Citrus Sinensis ID: 014485

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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-------340-------350-------360-------370-------380-------390-------400-------410-------420---
Protein Sequence
MNHCVPDFEFDDDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQPSFPADQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAEDRKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNMGMGIGMGMGMGRAWIWE
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccEEEEEEccccEEEEccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccHHHHHHHHHHcccEEEEcccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccHccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHcccccccccccccccccccccc
Coil and Loop (DISEMBL)
mnhcvpdfefdddhsiptssvlnrprksamaEEDVMELLWqngpvvlhnqnqrslkksqpsfpadqsapreipsshhhqqeqqDHLFMQEDEMAswlhyplndtnfdsdfctdllypapcitstttttatatatppvratrvrdsrpqlntattvasapplrppipppprrtenfglfarhmprevasgpsnsksvtirestvvdssdtpapgpdsrasEAMRsmegasgvnnnnrcrntsgagaaatssgggggssgardltmcemtvtsspggssasaeppaqkpaaedrkrkgretddeyhsedvelesadakkqsrgstsakRSRAAEVHNLSERRRRDRINEKMRALQELIprcnksdkaSMLDEAIEYLKSLQLQVQMMSMgcgvvpmmfpgvqqympnmgmgigmGMGMGRAWIWE
Flexible Loop (DISEMBL)
mnhcvpdfefdddhsiptssvlnrprKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQPSFPADQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCItstttttatatatppvratrvrdsrpqlntattvasapplrppippppRRTENFGLFARHMPrevasgpsnsksvtirestvvdssdtpapgpDSRASEAMRSMEgasgvnnnnrCRNTSGAgaaatssgggggSSGARDLTMCEMTVTSspggssasaeppaqkpaaedrkrkgretddeyhsedvelesadakkqsrgstsakrsraaevhnlserrrrdriNEKMRAlqeliprcnksdkASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNMGMGIGMGMGMGRAWIWE
Low Complexity Region (SEG)
MNHCVPDFEFDDDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQPSFPADQSAPREIPSShhhqqeqqdhLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCITStttttatatatppvratrvrDSRPQLNTATTVASApplrppipppprrTENFGLFARHMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNtsgagaaatssgggggssgaRDLTMCEMTVTsspggssasaeppaQKPAAEDRKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNmgmgigmgmgmgRAWIWE
Disordered region (IsUnstruct)
***********************************MELLWQNGPVVL********************************************EMASWLHYPLNDTNFDSDFCTDLLYPAPCITSTTTTT***********************************************************************************************************************************************************************************************************************************************LDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNMGMGIGMGMGMGRAWIW*
Disordered Region (DISOPRED)
**HCVPDFEFDDDH*****************EEDVMELLWQN************************************************************************LY*************************************************************************************************************************************************************************************************************************************NEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGV**MMFPG*************************
Disordered Region (DISEMBL)
MNHCVPDFEFDDDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQ*********************************DHLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPRE******************************************ASGVNNNNRCRNT******************ARDLTMCEMT*********************************************************************ERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNMGMGIGMGMGMGRAWIWE
Disordered Region (DISPRO)
***********DDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQ*********************************DHLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPC****************************************************************************************************************************************************************************************************************************RRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNMGMG**************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNHCVPDFEFDDDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQPSFPADQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAEDRKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNMGMGIGMGMGMGRAWIWE
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	423	2.2.26 [Sep-21-2011]
Q8GZM7	478	Transcription factor PIF1	yes	no	0.834	0.738	0.481	2e-72
Q9SVU7	445	Putative transcription fa	no	no	0.699	0.665	0.379	1e-40
Q9SVU6	413	Transcription factor bHLH	no	no	0.775	0.794	0.354	3e-40
O80536	524	Transcription factor PIF3	no	no	0.323	0.261	0.590	2e-36
Q8GT73	544	Transcription factor bHLH	no	no	0.817	0.636	0.356	2e-29
Q8L5W8	416	Transcription factor PIL1	no	no	0.281	0.286	0.526	4e-27
Q84LH8	444	Transcription factor PIF5	no	no	0.293	0.279	0.564	1e-26
Q9FUA4	373	Transcription factor SPAT	no	no	0.165	0.187	0.736	3e-23
Q7XHI7	307	Transcription factor bHLH	no	no	0.182	0.250	0.542	1e-22
Q9FHA2	210	Transcription factor ALC	no	no	0.179	0.361	0.641	2e-21

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

 Score =  273 bits (698), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 205/426 (48%), Positives = 256/426 (60%), Gaps = 73/426 (17%)

Query: 1   MNHCVPDFEFDDDHSIPTSSVLNR-PRKS--AMAEED-VMELLWQNGPVVLHNQNQRSLK 56
           M+H VPDF+ DDD+    +S LN  PRKS   M E+D +MELLWQNG VV+  QNQR L 
Sbjct: 1   MHHFVPDFDTDDDYVNNHNSSLNHLPRKSITTMGEDDDLMELLWQNGQVVV--QNQR-LH 57

Query: 57  KSQPSFPADQSAPREIPSSHHHQQEQQD-HLFMQEDEMASWLHYPLNDTNFDSDFCTDLL 115
             +PS     S P+ +PS    QQ   D +LF+QEDEM SWLHYPL D     DFC+DLL
Sbjct: 58  TKKPS----SSPPKLLPSMDPQQQPSSDQNLFIQEDEMTSWLHYPLRD----DDFCSDLL 109

Query: 116 YPAPCITSTTTTTATATAT-PPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTEN 174
           + A    + T T +  TA  PPV              ++T  S PP+R           N
Sbjct: 110 FSAAPTATATATVSQVTAARPPV--------------SSTNESRPPVR-----------N 144

Query: 175 FGLFAR-----HMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGAS 229
           F  F+R     +  R   SGP  SK+V +REST V  S TP+    + ASE        S
Sbjct: 145 FMNFSRLRGDFNNGRGGESGPLLSKAV-VRESTQVSPSATPS----AAASE--------S 191

Query: 230 GVNNNNRCRNTSGAGAAATSSGGG---GGSSGARDLTMCEMTVTSSPGGSSASAEPPAQK 286
           G+      R T G  ++A + GG     G + A      E+T TSS   S +  EP  +K
Sbjct: 192 GL-----TRRTDGTDSSAVAGGGAYNRKGKAVAMTAPAIEITGTSSSVVSKSEIEP--EK 244

Query: 287 PAAEDRKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRIN 346
              +DRKRK RE      +++ E  S + K+    +TS KRSRAAEVHNLSER+RRDRIN
Sbjct: 245 TNVDDRKRKEREATT---TDETESRSEETKQARVSTTSTKRSRAAEVHNLSERKRRDRIN 301

Query: 347 EKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMPNM 406
           E+M+ALQELIPRCNKSDKASMLDEAIEY+KSLQLQ+QMMSMGCG++PMM+PG+QQYMP+M
Sbjct: 302 ERMKALQELIPRCNKSDKASMLDEAIEYMKSLQLQIQMMSMGCGMMPMMYPGMQQYMPHM 361

Query: 407 GMGIGM 412
            MG+GM
Sbjct: 362 AMGMGM 367

Transcription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA).
Arabidopsis thaliana (taxid: 3702)

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

 Score =  167 bits (423), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 149/393 (37%), Positives = 194/393 (49%), Gaps = 97/393 (24%)

Query: 32  EEDVMELLWQNGPVVLHNQNQRS------LKKSQPSFPADQSAPREIPSSHHHQQEQQDH 85
           E+D++ELLWQ+G VV  NQ  R       + +   S   +++AP   P  H HQQ    +
Sbjct: 19  EDDIVELLWQSGQVVGTNQTHRQSYDPPPILRGSGSGRGEENAPLSQPPPHLHQQ----N 74

Query: 86  LFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCITSTTTTTATATATPPVRATRVRDS 145
           LF+QE EM SWLH+     N+   FC++LL   P             AT P        S
Sbjct: 75  LFIQEGEMYSWLHHSYRQ-NY---FCSELLNSTP-------------ATHP-------QS 110

Query: 146 RPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMP------REVASGPSNSKSVTIR 199
              L    T+A+            RR ENF  F+          R   +GPS S    +R
Sbjct: 111 SISLAPRQTIAT------------RRAENFMNFSWLRGNIFTGGRVDEAGPSFS---VVR 155

Query: 200 ESTVVDSSDTPAPGPDSRASEA--MRSMEG-ASGVNNNNRCRNTSGAGAAATSSGGGGGS 256
           ES  V S+ TP   P S A+E+  + + EG AS V+      +    G A      G  S
Sbjct: 156 ESMQVGSNTTP---PSSSATESCVIPATEGTASRVSGTLAAHDLGRKGKAVAVEAAGTPS 212

Query: 257 SGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAEDRKRKGRETDDEYHSEDVELESADAK 316
           SG     +C+           A  EP   +PA E  K K RE   E H            
Sbjct: 213 SG-----VCK-----------AETEPVQIQPATES-KLKARE---ETH----------GT 242

Query: 317 KQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLK 376
           +++RGSTS KRSR AE+HNL+ERRRR++INEKM+ LQ+LIPRCNKS K S LD+AIEY+K
Sbjct: 243 EEARGSTSRKRSRTAEMHNLAERRRREKINEKMKTLQQLIPRCNKSTKVSTLDDAIEYVK 302

Query: 377 SLQLQVQMMSMGCGVVPMMFPG-VQQYMPNMGM 408
           SLQ Q+Q M     + PMM  G  QQ+MP+M M
Sbjct: 303 SLQSQIQGM-----MSPMMNAGNTQQFMPHMAM 330

