Citrus Sinensis ID: 019960

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330---
Protein Sequence
MRTTKGNREEEDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVAKDLENPPSINQAMAKLRDVSSGEDSDHSQKRLRK
Secondary Structure (PSIPRED)
ccccccccccccccHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccccHHHccHHHHHHHHHHHHHHHHHHHHccccccHHcHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccHHcccccccEEcccEEEEcHHHHHHHHHHHHHHHHHccccccccEEEEEEEccccccccccccccccccccccccccccccccccccccccHHHHHHHHcc
Coil and Loop (DISEMBL)
mrttkgnreeedyeddefmskKEAASnitnsnakdgknsdkasvirskhsvTEQRRRSKINERFQILREiiphsdqkrdTASFLLEVIEYVQYLQEKVQKYEVSYqdwsaeptklmpwrnshwrvqnfatqphaikngsgpgsmfpgkfddnsismsptmltstqtpvesdpnrdiackpmdrqpevankgisismplqgnlpaparsdsvllhplqrpvsdaqsnecpattdtmnqqeeltveggtiNISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLgkranrglmpeasvakdlenppsINQAMAKLrdvssgedsdhsqkrlrk
Flexible Loop (DISEMBL)
mrttkgnreeedyeddefmskkeaasnitnsnakdgknsdkasvirskhsvteqrrrskineRFQIlreiiphsdqkrdTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTstqtpvesdpnrDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEAsvakdlenpPSINQAMAKlrdvssgedsdhsqkrlrk
Low Complexity Region (SEG)
MRTTKGNREEEDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVAKDLENPPSINQAMAKLRDVSSGEDSDHSQKRLRK
Disordered region (IsUnstruct)
***************************************************************FQILREIIPHS**KRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFA*****************************************************************************************************************VEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDL*************************************************
Disordered Region (DISOPRED)
********************************************************RSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKV***************************************************************************************************************************************************************LLNNLTQALESAGIDLSQANISV*****************************************************
Disordered Region (DISEMBL)
*******************SKKEAASNITNSN*************************SKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTML***********NRDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVAKDLENPPSINQAMAKL******************
Disordered Region (DISPRO)
*****************************************************QRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQD******KL*************************************************************AC*****QPEVANKGISISMP*****************************************EELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGK***********************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRTTKGNREEEDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVAKDLENPPSINQAMAKLRDVSSGEDSDHSQKRLRK
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	333	2.2.26 [Sep-21-2011]
Q9CAA4	311	Transcription factor BIM2	yes	no	0.849	0.909	0.599	3e-97
Q9FMB6	298	Transcription factor BIM3	no	no	0.789	0.882	0.374	9e-40
Q9LEZ3	529	Transcription factor BIM1	no	no	0.786	0.495	0.371	4e-38
O80536	524	Transcription factor PIF3	no	no	0.312	0.198	0.318	1e-07
Q9FHA2	210	Transcription factor ALC	no	no	0.198	0.314	0.447	2e-07
Q9SVU6	413	Transcription factor bHLH	no	no	0.267	0.215	0.336	3e-07
Q9CAD0	596	Transcription factor EGL1	no	no	0.159	0.088	0.518	6e-07
Q9FN69	637	Transcription factor GLAB	no	no	0.159	0.083	0.518	6e-07
Q9LSQ3	297	Transcription factor bHLH	no	no	0.165	0.185	0.446	1e-06
Q9ZUG9	350	Transcription factor bHLH	no	no	0.183	0.174	0.403	1e-06

>sp|Q9CAA4|BIM2_ARATH Transcription factor BIM2 OS=Arabidopsis thaliana GN=BIM2 PE=1 SV=1

 Score =  355 bits (911), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 181/302 (59%), Positives = 223/302 (73%), Gaps = 19/302 (6%)

Query: 1   MRTTKGNREEEDYEDDEFMSKKEA-ASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
           MRT KGN+EEEDY +++F SK+E  +SN T  + +D K +DKAS IRSKHSVTEQRRRSK
Sbjct: 1   MRTGKGNQEEEDYGEEDFNSKREGPSSNTTVHSNRDSKENDKASAIRSKHSVTEQRRRSK 60

Query: 60  INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
           INERFQILRE+IP+S+QKRDTASFLLEVI+YVQYLQEKVQKYE SY  WS EPTKL PWR
Sbjct: 61  INERFQILRELIPNSEQKRDTASFLLEVIDYVQYLQEKVQKYEGSYPGWSQEPTKLTPWR 120

Query: 120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACK 179
           N+HWRVQ+    P AI NGSGPG  FPGKF+DN+++ +P ++   Q P+ESD  R I   
Sbjct: 121 NNHWRVQSLGNHPVAINNGSGPGIPFPGKFEDNTVTSTPAIIAEPQIPIESDKARAITGI 180

Query: 180 PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQE 239
            ++ QPE+ +KG+    PLQ  LP                V   Q+NECPAT+D + Q  
Sbjct: 181 SIESQPELDDKGLP---PLQPILPM---------------VQGEQANECPATSDGLGQSN 222

Query: 240 ELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVA 299
           +L +EGGTI+ISS YS  LL++LTQAL++AGIDLSQA +SVQIDLGKRAN+GL  E   +
Sbjct: 223 DLVIEGGTISISSAYSHELLSSLTQALQNAGIDLSQAKLSVQIDLGKRANQGLTHEEPSS 282

Query: 300 KD 301
           K+
Sbjct: 283 KN 284

Positive brassinosteroid-signaling protein.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9FMB6|BIM3_ARATH Transcription factor BIM3 OS=Arabidopsis thaliana GN=BIM3 PE=1 SV=1

 Score =  164 bits (415), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 109/291 (37%), Positives = 155/291 (53%), Gaps = 28/291 (9%)

Query: 45  IRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQKYE 102
            RSKHS TEQRRRSKINERFQ L +IIP +  DQKRD ASFLLEVIEY+ +LQEKV  YE
Sbjct: 34  CRSKHSETEQRRRSKINERFQSLMDIIPQNQNDQKRDKASFLLEVIEYIHFLQEKVHMYE 93

Query: 103 VSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLT 162
            S+Q W   PTKL+PWRNSH  V      P  +K+ S           ++ ++ S   L 
Sbjct: 94  DSHQMWYQSPTKLIPWRNSHGSVAEENDHPQIVKSFSS----------NDKVAASSGFLL 143

Query: 163 STQTPVESDPNRDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSD 222
            T   V  D +  ++ K  +  P  A      + P          S   + H   +P + 
Sbjct: 144 DTYNSVNPDIDSAVSTKIPEHSPVSAVSSYLRTEP----------SLQFVQHDFWQPKTS 193

Query: 223 AQSNECPATTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQI 282
             +  C  T + +   E+ +      ++S++ SQ +LN LT+AL+S+G+++S+  ISVQ+
Sbjct: 194 CGTINC-FTNELLTSDEKTSA-----SLSTVCSQRVLNTLTEALKSSGVNMSETMISVQL 247

Query: 283 DLGKRANRGLMPEASVAKDLENPPSINQAMAKLRDVSSGEDSDHSQKRLRK 333
            L KR +R     A  ++D  N  +  +  +     S   D DHSQKR+R+
Sbjct: 248 SLRKREDREYSVAAFASEDNGNSIADEEGDSPTETRSFCNDIDHSQKRIRR 298

Positive brassinosteroid-signaling protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LEZ3|BIM1_ARATH Transcription factor BIM1 OS=Arabidopsis thaliana GN=BIM1 PE=1 SV=2

 Score =  159 bits (401), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 111/299 (37%), Positives = 171/299 (57%), Gaps = 37/299 (12%)

Query: 1   MRTTKGNREEEDYEDDE-FMSKKEAASNI--------TNSNAKDGKNSDKASVIRSKHSV 51
           +R+ KG+ +E+D +D+E F+ KKE++S            ++ +   N  K +  RSKHS 
Sbjct: 224 IRSAKGSSQEDDLDDEEDFIMKKESSSTSQSHRVDLRVKADVRGSPNDQKLNTPRSKHSA 283

Query: 52  TEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAE 111
           TEQRRRSKIN+RFQ+LR++IP+SDQKRD ASFLLEVIEY+Q+LQEK  KY  SYQ W+ E
Sbjct: 284 TEQRRRSKINDRFQMLRQLIPNSDQKRDKASFLLEVIEYIQFLQEKADKYVTSYQGWNHE 343

Query: 112 PTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESD 171
           P KL+ W++++    N    P         G  F  K ++   ++  ++L + Q  V   
Sbjct: 344 PAKLLNWQSNN----NQQLVPE--------GVAFAPKLEEEKNNIPVSVLATAQGVVIDH 391

Query: 172 PNRDIACK-PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPA 230
           P        P+  Q        S   P+    P P              V+ +++ E   
Sbjct: 392 PTTATTSPFPLSIQSN------SFFSPVIAGNPVPQ---------FHARVASSEAVEPSP 436

Query: 231 TTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRAN 289
           ++ +  ++E+  V  G I ISS+YSQGL+  L +ALE++G+DL++A+ISV+I+L K+++
Sbjct: 437 SSRSQKEEEDEEVLEGNIRISSVYSQGLVKTLREALENSGVDLTKASISVEIELAKQSS 495

Positive brassinosteroid-signaling protein. Transcription factor that bind specifically to the DNA sequence 5'-CANNTG-3'(E box). Can bind individually to the promoter as a homodimer or synergistically as a heterodimer with BZR2/BES1. Does not itself activate transcription but enhances BZR2/BES1-mediated target gene activation.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 57.8 bits (138), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 36/113 (31%), Positives = 64/113 (56%), Gaps = 9/113 (7%)

Query: 11  EDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREI 70
           ED E++    +KEA  + T   +K  ++++        H+++E+RRR +INE+ + L+E+
Sbjct: 317 EDVEEESGDGRKEAGPSRTGLGSKRSRSAEV-------HNLSERRRRDRINEKMRALQEL 369

Query: 71  IPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHW 123
           IP+ + K D AS L E IEY++ LQ +VQ   ++   +   P  + P    H+
Sbjct: 370 IPNCN-KVDKASMLDEAIEYLKSLQLQVQIMSMA-SGYYLPPAVMFPPGMGHY 420

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

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 30/67 (44%), Positives = 48/67 (71%), Gaps = 1/67 (1%)

Query: 37  KNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQE 96
           +NS K ++    H+++E++RRSKINE+ + L+++IP+S+ K D AS L E IEY++ LQ 
Sbjct: 86  RNSLKRNIDAQFHNLSEKKRRSKINEKMKALQKLIPNSN-KTDKASMLDEAIEYLKQLQL 144

Query: 97  KVQKYEV 103
           +VQ   V
Sbjct: 145 QVQTLAV 151

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

 Score = 56.6 bits (135), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 54/92 (58%), Gaps = 3/92 (3%)

