58

>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 = 57.8 bits (140), Expect = 2e-11
 Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 74  EVHKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQ 121
             H   ERKRRD I     +L++ +P+    K  +A +L++A +Y++ ++
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMR 53

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

 Score = 53.8 bits (129), Expect = 1e-08
 Identities = 23/109 (21%), Positives = 51/109 (46%), Gaps = 5/109 (4%)

Query: 64  SKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIP-NCNKVDKASMLEEAIDYLKTLQF 122
            + ++ K       + E+KRRD+ N  ++ L  ++P N  K+DK+++L+++ID+L+  + 
Sbjct: 4   EEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKE 63

Query: 123 QVMMMSMGTGVCMPSMMLPTGIIGMQQMHAVAPQMSHFPPMGIGMDGRM 171
                +      +     PT +   +    +   +  F  + I  DG +
Sbjct: 64  T---TAQSDASEIRQDWKPTFLSNEEFTQLMLEALDGF-FLAIMTDGSI 108

>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 = 48.7 bits (116), Expect = 2e-08
 Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 9/59 (15%)

Query: 70  KRTPEVHKRYERKRRDKINKKMRALQELIPNCNKVD-------KASMLEEAIDYLKTLQ 121
           KR    HK  E+ RR+++   +  L  LIP   K         KA+ +E A  Y++ LQ
Sbjct: 2   KRE--SHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 58

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

 Score = 50.8 bits (121), Expect = 1e-07
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 4/65 (6%)

Query: 62  RGSKSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYL 117
                 R K   E H + E++RRDK+N  +  L  L+P CN    K+DK ++L  A+ ++
Sbjct: 3   YAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHM 62

Query: 118 KTLQF 122
           KTL+ 
Sbjct: 63  KTLRG 67

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

 Score = 46.0 bits (109), Expect = 4e-07
 Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 74  EVHKRYERKRRDKINKKMRALQELIP---NCNKVDKASMLEEAIDYLKTLQ 121
             H   E+ RR  +   +  L+ L+P   + ++    S+L +A  ++K L+
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLE 53

>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 = 47.2 bits (111), Expect = 3e-06
 Identities = 20/133 (15%), Positives = 36/133 (27%), Gaps = 43/133 (32%)

Query: 33  LKRRYEDTEGSACPCDQYEKKLERKAVTVRGSKSNRKKRTPEVHKRYERKRRDKINKKMR 92
           +K               Y              + +R     +V  +Y   R     K  +
Sbjct: 98  IKTEQRQPSM---MTRMYI------------EQRDRLYNDNQVFAKYNVSRLQPYLKLRQ 142

Query: 93  ALQELIPN----------CNKVDKASMLEEAIDYLKTLQFQVMM------MSMGTGVCMP 136
           AL EL P             K    + +  A+D   + + Q  M      +++       
Sbjct: 143 ALLELRPAKNVLIDGVLGSGK----TWV--ALDVCLSYKVQCKMDFKIFWLNLKNCNS-- 194

Query: 137 SMMLPTGIIGMQQ 149
               P  ++ M Q
Sbjct: 195 ----PETVLEMLQ 203

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	268
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.68
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.66
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.65
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.64
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.63
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.61
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.57
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.57
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.54
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.54
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.49
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.32
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.31
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.26
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.18
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.95
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.94
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.54

>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=99.68  E-value=1.8e-17  Score=126.39  Aligned_cols=61  Identities=28%  Similarity=0.482  Sum_probs=57.0

Q ss_pred             CCcchhhhHHHHHHHHHHHHHHHHHhhCCCC-CCCchhhHHHHHHHHHHHHHHHHHhhhcCC
Q 038097           71 RTPEVHKRYERKRRDKINKKMRALQELIPNC-NKVDKASMLEEAIDYLKTLQFQVMMMSMGT  131 (268)
Q Consensus        71 ~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~-~K~dKasIL~~AI~YIk~Lq~qv~~L~~~~  131 (268)
                      .++..|+.+||+||++||++|.+|+.|||++ .|+||++||++||+||++||.+++.|+.++
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~   66 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN   66 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4577899999999999999999999999998 699999999999999999999999998654

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

Probab=99.66  E-value=1e-16  Score=119.40  Aligned_cols=60  Identities=27%  Similarity=0.494  Sum_probs=54.2