Arabidopsis thaliana (taxid: 3702)

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

 Score =  166 bits (421), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 145/409 (35%), Positives = 194/409 (47%), Gaps = 81/409 (19%)

Query: 22  LNRPRKSAMAEEDVMELLWQNGPVVLHNQNQR-------SLKKSQPSFPADQSAPREIPS 74
           L  P K  M E+D++ELL ++  VV  +Q Q         L+ S            + P 
Sbjct: 14  LISPEKYIMGEDDIVELLGKSSQVVTSSQTQTPSCDPPLILRGSGSGDGEGNGPLPQPPP 73

Query: 75  SHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCITSTTTTTATATAT 134
             +HQQ     LF+QEDEMASWLH P    N      + LLY     ++   + A+    
Sbjct: 74  PLYHQQS----LFIQEDEMASWLHQP----NRQDYLYSQLLYSG-VASTHPQSLASLEPP 124

Query: 135 PPVRATRVRDS-RPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPREVASG---- 189
           PP RA  +  + RP   T   +A             RR ENF   +R        G    
Sbjct: 125 PPPRAQYILAADRP---TGHILAE------------RRAENFMNISRQRGNIFLGGVEAV 169

Query: 190 PSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAAATS 249
           PSN        ST++ S+    P                    +    R T   G + T 
Sbjct: 170 PSN--------STLLSSATESIPA------------------THGTESRATVTGGVSRTF 203

Query: 250 SGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAE-----DRKRKGRETDDEYH 304
           +  G G  G       E   T S G   A  EP  ++PA E     +RKRK RE   E +
Sbjct: 204 AVPGLGPRG--KAVAIETAGTQSWGLCKAETEPVQRQPATETDITDERKRKTRE---ETN 258

Query: 305 SEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDK 364
            E+         +++R STS+KRSRAA +H LSERRRR +INE M+ALQEL+PRC K+D+
Sbjct: 259 VEN------QGTEEARDSTSSKRSRAAIMHKLSERRRRQKINEMMKALQELLPRCTKTDR 312

Query: 365 ASMLDEAIEYLKSLQLQVQMMSMGCGVV-PMMFPG--VQQYMPNMGMGI 410
           +SMLD+ IEY+KSLQ Q+QM SMG  ++ PMM+ G   QQYMP+M MG+
Sbjct: 313 SSMLDDVIEYVKSLQSQIQMFSMGHVMIPPMMYAGNIQQQYMPHMAMGM 361

Arabidopsis thaliana (taxid: 3702)

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

 Score =  154 bits (388), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 85/144 (59%), Positives = 100/144 (69%), Gaps = 7/144 (4%)

Query: 266 EMTVTSSPGGSSASAEPPAQKPAAEDRKRKGRETDDEYHSEDVELESADAKKQ---SRGS 322
           E  V  S  GS  S + P++ P+   +++     D + HSEDVE ES D +K+   SR  
Sbjct: 277 EKAVVCSSVGSGNSLDGPSESPSLSLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPSRTG 336

Query: 323 TSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQV 382
             +KRSR+AEVHNLSERRRRDRINEKMRALQELIP CNK DKASMLDEAIEYLKSLQLQV
Sbjct: 337 LGSKRSRSAEVHNLSERRRRDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKSLQLQV 396

Query: 383 QMMSMGCGVV---PMMF-PGVQQY 402
           Q+MSM  G      +MF PG+  Y
Sbjct: 397 QIMSMASGYYLPPAVMFPPGMGHY 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|Q8GT73|BH119_ARATH Transcription factor bHLH119 OS=Arabidopsis thaliana GN=BHLH119 PE=2 SV=2

 Score =  130 bits (328), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 146/410 (35%), Positives = 200/410 (48%), Gaps = 64/410 (15%)

Query: 17  PTSSV-LNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQPSFPADQSAPRE---- 71
           P SSV L  P   A +E+DV+ELLW++G VV   Q QR +    P F    S   E    
Sbjct: 92  PQSSVSLPPPPPIAPSEDDVVELLWKSGQVVQSIQTQRPIPP--PIFRGSGSGGGEETVL 149

Query: 72  -IPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDFCTDLLYPAPCITSTTTTTAT 130
            +P  H   Q    ++F+QEDEMASWL++PL    F S            + ST+ T   
Sbjct: 150 PLPPLHPSHQ----NIFIQEDEMASWLYHPLRQDYFSSG-----------VASTSATRPQ 194

Query: 131 ATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPREVASGP 190
           ++A+             Q+                 P  RRTENF  F R      + G 
Sbjct: 195 SSASLAPTPPPPSVPYGQI-----------------PVERRTENFMNFLRLRGNIFSGGR 237

Query: 191 SNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAAATSS 250
             +  V I EST + SS             +  +        +    R  +  G + T +
Sbjct: 238 VEAGPVVI-ESTQIGSSA---------TPSSSAAESCVIPATHGTESRAAAITGVSRTFA 287

Query: 251 GGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAEDRKRKGRETDDEYHSEDVEL 310
             G G  G    T  E   TS  G + A  E    +P     +R+ + T+D+   E +  
Sbjct: 288 VPGLGRRGKEVAT--ETAGTSYSGVNKAETERVQIQP-----ERETKITEDKKREETIA- 339

Query: 311 ESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDE 370
                 +++ GSTS KRSRAA++HNLSERRRR+RINE+M+ LQEL+PRC K+DK SML++
Sbjct: 340 -EIQGTEEAHGSTSRKRSRAADMHNLSERRRRERINERMKTLQELLPRCRKTDKVSMLED 398

Query: 371 AIEYLKSLQLQVQMMSMGCGVVPMMFP--GVQQYMPNMGMGIGMGMGMGR 418
            IEY+KSLQLQ+QMMSMG G++P M      QQ+MP+M MG+    GM R
Sbjct: 399 VIEYVKSLQLQIQMMSMGHGMMPPMMHEGNTQQFMPHMAMGM---KGMNR 445

Arabidopsis thaliana (taxid: 3702)

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

 Score =  122 bits (307), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 69/131 (52%), Positives = 88/131 (67%), Gaps = 12/131 (9%)

Query: 293 KRKGRETDDE---YHSEDVELESADAKKQSRGSTS---AKRSRAAEVHNLSERRRRDRIN 346
           KRK  + ++E   Y S + + ES DAK Q    T     KR R+ EVH L ER+RRD  N
Sbjct: 187 KRKYGDIEEEESTYLSNNSDDESDDAKTQVHARTRKPVTKRKRSTEVHKLYERKRRDEFN 246

Query: 347 EKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVV--PMMFPGVQQYMP 404
           +KMRALQ+L+P C K DKAS+LDEAI+Y+++LQLQVQMMSMG G++  P M P +  Y P
Sbjct: 247 KKMRALQDLLPNCYKDDKASLLDEAIKYMRTLQLQVQMMSMGNGLIRPPTMLP-MGHYSP 305

Query: 405 NMGMGIGMGMG 415
              MG+GM MG
Sbjct: 306 ---MGLGMHMG 313

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  121 bits (303), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 79/140 (56%), Positives = 97/140 (69%), Gaps = 16/140 (11%)

Query: 291 DRKRKG-RETDDEYHSE-DVELESAD----AKKQSRGSTSAKRSRAAEVHNLSERRRRDR 344
           DRKRK   + D E  S+ D+ L S D      K S+ S S +RSRAAEVHNLSERRRRDR
Sbjct: 212 DRKRKHVMDADQESVSQSDIGLTSTDDQTMGNKSSQRSGSTRRSRAAEVHNLSERRRRDR 271

Query: 345 INEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVV--------PMMF 396
           INE+M+ALQELIP C+++DKAS+LDEAI+YLKSLQ+Q+Q+M MG G+         PMMF
Sbjct: 272 INERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQLQVMWMGSGMAAAAAAAASPMMF 331

Query: 397 PGVQQ--YMPNMGMGIGMGM 414
           PGVQ   Y+  M M   M +
Sbjct: 332 PGVQSSPYINQMAMQSQMQL 351

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  109 bits (273), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 53/72 (73%), Positives = 60/72 (83%), Gaps = 2/72 (2%)

Query: 329 RAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSM- 387
           RAAEVHNLSE+RRR RINEKM+ALQ LIP  NK+DKASMLDEAIEYLK LQLQVQM++M 
Sbjct: 197 RAAEVHNLSEKRRRSRINEKMKALQSLIPNSNKTDKASMLDEAIEYLKQLQLQVQMLTMR 256

Query: 388 -GCGVVPMMFPG 398
            G  + P+  PG
Sbjct: 257 NGINLHPLCLPG 268

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  107 bits (268), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/94 (54%), Positives = 70/94 (74%), Gaps = 17/94 (18%)

Query: 317 KQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLK 376
           +++RGSTS KRSRAAE+HNL+ERRRR++INE+M+ LQ+LIPRCNKS K SML++ IEY+K
Sbjct: 138 EEARGSTSRKRSRAAEMHNLAERRRREKINERMKTLQQLIPRCNKSTKVSMLEDVIEYVK 197

Query: 377 SLQLQVQMMSMGCGVVPMMFPGVQQYMPNMGMGI 410
           SL++Q                 + Q+MP+M MG+
Sbjct: 198 SLEMQ-----------------INQFMPHMAMGM 214

Arabidopsis thaliana (taxid: 3702)