Query: 16  DEFMSKKEAASNITNSNAKDGKNSDKASVIRSK--HSVTEQRRRSKINERFQILREIIPH 73
           DE   K    +N+ N   ++ ++S  +   R+   H ++E+RRR KINE  + L+E++P 
Sbjct: 247 DERKRKTREETNVENQGTEEARDSTSSKRSRAAIMHKLSERRRRQKINEMMKALQELLPR 306

Query: 74  SDQKRDTASFLLEVIEYVQYLQEKVQKYEVSY 105
              K D +S L +VIEYV+ LQ ++Q + + +
Sbjct: 307 CT-KTDRSSMLDDVIEYVKSLQSQIQMFSMGH 337

Arabidopsis thaliana (taxid: 3702)

>sp|Q9CAD0|EGL1_ARATH Transcription factor EGL1 OS=Arabidopsis thaliana GN=BHLH2 PE=1 SV=1

 Score = 55.5 bits (132), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 39/54 (72%), Gaps = 1/54 (1%)

Query: 49  HSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE 102
           H+++E++RR K+NERF  LR IIP S  K D  S L + IEY+Q LQ++VQ+ E
Sbjct: 406 HALSEKKRREKLNERFMTLRSIIP-SISKIDKVSILDDTIEYLQDLQKRVQELE 458

Transcription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation but promotes trichome formation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Involved in seed mucilage production. Activates the transcription of GL2.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FN69|GL3_ARATH Transcription factor GLABRA 3 OS=Arabidopsis thaliana GN=GL3 PE=1 SV=1

 Score = 55.5 bits (132), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 28/54 (51%), Positives = 38/54 (70%), Gaps = 1/54 (1%)

Query: 49  HSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE 102
           H+V E++RR K+NERF  LR+IIP S  K D  S L + IEY+Q L+ +VQ+ E
Sbjct: 442 HAVLEKKRREKLNERFMTLRKIIP-SINKIDKVSILDDTIEYLQELERRVQELE 494

Transcription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication. Regulates also trichome cell wall maturation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Activates the transcription of GL2.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSQ3|BH082_ARATH Transcription factor bHLH82 OS=Arabidopsis thaliana GN=BHLH82 PE=2 SV=1

 Score = 54.7 bits (130), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/56 (44%), Positives = 41/56 (73%), Gaps = 1/56 (1%)

Query: 49  HSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVS 104
           HS+ E+ RR +I ER + L+E++P+++ K D AS L E+IEYV++LQ +V+   +S
Sbjct: 110 HSIAERLRRERIAERMKSLQELVPNTN-KTDKASMLDEIIEYVRFLQLQVKVLSMS 164

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZUG9|BH066_ARATH Transcription factor bHLH66 OS=Arabidopsis thaliana GN=BHLH66 PE=2 SV=1

 Score = 54.3 bits (129), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 42/62 (67%), Gaps = 1/62 (1%)

Query: 49  HSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDW 108
           HS+ E+ RR +I ER + L+E++P+ + K D AS L E+I+YV++LQ +V+   +S    
Sbjct: 149 HSIAERLRRERIAERMKALQELVPNGN-KTDKASMLDEIIDYVKFLQLQVKVLSMSRLGG 207

Query: 109 SA 110
           +A
Sbjct: 208 AA 209

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	333
255547053	348	conserved hypothetical protein [Ricinus	0.888	0.850	0.706	1e-122
302398603	334	BHLH domain class transcription factor [	0.987	0.985	0.681	1e-122
359806380	336	uncharacterized protein LOC100816055 [Gl	0.996	0.988	0.660	1e-121
357488103	335	Transcription factor BIM2 [Medicago trun	0.993	0.988	0.660	1e-119
359473634	328	PREDICTED: transcription factor BIM2-lik	0.981	0.996	0.665	1e-119
217074640	335	unknown [Medicago truncatula] gi|3884906	0.993	0.988	0.654	1e-117
358249202	335	uncharacterized protein LOC100795416 [Gl	0.993	0.988	0.651	1e-116
357488105	326	Transcription factor BIM2 [Medicago trun	0.966	0.987	0.633	1e-111
224108629	322	predicted protein [Populus trichocarpa]	0.897	0.928	0.639	1e-109
449452819	325	PREDICTED: transcription factor BIM2-lik	0.972	0.996	0.593	1e-105

>gi|255547053|ref|XP_002514584.1| conserved hypothetical protein [Ricinus communis] gi|223546188|gb|EEF47690.1| conserved hypothetical protein [Ricinus communis]

 Score =  444 bits (1141), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 219/310 (70%), Positives = 251/310 (80%), Gaps = 14/310 (4%)

Query: 34  KDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQY 93
           KDGKNSDKA+ IRSKHSVTEQRRRSKINERFQILR++IPHSDQKRDTASFLLEVIEYVQY
Sbjct: 41  KDGKNSDKANAIRSKHSVTEQRRRSKINERFQILRDLIPHSDQKRDTASFLLEVIEYVQY 100

Query: 94  LQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNS 153
           LQEKVQKYE SYQ WS+EPTKLMPWRNSHWRVQ+F   P  IKNGSGPGS  PGKFD+N+
Sbjct: 101 LQEKVQKYEGSYQGWSSEPTKLMPWRNSHWRVQSFIGHPQPIKNGSGPGSTIPGKFDENT 160

Query: 154 ISMSPTMLTSTQTPVESDPNRDIACKPMDRQPEVANKGI--------SISMPLQ--GNLP 203
           I+++PTMLT  Q  VESDP+RD+ CK MDR PEVANK +        +I +P+   G + 
Sbjct: 161 IAINPTMLTGAQNQVESDPSRDVTCKAMDRHPEVANKVLLHPVSLQTTIPIPVHSDGAIA 220

Query: 204 APARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEELTVEGGTINISSIYSQGLLNNLT 263
            P  SD  + HPLQ+PV+DAQS + P T+  +NQQEELT+EGGTI+ISS+YSQGLLNNLT
Sbjct: 221 HPVHSDGAIAHPLQQPVTDAQSADFPITSGALNQQEELTIEGGTISISSVYSQGLLNNLT 280

Query: 264 QALESAGIDLSQANISVQIDLGKRANRGLMPEASVAKDLENPP-SINQAMAKLRDVSSGE 322
           ++L+SAG+DLS ANISVQIDLGKRANRGL    S  KD   PP S NQ  A LRDVSSGE
Sbjct: 281 RSLQSAGVDLSDANISVQIDLGKRANRGLASGTSTTKD---PPLSNNQVAAHLRDVSSGE 337

Query: 323 DSDHSQKRLR 332
           DSD +QKRL+
Sbjct: 338 DSDQAQKRLK 347

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302398603|gb|ADL36596.1| BHLH domain class transcription factor [Malus x domestica]

 Score =  443 bits (1140), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 229/336 (68%), Positives = 272/336 (80%), Gaps = 7/336 (2%)

Query: 1   MRTT-KGNREEEDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
           MRT  KGN+EE++Y+++EF S+KE  S  +NSN+KD KN+DKAS IRSKHSVTEQRRRSK
Sbjct: 1   MRTAAKGNQEEDEYDEEEFGSRKEGPS--SNSNSKDAKNNDKASAIRSKHSVTEQRRRSK 58

Query: 60  INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
           INERFQILR++IPHSDQKRDTASFLLEVIEYVQYLQEKV KYE SYQ WS EPTKLMPWR
Sbjct: 59  INERFQILRDLIPHSDQKRDTASFLLEVIEYVQYLQEKVHKYEGSYQGWSPEPTKLMPWR 118

Query: 120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLT-STQTPVESDPNRDIAC 178
           NSHWRVQ+F   P AIK+ + P   FPGKFD+++IS++P ML  ST  PVESDP+RD+A 
Sbjct: 119 NSHWRVQSFVGNPQAIKSDAAPMLPFPGKFDESNISINPNMLANSTPNPVESDPSRDVAS 178

Query: 179 KPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPAT--TDTMN 236
           K +DRQPE+ NKGI + MPL  N+  P RSD VL HPLQ  +SDAQS +CP T  +D ++
Sbjct: 179 KIVDRQPEIVNKGIPLPMPLP-NIAPPVRSDGVLAHPLQGQISDAQSTQCPTTSASDVLS 237

Query: 237 QQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEA 296
           QQEELT+EGGTI+ISS+YSQGLLN+L+QAL+SAG+DLSQA+ISVQIDLG RANRGL    
Sbjct: 238 QQEELTIEGGTISISSVYSQGLLNSLSQALQSAGVDLSQASISVQIDLGNRANRGLPSVT 297

Query: 297 SVAKDLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
             +KD +NP S NQ  A  RD  SGEDSD + KRL+
Sbjct: 298 PASKDNDNPHSSNQTTAHFRDAGSGEDSDQAHKRLK 333

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359806380|ref|NP_001241235.1| uncharacterized protein LOC100816055 [Glycine max] gi|255635096|gb|ACU17906.1| unknown [Glycine max]

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 220/333 (66%), Positives = 267/333 (80%), Gaps = 1/333 (0%)

Query: 1   MRTTKGNREEEDYEDDEF-MSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
           MR  KG++EE++YE++EF  SKK+  S+  N+N  DGK  DKAS IRSKHSVTEQRRRSK
Sbjct: 1   MRAGKGSQEEDEYEEEEFGSSKKQGTSSAPNTNKADGKAIDKASAIRSKHSVTEQRRRSK 60

Query: 60  INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
           INERFQILR++IPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE SYQ W  EP+KLMPWR
Sbjct: 61  INERFQILRDLIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEGSYQGWGQEPSKLMPWR 120

Query: 120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACK 179
           NSHWRVQ+FA QP A+KNG GP S FPGKFD++++S+SPTML  +Q  ++ D +RDI  K
Sbjct: 121 NSHWRVQSFAGQPTAVKNGLGPVSPFPGKFDESNVSISPTMLNGSQNTIDPDQSRDIVNK 180

Query: 180 PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQE 239
             +RQP++ +KGI + + +  N+  P RSD VL HPLQ  VS+AQS ECP T++  NQQ+
Sbjct: 181 TAERQPDLVSKGIPLPLAMHANMSVPVRSDGVLAHPLQGTVSNAQSTECPTTSEPQNQQD 240

Query: 240 ELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVA 299
           EL+VEGGTI+ISS YSQGLLNNLTQAL+SAG+DLSQA+ISVQI+LGKRAN+GL    S  
Sbjct: 241 ELSVEGGTISISSAYSQGLLNNLTQALQSAGLDLSQASISVQINLGKRANKGLNCGTSSL 300

Query: 300 KDLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
           K  +NP S NQ +A  RD  SGEDSD +QKR++
Sbjct: 301 KHHDNPSSNNQTIAHFRDAGSGEDSDQAQKRMK 333

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357488103|ref|XP_003614339.1| Transcription factor BIM2 [Medicago truncatula] gi|355515674|gb|AES97297.1| Transcription factor BIM2 [Medicago truncatula]