Q ss_pred             ccCCcchhhhHHHHHHHHHHHHHHHHHhhCCCC-CCCchhhHHHHHHHHHHHHHHHHHhhh
Q 038097           69 KKRTPEVHKRYERKRRDKINKKMRALQELIPNC-NKVDKASMLEEAIDYLKTLQFQVMMMS  128 (268)
Q Consensus        69 r~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~-~K~dKasIL~~AI~YIk~Lq~qv~~L~  128 (268)
                      ...+|..|+.+||+||++||++|.+|+.|||.. .|+||++||++||+||+.||.++.-|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            344578999999999999999999999999975 499999999999999999999987664

>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=99.65  E-value=4.3e-17  Score=118.79  Aligned_cols=54  Identities=31%  Similarity=0.449  Sum_probs=48.9

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC-------CCCchhhHHHHHHHHHHHHHHHHH
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC-------NKVDKASMLEEAIDYLKTLQFQVM  125 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~-------~K~dKasIL~~AI~YIk~Lq~qv~  125 (268)
                      +|.+|+.+||+||++||.+|.+|+.|||.+       .|++||+||++||+||++||++++
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            367899999999999999999999999976       377899999999999999998753

>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=99.64  E-value=4.8e-17  Score=118.53  Aligned_cols=56  Identities=32%  Similarity=0.542  Sum_probs=51.0

Q ss_pred             cCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC------CCchhhHHHHHHHHHHHHHHHHH
Q 038097           70 KRTPEVHKRYERKRRDKINKKMRALQELIPNCN------KVDKASMLEEAIDYLKTLQFQVM  125 (268)
Q Consensus        70 ~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~------K~dKasIL~~AI~YIk~Lq~qv~  125 (268)
                      ..++..|+.+||+||++||++|.+|+.|||.+.      |++|++||++||+||++||++++
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            345778999999999999999999999999986      78999999999999999998753

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

Probab=99.63  E-value=3.4e-16  Score=127.04  Aligned_cols=64  Identities=28%  Similarity=0.513  Sum_probs=51.6

Q ss_pred             CcccCCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHHhhhcC
Q 038097           67 NRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQFQVMMMSMG  130 (268)
Q Consensus        67 ~kr~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~----K~dKasIL~~AI~YIk~Lq~qv~~L~~~  130 (268)
                      .++.+++..|+.+||+||++||++|.+|+.|||.+.    |++|++||++||+||++||.+++.|...
T Consensus        22 ~k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           22 AKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            444556789999999999999999999999999985    7889999999999999999999999754

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

Probab=99.61  E-value=1.3e-16  Score=119.43  Aligned_cols=55  Identities=40%  Similarity=0.662  Sum_probs=50.7

Q ss_pred             cccCCcchhhhHHHHHHHHHHHHHHHHHhhCCCC----CCCchhhHHHHHHHHHHHHHH
Q 038097           68 RKKRTPEVHKRYERKRRDKINKKMRALQELIPNC----NKVDKASMLEEAIDYLKTLQF  122 (268)
Q Consensus        68 kr~~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~----~K~dKasIL~~AI~YIk~Lq~  122 (268)
                      +..+++..|+.+||+||++||++|.+|+.|||.|    .|+|||+||+.||+||+.|+.
T Consensus         5 k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            5 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            4556788999999999999999999999999987    599999999999999999975

>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=99.57  E-value=2.2e-15  Score=114.05  Aligned_cols=59  Identities=25%  Similarity=0.487  Sum_probs=55.3

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHHHhhhcC
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC--NKVDKASMLEEAIDYLKTLQFQVMMMSMG  130 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~--~K~dKasIL~~AI~YIk~Lq~qv~~L~~~  130 (268)
                      +|..|+.+||+||+.||++|..|+.+||.+  .|++|++||..||+||+.|+.+++.|..+
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e   72 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD   72 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999999999987  49999999999999999999999999864

>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=99.57  E-value=2.5e-15  Score=114.35  Aligned_cols=59  Identities=25%  Similarity=0.487  Sum_probs=54.6