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

 Score =  103 bits (258), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 50/78 (64%), Positives = 62/78 (79%), Gaps = 2/78 (2%)

Query: 324 SAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQ 383
           S KR+  A+ HNLSE++RR +INEKM+ALQ+LIP  NK+DKASMLDEAIEYLK LQLQVQ
Sbjct: 88  SLKRNIDAQFHNLSEKKRRSKINEKMKALQKLIPNSNKTDKASMLDEAIEYLKQLQLQVQ 147

Query: 384 MMSM--GCGVVPMMFPGV 399
            +++  G G+ PM  P V
Sbjct: 148 TLAVMNGLGLNPMRLPQV 165

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)

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	423
449443927	529	PREDICTED: transcription factor PIF1-lik	0.893	0.714	0.591	1e-106
255560265	572	Phytochrome-interacting factor, putative	0.919	0.680	0.582	1e-105
224069945	615	predicted protein [Populus trichocarpa]	0.905	0.622	0.535	1e-103
359480088	517	PREDICTED: transcription factor PIF1-lik	0.851	0.696	0.555	3e-99
297744279	479	unnamed protein product [Vitis vinifera]	0.761	0.672	0.519	4e-90
356505096	517	PREDICTED: transcription factor PIF1-lik	0.860	0.704	0.515	2e-88
449468728	553	PREDICTED: transcription factor PIF1-lik	0.872	0.667	0.486	1e-83
449515805	549	PREDICTED: transcription factor PIF1-lik	0.862	0.664	0.484	9e-83
356545930	476	PREDICTED: transcription factor PIF1-lik	0.770	0.684	0.493	8e-78
356536868	491	PREDICTED: transcription factor PIF1-lik	0.803	0.692	0.471	7e-73

>gi|449443927|ref|XP_004139727.1| PREDICTED: transcription factor PIF1-like [Cucumis sativus]

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 243/411 (59%), Positives = 280/411 (68%), Gaps = 33/411 (8%)

Query: 1   MNHCVPDFEFDDDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQP 60
           MNHCVPDFE  DD S+PT S L RPRKS++ ++DVMELLWQNG VV H+QNQRS +KS P
Sbjct: 7   MNHCVPDFEMADDFSLPTFSSLTRPRKSSLPDDDVMELLWQNGQVVTHSQNQRSFRKSPP 66

Query: 61  S-----FPADQSAPREI-PSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDFCTDL 114
           S      P +Q+A REI PS+   Q E+   LFMQEDEMASWL+YPL +   D +FC+DL
Sbjct: 67  SKFDVSIPQEQAATREIRPST---QLEEHHELFMQEDEMASWLNYPLVE---DHNFCSDL 120

Query: 115 LYPAPCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTEN 174
           L+PA               T P+ A    D RP   +AT   +  P  P  P      + 
Sbjct: 121 LFPA--------------ITAPLCANPQPDIRP---SATATLTLTPRPPIPPCRRPEVQT 163

Query: 175 FGLFARHMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNN 234
              F+R+    V S PSNSK V +RESTVVDS DTP+ GP+SRASE  R           
Sbjct: 164 SVQFSRNK-ATVESEPSNSK-VMVRESTVVDSCDTPSVGPESRASEMARRKLVEVVNGGG 221

Query: 235 NRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAEDRKR 294
            R     G+     +S GG G  G +++  CEMTVTSSPGGSSASAEP   K A +DRKR
Sbjct: 222 VRYEIARGSDGVRGASVGGDGI-GEKEMMTCEMTVTSSPGGSSASAEPACPKLAVDDRKR 280

Query: 295 KGRETDD-EYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQ 353
           KGR  DD E  SEDVE ESAD KKQ RGSTS KRSRAAEVHNLSERRRRDRINEKM+ALQ
Sbjct: 281 KGRALDDTECQSEDVEYESADPKKQLRGSTSTKRSRAAEVHNLSERRRRDRINEKMKALQ 340

Query: 354 ELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMP 404
           ELIPRCNK+DKASMLDEAIEYLK+LQLQVQMMSMGCG++PMMFPGVQQY+P
Sbjct: 341 ELIPRCNKTDKASMLDEAIEYLKTLQLQVQMMSMGCGMMPMMFPGVQQYLP 391

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255560265|ref|XP_002521150.1| Phytochrome-interacting factor, putative [Ricinus communis] gi|223539719|gb|EEF41301.1| Phytochrome-interacting factor, putative [Ricinus communis]

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 260/446 (58%), Positives = 291/446 (65%), Gaps = 57/446 (12%)

Query: 1   MNHCVPDFEFDDDHSIPTSSVLNRPRKSAMAEED-VMELLWQNGPVVLHNQNQRSLKKSQ 59
           M+H VPDFE DDD +IPTSS L RP+KS  + ED  MELLW NG VV+  Q   SLKK Q
Sbjct: 1   MSHYVPDFEMDDDCAIPTSSTLVRPKKSITSTEDEFMELLWHNGQVVVQTQ---SLKKPQ 57

Query: 60  PS--------FPADQSAPREIPSSHHHQQEQQDH---------------LFMQEDEMASW 96
                      P DQS PR++  +        ++               LFMQEDEMASW
Sbjct: 58  QQHHKYDDAVIPVDQSNPRDVIRTAQEHHNHNNNSNNNNNNNNNTHNSNLFMQEDEMASW 117

Query: 97  LHYPLNDTNFDSDFCTDLLYP----APCITSTTTTTATATATP----PVRATR---VRDS 145
           LHYP+NDTNFD DFC DLLYP    A C+TSTTT T T T T     PVR+     +R  
Sbjct: 118 LHYPINDTNFDQDFCADLLYPTSAAAACVTSTTTNTTTTTTTNNSFAPVRSLHNPEIRSQ 177

Query: 146 RPQLNTATTVASAPPLRPPIPPPPRR--TENFGLFARHMPREVA----SGPSNSKSVTIR 199
           +P + +AT  AS    RPPIPP  R    +NF  F+RH  R+ A    SGPS  K V  R
Sbjct: 178 QPPV-SATATAS----RPPIPPTRRAQVVQNFAYFSRHRARDGANVAESGPSKVKPVA-R 231

Query: 200 ESTVVDSSDTP-APGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAAATSSGGGGGSSG 258
           ESTVVDSS+TP     DSR SEA          +  +       A A   SS G   ++ 
Sbjct: 232 ESTVVDSSETPEGIALDSRISEAA----FGRSTSGGDNGGVGGAAAACGASSRGNNNNNN 287

Query: 259 ARDLTMCEMTVTSSPGGSSASAEPPA-QKPAAEDRKRKGRETDDEY-HSEDVELESADAK 316
               T CEMTVTSSPGGSSASAEPP  Q+P A+DRKRKGRE + EY HSEDVE ESADAK
Sbjct: 288 REMTTTCEMTVTSSPGGSSASAEPPQPQRPPADDRKRKGREEETEYYHSEDVEFESADAK 347

Query: 317 KQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLK 376
           KQ+RGSTS KRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLK
Sbjct: 348 KQARGSTSTKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLK 407

Query: 377 SLQLQVQMMSMGCGVVPMMFPGVQQY 402
           SLQLQVQMMSMGC +VPMMFPG+QQY
Sbjct: 408 SLQLQVQMMSMGCSMVPMMFPGIQQY 433

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224069945|ref|XP_002303090.1| predicted protein [Populus trichocarpa] gi|222844816|gb|EEE82363.1| predicted protein [Populus trichocarpa]

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 246/459 (53%), Positives = 275/459 (59%), Gaps = 76/459 (16%)

Query: 1   MNHCVPDFEFDDDHSIPTS-SVLNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQ 59
           MN  VPDFE DDD+S+P   S   RPRK AM EE++MELLWQNG VV+H+Q  RS KKS 
Sbjct: 1   MNPYVPDFEMDDDYSLPPPPSTHTRPRKPAMQEEEIMELLWQNGQVVMHSQ--RSQKKSS 58

Query: 60  P--------SFPADQ-SAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDF 110
           P          PADQ    +EI SSH  QQE   HLFMQEDEMASWL++PLNDTNFD DF
Sbjct: 59  PPPSELDDAVLPADQLPGTKEIRSSHDQQQEHH-HLFMQEDEMASWLNHPLNDTNFDHDF 117

Query: 111 CTDLLYPAPCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVA-SAPPLRPPIPPPP 169
           C DLLYP    T++ T  A  T      A+ VR +  ++   +  A SAP    P     
Sbjct: 118 CADLLYPPTASTASITREAAVTN---AAASTVRGATQRMEARSYPAVSAPRPPIPPVRRA 174

Query: 170 RRTENFGLFARHMPREVA-SGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGA 228
              +NF  F+RH    V+ SG SNSKSV +RESTVVDS +TP            R  E A
Sbjct: 175 EVVQNFAYFSRHRAGGVSESGRSNSKSV-VRESTVVDSCETPT----------ARISETA 223

Query: 229 SGVNNNNRCRNTSGAGAAATSSGGGGGSSGARDLTM-CEMTVTSSPGGSSASAEPPAQKP 287
              + +N C   +GA  A T S     SS    +T  CEMT TSSPG SSASAE PA   
Sbjct: 224 FARSADNTCGTINGAAVAGTVSSAP--SSNRETMTNPCEMTSTSSPGCSSASAELPALMS 281

Query: 288 AAEDRKRKGRETDDEYHSE----------------------------------------- 306
             EDRKRKGRE + E HSE                                         
Sbjct: 282 PVEDRKRKGREEEAECHSEFIAISITMAHGNQPQSVAIRQKTQNSADSSKPLQGRRDAAN 341