 Score =  434 bits (1116), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 220/333 (66%), Positives = 266/333 (79%), Gaps = 2/333 (0%)

Query: 1   MRTTKGNREEEDYEDDEFMS-KKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
           M+  K N EE++Y+DDEF S KK+A S++ N+N KDGK +DKASVIRSKHSVTEQRRRSK
Sbjct: 1   MKAGKVNHEEDEYDDDEFNSNKKQATSSVPNTN-KDGKATDKASVIRSKHSVTEQRRRSK 59

Query: 60  INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
           INERFQILR++IP  DQKRDTASFLLEVIEYVQYLQE+VQKYE SYQ WS EP+KLMPWR
Sbjct: 60  INERFQILRDLIPQCDQKRDTASFLLEVIEYVQYLQERVQKYEGSYQGWSQEPSKLMPWR 119

Query: 120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACK 179
           NSHWR QNF  QP  +KNGSGP   FPGKFD+NS+ +SPTML+ +   ++ DP RDI  K
Sbjct: 120 NSHWRAQNFVGQPPIVKNGSGPVLPFPGKFDENSVGISPTMLSGSHNMIDHDPTRDIVGK 179

Query: 180 PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQE 239
             +RQP++A+KGI + M +  N+  P RSD VL HPLQ  VSDAQS ECP T++ +NQQ+
Sbjct: 180 TAERQPDLASKGIPLPMAMHANMSVPVRSDGVLSHPLQGTVSDAQSTECPTTSEQLNQQD 239

Query: 240 ELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVA 299
           +LTVEGGTI+ISS+YSQGLLNNLTQAL+SAG+DLS+ANISVQIDLGKRAN+     AS  
Sbjct: 240 DLTVEGGTISISSVYSQGLLNNLTQALQSAGLDLSKANISVQIDLGKRANKDPSGTASSP 299

Query: 300 KDLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
           K+ +NP   NQ+ A  RD  + EDSD +QKR++
Sbjct: 300 KNHDNPLCCNQSFAHFRDGGNREDSDQAQKRMK 332

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359473634|ref|XP_002266685.2| PREDICTED: transcription factor BIM2-like [Vitis vinifera] gi|297738196|emb|CBI27397.3| unnamed protein product [Vitis vinifera]

 Score =  434 bits (1116), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 221/332 (66%), Positives = 262/332 (78%), Gaps = 5/332 (1%)

Query: 1   MRTTKGNREEEDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKI 60
           M+  KG+REEE+ E++E +S K+          KDGKN DKA+ +RSKHSVTEQRRRSKI
Sbjct: 1   MKQDKGHREEEEEEEEEELSMKKEGP----LTKKDGKNHDKANAMRSKHSVTEQRRRSKI 56

Query: 61  NERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRN 120
           NERFQILR++IPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE SYQ  + EPTKLMPWRN
Sbjct: 57  NERFQILRDLIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEGSYQGLTPEPTKLMPWRN 116

Query: 121 SHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACKP 180
           SHWRVQ+F   P AI NGSGPGS F GKFD+N+I+++ TML   Q PVESD +RD  CK 
Sbjct: 117 SHWRVQSFVGHPQAINNGSGPGSAFSGKFDENNINITSTMLVKAQNPVESDLSRDATCKA 176

Query: 181 MDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEE 240
           MD Q E  NK I + + LQ N+ AP +S+  L+HPLQ PVSDAQS +CP T++T++++EE
Sbjct: 177 MDHQSEF-NKAIVMPISLQSNMSAPVQSEGGLVHPLQGPVSDAQSADCPITSETLSKKEE 235

Query: 241 LTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVAK 300
           L +EGGTI+ISS YSQGLLN LTQAL+S+G+DLSQA+ISVQIDLGKRANRGL    S+AK
Sbjct: 236 LMIEGGTISISSAYSQGLLNTLTQALQSSGVDLSQASISVQIDLGKRANRGLPSGTSIAK 295

Query: 301 DLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
           D ENPP  N  +A  RD SS EDSD SQKRL+
Sbjct: 296 DHENPPPSNHIIAHHRDASSAEDSDQSQKRLK 327

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|217074640|gb|ACJ85680.1| unknown [Medicago truncatula] gi|388490634|gb|AFK33383.1| unknown [Medicago truncatula]

 Score =  429 bits (1102), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 218/333 (65%), Positives = 265/333 (79%), Gaps = 2/333 (0%)

Query: 1   MRTTKGNREEEDYEDDEFMS-KKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
           M+  K N EE++Y+DDEF S KK+A S++ N++ KDGK +DKASVIRSKHSVTEQRRRSK
Sbjct: 1   MKAGKVNHEEDEYDDDEFNSNKKQATSSVPNTD-KDGKATDKASVIRSKHSVTEQRRRSK 59

Query: 60  INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
           INERFQILR++IP  DQKRDTASFLLEVIEYVQYLQE+VQKYE SYQ WS EP+KLMPWR
Sbjct: 60  INERFQILRDLIPQCDQKRDTASFLLEVIEYVQYLQERVQKYEGSYQGWSQEPSKLMPWR 119

Query: 120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACK 179
           NSHWR QNF  QP  +KNGSGP   FPGKFD+NS+ +SPTML+ +   ++ DP RDI  K
Sbjct: 120 NSHWRAQNFVGQPPIVKNGSGPVLPFPGKFDENSVGISPTMLSGSHNMMDHDPTRDIVGK 179

Query: 180 PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQE 239
             +RQP++A+KGI + M +  N+  P RSD VL H LQ  VSDAQS ECP T++ +NQQ+
Sbjct: 180 TAERQPDLASKGIPLPMAMHANMSVPVRSDGVLSHSLQGTVSDAQSTECPTTSEQLNQQD 239

Query: 240 ELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVA 299
           +LTVEGGTI+ISS+YSQGLLNNLTQAL+SAG+DLS+ANISVQIDLGKRAN+     AS  
Sbjct: 240 DLTVEGGTISISSVYSQGLLNNLTQALQSAGLDLSKANISVQIDLGKRANKDPSGTASSP 299

Query: 300 KDLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
           K+ +NP   NQ+ A  RD  + EDSD +QKR++
Sbjct: 300 KNHDNPLCCNQSFAHFRDGGNREDSDQAQKRMK 332

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358249202|ref|NP_001239754.1| uncharacterized protein LOC100795416 [Glycine max] gi|255635070|gb|ACU17893.1| unknown [Glycine max]

 Score =  425 bits (1092), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 217/333 (65%), Positives = 260/333 (78%), Gaps = 2/333 (0%)

Query: 1   MRTTKGNREEEDYEDDEF-MSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
           MR  KG++EE++YE++EF  SKK+  S+  N+N KDGK  DKAS IRSKHSVTEQRRRSK
Sbjct: 1   MRAGKGSQEEDEYEEEEFGSSKKQGTSSAPNAN-KDGKAIDKASAIRSKHSVTEQRRRSK 59

Query: 60  INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
           INERFQILR++IPHSDQKRDTASFLLEV+EYVQYLQEKVQKYE SYQ W  EP KLMPWR
Sbjct: 60  INERFQILRDLIPHSDQKRDTASFLLEVMEYVQYLQEKVQKYEGSYQGWGQEPLKLMPWR 119

Query: 120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACK 179
           NSHWRVQ+FA QP A+KNG GP S FP KFD+++ S+SPTML+ TQ  ++   +RDI  K
Sbjct: 120 NSHWRVQSFAGQPTAVKNGLGPVSPFPVKFDESNASISPTMLSGTQNTIDPYQSRDIVNK 179

Query: 180 PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQE 239
             +RQP++ NKG+ + + +  N+  P RSD VL HPL   VSD QS ECP T++  NQQ+
Sbjct: 180 TAERQPDLVNKGMPLPLAMHANMSVPVRSDGVLAHPLHGTVSDPQSTECPTTSEPQNQQD 239

Query: 240 ELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVA 299
           E TVEGGTI+ISS YSQGLLNNLTQAL+SAG+DLSQA+ISVQI+LGKR N+GL    S  
Sbjct: 240 EFTVEGGTISISSAYSQGLLNNLTQALQSAGLDLSQASISVQINLGKRGNKGLSCGTSSP 299

Query: 300 KDLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
           K  +NP S NQ +A  RD  SGEDSD  QKR++
Sbjct: 300 KHHDNPSSNNQTIAHFRDAGSGEDSDQVQKRMK 332

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357488105|ref|XP_003614340.1| Transcription factor BIM2 [Medicago truncatula] gi|355515675|gb|AES97298.1| Transcription factor BIM2 [Medicago truncatula]

 Score =  407 bits (1046), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 211/333 (63%), Positives = 257/333 (77%), Gaps = 11/333 (3%)

Query: 1   MRTTKGNREEEDYEDDEFMS-KKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
           M+  K N EE++Y+DDEF S KK+A S++ N+N KDGK +DKASVIRSKHSVTEQRRRSK
Sbjct: 1   MKAGKVNHEEDEYDDDEFNSNKKQATSSVPNTN-KDGKATDKASVIRSKHSVTEQRRRSK 59

Query: 60  INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
           INERFQILR++IP  DQKRDTASFLLE         E+VQKYE SYQ WS EP+KLMPWR
Sbjct: 60  INERFQILRDLIPQCDQKRDTASFLLE---------ERVQKYEGSYQGWSQEPSKLMPWR 110

Query: 120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACK 179
           NSHWR QNF  QP  +KNGSGP   FPGKFD+NS+ +SPTML+ +   ++ DP RDI  K
Sbjct: 111 NSHWRAQNFVGQPPIVKNGSGPVLPFPGKFDENSVGISPTMLSGSHNMIDHDPTRDIVGK 170

Query: 180 PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQE 239
             +RQP++A+KGI + M +  N+  P RSD VL HPLQ  VSDAQS ECP T++ +NQQ+
Sbjct: 171 TAERQPDLASKGIPLPMAMHANMSVPVRSDGVLSHPLQGTVSDAQSTECPTTSEQLNQQD 230

Query: 240 ELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVA 299
           +LTVEGGTI+ISS+YSQGLLNNLTQAL+SAG+DLS+ANISVQIDLGKRAN+     AS  
Sbjct: 231 DLTVEGGTISISSVYSQGLLNNLTQALQSAGLDLSKANISVQIDLGKRANKDPSGTASSP 290

Query: 300 KDLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
           K+ +NP   NQ+ A  RD  + EDSD +QKR++
Sbjct: 291 KNHDNPLCCNQSFAHFRDGGNREDSDQAQKRMK 323

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224108629|ref|XP_002314914.1| predicted protein [Populus trichocarpa] gi|222863954|gb|EEF01085.1| predicted protein [Populus trichocarpa]

 Score =  399 bits (1025), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 204/319 (63%), Positives = 245/319 (76%), Gaps = 20/319 (6%)