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHHHhhhcC
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC--NKVDKASMLEEAIDYLKTLQFQVMMMSMG  130 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~--~K~dKasIL~~AI~YIk~Lq~qv~~L~~~  130 (268)
                      +|..|+..||+||+.||++|.+|+++||.+  .|++|++||.+||+||+.|+.+++.|+.+
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e   62 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD   62 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            367899999999999999999999999986  59999999999999999999999888754

>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=99.54  E-value=5.3e-15  Score=114.27  Aligned_cols=58  Identities=26%  Similarity=0.445  Sum_probs=53.6

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHhhhc
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQFQVMMMSM  129 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~---~K~dKasIL~~AI~YIk~Lq~qv~~L~~  129 (268)
                      +|..||..||+||+.||++|..|+.+||.+   .|++|++||.+||+||++|+.+++.+..
T Consensus         6 ~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~   66 (88)
T 1nkp_A            6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS   66 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467899999999999999999999999986   4999999999999999999999888764

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

Probab=99.54  E-value=4.7e-15  Score=111.78  Aligned_cols=58  Identities=29%  Similarity=0.395  Sum_probs=50.0

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC---CCC-chhhHHHHHHHHHHHHHHHHHhhhc
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC---NKV-DKASMLEEAIDYLKTLQFQVMMMSM  129 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~---~K~-dKasIL~~AI~YIk~Lq~qv~~L~~  129 (268)
                      +|..||..||+||+.||++|.+|+.+||.+   .|. +|++||.+||+||++||+++++++.
T Consensus         5 rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            467899999999999999999999999953   365 7999999999999999999999874

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

Probab=99.49  E-value=4.7e-14  Score=107.22  Aligned_cols=58  Identities=21%  Similarity=0.252  Sum_probs=53.7

Q ss_pred             cchhhhHHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHhhhcC
Q 038097           73 PEVHKRYERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQFQVMMMSMG  130 (268)
Q Consensus        73 r~~H~~~ERrRR~~In~~~~~L~~LVP~~---~K~dKasIL~~AI~YIk~Lq~qv~~L~~~  130 (268)
                      |..||..||+||+.||++|.+|+++||.+   .|.+|++||.+|++||+.|+.+.+.|..+
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e   62 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ   62 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            56899999999999999999999999976   48999999999999999999999888754

>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=99.32  E-value=1.1e-12  Score=96.80  Aligned_cols=54  Identities=24%  Similarity=0.382  Sum_probs=49.4

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHHH
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC--NKVDKASMLEEAIDYLKTLQFQVM  125 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~--~K~dKasIL~~AI~YIk~Lq~qv~  125 (268)
                      +|..||..||+|+..||+.|..|+++||..  .|++|+.||..||+||.+|++.++
T Consensus        12 rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           12 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             hhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            467899999999999999999999999975  499999999999999999998653

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

Probab=99.31  E-value=2.5e-12  Score=92.72  Aligned_cols=53  Identities=23%  Similarity=0.303  Sum_probs=48.7

Q ss_pred             cchhhhHHHHHHHHHHHHHHHHHhhCCCCC---CCchhhHHHHHHHHHHHHHHHHH
Q 038097           73 PEVHKRYERKRRDKINKKMRALQELIPNCN---KVDKASMLEEAIDYLKTLQFQVM  125 (268)
Q Consensus        73 r~~H~~~ERrRR~~In~~~~~L~~LVP~~~---K~dKasIL~~AI~YIk~Lq~qv~  125 (268)
                      |..||..||+|+..||++|..|+.+||...   |++|+.||..||+||..|++.++
T Consensus         3 R~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            3 RMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            567999999999999999999999999764   99999999999999999998763

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

Probab=99.26  E-value=5.6e-12  Score=117.45  Aligned_cols=84  Identities=24%  Similarity=0.386  Sum_probs=57.0

Q ss_pred             cccCCcchhhhHHHHHHHHHHHHHHHHHhhCC-CCCCCchhhHHHHHHHHHHHHHHHHHhhh--cCCCCCCCCcCCCCcc
Q 038097           68 RKKRTPEVHKRYERKRRDKINKKMRALQELIP-NCNKVDKASMLEEAIDYLKTLQFQVMMMS--MGTGVCMPSMMLPTGI  144 (268)
Q Consensus        68 kr~~~r~~H~~~ERrRR~~In~~~~~L~~LVP-~~~K~dKasIL~~AI~YIk~Lq~qv~~L~--~~~~~~~p~~~l~~~i  144 (268)
                      +...+|..|+.+||+||++||+.|.+|+.||| ...|+||++||+.||+|||.|+.......  .....+.|.++...  
T Consensus         8 ~~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--   85 (361)
T 4f3l_A            8 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNE--   85 (361)
T ss_dssp             -----------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHHTSCSCGGGTSCCSCTTSCHH--
T ss_pred             ccchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhcccccccccccccCcccccHH--
Confidence            34456778999999999999999999999999 55699999999999999999987643221  11235667666554  