Query: 307 ---DVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSD 363
              D E ESADAKK+ RGS S+KRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSD
Sbjct: 342 PLKDAEFESADAKKRIRGSMSSKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSD 401

Query: 364 KASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQY 402
           KASMLDEAIEYLKSLQLQVQMMSMGC +VPMMFPG QQY
Sbjct: 402 KASMLDEAIEYLKSLQLQVQMMSMGCSMVPMMFPGFQQY 440

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359480088|ref|XP_002263397.2| PREDICTED: transcription factor PIF1-like [Vitis vinifera]

 Score =  368 bits (945), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 237/427 (55%), Positives = 268/427 (62%), Gaps = 67/427 (15%)

Query: 1   MNHCVPDFEFDDDHSIPTSSVLNRPRKSA-MAEED-VMELLWQNGPVVLHNQNQRSLKKS 58
           MNHCVPDFE DD+ +IP    L RP+KSA M E+D +MELLWQNG VV+  QNQRS KKS
Sbjct: 1   MNHCVPDFEVDDEDAIP----LTRPKKSAAMVEDDEIMELLWQNGQVVMQIQNQRSFKKS 56

Query: 59  QPS--------FPADQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDF 110
           QPS         P +QS  R    S     E    LFMQEDEMASWLHYPL+D      F
Sbjct: 57  QPSKFPIQDAVLPPEQSKIR----SSAPVDESSAQLFMQEDEMASWLHYPLDD------F 106

Query: 111 CTDLLYPAPCITSTTTTTATATATPPVRATRVRDSR-PQLNTATTVASAPPLRPPIPPPP 169
           C DLL P PC+ ++          PP R     D R P+   A T       +PPIPP  
Sbjct: 107 CADLLDPTPCVNASP---------PPARPNLSPDVRQPEERPAAT-------KPPIPPAR 150

Query: 170 R-----RTENFGLFARHMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRS 224
           R     +  NF  F R    E +  PS+S+   + ESTVVDSSDTP     SR S A   
Sbjct: 151 RVELDSKVHNFLHFPRKSTAE-SGEPSSSRPAGM-ESTVVDSSDTPGVCQQSRTSPA--- 205

Query: 225 MEGASGVNNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSP-----GGSSAS 279
            E       N+      GA  AATS+ G        + T  E+T+TSSP     GGS+++
Sbjct: 206 -EWCKAELANSGYGTIGGATEAATSAAG--------EHTTFELTMTSSPEGSGSGGSASA 256

Query: 280 AEPPAQKPAAEDRKRKGRETDD--EYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLS 337
              P  K  A+DRKRKGRE DD  EY SEDVE ESADAKKQ RGS +AKRSRAAEVHNLS
Sbjct: 257 GAEPTPKAPADDRKRKGREGDDTAEYQSEDVEFESADAKKQVRGSATAKRSRAAEVHNLS 316

Query: 338 ERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFP 397
           ERRRRDRINEKM+ALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGC +VPMM+P
Sbjct: 317 ERRRRDRINEKMKALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCSMVPMMYP 376

Query: 398 GVQQYMP 404
           GVQQYMP
Sbjct: 377 GVQQYMP 383

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744279|emb|CBI37249.3| unnamed protein product [Vitis vinifera]

 Score =  338 bits (866), Expect = 4e-90,   Method: Compositional matrix adjust.
 Identities = 222/427 (51%), Positives = 252/427 (59%), Gaps = 105/427 (24%)

Query: 1   MNHCVPDFEFDDDHSIPTSSVLNRPRKSA-MAEED-VMELLWQNGPVVLHNQNQRSLKKS 58
           MNHCVPDFE DD+ +IP    L RP+KSA M E+D +MELLWQNG VV+  QNQRS KKS
Sbjct: 1   MNHCVPDFEVDDEDAIP----LTRPKKSAAMVEDDEIMELLWQNGQVVMQIQNQRSFKKS 56

Query: 59  QPS--------FPADQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTNFDSDF 110
           QPS         P +QS  R    S     E    LFMQEDEMASWLHYPL+      DF
Sbjct: 57  QPSKFPIQDAVLPPEQSKIR----SSAPVDESSAQLFMQEDEMASWLHYPLD------DF 106

Query: 111 CTDLLYPAPCITSTTTTTATATATPPVRATRVRDSR-PQLNTATTVASAPPLRPPIPPPP 169
           C DLL P PC+ ++          PP R     D R P+   A T       +PPIPP  
Sbjct: 107 CADLLDPTPCVNAS---------PPPARPNLSPDVRQPEERPAAT-------KPPIPPAR 150

Query: 170 R-----RTENFGLFARHMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRS 224
           R     +  NF  F R    E +  PS+S+   + ESTV                     
Sbjct: 151 RVELDSKVHNFLHFPRKSTAE-SGEPSSSRPAGM-ESTV--------------------- 187

Query: 225 MEGASGVNNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSP-----GGSSAS 279
                                AATS+ G        + T  E+T+TSSP     GGS+++
Sbjct: 188 ---------------------AATSAAG--------EHTTFELTMTSSPEGSGSGGSASA 218

Query: 280 AEPPAQKPAAEDRKRKGRETDD--EYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLS 337
              P  K  A+DRKRKGRE DD  EY SEDVE ESADAKKQ RGS +AKRSRAAEVHNLS
Sbjct: 219 GAEPTPKAPADDRKRKGREGDDTAEYQSEDVEFESADAKKQVRGSATAKRSRAAEVHNLS 278

Query: 338 ERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFP 397
           ERRRRDRINEKM+ALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGC +VPMM+P
Sbjct: 279 ERRRRDRINEKMKALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCSMVPMMYP 338

Query: 398 GVQQYMP 404
           GVQQYMP
Sbjct: 339 GVQQYMP 345

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356505096|ref|XP_003521328.1| PREDICTED: transcription factor PIF1-like [Glycine max]

 Score =  332 bits (852), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 215/417 (51%), Positives = 254/417 (60%), Gaps = 53/417 (12%)

Query: 2   NHCVPDFEF--DDDHSIP--TSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKK 57
           NHCVPDF+   D DH  P  T S L R +K ++A++D+MELLW NG VV+ +QNQRSL+K
Sbjct: 6   NHCVPDFDIQMDHDHEYPILTPSALPRQKKPSIADDDIMELLWHNGQVVVQSQNQRSLRK 65

Query: 58  SQP------SFPADQSAPREI-PSSHHHQQEQQDHLFMQEDEMASWLHYPLNDTN--FDS 108
             P      + PA  S  REI P   +  Q    HLFM E EMASWLHYP++D     D 
Sbjct: 66  LPPVTNSHDASPAGPSMTREIRPLVENFNQ----HLFMHEGEMASWLHYPIDDDEPALDQ 121

Query: 109 DFCTDLLYPAPCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPP 168
            F  D LY  P   + ++   T   T  +   R   + P+                    
Sbjct: 122 SFGADFLYSPPTTANNSSFMQTLGHTSQLTELRPMSANPRPPIPPPRRPE---------- 171

Query: 169 PRRTENFGLFARHMPREVASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGA 228
            +RT NF  F+RH  R  A+ PS       RESTVVDS DT A    SR SE +RS    
Sbjct: 172 -QRTPNFAYFSRHNTR--AAEPS--VKAAARESTVVDSCDTEAAA--SRVSETVRSAAEG 224

Query: 229 SGVNNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPA 288
                       +G  A +TS+GGG      R   M ++T+TSSPGGSS+  EP     A
Sbjct: 225 -----------GAGVAAPSTSAGGG------RSTMMYDLTMTSSPGGSSSCDEPVQVAAA 267

Query: 289 AEDRKRKGRETDD-EYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINE 347
            EDRKRKGRE ++ E  SEDV+ ES +AKKQ  GSTS KRSRAAEVHNLSERRRRDRINE
Sbjct: 268 EEDRKRKGREAEEWECQSEDVDFES-EAKKQVCGSTSTKRSRAAEVHNLSERRRRDRINE 326

Query: 348 KMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMP 404
           KM+ALQELIPRCNKSDKASMLDEAI YLKSLQLQVQMMSMGCG+VP+MFPG+QQYMP
Sbjct: 327 KMKALQELIPRCNKSDKASMLDEAISYLKSLQLQVQMMSMGCGMVPVMFPGIQQYMP 383

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468728|ref|XP_004152073.1| PREDICTED: transcription factor PIF1-like [Cucumis sativus]

 Score =  317 bits (811), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 200/411 (48%), Positives = 257/411 (62%), Gaps = 42/411 (10%)

Query: 1   MNHCVPDFEFDDDHSIPTSSVLNRPRK-SAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQ 59
           MN+CVPDFE D+D  +P+SS +    K S+M + +VMELL QNG VV+ + NQ+S  KS 
Sbjct: 1   MNYCVPDFETDEDSLLPSSSSVPSRSKTSSMLDGEVMELLCQNGQVVMQSPNQKSRMKSP 60

Query: 60  PSFPADQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPL-NDTNFDSDFCTDLLYPA 118
            S  A+Q   R+   +    Q+++  LFMQEDEM SWLHYPL +D+  ++ F  +LLYP+
Sbjct: 61  QSTTAEQITNRD---TRPMSQQEEPQLFMQEDEMISWLHYPLVDDSTLENSFRDELLYPS 117