Query: 18  FMSKKEAASN---ITNSN-AKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPH 73
           F S+K+  S+   I N+N  KDGK+SDKA+ IRSKHSVTEQ+RRSKINERFQILR++IPH
Sbjct: 19  FGSRKDGPSSNFTIDNTNSCKDGKHSDKANAIRSKHSVTEQKRRSKINERFQILRDLIPH 78

Query: 74  SDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPH 133
           SDQKRDTASFLLEVIEYVQYLQEKVQKYE  Y  WS EP KLMPWRNSHWR+Q+F   P 
Sbjct: 79  SDQKRDTASFLLEVIEYVQYLQEKVQKYEGPYPGWSPEPAKLMPWRNSHWRLQSFVGHPQ 138

Query: 134 AIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACKPMDRQPEVANKGIS 193
           A KNGSG G+ FPGK D+N+I+++P ML ST   +ESD    + CK ++ QPE+AN    
Sbjct: 139 ATKNGSGLGAAFPGKLDENNITLTPAMLPSTPNLIESD---HVTCKVLEHQPELAN---- 191

Query: 194 ISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEELTVEGGTINISSI 253
            ++P    +PAPARSD ++  PL++PVSDAQS ECP T++ +NQQ EL +E GTI+ISS+
Sbjct: 192 -ALP----MPAPARSDGLVAPPLEQPVSDAQSAECPITSEMLNQQ-ELAIEAGTISISSV 245

Query: 254 YSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVAKDLENPPSINQAMA 313
           YSQ LLN LTQAL+SA +DLSQANISVQIDLGKRAN+GL    S +KD   P   NQ M 
Sbjct: 246 YSQELLNTLTQALQSASVDLSQANISVQIDLGKRANKGLASGTSTSKD---PQDCNQVMT 302

Query: 314 KLRDVSSGEDSDHSQKRLR 332
            LRD S GEDSD +QKRL+
Sbjct: 303 HLRDASEGEDSDQAQKRLK 321

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449452819|ref|XP_004144156.1| PREDICTED: transcription factor BIM2-like [Cucumis sativus] gi|449530757|ref|XP_004172359.1| PREDICTED: transcription factor BIM2-like [Cucumis sativus]

 Score =  389 bits (999), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 197/332 (59%), Positives = 255/332 (76%), Gaps = 8/332 (2%)

Query: 1   MRTTKGNREEEDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKI 60
           MRT K N+E+++Y++DE + K+E  S  + SNA + KN+DKA+ IRSKHSVTEQRRRSKI
Sbjct: 1   MRTGKSNQEDDEYDEDELVGKREGPS--STSNAINAKNNDKANAIRSKHSVTEQRRRSKI 58

Query: 61  NERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRN 120
           NERFQILR++IPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE SYQ+WS EPTKL+PWRN
Sbjct: 59  NERFQILRDLIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEGSYQNWSGEPTKLIPWRN 118

Query: 121 SHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACKP 180
           SHWR+Q F     ++KNGS  G  + GKFDDN+IS+SP ML S+Q P++S   RDI    
Sbjct: 119 SHWRMQTFVGHQQSVKNGSASGPTYSGKFDDNNISISPAMLASSQNPLDSHSGRDIL--- 175

Query: 181 MDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPATTDTMNQQEE 240
             ++ ++ NK +   M L+GN+ A  RSD+VL H L  P+SD Q+ ECP T +  NQ EE
Sbjct: 176 --QEADITNK-VPHPMSLEGNMHASIRSDTVLDHSLHIPISDPQATECPITNNASNQPEE 232

Query: 241 LTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRANRGLMPEASVAK 300
           + +EGGTI++SS+YS+G +N+L QAL+S G+DLSQA+ISVQIDLGKRAN+G+     + K
Sbjct: 233 MGIEGGTISVSSVYSEGFMNSLAQALQSTGLDLSQASISVQIDLGKRANKGMPFGTPIFK 292

Query: 301 DLENPPSINQAMAKLRDVSSGEDSDHSQKRLR 332
           +  NP S + AMA + D+ SG+DS+ ++KRLR
Sbjct: 293 ETGNPSSNHPAMANVGDLGSGDDSEQAKKRLR 324

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	333
TAIR|locus:2205455	311	BIM2 "AT1G69010" [Arabidopsis	0.804	0.861	0.526	7.4e-66
UNIPROTKB|Q6ZBQ2	508	P0605H02.26 "BHLH protein fami	0.885	0.580	0.418	8.3e-51
UNIPROTKB|Q69JI7	504	OSJNBa0026C08.39-1 "BHLH prote	0.888	0.587	0.388	4.1e-49
TAIR|locus:2152262	298	BIM3 "AT5G38860" [Arabidopsis	0.465	0.520	0.460	7.5e-42
UNIPROTKB|Q6Z339	344	B1121A12.20 "Os02g0726700 prot	0.591	0.572	0.358	5.8e-27
TAIR|locus:2155503	210	ALC "AT5G67110" [Arabidopsis t	0.381	0.604	0.335	7.8e-09
TAIR|locus:2090847	494	ICE1 "AT3G26744" [Arabidopsis	0.309	0.208	0.3	3.5e-08
UNIPROTKB|Q5NAE0	565	P0498A12.33 "Putative BP-5 pro	0.330	0.194	0.376	7.8e-08
TAIR|locus:2053733	430	PIF4 "AT2G43010" [Arabidopsis	0.273	0.211	0.381	1.4e-07
TAIR|locus:2117773	413	AT4G28790 [Arabidopsis thalian	0.267	0.215	0.336	3.6e-07

TAIR|locus:2205455 BIM2 "AT1G69010" [Arabidopsis thaliana (taxid:3702)]

 Score = 670 (240.9 bits), Expect = 7.4e-66, P = 7.4e-66
 Identities = 148/281 (52%), Positives = 190/281 (67%)

Query:     1 MRTTKGNREEEDYEDDEFMSKKEA-ASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSK 59
             MRT KGN+EEEDY +++F SK+E  +SN T  + +D K +DKAS IRSKHSVTEQRRRSK
Sbjct:     1 MRTGKGNQEEEDYGEEDFNSKREGPSSNTTVHSNRDSKENDKASAIRSKHSVTEQRRRSK 60

Query:    60 INERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWR 119
             INERFQILRE+IP+S+QKRDTASFLLEVI+YVQYLQEKVQKYE SY  WS EPTKL PWR
Sbjct:    61 INERFQILRELIPNSEQKRDTASFLLEVIDYVQYLQEKVQKYEGSYPGWSQEPTKLTPWR 120

Query:   120 NSHWRVQNFATQPHAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESDPNRDIACK 179
             N+HWRVQ+    P AI NGSGPG  FPGKF+DN+++ +P ++   Q P+ESD  R I   
Sbjct:   121 NNHWRVQSLGNHPVAINNGSGPGIPFPGKFEDNTVTSTPAIIAEPQIPIESDKARAITGI 180

Query:   180 PMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDA--QSNECPATTDTMNQ 237
              ++ QPE+ +KG+    PLQ  LP   + +     P     SD   QSN+      T++ 
Sbjct:   181 SIESQPELDDKGLP---PLQPILPM-VQGEQANECPA---TSDGLGQSNDLVIEGGTISI 233

Query:   238 QEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQ-AN 277
                 + E  +    ++ + G+  +L+QA  S  IDL + AN
Sbjct:   234 SSAYSHELLSSLTQALQNAGI--DLSQAKLSVQIDLGKRAN 272

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

UNIPROTKB|Q6ZBQ2 P0605H02.26 "BHLH protein family-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 528 (190.9 bits), Expect = 8.3e-51, P = 8.3e-51
 Identities = 144/344 (41%), Positives = 202/344 (58%)

Query:    14 EDDEFMSKKEAASNITNSNAK-DGKN---SDKA------SVIRSKHSVTEQRRRSKINER 63
             +DD   +++E +S++     + +GK    S  A      +  RSKHS TEQRRRSKIN+R
Sbjct:   181 DDDGHAARREVSSSLKELTVRVEGKGGSCSGSAGTDQMPNTPRSKHSATEQRRRSKINDR 240

Query:    64 FQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRN--- 120
             FQ+LR+++PH+DQKRD ASFLLEVIEY+++LQEKVQKYEVSY +W+ E  K++PW N   
Sbjct:   241 FQLLRDLLPHNDQKRDKASFLLEVIEYIRFLQEKVQKYEVSYPEWNQENAKVVPWTNIYF 300

Query:   121 -SHWR-VQNFATQP--HA------IKNGSGPGSMFP--GKFDDNSISMSPTMLTSTQTPV 168
              S W+  QN    P  H+      +KNGS P  MFP  G  D+N+ ++     +  Q   
Sbjct:   301 RSSWKNAQNKGQVPADHSPDPPELLKNGS-P-YMFPFTGNSDNNN-AVETAAASGAQDQA 357

Query:   169 ESDPNRDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNEC 228
             E+DP        M R   V+ +  S+  P   N+     +D V   P  + V  + +   
Sbjct:   358 ETDP--------MSR---VSYR--SVDTPSPNNV-----ADKVTSQPHAQLVRPSPAENH 399

Query:   229 PATTDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRA 288
                 D +N  + L ++ GTI++SS YSQ LLN L  ALE++GIDLSQA+ISVQI+LGKRA
Sbjct:   400 TVNCDKLNNSD-LAIDEGTISLSSQYSQELLNKLNHALENSGIDLSQASISVQINLGKRA 458

Query:   289 NRGLMPEA-SVAKDLENPPSINQAMAK-LRDVSSGEDSDHSQKR 330
              +   P A S +K+L +P S +QAM + LR     E+   + KR
Sbjct:   459 MKRSTPAATSTSKELTDPASNSQAMGRQLRLGDGAEEHRQASKR 502

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q69JI7 OSJNBa0026C08.39-1 "BHLH protein family-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 133/342 (38%), Positives = 193/342 (56%)

Query:    14 EDDEFMSKKEAASNITNSNAK-DGKNSD--------KASVIRSKHSVTEQRRRSKINERF 64
             +DD   +++E +S++     + DGK           + S  RSKHS TEQRRRSKIN+RF
Sbjct:   178 DDDGVAARREVSSSLKELTVRVDGKGGSCSGSGTDQRPSSPRSKHSATEQRRRSKINDRF 237

Query:    65 QILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRN---- 120
             QILRE++PHSDQKRD A+FLLEVIEY+++LQEKVQK+E S  +W+ E  K++PW N    
Sbjct:   238 QILRELLPHSDQKRDKATFLLEVIEYIRFLQEKVQKFEASVPEWNQENAKILPWSNIYFR 297

Query:   121 SHWR-VQNFATQP--------HAIKNGSGPGSMFPGKFDDNSISMSPTMLTSTQTPVESD 171
             S W+  Q+    P          I+NGS  G  F GK DDN   ++    +  Q  VE+D
Sbjct:   298 SFWKNSQSKGQNPGDDLPDPSQFIRNGSSSGYNFTGKPDDNHNMVTSAAASGAQELVETD 357