Q ss_pred             cchhhhhhhc
Q 038097          145 IGMQQMHAVA  154 (268)
Q Consensus       145 ~~l~~~~~~a  154 (268)
                       ++.+++.++
T Consensus        86 -~~~~~~l~a   94 (361)
T 4f3l_A           86 -EFTQLMLEA   94 (361)
T ss_dssp             -HHHHHHHHH
T ss_pred             -HHHHHHHHh
Confidence             667666554

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

Probab=99.18  E-value=1.1e-11  Score=116.80  Aligned_cols=83  Identities=28%  Similarity=0.416  Sum_probs=62.5

Q ss_pred             cccCCcchhhhHHHHHHHHHHHHHHHHHhhCC----CCCCCchhhHHHHHHHHHHHHHHHHHhhhcCCCCCCCCcCCCCc
Q 038097           68 RKKRTPEVHKRYERKRRDKINKKMRALQELIP----NCNKVDKASMLEEAIDYLKTLQFQVMMMSMGTGVCMPSMMLPTG  143 (268)
Q Consensus        68 kr~~~r~~H~~~ERrRR~~In~~~~~L~~LVP----~~~K~dKasIL~~AI~YIk~Lq~qv~~L~~~~~~~~p~~~l~~~  143 (268)
                      |...+|.+|+.+||+||++||+.|.+|+.|||    ...|+||++||+.||+|||.|+.......  ...+.|.++... 
T Consensus         9 ~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~-   85 (387)
T 4f3l_B            9 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYT--EANYKPTFLSDD-   85 (387)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC--------CCSSCTTSCHH-
T ss_pred             hhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhccccccc--ccccCcccCCHH-
Confidence            33455789999999999999999999999999    45699999999999999999985433222  234567766555 


Q ss_pred             ccchhhhhhhcC
Q 038097          144 IIGMQQMHAVAP  155 (268)
Q Consensus       144 i~~l~~~~~~a~  155 (268)
                        +|.+++.++.
T Consensus        86 --~~~~~ll~~~   95 (387)
T 4f3l_B           86 --ELKHLILRAA   95 (387)
T ss_dssp             --HHHHHHHHTC
T ss_pred             --HHHHHHHhcC
Confidence              7777776654

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

Probab=98.95  E-value=1.9e-10  Score=84.61  Aligned_cols=46  Identities=26%  Similarity=0.447  Sum_probs=41.9

Q ss_pred             hhHHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHH
Q 038097           77 KRYERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQF  122 (268)
Q Consensus        77 ~~~ERrRR~~In~~~~~L~~LVP~~---~K~dKasIL~~AI~YIk~Lq~  122 (268)
                      +..||+|+..||++|..||++||..   .|++|..||+.||+||..||.
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            4568899999999999999999976   499999999999999999984

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

Probab=98.94  E-value=9.9e-10  Score=83.76  Aligned_cols=46  Identities=30%  Similarity=0.546  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHHhhhc
Q 038097           84 RDKINKKMRALQELIPNCN----KVDKASMLEEAIDYLKTLQFQVMMMSM  129 (268)
Q Consensus        84 R~~In~~~~~L~~LVP~~~----K~dKasIL~~AI~YIk~Lq~qv~~L~~  129 (268)
                      |+.||++|.+|+.|||.+.    |.+|++||.+|||||++||++++.+.+
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e   53 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKD   53 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999999999864    889999999999999999988877664

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

Probab=98.54  E-value=2e-07  Score=73.06  Aligned_cols=50  Identities=28%  Similarity=0.367  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHhhhc
Q 038097           80 ERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQFQVMMMSM  129 (268)
Q Consensus        80 ERrRR~~In~~~~~L~~LVP~~---~K~dKasIL~~AI~YIk~Lq~qv~~L~~  129 (268)
                      |+.|-..||++|..|+.+||..   .|++|..+|..||+||+.|+..++.-..
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~~   85 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLK   85 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            4677789999999999999975   3999999999999999999998876554