Query: 119 PCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPP-----PPRRTE 173
               +  +    A  +  VR T   + RP     TT  S    RPPIPP     P  +  
Sbjct: 118 ----NPQSIEQNAVVSAQVRTTDGMEFRPLTAMTTTATSTMVARPPIPPMRRTEPETKVN 173

Query: 174 NFGLFARHMPREVASGPSNSKSVTIRESTVV--DSSDTPAPGPDSRASEAMRSMEGASGV 231
           +FG F+ H  R + S PSNSK++ +RESTVV   SS+T    P++R+SE  R+      +
Sbjct: 174 SFGRFSGH-ARRIESAPSNSKNM-VRESTVVGSTSSNTMVLTPETRSSEVQRT-----AI 226

Query: 232 NNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAED 291
            +   C      G AA S+G GG         + +M V+ +        EP  +  + ED
Sbjct: 227 TDIPSCGLACSGGVAAPSTGNGG--------ELMKMIVSET--------EPVQRTTSLED 270

Query: 292 RKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRA 351
           RKRKG+ETDD   S+ +   +    KQ RGSTS KRSRAAEVHNLSERRRRDRINEKM+A
Sbjct: 271 RKRKGKETDD---SDYLCYSTLKGSKQVRGSTSTKRSRAAEVHNLSERRRRDRINEKMKA 327

Query: 352 LQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQY 402
           LQELIPRCNK+DKASMLDEAIEYLK+LQLQVQMMSMGCG+VPMMFPG QQ+
Sbjct: 328 LQELIPRCNKADKASMLDEAIEYLKTLQLQVQMMSMGCGMVPMMFPGAQQF 378

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449515805|ref|XP_004164938.1| PREDICTED: transcription factor PIF1-like [Cucumis sativus]

 Score =  313 bits (803), Expect = 9e-83,   Method: Compositional matrix adjust.
 Identities = 199/411 (48%), Positives = 255/411 (62%), Gaps = 46/411 (11%)

Query: 1   MNHCVPDFEFDDDHSIPTSSVLNRPRK-SAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQ 59
           MN+CVPDFE D+D  +P+SS +    K S+M + +VMELL QNG VV+ + NQ+S  KS 
Sbjct: 1   MNYCVPDFETDEDSLLPSSSSVPSRSKTSSMLDGEVMELLCQNGQVVMQSPNQKSRMKSP 60

Query: 60  PSFPADQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPL-NDTNFDSDFCTDLLYPA 118
            S  A+Q   R+   +    Q+++  LFMQEDEM SWLHYPL +D+  ++ F  +LLYP+
Sbjct: 61  QSTTAEQITNRD---TRPMSQQEEPQLFMQEDEMISWLHYPLVDDSTLENSFRDELLYPS 117

Query: 119 PCITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPP-----PPRRTE 173
               +  +    A  +  VR T   + RP     TT  S    RPPIPP     P  +  
Sbjct: 118 ----NPQSIEQNAVVSAQVRTTDGMEFRPLTAMTTTATSTMVARPPIPPMRRTEPETKVN 173

Query: 174 NFGLFARHMPREVASGPSNSKSVTIRESTVV--DSSDTPAPGPDSRASEAMRSMEGASGV 231
           +FG F+ H  R + S PSNSK++ +RESTVV   SS+T    P++R+SE  R+      +
Sbjct: 174 SFGRFSGH-ARRIESAPSNSKNM-VRESTVVGSTSSNTMVLTPETRSSEVQRT-----AI 226

Query: 232 NNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAED 291
            +   C      G AA S+G GG         + +M V+ +        EP  +  + ED
Sbjct: 227 TDIPSCGLACSGGVAAPSTGNGG--------ELMKMIVSET--------EPVQRTTSLED 270

Query: 292 RKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRA 351
           RKRKG+ETDD  +          + KQ RGSTS KRSRAAEVHNLSERRRRDRINEKM+A
Sbjct: 271 RKRKGKETDDSDYL-------CYSTKQVRGSTSTKRSRAAEVHNLSERRRRDRINEKMKA 323

Query: 352 LQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQY 402
           LQELIPRCNK+DKASMLDEAIEYLK+LQLQVQMMSMGCG+VPMMFPG QQ+
Sbjct: 324 LQELIPRCNKADKASMLDEAIEYLKTLQLQVQMMSMGCGMVPMMFPGAQQF 374

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356545930|ref|XP_003541386.1| PREDICTED: transcription factor PIF1-like [Glycine max]

 Score =  297 bits (760), Expect = 8e-78,   Method: Compositional matrix adjust.
 Identities = 186/377 (49%), Positives = 225/377 (59%), Gaps = 51/377 (13%)

Query: 36  MELLWQNGPVVLHNQNQRSLKKSQPSFPADQS------APREIPSSHHHQQEQQDHLFMQ 89
           MELLWQNG VV+ +QNQR  +K  P  P + +      + REI SS         HLFMQ
Sbjct: 1   MELLWQNGQVVMQSQNQRPFRK--PPQPPEANGGDGAISAREIRSSEAENYNNSQHLFMQ 58

Query: 90  EDEMASWLHYPLNDTN--FDS-DFCTDLLYPAPCITSTTTTTATATATPPVRATRVRDSR 146
           EDEMA+WLHYP+++    FD  DF  D+ YP P  T++    + A  +   R T +    
Sbjct: 59  EDEMAAWLHYPIHEDPPPFDHHDFGADIFYPPPNATASQNRGSAAVQSS-FRTTELWHPA 117

Query: 147 PQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPREVASGPSNSKSVTIRESTVVDS 206
           P+                    P R  NF  F +H      +  S+SK+    + TVVDS
Sbjct: 118 PRPPIPPPRRPEHA--------PSRIHNFAHFTKH-----GNASSSSKAAAAAQPTVVDS 164

Query: 207 SDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAAATSSGGGGGSSGARDLTMCE 266
            +TP                  +   +    R  + AG  A S GG       R+   C+
Sbjct: 165 CETPV-----------------ATAEHAETGRARAAAGKTAVSDGG-------RETATCD 200

Query: 267 MTVTSSPGGSSASAEPPAQKPAAEDRKRKGRETDD-EYHSEDVELESADAKKQSRGSTSA 325
           +TVTSSPG SS SAEP  ++P A DRKRKGRE ++ E+ SEDV+ ES +AKKQ  GSTS 
Sbjct: 201 VTVTSSPGDSSGSAEPVEREPMA-DRKRKGREHEESEFQSEDVDFESPEAKKQVHGSTST 259

Query: 326 KRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMM 385
           KRSRAAEVHNLSERRRRDRINEKM+ALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMM
Sbjct: 260 KRSRAAEVHNLSERRRRDRINEKMKALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMM 319

Query: 386 SMGCGVVPMMFPGVQQY 402
           SMG G+VPMMFPG+QQY
Sbjct: 320 SMGYGMVPMMFPGIQQY 336

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536868|ref|XP_003536955.1| PREDICTED: transcription factor PIF1-like [Glycine max]

 Score =  280 bits (717), Expect = 7e-73,   Method: Compositional matrix adjust.
 Identities = 187/397 (47%), Positives = 236/397 (59%), Gaps = 57/397 (14%)

Query: 11  DDDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGPVVLHNQNQRSLKKSQPSFPADQSAP- 69
           D+++ IP S      +K +   +++MELLWQNG VV+ NQNQR  +K  P+   D   P 
Sbjct: 5   DEEYPIPVS------KKPSTQNDEIMELLWQNGQVVMQNQNQRPFRKQPPTTDGDGPIPA 58

Query: 70  REIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDT--NFD-SDFCTDLLYPAPCITSTTT 126
           REI SS       Q HLFMQEDEMASWLHYP+++    FD  DFC D+LYP P  T++  
Sbjct: 59  REIRSSEAENYNSQ-HLFMQEDEMASWLHYPIHEDPPPFDHHDFCADILYPPPNATASQN 117

Query: 127 TTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPREV 186
            ++ +  +  VR T ++   P+            L         R  NF  FA+H     
Sbjct: 118 QSSASVQS-SVRTTELQHPAPRPPIPPPRRQEHTL--------SRIHNFTHFAKHGNASS 168

Query: 187 ASGPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAA 246
           +S  +     T+  +  V+                                   +G  + 
Sbjct: 169 SSKAAAPAQPTVATAEHVE-----------------------------------TGRASV 193

Query: 247 ATSSGGGGGSSGARDLTMCEMTVTSSPGGSSASAEPPAQKPAAEDRKRKGR-ETDDEYHS 305
           + ++G    S G R+   C++TVTSSPGGSS SAEP  ++P   +RKRKGR + + EY S
Sbjct: 194 SAAAGKTPASDGGRETATCDVTVTSSPGGSSGSAEPVQREPVV-NRKRKGREQEESEYQS 252

Query: 306 EDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKA 365
           EDV+ ES +AKKQ RGSTS KRS AAEVHNLSERRRRDRINEKM+ALQELIPRCNKSDKA
Sbjct: 253 EDVDFESPEAKKQVRGSTSTKRSHAAEVHNLSERRRRDRINEKMKALQELIPRCNKSDKA 312

Query: 366 SMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQY 402
           SMLDEAIEYLKSLQLQVQMMSMGCG+VPM+FPG+QQY
Sbjct: 313 SMLDEAIEYLKSLQLQVQMMSMGCGMVPMIFPGIQQY 349