Query:   172 PNRDIACKPMDRQPEVANKGISISMPLQGNLPAPARSDSVLLHPLQRPVSDAQSNECPAT 231
                 ++ +  +    + N   +++   Q    +PA  D                 +C   
Sbjct:   358 HAASVSYRSAETPTNITN---NVTSQAQAQWASPAGVD-----------------DCAMN 397

Query:   232 TDTMNQQEELTVEGGTINISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRA-NR 290
             ++ +N Q+ L ++ GTI++SS YSQ LL  LT ALES+G+DLSQ++ISVQI+LGKRA  R
Sbjct:   398 SEMLNNQQ-LAIDEGTISLSSQYSQQLLGTLTHALESSGVDLSQSSISVQINLGKRAVKR 456

Query:   291 GLMPEASVAKDLENPPSINQAMA-KLRDVSSG-EDSDHSQKR 330
                  +S +K+L +  + N+ M  +L  +  G E+  H  KR
Sbjct:   457 PGADGSSSSKELPSTSANNENMGHQLTMLGGGTEELPHPTKR 498

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2152262 BIM3 "AT5G38860" [Arabidopsis thaliana (taxid:3702)]

 Score = 313 (115.2 bits), Expect = 7.5e-42, Sum P(2) = 7.5e-42
 Identities = 75/163 (46%), Positives = 97/163 (59%)

Query:    15 DDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHS 74
             DD+   + +  SN+ + N       ++ S  RSKHS TEQRRRSKINERFQ L +IIP +
Sbjct:     7 DDQL--EADVYSNLPSRNDSSTGRRNRNSC-RSKHSETEQRRRSKINERFQSLMDIIPQN 63

Query:    75 --DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQP 132
               DQKRD ASFLLEVIEY+ +LQEKV  YE S+Q W   PTKL+PWRNSH  V      P
Sbjct:    64 QNDQKRDKASFLLEVIEYIHFLQEKVHMYEDSHQMWYQSPTKLIPWRNSHGSVAEENDHP 123

Query:   133 HAIKNGSGPGSMFP--GKFDDNSISMSPTMLTSTQTPV-ESDP 172
               +K+ S    +    G   D   S++P + ++  T + E  P
Sbjct:   124 QIVKSFSSNDKVAASSGFLLDTYNSVNPDIDSAVSTKIPEHSP 166

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

UNIPROTKB|Q6Z339 B1121A12.20 "Os02g0726700 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 273 (101.2 bits), Expect = 5.8e-27, Sum P(2) = 5.8e-27
 Identities = 76/212 (35%), Positives = 111/212 (52%)

Query:    29 TNSNAKDGKNS-DKA-SVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLE 86
             T +  +   +S D+  S  RSKHS TEQRRR+KIN+R +ILRE++PH+DQKRD ASFL E
Sbjct:   128 TRAEGRSSASSADQGPSTPRSKHSATEQRRRTKINDRLEILRELLPHTDQKRDKASFLSE 187

Query:    87 VIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRN----SHWRVQNFATQPHAIKNGSGPG 142
             VIEY+++LQEKVQKYE +  + + E +K MPW      S WR     +Q           
Sbjct:   188 VIEYIRFLQEKVQKYEEADPERNHEDSKSMPWAKVYYRSCWRNTKNTSQVQGEDLSPSTQ 247

Query:   143 SMFPGKFDDNSISMSPTMLTSTQ--TPVESDPNRDIACKP--MDRQPEVANKG--ISISM 196
              M   ++    IS +   L +TQ  T   +  +      P  +++    +N+   +S+S 
Sbjct:   248 DMNNEQYGPKHISAAQPALFNTQSVTSTTTSSSHMATGTPQNLEKNSTPSNQPPWLSMST 307

Query:   197 PLQGNLPA---PARSDSVLLHPLQRPVSDAQS 225
               Q + P    P + +   LH     +S A S
Sbjct:   308 MRQESEPGNKMPNKHEKQTLHDENHSISSAYS 339

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2155503 ALC "AT5G67110" [Arabidopsis thaliana (taxid:3702)]

 Score = 147 (56.8 bits), Expect = 7.8e-09, P = 7.8e-09
 Identities = 45/134 (33%), Positives = 73/134 (54%)

Query:    31 SNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEY 90
             S AK  +NS K ++    H+++E++RRSKINE+ + L+++IP+S+ K D AS L E IEY
Sbjct:    81 SGAKQ-RNSLKRNIDAQFHNLSEKKRRSKINEKMKALQKLIPNSN-KTDKASMLDEAIEY 138

Query:    91 VQYLQEKVQKYEVSYQDWSAEPTKL--MPWRNSHWRVQNFATQPHAIKNG-SGPGSMFPG 147
             ++ LQ +VQ   V        P +L  +P   +H R+     Q   ++   + P S+ P 
Sbjct:   139 LKQLQLQVQTLAVM-NGLGLNPMRLPQVP-PPTHTRINETLEQDLNLETLLAAPHSLEPA 196

Query:   148 KFDDNSISMSPTML 161
             K        + T+L
Sbjct:   197 KTSQGMCFSTATLL 210

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;ISS;IDA

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

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

GO:0010047 "fruit dehiscence" evidence=IMP

TAIR|locus:2090847 ICE1 "AT3G26744" [Arabidopsis thaliana (taxid:3702)]

 Score = 123 (48.4 bits), Expect = 3.5e-08, Sum P(2) = 3.5e-08
 Identities = 33/110 (30%), Positives = 56/110 (50%)

Query:    12 DYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREII 71
             +YE DE     +AA ++       GK   K   + +K+ + E+RRR K+N+R  +LR ++
Sbjct:   275 NYESDEINESGKAAESVQIGGG--GKGKKKG--MPAKNLMAERRRRKKLNDRLYMLRSVV 330

Query:    72 PHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMPWRNS 121
             P    K D AS L + I+Y++ L +++       +  S  P  L P  +S
Sbjct:   331 PKIS-KMDRASILGDAIDYLKELLQRINDLHNELE--STPPGSLPPTSSS 377

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009409 "response to cold" evidence=IEP

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

GO:0050826 "response to freezing" evidence=RCA;IMP

GO:0010440 "stomatal lineage progression" evidence=IMP

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

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0009793 "embryo development ending in seed dormancy" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0009909 "regulation of flower development" evidence=RCA

GO:0009933 "meristem structural organization" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

GO:0010182 "sugar mediated signaling pathway" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0019915 "lipid storage" evidence=RCA

GO:0043687 "post-translational protein modification" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

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

 Score = 152 (58.6 bits), Expect = 7.8e-08, P = 7.8e-08
 Identities = 44/117 (37%), Positives = 63/117 (53%)

Query:    34 KDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQY 93
             K G  S K S     H+++E+RRR +INE+ + L+E+IP+ + K D AS L E IEY++ 
Sbjct:   302 KSGTRSTKRSRTAEVHNLSERRRRDRINEKMRALQELIPNCN-KIDKASMLDEAIEYLKT 360

Query:    94 LQEKVQKYEVSYQDWSAEPTKLMPWRNSHWRVQNFATQPHAIKNGSGPGSMFPGKFD 150
             LQ +VQ   +S       P  L+P    H ++   A  PH +  G G G    G FD
Sbjct:   361 LQLQVQM--MSMGTGLCIPPMLLPTAMQHLQIPPMAHFPH-LGMGLGYGM---GVFD 411

GO:0005634 "nucleus" evidence=IC

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

 Score = 148 (57.2 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 37/97 (38%), Positives = 58/97 (59%)

Query:     3 TTKGNREEEDYEDDEFMSKKEAASNITNSNAKDGKNSDKASVIRSKHSVTEQRRRSKINE 62
             TT   R+  ++ D E +S  +A  N +N  +   + S  A V    H+++E+RRR +INE
Sbjct:   221 TTDRKRKRINHTD-ESVSLSDAIGNKSNQRSGSNRRSRAAEV----HNLSERRRRDRINE 275

Query:    63 RFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQ 99
             R + L+E+IPH   K D AS L E I+Y++ LQ ++Q
Sbjct:   276 RMKALQELIPHCS-KTDKASILDEAIDYLKSLQLQLQ 311

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:2117773 AT4G28790 [Arabidopsis thaliana (taxid:3702)]

 Score = 144 (55.7 bits), Expect = 3.6e-07, P = 3.6e-07
 Identities = 31/92 (33%), Positives = 54/92 (58%)

Query:    16 DEFMSKKEAASNITNSNAKDGKNSDKASVIRSK--HSVTEQRRRSKINERFQILREIIPH 73
             DE   K    +N+ N   ++ ++S  +   R+   H ++E+RRR KINE  + L+E++P 
Sbjct:   247 DERKRKTREETNVENQGTEEARDSTSSKRSRAAIMHKLSERRRRQKINEMMKALQELLPR 306

Query:    74 SDQKRDTASFLLEVIEYVQYLQEKVQKYEVSY 105
                K D +S L +VIEYV+ LQ ++Q + + +
Sbjct:   307 CT-KTDRSSMLDDVIEYVKSLQSQIQMFSMGH 337

GO:0005634 "nucleus" evidence=ISM

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9CAA4	BIM2_ARATH	No assigned EC number	0.5993	0.8498	0.9099	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	333
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	4e-13
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	5e-12
smart00353	53	smart00353, HLH, helix loop helix domain	6e-11

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

 Score = 62.5 bits (153), Expect = 4e-13
 Identities = 21/51 (41%), Positives = 33/51 (64%), Gaps = 1/51 (1%)

Query: 46 RSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQ 95
          R  H+  E+RRR +IN+ F+ LRE++P   ++K   A  L   IEY+++LQ
Sbjct: 2  RKAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

>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 = 59.9 bits (146), Expect = 5e-12
 Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 46 RSKHSVTEQRRRSKINERFQILREIIP--HSDQKRDTASFLLEVIEYVQYLQEKVQ 99
          R  H++ E+RRR +IN+ F  LR ++P     +K   A  L + ++Y++ LQE +Q
Sbjct: 5  REAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 56.8 bits (138), Expect = 6e-11
 Identities = 23/50 (46%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 53  EQRRRSKINERFQILREIIP--HSDQKRDTASFLLEVIEYVQYLQEKVQK 100
           E+RRR KINE F  LR ++P    ++K   A  L   IEY++ LQE++QK
Sbjct: 4   ERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	333
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.45
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.42
smart00353	53	HLH helix loop helix domain.	99.32
KOG1318	411	consensus Helix loop helix transcription factor EB	99.2
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.12
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.71
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.53
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.53
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.47
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.26
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.96
KOG0561	373	consensus bHLH transcription factor [Transcription	97.7
KOG3910	632	consensus Helix loop helix transcription factor [T	97.44
PLN03217	93	transcription factor ATBS1; Provisional	96.49
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	95.35
KOG3898	254	consensus Transcription factor NeuroD and related	93.68
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	91.78
KOG4395	285	consensus Transcription factor Atonal, contains HT	89.4
KOG3582	856	consensus Mlx interactors and related transcriptio	87.47
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	85.59
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	84.34