---

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	268
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-13
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	3e-13
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	3e-13
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-12
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-12
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	8e-12
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-11
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	4e-11

>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 = 62.1 bits (151), Expect = 1e-13
 Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 84  RDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQFQVMMMSM 129
           R  IN K+  L++L+   + K+ K+ +L +AIDY+K LQ     +  
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQ 47

>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 = 61.4 bits (149), Expect = 3e-13
 Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 76  HKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQFQVMMMSM 129
           H   ERKRRD I     +L++ +P+    K  +A +L++A +Y++ ++ +      
Sbjct: 6   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ 61

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

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

 Score = 61.5 bits (149), Expect = 3e-13
 Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 3/64 (4%)

Query: 65  KSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQFQ 123
           +S  +KRT   H   E++ R  IN K+  L++L+     K++K+++L +AIDY++ LQ  
Sbjct: 1   QSRGEKRTA--HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHS 58

Query: 124 VMMM 127
              +
Sbjct: 59  NQKL 62

>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 = 59.5 bits (144), Expect = 1e-12
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 7/58 (12%)

Query: 74  EVHKRYERKRRDKINKKMRALQELIPNCN-------KVDKASMLEEAIDYLKTLQFQV 124
           E HK  E+ RR+++   +  L  LIP             KA+ +E A  Y++ LQ   
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

>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 = 59.4 bits (144), Expect = 1e-12
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 8/61 (13%)

Query: 67  NRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN------KVDKASMLEEAIDYLKTL 120
           + K+R    H   ER+RRDKIN  +  L ++IP+ +         K  +L +A DY++ L
Sbjct: 2   DEKRRA--QHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

Query: 121 Q 121
           +
Sbjct: 60  R 60

>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 = 58.0 bits (140), Expect = 8e-12
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 6/66 (9%)

Query: 67  NRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN---KVDKASMLEEAIDYLKTLQFQ 123
           N K+RT   H   ER+RR+++ +   AL++ IP      K  K  +L++A  Y+ ++Q +
Sbjct: 4   NVKRRT---HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAE 60

Query: 124 VMMMSM 129
              +  
Sbjct: 61  EQKLIS 66

>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 = 57.2 bits (138), Expect = 1e-11
 Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 74  EVHKRYERKRRDKINKKMRALQELIPNCN---KVDKASMLEEAIDYLKTLQFQVMMMSM 129
             H   E+ RR  +   +  L+ L+P      +    S+L +A  ++K L+        
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH 61

>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 = 55.3 bits (133), Expect = 4e-11
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 65  KSNRKKRTPEVHKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQF 122
           +        +     ER+R  K+N+    L+    +    ++ K  +L  AI Y++ LQ 
Sbjct: 5   RKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQA 64

Query: 123 QV 124
            +
Sbjct: 65  LL 66

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	268
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.61
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.61
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.59
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.58
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.55
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.54
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.53
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.39

>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=99.61  E-value=1.8e-16  Score=113.42  Aligned_cols=53  Identities=32%  Similarity=0.466  Sum_probs=48.5

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC-------CCCchhhHHHHHHHHHHHHHHHH
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC-------NKVDKASMLEEAIDYLKTLQFQV  124 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~-------~K~dKasIL~~AI~YIk~Lq~qv  124 (268)
                      +|..|+.+||+||++||++|.+|++|||.+       .|+||++||++||+||++||+++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            356899999999999999999999999953       48999999999999999999865

>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=99.61  E-value=1.3e-16  Score=119.00  Aligned_cols=60  Identities=28%  Similarity=0.495  Sum_probs=55.5

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCCC-CCchhhHHHHHHHHHHHHHHHHHhhhcCC
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQFQVMMMSMGT  131 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~-K~dKasIL~~AI~YIk~Lq~qv~~L~~~~  131 (268)
                      +|..|+.+||+||++||++|.+|++|||++. |+||++||.+||+||+.|+.+++.|..++
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~   66 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN   66 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999875 99999999999999999999999987643