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	423
TAIR|locus:2061634	478	PIL5 "phytochrome interacting	0.333	0.294	0.590	2.9e-64
TAIR|locus:4010713915	544	AT4G28811 [Arabidopsis thalian	0.260	0.202	0.568	9.4e-45
TAIR|locus:2012345	524	PIF3 "AT1G09530" [Arabidopsis	0.278	0.225	0.632	2.1e-40
TAIR|locus:2053733	430	PIF4 "AT2G43010" [Arabidopsis	0.250	0.246	0.637	8.3e-39
TAIR|locus:2077680	444	PIL6 "AT3G59060" [Arabidopsis	0.260	0.247	0.604	1.7e-38
UNIPROTKB|Q8GRJ1	417	OJ1343_B12.103 "Transcription	0.222	0.225	0.712	2.4e-37
UNIPROTKB|Q5NAE0	565	P0498A12.33 "Putative BP-5 pro	0.264	0.198	0.631	9.4e-36
TAIR|locus:2117788	445	AT4G28800 [Arabidopsis thalian	0.210	0.2	0.618	1.7e-35
TAIR|locus:2117773	413	AT4G28790 [Arabidopsis thalian	0.252	0.259	0.554	2.4e-35
TAIR|locus:4010713916	307	AT4G28815 [Arabidopsis thalian	0.191	0.263	0.588	1.2e-32

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

 Score = 429 (156.1 bits), Expect = 2.9e-64, Sum P(2) = 2.9e-64
 Identities = 85/144 (59%), Positives = 106/144 (73%)

Query:   262 LTMCEMTVTXXXXXXXXXXXXXXQKPAAEDRKRKGRETDDEYHSEDVELESADAKKQSRG 321
             +T   + +T              +K   +DRKRK RE      +++ E  S + K+    
Sbjct:   220 MTAPAIEITGTSSSVVSKSEIEPEKTNVDDRKRKEREATT---TDETESRSEETKQARVS 276

Query:   322 STSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQ 381
             +TS KRSRAAEVHNLSER+RRDRINE+M+ALQELIPRCNKSDKASMLDEAIEY+KSLQLQ
Sbjct:   277 TTSTKRSRAAEVHNLSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQLQ 336

Query:   382 VQMMSMGCGVVPMMFPGVQQYMPN 405
             +QMMSMGCG++PMM+PG+QQYMP+
Sbjct:   337 IQMMSMGCGMMPMMYPGMQQYMPH 360

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0015995 "chlorophyll biosynthetic process" evidence=IMP

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

GO:0010313 "phytochrome binding" evidence=IDA

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

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

GO:0010099 "regulation of photomorphogenesis" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

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

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

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

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

GO:0006783 "heme biosynthetic process" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0009686 "gibberellin biosynthetic process" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0048608 "reproductive structure development" evidence=RCA

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

 Score = 327 (120.2 bits), Expect = 9.4e-45, Sum P(3) = 9.4e-45
 Identities = 66/116 (56%), Positives = 92/116 (79%)

Query:   293 KRKGRETDDEYHSEDV-ELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRA 351
             +R+ + T+D+   E + E++  +   ++ GSTS KRSRAA++HNLSERRRR+RINE+M+ 
Sbjct:   323 ERETKITEDKKREETIAEIQGTE---EAHGSTSRKRSRAADMHNLSERRRRERINERMKT 379

Query:   352 LQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVP-MMFPG-VQQYMPN 405
             LQEL+PRC K+DK SML++ IEY+KSLQLQ+QMMSMG G++P MM  G  QQ+MP+
Sbjct:   380 LQELLPRCRKTDKVSMLEDVIEYVKSLQLQIQMMSMGHGMMPPMMHEGNTQQFMPH 435

GO:0005634 "nucleus" evidence=ISM

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

 Score = 356 (130.4 bits), Expect = 2.1e-40, Sum P(2) = 2.1e-40
 Identities = 79/125 (63%), Positives = 93/125 (74%)

Query:   285 QKPAAEDRKRKGRETDDEYHSEDVELESADAKKQ---SRGSTSAKRSRAAEVHNLSERRR 341
             + P+   +++     D + HSEDVE ES D +K+   SR    +KRSR+AEVHNLSERRR
Sbjct:   296 ESPSLSLKRKHSNIQDIDCHSEDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRR 355

Query:   342 RDRINEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGV-VP--MMFP- 397
             RDRINEKMRALQELIP CNK DKASMLDEAIEYLKSLQLQVQ+MSM  G  +P  +MFP 
Sbjct:   356 RDRINEKMRALQELIPNCNKVDKASMLDEAIEYLKSLQLQVQIMSMASGYYLPPAVMFPP 415

Query:   398 GVQQY 402
             G+  Y
Sbjct:   416 GMGHY 420

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

GO:0042802 "identical protein binding" evidence=IPI

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

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

GO:0009704 "de-etiolation" evidence=IMP

GO:0007623 "circadian rhythm" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

GO:0007165 "signal transduction" evidence=TAS

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

 Score = 331 (121.6 bits), Expect = 8.3e-39, Sum P(2) = 8.3e-39
 Identities = 74/116 (63%), Positives = 86/116 (74%)

Query:   291 DRKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMR 350
             DRKRK     DE     V L  A   K ++ S S +RSRAAEVHNLSERRRRDRINE+M+
Sbjct:   223 DRKRKRINHTDE----SVSLSDAIGNKSNQRSGSNRRSRAAEVHNLSERRRRDRINERMK 278

Query:   351 ALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVV------PMMFPGVQ 400
             ALQELIP C+K+DKAS+LDEAI+YLKSLQLQ+Q+M MG G+       PMMFPGVQ
Sbjct:   279 ALQELIPHCSKTDKASILDEAIDYLKSLQLQLQVMWMGSGMAAAAASAPMMFPGVQ 334

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

 Score = 328 (120.5 bits), Expect = 1.7e-38, Sum P(2) = 1.7e-38
 Identities = 75/124 (60%), Positives = 91/124 (73%)

Query:   291 DRKRKG-RETDDEYHSE-DVELESAD----AKKQSRGSTSAKRSRAAEVHNLSERRRRDR 344
             DRKRK   + D E  S+ D+ L S D      K S+ S S +RSRAAEVHNLSERRRRDR
Sbjct:   212 DRKRKHVMDADQESVSQSDIGLTSTDDQTMGNKSSQRSGSTRRSRAAEVHNLSERRRRDR 271

Query:   345 INEKMRALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVV--------PMMF 396
             INE+M+ALQELIP C+++DKAS+LDEAI+YLKSLQ+Q+Q+M MG G+         PMMF
Sbjct:   272 INERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQLQVMWMGSGMAAAAAAAASPMMF 331

Query:   397 PGVQ 400
             PGVQ
Sbjct:   332 PGVQ 335

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009693 "ethylene biosynthetic process" evidence=IMP

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

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

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

GO:0006546 "glycine catabolic process" evidence=RCA

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

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

GO:0006766 "vitamin metabolic process" evidence=RCA

GO:0007623 "circadian rhythm" evidence=RCA

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

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

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

GO:0009106 "lipoate metabolic process" evidence=RCA

GO:0009108 "coenzyme biosynthetic process" evidence=RCA

GO:0009117 "nucleotide metabolic process" evidence=RCA

GO:0009630 "gravitropism" evidence=RCA

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

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

GO:0009965 "leaf morphogenesis" evidence=RCA

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

GO:0015995 "chlorophyll biosynthetic process" evidence=RCA

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

GO:0019344 "cysteine biosynthetic process" evidence=RCA

GO:0019748 "secondary metabolic process" evidence=RCA

GO:0019761 "glucosinolate biosynthetic process" evidence=RCA

GO:0030003 "cellular cation homeostasis" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

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

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

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

 Score = 346 (126.9 bits), Expect = 2.4e-37, Sum P(2) = 2.4e-37
 Identities = 67/94 (71%), Positives = 79/94 (84%)

Query:   311 ESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDE 370
             E AD  + S+   + +R+RAAEVHNLSERRRRDRINEK+RALQEL+P CNK+DKAS+LDE
Sbjct:   210 EVADETRPSKRPAAKRRTRAAEVHNLSERRRRDRINEKLRALQELVPHCNKTDKASILDE 269

Query:   371 AIEYLKSLQLQVQMMSMGCGVVPMMFPGVQQYMP 404
             AIEYLKSLQ+QVQ+M M  G+VPMMFPG  Q MP
Sbjct:   270 AIEYLKSLQMQVQIMWMTTGIVPMMFPGTHQLMP 303

GO:0005634 "nucleus" evidence=IC

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

 Score = 340 (124.7 bits), Expect = 9.4e-36, Sum P(3) = 9.4e-36
 Identities = 72/114 (63%), Positives = 85/114 (74%)

Query:   292 RKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRA 351
             +KRK +   +   S+D +L+      +  G+ S KRSR AEVHNLSERRRRDRINEKMRA
Sbjct:   275 QKRKCQAQAECSASQDDDLDDEPGVLRKSGTRSTKRSRTAEVHNLSERRRRDRINEKMRA 334

Query:   352 LQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCG--VVPMMFPGVQQYM 403
             LQELIP CNK DKASMLDEAIEYLK+LQLQVQMMSMG G  + PM+ P   Q++
Sbjct:   335 LQELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMSMGTGLCIPPMLLPTAMQHL 388

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2117788 AT4G28800 [Arabidopsis thaliana (taxid:3702)]

 Score = 280 (103.6 bits), Expect = 1.7e-35, Sum P(2) = 1.7e-35
 Identities = 60/97 (61%), Positives = 74/97 (76%)