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

Probab=99.45  E-value=7.5e-14  Score=102.19  Aligned_cols=51  Identities=43%  Similarity=0.711  Sum_probs=48.0

Q ss_pred             ccccCchHHHHHHHHHHHHHHHHhccCCCC----CCCCChhhhhHHHHHHHHHHH
Q 019960           45 IRSKHSVTEQRRRSKINERFQILREIIPHS----DQKRDTASFLLEVIEYVQYLQ   95 (333)
Q Consensus        45 rr~~H~~~ERrRR~rINe~f~~LrsLVP~~----~~K~DKasIL~~AIeYIk~Lq   95 (333)
                      +|..|+..||+||++||+.|.+|+.+||.+    ..|++|++||..||+||++||
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            467899999999999999999999999986    479999999999999999997

; 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=99.42  E-value=2.1e-13  Score=100.00  Aligned_cols=55  Identities=35%  Similarity=0.625  Sum_probs=51.6

Q ss_pred             cccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHH
Q 019960           44 VIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      .++..|+..||+||++||+.|..|+.+||..  ..|+||++||..||+||++|+.++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            4678899999999999999999999999998  589999999999999999999875

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=99.32  E-value=3.6e-12  Score=91.89  Aligned_cols=50  Identities=44%  Similarity=0.672  Sum_probs=46.1

Q ss_pred             chHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960           50 SVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQ   99 (333)
Q Consensus        50 ~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~   99 (333)
                      +..||+||.+||++|..|+.+||.+  ..|++|++||..||+||++|+.+++
T Consensus         1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~   52 (53)
T smart00353        1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ   52 (53)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence            4689999999999999999999964  4799999999999999999998875

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

Probab=99.20  E-value=1.5e-11  Score=123.15  Aligned_cols=59  Identities=32%  Similarity=0.573  Sum_probs=55.4

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQ   99 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~   99 (333)
                      |.+.+|..|+++|||||++||++|++|..|||.|   +.|+.|..||..+++||++||+..+
T Consensus       229 rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q  290 (411)
T KOG1318|consen  229 RDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ  290 (411)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence            7888999999999999999999999999999998   5689999999999999999988666

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.12  E-value=2e-11  Score=111.17  Aligned_cols=89  Identities=26%  Similarity=0.351  Sum_probs=68.9

Q ss_pred             cccccccCchHHHHHHHHHHHHHHHHhccCCCC------CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCcccc
Q 019960           42 ASVIRSKHSVTEQRRRSKINERFQILREIIPHS------DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKL  115 (333)
Q Consensus        42 ~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~------~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~~~l  115 (333)
                      +.+||..|.-+||+||+.||..+..|+.|||.|      ..|+.||.||.++|+||.+|..+..+-+.+...|+.+...|
T Consensus        59 k~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL  138 (229)
T KOG1319|consen   59 KDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTAL  138 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            567899999999999999999999999999987      23889999999999999999988887777766666555433


Q ss_pred             cc-CCCCcccccccCC
Q 019960          116 MP-WRNSHWRVQNFAT  130 (333)
Q Consensus       116 ~p-~~n~~~~~~s~~d  130 (333)
                      .- ..+++..+....+
T Consensus       139 ~iIk~~YEqM~~~~qd  154 (229)
T KOG1319|consen  139 KIIKVNYEQMVKAHQD  154 (229)
T ss_pred             HHHHHHHHHHHHhccc
Confidence            22 2333334444333

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

Probab=98.71  E-value=6.8e-09  Score=98.52  Aligned_cols=61  Identities=25%  Similarity=0.429  Sum_probs=53.3

Q ss_pred             CCcccccccccCchHHHHHHHHHHHHHHHHhccCCCC---C----CCCChhhhhHHHHHHHHHHHHHH
Q 019960           38 NSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHS---D----QKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        38 ~~~k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~----~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      .......|+..|-+.|||||+|||+.+.+|++|||.+   +    .|++||.||+-|++|++.|+...
T Consensus        25 ~~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~   92 (250)
T KOG4304|consen   25 SSKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ   92 (250)
T ss_pred             chhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence            3336677889999999999999999999999999965   1    58999999999999999998643

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

Probab=98.53  E-value=1.2e-07  Score=89.26  Aligned_cols=76  Identities=30%  Similarity=0.451  Sum_probs=62.8

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCCCCC-CC-hhhhhHHHHHHHHHHHHHHHHHHhhhcccccCccccc
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQK-RD-TASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLM  116 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K-~D-KasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~~~l~  116 (333)
                      .....|..|+..||+||..|+++|..|+.+||..+.. .. .++||++|++||+.|+.+....+..++.+..+..+|.
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~  132 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSRENRKLK  132 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence            5566789999999999999999999999999987433 33 5999999999999999988877777666666555444

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

Probab=98.53  E-value=1.6e-07  Score=89.11  Aligned_cols=74  Identities=24%  Similarity=0.359  Sum_probs=63.0

Q ss_pred             CCCCcccccccccCchHHHHHHHHHHHHHHHH-hccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccc
Q 019960           36 GKNSDKASVIRSKHSVTEQRRRSKINERFQIL-REIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWS  109 (333)
Q Consensus        36 g~~~~k~~~rr~~H~~~ERrRR~rINe~f~~L-rsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~  109 (333)
                      .|.+.-...||++-.+.||||-.|+||.|.+| |.-.++.++++.|+.||..||+||..||.-++++......+.
T Consensus       109 ckrks~svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~~  183 (284)
T KOG3960|consen  109 CKRKSTSVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGLA  183 (284)
T ss_pred             ccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhhh
Confidence            34444556688888999999999999999999 667888889999999999999999999999998887665544

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

Probab=98.47  E-value=1.6e-07  Score=101.10  Aligned_cols=57  Identities=26%  Similarity=0.457  Sum_probs=51.9

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCCC---CCCChhhhhHHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHSD---QKRDTASFLLEVIEYVQYLQEK   97 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~---~K~DKasIL~~AIeYIk~Lq~~   97 (333)
                      +....|.+|+.+|||||+++|..|.+|.+|||.|.   .|+||..||..||.+||.+++.
T Consensus        16 k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   16 KDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             hhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            33345999999999999999999999999999985   8999999999999999999874

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.26  E-value=3.1e-07  Score=99.52  Aligned_cols=67  Identities=27%  Similarity=0.477  Sum_probs=60.5

Q ss_pred             ccccccCchHHHHHHHHHHHHHHHHhccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccc
Q 019960           43 SVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWS  109 (333)
Q Consensus        43 ~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~  109 (333)
                      ..+|.+||++|||.|..||+++.+|+++||+...|+.|..+|..||+||++|+...+.+......+.
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            3679999999999999999999999999999888999999999999999999998887776655444

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

Probab=97.96  E-value=7.1e-06  Score=76.26  Aligned_cols=65  Identities=23%  Similarity=0.402  Sum_probs=56.2

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHHHHHhhh
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQKYEVSY  105 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~  105 (333)
                      ....++..++..||.|=..+|..|.+||.+||..   ++|+.|+.+|..||.||++|+.-++.-+...
T Consensus       105 ~~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~  172 (228)
T KOG4029|consen  105 QTSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL  172 (228)
T ss_pred             chhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence            4556777888999999999999999999999964   5799999999999999999998877666443

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.70  E-value=2.8e-05  Score=75.82  Aligned_cols=59  Identities=27%  Similarity=0.456  Sum_probs=51.2

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKVQ   99 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~v~   99 (333)
                      .++-||.--|-.||||=.-||..|..||.|||.. ..|++||.||..+.+||..|+.+..
T Consensus        56 erRmRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt  115 (373)
T KOG0561|consen   56 ERRMRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKT  115 (373)
T ss_pred             HHHHHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccc
Confidence            3445677778889999999999999999999976 4699999999999999999976443

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.44  E-value=0.00011  Score=75.69  Aligned_cols=61  Identities=18%  Similarity=0.290  Sum_probs=52.0

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQKY  101 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~~L  101 (333)
                      |...||...++.||-|-..||+.|++|..+.--.   ++.-.|.-||..||.-|-.|++||++-
T Consensus       522 REkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  522 REKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            5667899999999999999999999998876432   345569999999999999999999853

>PLN03217 transcription factor ATBS1; Provisional

Probab=96.49  E-value=0.0047  Score=50.55  Aligned_cols=52  Identities=19%  Similarity=0.387  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHhccCCCC-----CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhccc
Q 019960           57 RSKINERFQILREIIPHS-----DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDW  108 (333)
Q Consensus        57 R~rINe~f~~LrsLVP~~-----~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l  108 (333)
                      -+.|++.+..|+.|+|..     ..|..-+-+|.++..||+.|+.+|..|....-++
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~L   75 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSEL   75 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999964     2366777899999999999999999999876443

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=95.35  E-value=0.007  Score=54.36  Aligned_cols=54  Identities=30%  Similarity=0.435  Sum_probs=48.3

Q ss_pred             cccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHH
Q 019960           44 VIRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEK   97 (333)
Q Consensus        44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~   97 (333)
                      ..|..|++.||+|-..+|+.|..||.+||.. ..|.+|+-.|.-|-.||-+|=.-
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v  131 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV  131 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence            4677899999999999999999999999976 46999999999999999998543

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

Probab=93.68  E-value=0.068  Score=51.17  Aligned_cols=56  Identities=29%  Similarity=0.423  Sum_probs=49.7

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQE   96 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~   96 (333)
                      ....+|.+-|..||+|=-.+|+.|..||.+||..  +.|+.|+..|.-|-.||..|++
T Consensus        68 ~~~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~  125 (254)
T KOG3898|consen   68 ALTLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE  125 (254)
T ss_pred             hhhhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence            4566788889999999999999999999999943  6899999999999999998874

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

Probab=91.78  E-value=0.12  Score=55.80  Aligned_cols=50  Identities=30%  Similarity=0.438  Sum_probs=42.6

Q ss_pred             cccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHH
Q 019960           44 VIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQY   93 (333)
Q Consensus        44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~   93 (333)
                      .||++-.-+-|.||.|-|+-|.+|..+||-.   ...+|||+|+.-||-|++-
T Consensus        45 ~rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   45 LRKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             HHhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            3466666778999999999999999999942   4689999999999999974

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

Probab=89.40  E-value=0.52  Score=45.66  Aligned_cols=56  Identities=27%  Similarity=0.317  Sum_probs=49.6

Q ss_pred             ccccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHH
Q 019960           43 SVIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        43 ~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      ..+|..-+..||+|=..+|..|..||..||..  +.|++|-..|.-|-.||--|-..+
T Consensus       172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l  229 (285)
T KOG4395|consen  172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL  229 (285)
T ss_pred             HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence            35677888999999999999999999999975  689999999999999998886554