>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=99.59  E-value=3.3e-16  Score=113.74  Aligned_cols=54  Identities=24%  Similarity=0.372  Sum_probs=50.1

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCCC--CCchhhHHHHHHHHHHHHHHHHH
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNCN--KVDKASMLEEAIDYLKTLQFQVM  125 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~--K~dKasIL~~AI~YIk~Lq~qv~  125 (268)
                      ++..|+..||+||++||++|.+|++|||.+.  |+||++||+.||+||++||+.++
T Consensus        12 rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          12 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            4678999999999999999999999999875  88999999999999999998764

>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=99.58  E-value=1.4e-15  Score=112.95  Aligned_cols=58  Identities=21%  Similarity=0.242  Sum_probs=53.8

Q ss_pred             cchhhhHHHHHHHHHHHHHHHHHhhCCCCC---CCchhhHHHHHHHHHHHHHHHHHhhhcC
Q 038097           73 PEVHKRYERKRRDKINKKMRALQELIPNCN---KVDKASMLEEAIDYLKTLQFQVMMMSMG  130 (268)
Q Consensus        73 r~~H~~~ERrRR~~In~~~~~L~~LVP~~~---K~dKasIL~~AI~YIk~Lq~qv~~L~~~  130 (268)
                      |..||.+||+||++||++|.+|+++||.+.   |++|++||.+||+||+.|+.+++.|...
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~   62 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ   62 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999764   8999999999999999999999988754

>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=99.55  E-value=5.5e-16  Score=111.47  Aligned_cols=54  Identities=33%  Similarity=0.562  Sum_probs=49.1

Q ss_pred             CCcchhhhHHHHHHHHHHHHHHHHHhhCCCCC------CCchhhHHHHHHHHHHHHHHHH
Q 038097           71 RTPEVHKRYERKRRDKINKKMRALQELIPNCN------KVDKASMLEEAIDYLKTLQFQV  124 (268)
Q Consensus        71 ~~r~~H~~~ERrRR~~In~~~~~L~~LVP~~~------K~dKasIL~~AI~YIk~Lq~qv  124 (268)
                      .+|..|+.+||+||++||++|.+|++|||.+.      |++|++||.+||+||+.||++.
T Consensus         4 ~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           4 KRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            34568999999999999999999999999764      8999999999999999998764

>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=99.54  E-value=2.5e-15  Score=112.43  Aligned_cols=59  Identities=25%  Similarity=0.487  Sum_probs=54.1

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHHHhhhcC
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC--NKVDKASMLEEAIDYLKTLQFQVMMMSMG  130 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~--~K~dKasIL~~AI~YIk~Lq~qv~~L~~~  130 (268)
                      +|..|+.+||+||++||++|.+|+++||.+  .|++|++||..||+||+.|+.+++.|...
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~   62 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD   62 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            367899999999999999999999999975  48999999999999999999999888754

>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=99.53  E-value=3.3e-15  Score=112.94  Aligned_cols=59  Identities=25%  Similarity=0.433  Sum_probs=54.1

Q ss_pred             CcchhhhHHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHhhhcC
Q 038097           72 TPEVHKRYERKRRDKINKKMRALQELIPNC---NKVDKASMLEEAIDYLKTLQFQVMMMSMG  130 (268)
Q Consensus        72 ~r~~H~~~ERrRR~~In~~~~~L~~LVP~~---~K~dKasIL~~AI~YIk~Lq~qv~~L~~~  130 (268)
                      +|..|+.+||+||++||++|..|+++||++   .|.+|++||..||+||++|+.+++.|..+
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~   67 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISE   67 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456899999999999999999999999976   38999999999999999999999988754

>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=99.39  E-value=3.9e-14  Score=100.49  Aligned_cols=48  Identities=33%  Similarity=0.494  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHHhhCCCCC-CCchhhHHHHHHHHHHHHHHHHHhhhcCC
Q 038097           84 RDKINKKMRALQELIPNCN-KVDKASMLEEAIDYLKTLQFQVMMMSMGT  131 (268)
Q Consensus        84 R~~In~~~~~L~~LVP~~~-K~dKasIL~~AI~YIk~Lq~qv~~L~~~~  131 (268)
                      |++||++|.+|++|||++. |+|||+||.+||+||++||.+++.|+.++
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~   49 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQEN   49 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999985 99999999999999999999999998654