Query:   311 ESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDE 370
             E     +++RGSTS KRSR AE+HNL+ERRRR++INEKM+ LQ+LIPRCNKS K S LD+
Sbjct:   237 EETHGTEEARGSTSRKRSRTAEMHNLAERRRREKINEKMKTLQQLIPRCNKSTKVSTLDD 296

Query:   371 AIEYLKSLQLQVQ-MMSMGCGVVPMMFPG-VQQYMPN 405
             AIEY+KSLQ Q+Q MMS      PMM  G  QQ+MP+
Sbjct:   297 AIEYVKSLQSQIQGMMS------PMMNAGNTQQFMPH 327

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2117773 AT4G28790 [Arabidopsis thaliana (taxid:3702)]

 Score = 298 (110.0 bits), Expect = 2.4e-35, Sum P(2) = 2.4e-35
 Identities = 66/119 (55%), Positives = 88/119 (73%)

Query:   290 EDRKRKGRETDDEYHSEDVELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKM 349
             ++RKRK RE        +VE +  +   ++R STS+KRSRAA +H LSERRRR +INE M
Sbjct:   247 DERKRKTRE------ETNVENQGTE---EARDSTSSKRSRAAIMHKLSERRRRQKINEMM 297

Query:   350 RALQELIPRCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVP-MMFPG--VQQYMPN 405
             +ALQEL+PRC K+D++SMLD+ IEY+KSLQ Q+QM SMG  ++P MM+ G   QQYMP+
Sbjct:   298 KALQELLPRCTKTDRSSMLDDVIEYVKSLQSQIQMFSMGHVMIPPMMYAGNIQQQYMPH 356

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:4010713916 AT4G28815 [Arabidopsis thaliana (taxid:3702)]

 Score = 259 (96.2 bits), Expect = 1.2e-32, Sum P(3) = 1.2e-32
 Identities = 50/85 (58%), Positives = 67/85 (78%)

Query:   317 KQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSDKASMLDEAIEYLK 376
             +++RGSTS KRSRAAE+HNL+ERRRR++INE+M+ LQ+LIPRCNKS K SML++ IEY+K
Sbjct:   138 EEARGSTSRKRSRAAEMHNLAERRRREKINERMKTLQQLIPRCNKSTKVSMLEDVIEYVK 197

Query:   377 SLQLQVQM----MSMGCGVVPMMFP 397
             SL++Q+      M+MG    P   P
Sbjct:   198 SLEMQINQFMPHMAMGMNQPPAYIP 222

GO:0005634 "nucleus" evidence=ISM

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_II002531 hypothetical protein (615 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	423
smart00353	53	smart00353, HLH, helix loop helix domain	9e-17
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	4e-16
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	1e-13
PHA03307	1352	PHA03307, PHA03307, transcriptional regulator ICP4	3e-04
PRK07003	830	PRK07003, PRK07003, DNA polymerase III subunits ga	3e-04

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

 Score = 73.4 bits (181), Expect = 9e-17
 Identities = 25/52 (48%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 335 NLSERRRRDRINEKMRALQELIPRCN---KSDKASMLDEAIEYLKSLQLQVQ 383
           N  ERRRR +INE    L+ L+P      K  KA +L  AIEY+KSLQ ++Q
Sbjct: 1   NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQ 52

Length = 53

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

 Score = 71.9 bits (177), Expect = 4e-16
 Identities = 26/55 (47%), Positives = 36/55 (65%), Gaps = 3/55 (5%)

Query: 332 EVHNLSERRRRDRINEKMRALQELIP---RCNKSDKASMLDEAIEYLKSLQLQVQ 383
           E HNL ERRRR+RIN+    L+ L+P      K  KA +L +A++Y+KSLQ  +Q
Sbjct: 6   EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 64.4 bits (158), Expect = 1e-13
 Identities = 26/50 (52%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 332 EVHNLSERRRRDRINEKMRALQELIPRCN--KSDKASMLDEAIEYLKSLQ 379
           + HN  ERRRRDRIN+    L+EL+P     K  KA +L  AIEY+K LQ
Sbjct: 3   KAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 45/237 (18%), Positives = 58/237 (24%), Gaps = 35/237 (14%)

Query: 133 ATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENFGLFARHMPREVASGPSN 192
           A   V A      R +  T                         L      RE +  P  
Sbjct: 51  AAVTVVAGAAACDRFEPPTGPPPGPGTEAPANESRSTPTWSLSTLAPASPAREGSPTPPG 110

Query: 193 SKSVTIRESTVVDSSDTPAPGPDSRASEAMRSMEGASGVNNNNRCRNTSGAGAAATSSGG 252
             S      T   +S  P+P PD      M    G+ G        +   AGA+  +   
Sbjct: 111 PSSPDPPPPTPPPASPPPSPAPDLS---EMLRPVGSPG---PPPAASPPAAGASPAAVAS 164

Query: 253 GGGSSG--ARDLTMCEMTVTSSPGGS-----------------------SASAEPPAQKP 287
              SS   A  L+  E T  +                            SASA  PA  P
Sbjct: 165 DAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAP 224

Query: 288 AAEDRKRKGRETDDEYHSEDVEL----ESADAKKQSRGSTSAKRSRAAEVHNLSERR 340
                   G  + D   SE        E+     +    T   R   A   N    R
Sbjct: 225 GRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSR 281

Length = 1352

>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated

 Score = 42.9 bits (101), Expect = 3e-04
 Identities = 45/213 (21%), Positives = 63/213 (29%), Gaps = 34/213 (15%)

Query: 117 PAPCITSTTTTTATA-TATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENF 175
           PAP   +     A+A  A   V         P+   A   A+     PP  P P  T + 
Sbjct: 381 PAPGARAAAAVGASAVPAVTAVTGAAGAALAPK--AAAAAAATRAEAPPAAPAPPATADR 438

Query: 176 GLFARHMPREVAS------------GPSNSKSVTIRESTVVDSSDTPAPGPDSRASEAMR 223
           G  A      V +               +++      S    +SD P       A  A  
Sbjct: 439 GDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPRAAA 498

Query: 224 SMEGASGVNNNNRC------------------RNTSGAGAAATSSGGGGGSSGARD-LTM 264
                     + R                          AAA  +   GG++ A D L  
Sbjct: 499 PSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAAAAPAARAGGAAAALDVLRN 558

Query: 265 CEMTVTSSPGGSSASAEPPAQKPAAEDRKRKGR 297
             M V+S  G  +A+A  PA  PAA  +    R
Sbjct: 559 AGMRVSSDRGARAAAAAKPAAAPAAAPKPAAPR 591

Length = 830

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	423
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.39
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.39
smart00353	53	HLH helix loop helix domain.	99.3
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	99.2
KOG1318	411	consensus Helix loop helix transcription factor EB	99.16
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.99
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.91
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.07
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.05
KOG0561	373	consensus bHLH transcription factor [Transcription	97.81
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.76
KOG3910	632	consensus Helix loop helix transcription factor [T	97.57
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.43
PLN03217	93	transcription factor ATBS1; Provisional	97.37
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	92.97
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	91.46
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	89.7
KOG3898	254	consensus Transcription factor NeuroD and related	86.56
KOG4395	285	consensus Transcription factor Atonal, contains HT	84.75
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	81.4

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

Probab=99.39  E-value=5.7e-13  Score=100.64  Aligned_cols=53  Identities=47%  Similarity=0.752  Sum_probs=49.8

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHHHH
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQLQV  382 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~qv  382 (423)
                      .+..|+..||+||++||+.|..|+.+||.+   .|+||++||+.||+||++|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            456799999999999999999999999998   79999999999999999999876

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

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

Probab=99.39  E-value=4.9e-13  Score=100.85  Aligned_cols=49  Identities=55%  Similarity=0.883  Sum_probs=46.4

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCC-----CCCchhhhHHHHHHHHHHHH
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRC-----NKSDKASMLDEAIEYLKSLQ  379 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~-----~K~DKASIL~eAIeYIK~LQ  379 (423)
                      +..|+..||+||++||+.|..|+++||.+     .|++|++||+.||+||++||
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            45799999999999999999999999998     58999999999999999997

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

>smart00353 HLH helix loop helix domain

Probab=99.30  E-value=5.6e-12  Score=93.68  Aligned_cols=49  Identities=51%  Similarity=0.716  Sum_probs=45.5

Q ss_pred             chHHHHHHHHHHHHHHHHHhccCC---CCCCchhhhHHHHHHHHHHHHHHHH
Q 014485          335 NLSERRRRDRINEKMRALQELIPR---CNKSDKASMLDEAIEYLKSLQLQVQ  383 (423)
Q Consensus       335 ~~~ERrRRdrINe~~~~Lr~LVP~---~~K~DKASIL~eAIeYIK~LQ~qvq  383 (423)
                      +..||+||++||+.|..|+.+||.   ..|++|++||.+||+||+.|+.+++
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            468999999999999999999995   5599999999999999999999876

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

Probab=99.20  E-value=1.2e-11  Score=135.99  Aligned_cols=91  Identities=23%  Similarity=0.312  Sum_probs=76.7