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

Probab=87.47  E-value=0.16  Score=54.84  Aligned_cols=76  Identities=21%  Similarity=0.271  Sum_probs=60.1

Q ss_pred             cccccccCchHHHHHHHHHHHHHHHHhccCCCC----CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCcccccc
Q 019960           42 ASVIRSKHSVTEQRRRSKINERFQILREIIPHS----DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMP  117 (333)
Q Consensus        42 ~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~----~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~~~l~p  117 (333)
                      ...+...|+-+|++||.+|+-+|..|-.++-+.    ..|+.+..-+...++||-.++.+...+..+...+..+...++.
T Consensus       648 ~k~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr~~~s~~~A  727 (856)
T KOG3582|consen  648 AKNRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKEISELNA  727 (856)
T ss_pred             ccCCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhhhHHHHH
Confidence            446788999999999999999999999988754    3588888889999999999987776666555555555544443

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=85.59  E-value=0.69  Score=49.13  Aligned_cols=39  Identities=26%  Similarity=0.473  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHH
Q 019960           54 QRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQ   92 (333)
Q Consensus        54 RrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk   92 (333)
                      +|-|+|+|.-+..|.+|+|-.   ..|+||.+||.-++.|++
T Consensus        34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            566899999999999999964   479999999999999987

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=84.34  E-value=0.99  Score=46.60  Aligned_cols=44  Identities=25%  Similarity=0.357  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHH
Q 019960           51 VTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYL   94 (333)
Q Consensus        51 ~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~L   94 (333)
                      -+-|.||++-|..|.+|..++|-.   ...+||++|+.-+..|||.-
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            456889999999999999999954   45799999999999999854

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	333
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	7e-18
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	5e-12
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	5e-12
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	5e-12
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-10
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	5e-07
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	1e-04
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	5e-04

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

 Score = 76.3 bits (188), Expect = 7e-18
 Identities = 17/57 (29%), Positives = 37/57 (64%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE 102
           R+ H+  E+R RS IN++   L++++  ++ K + ++ L + I+Y+++LQ   QK +
Sbjct: 7   RTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLK 63

>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 = 59.7 bits (145), Expect = 5e-12
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIP-----HSDQKRDTASFLLEVIEYVQYLQEKVQK 100
           R++H+  E+RRR KIN     L +IIP      +   +     L +  +Y+Q L++   +
Sbjct: 6   RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65

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

 Score = 60.1 bits (146), Expect = 5e-12
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIPH-SDQKRDTASFLLEVIEYVQYLQEKVQKYEVS 104
           R+ H+  E++RR  I + F  LR+ +P    +K   A  L +  EY+QY++ K   ++  
Sbjct: 3   RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD 62

Query: 105 YQDWSAEPTKLM 116
             D   +   L 
Sbjct: 63  IDDLKRQNALLE 74

>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 = 60.0 bits (146), Expect = 5e-12
 Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 30  NSNAKDGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPH-SDQKRDTASFLLEVI 88
           N + +   ++DK    R+ H+  E++RR  I + F  LR+ +P    +K   A  L +  
Sbjct: 1   NDDIEVESDADK----RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKAT 56

Query: 89  EYVQYLQEKVQKYE 102
           EY+QY++ K   ++
Sbjct: 57  EYIQYMRRKNHTHQ 70

>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 = 56.6 bits (137), Expect = 1e-10
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 6/69 (8%)

Query: 36  GKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIP--HSDQKRDTASFLLEVIEYVQY 93
           G  + K    R  H+V E++RR+++   F  LR+ IP   +++K      L +   Y+  
Sbjct: 1   GHMNVK----RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILS 56

Query: 94  LQEKVQKYE 102
           +Q + QK  
Sbjct: 57  VQAEEQKLI 65

>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 = 5e-07
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIP--HSDQKRDTASFLLEVIEYVQYLQEKVQKYEV 103
           RS H+  E+ RR+ +    + L+ ++P      +  T S L +   +++ L++  +K   
Sbjct: 2   RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH 61

Query: 104 SYQDWSAEPTKL 115
                  E   L
Sbjct: 62  QIDQLQREQRHL 73

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

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 46  RSKHSVTEQRRRSKINERFQIL-REIIPH--SDQKRDTASFLLEVIEYVQYLQEKVQKYE 102
           R+ H+  E++RR  INE F+ L R    H  SD+ +     L + ++ +  L+++V++  
Sbjct: 6   RAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN 65

Query: 103 VS 104
           ++
Sbjct: 66  LN 67

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

 Score = 40.8 bits (95), Expect = 5e-04
 Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 9/97 (9%)

Query: 35  DGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHSD---QKRDTASFLLEVIEYV 91
             ++  +    R  HS  E+RRR K+N     L  ++P  +   +K D  + L   ++++
Sbjct: 3   YAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHM 62

Query: 92  QYLQEKVQKY-EVSYQDWSAEPTKLMPWRNSHWRVQN 127
                K  +     Y + + +PT L      H  ++ 
Sbjct: 63  -----KTLRGATNPYTEANYKPTFLSDDELKHLILRA 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	333
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.69
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.65
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.63
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.6
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.59
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.59
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.57
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.56
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.52
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.48
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.47
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.3
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.26
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.05
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.9
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.8
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.75
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.42

>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=99.69  E-value=1.5e-17  Score=131.44  Aligned_cols=68  Identities=25%  Similarity=0.443  Sum_probs=62.8

Q ss_pred             ccccccCchHHHHHHHHHHHHHHHHhccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHhhhccccc
Q 019960           43 SVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSA  110 (333)
Q Consensus        43 ~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~  110 (333)
                      ..+|.+|+++||+||++||++|.+|++|||+++.|+||++||.+||+||++||.+++.|+.+...+..
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   71 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45789999999999999999999999999998789999999999999999999999999988766543

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

Probab=99.65  E-value=1.7e-16  Score=133.30  Aligned_cols=71  Identities=27%  Similarity=0.459  Sum_probs=53.0

Q ss_pred             CCCCCcccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHHHHHhhh
Q 019960           35 DGKNSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQKYEVSY  105 (333)
Q Consensus        35 ~g~~~~k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~  105 (333)
                      +.+...+...+|.+|+++||+||++||++|.+|++|||.+   +.|++|++||..||+||++||.+++.|+...
T Consensus        17 ~~~~~~k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~   90 (118)
T 4ati_A           17 EARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLE   90 (118)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             hHHHHhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3333446777899999999999999999999999999987   3589999999999999999999999998653

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

Probab=99.63  E-value=1.5e-16  Score=123.29  Aligned_cols=63  Identities=22%  Similarity=0.352  Sum_probs=58.1

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHh
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEV  103 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~  103 (333)
                      +...+|.+|+++||+||++||++|.+|+.|||.+..|+||++||..||+||++||.++.-|+.
T Consensus         4 k~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~~   66 (71)
T 4h10_B            4 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLEH   66 (71)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             hhhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHHh
Confidence            456789999999999999999999999999998767999999999999999999999887763

>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=99.60  E-value=5e-16  Score=121.71  Aligned_cols=69  Identities=28%  Similarity=0.489  Sum_probs=62.9

Q ss_pred             cccccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhccccc
Q 019960           42 ASVIRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSA  110 (333)
Q Consensus        42 ~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~  110 (333)
                      ...+|..|+..||+||.+||++|..|+.+||.+ ..|++|++||..||+||++|+.+++.|+.+.+.+..
T Consensus         9 ~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~~   78 (80)
T 1hlo_A            9 DADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   78 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             hHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            345789999999999999999999999999986 469999999999999999999999999998876653

>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=99.59  E-value=3.7e-16  Score=122.96  Aligned_cols=69  Identities=28%  Similarity=0.506  Sum_probs=62.5

Q ss_pred             ccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCcc
Q 019960           45 IRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPT  113 (333)
Q Consensus        45 rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~~  113 (333)
                      +|..|+..||+||.+||++|..|+++||.+ ..|++|++||..||+||++|+.+++.|+.+.+.+..+..
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~~   71 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQNA   71 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            578999999999999999999999999985 579999999999999999999999999988777765543

>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=99.59  E-value=4.7e-16  Score=117.20  Aligned_cols=56  Identities=32%  Similarity=0.494  Sum_probs=51.3

Q ss_pred             ccccccCchHHHHHHHHHHHHHHHHhccCCCCC-----CCCChhhhhHHHHHHHHHHHHHH
Q 019960           43 SVIRSKHSVTEQRRRSKINERFQILREIIPHSD-----QKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        43 ~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~-----~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      ..+|..|+++||+||++||++|.+|+.|||.+.     .|++|++||..||+||++||.++
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999999883     37899999999999999999764

>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=99.57  E-value=5.9e-16  Score=117.06  Aligned_cols=54  Identities=24%  Similarity=0.372  Sum_probs=49.5

Q ss_pred             ccccCchHHHHHHHHHHHHHHHHhccCCCC------CCCCChhhhhHHHHHHHHHHHHHH
Q 019960           45 IRSKHSVTEQRRRSKINERFQILREIIPHS------DQKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        45 rr~~H~~~ERrRR~rINe~f~~LrsLVP~~------~~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      +|.+|+++||+||++||.+|.+|+.|||.+      ..+++||+||+.||+||++||+++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999965      357889999999999999999765

>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=99.56  E-value=1.2e-15  Score=122.15  Aligned_cols=70  Identities=26%  Similarity=0.360  Sum_probs=61.3

Q ss_pred             ccccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCc
Q 019960           43 SVIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEP  112 (333)
Q Consensus        43 ~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~  112 (333)
                      ..+|..|++.||+||.+||++|..|+.+||.+  ..|++|++||.+||+||++|+.+.+.+....+.+..+.
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~n   75 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKRR   75 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34788999999999999999999999999986  36999999999999999999999998877665554443

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

Probab=99.52  E-value=1.8e-15  Score=117.61  Aligned_cols=56  Identities=27%  Similarity=0.409  Sum_probs=51.5

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQE   96 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~   96 (333)
                      +...+|.+|+++||+||++||+.|.+|+.|||.|   ..|+||++||+.||+||+.|+.
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            4567899999999999999999999999999976   3799999999999999999974

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

Probab=99.48  E-value=1.1e-14  Score=113.99  Aligned_cols=60  Identities=23%  Similarity=0.376  Sum_probs=49.7

Q ss_pred             cccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCC-ChhhhhHHHHHHHHHHHHHHHHHHh
Q 019960           44 VIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKR-DTASFLLEVIEYVQYLQEKVQKYEV  103 (333)
Q Consensus        44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~-DKasIL~~AIeYIk~Lq~~v~~Le~  103 (333)
                      .+|..|++.||+||..||++|.+|+.+||.+  ..|. +|+.||..||+||++||+++++++.
T Consensus         4 ~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             hHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            5789999999999999999999999999953  2354 7999999999999999999998774

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

Probab=99.47  E-value=2.5e-14  Score=112.78  Aligned_cols=67  Identities=21%  Similarity=0.321  Sum_probs=59.9

Q ss_pred             cccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCc
Q 019960           46 RSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEP  112 (333)
Q Consensus        46 r~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~  112 (333)
                      |..|+..||+||..||++|..|+++||.+  ..|.+|+.||..||+||+.|+.+.+.|..+.+.+..+.
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e~   70 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQ   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999999999999965  47999999999999999999999999988877665443

>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=99.30  E-value=1.5e-12  Score=99.96  Aligned_cols=57  Identities=28%  Similarity=0.421  Sum_probs=52.1

Q ss_pred             cccccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHHH
Q 019960           42 ASVIRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        42 ~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      ...+|..|+..||+|+..||+.|..||.+||.. +.|++|+.||..||+||.+|++.+
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            445788899999999999999999999999975 579999999999999999999764

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

Probab=99.26  E-value=3.7e-12  Score=95.43  Aligned_cols=55  Identities=25%  Similarity=0.318  Sum_probs=50.5

Q ss_pred             ccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960           45 IRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQ   99 (333)
Q Consensus        45 rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~   99 (333)
                      +|..|+..||+|+..||+.|..||.+||..  +.|++|+.||..||+||.+|++.++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            577899999999999999999999999975  5799999999999999999998653

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

Probab=99.05  E-value=1.1e-10  Score=111.47  Aligned_cols=57  Identities=23%  Similarity=0.413  Sum_probs=43.2

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCCCCCCChhhhhHHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEK   97 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K~DKasIL~~AIeYIk~Lq~~   97 (333)
                      +...+|..|+.+||+||++||+.|.+|+.|||....|+||++||..||+||+.|+..
T Consensus         8 ~~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A            8 KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             -----------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             ccchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            566789999999999999999999999999995568999999999999999999864

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

Probab=98.90  E-value=5.6e-10  Score=108.06  Aligned_cols=56  Identities=27%  Similarity=0.409  Sum_probs=49.9

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQE   96 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~   96 (333)
                      +...+|.+|+.+||+||++||+.|.+|+.|||.+   ..|+||++||..||+|||.|+.
T Consensus         9 ~~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B            9 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hhhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            5567899999999999999999999999999953   4799999999999999999974

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

Probab=98.80  E-value=9.8e-10  Score=84.40  Aligned_cols=48  Identities=23%  Similarity=0.340  Sum_probs=43.4

Q ss_pred             CchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHH
Q 019960           49 HSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQE   96 (333)
Q Consensus        49 H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~   96 (333)
                      -+..||+|...||+.|..||.+||..  +.|++|+.||..||+||..||.
T Consensus        18 a~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           18 AAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CBCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            34568999999999999999999976  6799999999999999999984

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

Probab=98.75  E-value=1e-08  Score=81.46  Aligned_cols=49  Identities=29%  Similarity=0.473  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHHHHHhh
Q 019960           56 RRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQKYEVS  104 (333)
Q Consensus        56 RR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~  104 (333)
                      -|.+||++|.+|..|||.+   +.|++|++||..+|+||++||..++.+...
T Consensus         3 ~R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~   54 (83)
T 4ath_A            3 MRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   54 (83)
T ss_dssp             CHHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHH
T ss_pred             chhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3899999999999999975   468999999999999999999877765543

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

Probab=98.42  E-value=3.8e-07  Score=74.40  Aligned_cols=50  Identities=22%  Similarity=0.344  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHHHHH
Q 019960           53 EQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQKYE  102 (333)
Q Consensus        53 ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~~Le  102 (333)
                      ||.|-..||+.|..||.+||..  ++|++|+.+|..||+||.+|+..++.-.
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~   84 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHL   84 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            5778889999999999999975  6899999999999999999998776533

---

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	333
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-12
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	3e-12
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	3e-12
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	5e-12
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	7e-12
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	8e-12
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	2e-11
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	5e-11

>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 = 59.9 bits (145), Expect = 1e-12
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 6/60 (10%)

Query: 46 RSKHSVTEQRRRSKINERFQILREIIP------HSDQKRDTASFLLEVIEYVQYLQEKVQ 99
          R  H   EQ RR+++      L  +IP      +       A+ +     Y+++LQ+   
Sbjct: 3  RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

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

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

 Score = 59.9 bits (145), Expect = 3e-12
 Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIPH--SDQKRDTASFLLEVIEYVQYLQEKVQKYE 102
           R  H+V E++RR+++   F  LR+ IP   +++K      L +   Y+  +Q + QK  
Sbjct: 7   RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLI 65

>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 = 59.0 bits (143), Expect = 3e-12
 Identities = 14/46 (30%), Positives = 27/46 (58%)

Query: 57  RSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE 102
           RS IN++   L++++  +D K   +  L + I+Y++YLQ+   K  
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLR 46

>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 = 58.7 bits (142), Expect = 5e-12
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKVQKYEVS 104
           R+ H+  E++RR  I + F  LR+ +P    +K   A  L +  EY+QY++ K   ++  
Sbjct: 3   RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD 62

Query: 105 YQDWSAEPTKL 115
             D   +   L
Sbjct: 63  IDDLKRQNALL 73

>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 = 58.0 bits (140), Expect = 7e-12
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 46 RSKHSVTEQRRRSKINERFQILREIIPHSDQKR-DTASFLLEVIEYVQYLQEKVQ 99
          R   ++ E+RR SK+NE F+ L+     +  +R      L   I Y++ LQ  ++
Sbjct: 13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR 67

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

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

 Score = 57.9 bits (140), Expect = 8e-12
 Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIPHS-----DQKRDTASFLLEVIEYVQYLQEKVQK 100
           R++H+  E+RRR KIN     L +IIP S        +     L +  +Y+Q L++   +
Sbjct: 6   RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNHR 65

>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 = 2e-11
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQKYEV 103
           RS H+  E+ RR+ +    + L+ ++P      +  T S L +   +++ L++  +K   
Sbjct: 2   RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH 61

Query: 104 SYQDWSAEPTKLM 116
                  E   L 
Sbjct: 62  QIDQLQREQRHLK 74

>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 = 55.7 bits (134), Expect = 5e-11
 Identities = 17/57 (29%), Positives = 37/57 (64%)

Query: 46  RSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYE 102
           R+ H+  E+R RS IN++   L++++  ++ K + ++ L + I+Y+++LQ   QK +
Sbjct: 7   RTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLK 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	333
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.56
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.56
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.55
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.55
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.48
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.42

>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=99.62  E-value=1.3e-16  Score=123.07  Aligned_cols=66  Identities=26%  Similarity=0.452  Sum_probs=60.9

Q ss_pred             cccccCchHHHHHHHHHHHHHHHHhccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccc
Q 019960           44 VIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWS  109 (333)
Q Consensus        44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~  109 (333)
                      .+|..|+.+||+||++||++|..|++|||++..|++|++||..||+||++|+.+++.|..+...+.
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk   70 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467889999999999999999999999999878999999999999999999999999998766543

>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=99.57  E-value=5.6e-16  Score=118.92  Aligned_cols=67  Identities=21%  Similarity=0.321  Sum_probs=60.0

Q ss_pred             cccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCc
Q 019960           46 RSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEP  112 (333)
Q Consensus        46 r~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~  112 (333)
                      |..|+..||+||++||++|.+|+++||.+  ..|++|++||..||+||++|+.+++.|..+.+.+..+.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~~   70 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQREQ   70 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            57899999999999999999999999975  46899999999999999999999999988876665443

>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=99.56  E-value=7.2e-16  Score=114.17  Aligned_cols=54  Identities=24%  Similarity=0.372  Sum_probs=49.6

Q ss_pred             ccccCchHHHHHHHHHHHHHHHHhccCCCC------CCCCChhhhhHHHHHHHHHHHHHH
Q 019960           45 IRSKHSVTEQRRRSKINERFQILREIIPHS------DQKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        45 rr~~H~~~ERrRR~rINe~f~~LrsLVP~~------~~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      +|..|+.+||+||++||++|.+|+.|||.+      ..|++|+.||+.||+||++||+++
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            578999999999999999999999999952      479999999999999999999764

>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=99.56  E-value=5.6e-16  Score=119.94  Aligned_cols=67  Identities=28%  Similarity=0.523  Sum_probs=60.2

Q ss_pred             ccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccC
Q 019960           45 IRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAE  111 (333)
Q Consensus        45 rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e  111 (333)
                      +|..|+..||+||++||+.|..|+++||.+ +.|++|++||..||+||++|+.+++.|....+.+..+
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~   69 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQ   69 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999975 5799999999999999999999999888776655443

>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=99.55  E-value=7.4e-16  Score=115.98  Aligned_cols=59  Identities=27%  Similarity=0.416  Sum_probs=52.9

Q ss_pred             ccccccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960           41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKVQ   99 (333)
Q Consensus        41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~v~   99 (333)
                      ....+|..|+..||+||.+||++|..|+.|||.+ ..|++|++||..||+||++||+.++
T Consensus         8 ~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_           8 TNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            3445788999999999999999999999999987 4689999999999999999997664

>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=99.55  E-value=6.3e-16  Score=120.85  Aligned_cols=70  Identities=26%  Similarity=0.361  Sum_probs=61.5

Q ss_pred             cccccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccC
Q 019960           42 ASVIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAE  111 (333)
Q Consensus        42 ~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e  111 (333)
                      ...+|..|+.+||+||++||+.|..|+++||++  ..|++|++||..||+||++|+.+++.|....+.+..+
T Consensus         3 ~~~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~   74 (88)
T d1nkpa_           3 MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKR   74 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            346788999999999999999999999999975  4689999999999999999999999988776655433

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

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

Probab=99.48  E-value=5.4e-15  Score=110.00  Aligned_cols=55  Identities=33%  Similarity=0.502  Sum_probs=50.1

Q ss_pred             cccccCchHHHHHHHHHHHHHHHHhccCCCC-----CCCCChhhhhHHHHHHHHHHHHHH
Q 019960           44 VIRSKHSVTEQRRRSKINERFQILREIIPHS-----DQKRDTASFLLEVIEYVQYLQEKV   98 (333)
Q Consensus        44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-----~~K~DKasIL~~AIeYIk~Lq~~v   98 (333)
                      .+|..|+.+||+||++||+.|.+|++|||.+     ..|++|+.||..||+||++||++.
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            4688999999999999999999999999965     359999999999999999998754

>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=99.42  E-value=2.4e-14  Score=105.43  Aligned_cols=53  Identities=26%  Similarity=0.440  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHhccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccc
Q 019960           57 RSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWS  109 (333)
Q Consensus        57 R~rINe~f~~LrsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~  109 (333)
                      |++||++|.+|+++||++..|+|||+||.+||+||++||.+++.|+.++..+.
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~   53 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK   53 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67899999999999999878999999999999999999999999998876554