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCCC----CCchhhhHHHHHHHHHHHHHHH-HHhccCCCCCCCCC--chhhhcc
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRCN----KSDKASMLDEAIEYLKSLQLQV-QMMSMGCGVVPMMF--PGVQQYM  403 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~----K~DKASIL~eAIeYIK~LQ~qv-q~Ls~~~~~~P~~~--pg~q~~m  403 (423)
                      +++|+.+||||||++|..|.+|.+|||.|.    |+||.+||.+||.+||.+++.- +.-+.+..-.|.++  ++|.|+|
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~~~~~~~~~~d~KpSflS~~eL~~Lm  100 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQESENSSIDQDYKPSFLSNDELTHLI  100 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhhhcccccccccccccccchHHHHHHH
Confidence            678999999999999999999999999985    9999999999999999998863 22222333345444  3799999


Q ss_pred             cccCCCCcccccCCccccc
Q 014485          404 PNMGMGIGMGMGMGRAWIW  422 (423)
Q Consensus       404 ~~~g~gm~~~~g~~~~~i~  422 (423)
                      ..+..||-|+++|+ |+|.
T Consensus       101 LeAlDGF~fvV~cd-G~Iv  118 (803)
T KOG3561|consen  101 LEALDGFLFVVNCD-GRIV  118 (803)
T ss_pred             HHHhcCeEEEEecC-ceEE
Confidence            99999999999999 9883

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

Probab=99.16  E-value=3e-11  Score=124.52  Aligned_cols=62  Identities=39%  Similarity=0.739  Sum_probs=54.4

Q ss_pred             ccchhhhhccchHHHHHHHHHHHHHHHHHhccCCCC----CCchhhhHHHHHHHHHHHHHHHHHhc
Q 014485          325 AKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN----KSDKASMLDEAIEYLKSLQLQVQMMS  386 (423)
Q Consensus       325 ~kr~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~----K~DKASIL~eAIeYIK~LQ~qvq~Ls  386 (423)
                      .|.+++|..||++|||||++||++|++|..|||.|+    |..|..||..+++||+.||+..+...
T Consensus       228 ~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~  293 (411)
T KOG1318|consen  228 ERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR  293 (411)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence            344556788999999999999999999999999995    77899999999999999988776443

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

Probab=98.99  E-value=1.5e-10  Score=113.00  Aligned_cols=78  Identities=27%  Similarity=0.361  Sum_probs=58.3

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHHhccCCC--------CCCchhhhHHHHHHHHHHHHHHHHHhccC-C--CCCCCCCc
Q 014485          329 RAAEVHNLSERRRRDRINEKMRALQELIPRC--------NKSDKASMLDEAIEYLKSLQLQVQMMSMG-C--GVVPMMFP  397 (423)
Q Consensus       329 ~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--------~K~DKASIL~eAIeYIK~LQ~qvq~Ls~~-~--~~~P~~~p  397 (423)
                      .++..|.++|||||+|||+.|.+|++||+.+        .|++||.||+.||+|+|.||...+.--.. .  .....+--
T Consensus        31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~~~~~~~~~~~~d~f~~  110 (250)
T KOG4304|consen   31 YRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQAAAQAAPAALPVDSFRA  110 (250)
T ss_pred             HhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccccccccccccccchhhhc
Confidence            3456699999999999999999999999955        58899999999999999999766544433 1  11222333


Q ss_pred             hhhhccccc
Q 014485          398 GVQQYMPNM  406 (423)
Q Consensus       398 g~q~~m~~~  406 (423)
                      ||..++.-.
T Consensus       111 Gf~ec~~EV  119 (250)
T KOG4304|consen  111 GFRECAAEV  119 (250)
T ss_pred             cHHHHHHHH
Confidence            776654433

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.91  E-value=1e-09  Score=103.20  Aligned_cols=59  Identities=32%  Similarity=0.573  Sum_probs=51.8

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHHhccCCCC-------CCchhhhHHHHHHHHHHHHHHHHHhc
Q 014485          328 SRAAEVHNLSERRRRDRINEKMRALQELIPRCN-------KSDKASMLDEAIEYLKSLQLQVQMMS  386 (423)
Q Consensus       328 ~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~-------K~DKASIL~eAIeYIK~LQ~qvq~Ls  386 (423)
                      .+++..|...||+||+.||.++..|+.|||.|.       |+.||.||.++|+||.+|+.++..-+
T Consensus        60 ~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe  125 (229)
T KOG1319|consen   60 DRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQE  125 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344567999999999999999999999999884       88999999999999999987765444

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.07  E-value=1.5e-06  Score=97.11  Aligned_cols=62  Identities=32%  Similarity=0.540  Sum_probs=55.7

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHHhccCCCC-CCchhhhHHHHHHHHHHHHHHHHHhccCC
Q 014485          328 SRAAEVHNLSERRRRDRINEKMRALQELIPRCN-KSDKASMLDEAIEYLKSLQLQVQMMSMGC  389 (423)
Q Consensus       328 ~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~-K~DKASIL~eAIeYIK~LQ~qvq~Ls~~~  389 (423)
                      +.+|.+||.+|||.|-.|||+|.+|+++||+.. |+.|..+|..||+||++|+...+.|...+
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~  336 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLEN  336 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhh
Confidence            345678999999999999999999999999875 99999999999999999999888877543

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

Probab=98.05  E-value=8.1e-06  Score=79.46  Aligned_cols=53  Identities=30%  Similarity=0.502  Sum_probs=45.9

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCCC--CC-chhhhHHHHHHHHHHHHHHH
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRCN--KS-DKASMLDEAIEYLKSLQLQV  382 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~--K~-DKASIL~eAIeYIK~LQ~qv  382 (423)
                      ++..||..||+||+.|++.|..|+.+||...  |. ..++||++|++||+.|+.+.
T Consensus        59 ~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~  114 (232)
T KOG2483|consen   59 SRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKS  114 (232)
T ss_pred             chhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHH
Confidence            4567999999999999999999999999864  22 37999999999999996554

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.81  E-value=2.1e-05  Score=79.05  Aligned_cols=60  Identities=30%  Similarity=0.464  Sum_probs=52.1

Q ss_pred             hhhhccchHHHHHHHHHHHHHHHHHhccCCC--CCCchhhhHHHHHHHHHHHHHHHHHhccC
Q 014485          329 RAAEVHNLSERRRRDRINEKMRALQELIPRC--NKSDKASMLDEAIEYLKSLQLQVQMMSMG  388 (423)
Q Consensus       329 ~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--~K~DKASIL~eAIeYIK~LQ~qvq~Ls~~  388 (423)
                      -+|+.-|..||||=..||.+|..||.|+|..  .|+.||.||+.+.+||..|..+.-.|--+
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~q  120 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQ  120 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccc
Confidence            4567889999999999999999999999986  49999999999999999998766554433

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

Probab=97.76  E-value=6.9e-05  Score=73.77  Aligned_cols=55  Identities=29%  Similarity=0.432  Sum_probs=47.2

Q ss_pred             ccchHHHHHHHHHHHHHHHHHh-ccCCCC-CCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          333 VHNLSERRRRDRINEKMRALQE-LIPRCN-KSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       333 ~H~~~ERrRRdrINe~~~~Lr~-LVP~~~-K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      +-.+.||||=.|+||.|.+|+. -.++.+ ++-|+.||..||+||..||.-++.+..
T Consensus       121 AATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~  177 (284)
T KOG3960|consen  121 AATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQ  177 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3568999999999999999954 456554 789999999999999999998888764

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.57  E-value=0.00024  Score=75.47  Aligned_cols=59  Identities=29%  Similarity=0.313  Sum_probs=50.4

Q ss_pred             chhhhhccchHHHHHHHHHHHHHHHHHhccCCCCCC----chhhhHHHHHHHHHHHHHHHHHh
Q 014485          327 RSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKS----DKASMLDEAIEYLKSLQLQVQMM  385 (423)
Q Consensus       327 r~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~K~----DKASIL~eAIeYIK~LQ~qvq~L  385 (423)
                      .+++|...|..||.|-..|||.|++|..+.--.-|.    .|.-||..||..|-.|++||.+-
T Consensus       523 EkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  523 EKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            344567799999999889999999999987766555    48999999999999999999654

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

Probab=97.43  E-value=0.00013  Score=69.92  Aligned_cols=58  Identities=24%  Similarity=0.362  Sum_probs=50.0

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCC----CCCCchhhhHHHHHHHHHHHHHHHHHhccC
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPR----CNKSDKASMLDEAIEYLKSLQLQVQMMSMG  388 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~----~~K~DKASIL~eAIeYIK~LQ~qvq~Ls~~  388 (423)
                      +..+|..||.|=..+|..|..||.+||.    .+|+.|..+|..||.||++|+.-++.-...
T Consensus       110 ~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  110 RQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            3447777999999999999999999995    458999999999999999999877666543

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.37  E-value=0.00023  Score=59.97  Aligned_cols=48  Identities=29%  Similarity=0.511  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHhccCCC------CCCchhhhHHHHHHHHHHHHHHHHHhccCC
Q 014485          342 RDRINEKMRALQELIPRC------NKSDKASMLDEAIEYLKSLQLQVQMMSMGC  389 (423)
Q Consensus       342 RdrINe~~~~Lr~LVP~~------~K~DKASIL~eAIeYIK~LQ~qvq~Ls~~~  389 (423)
                      -|.|+|.+..|++|+|..      .|..-+-||++|+.||+.|+.+|..|++.+
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerL   72 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERL   72 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999965      366778899999999999999999998643

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=92.97  E-value=0.052  Score=50.54  Aligned_cols=51  Identities=31%  Similarity=0.447  Sum_probs=46.1

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCC--CCCchhhhHHHHHHHHHHHHHH
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRC--NKSDKASMLDEAIEYLKSLQLQ  381 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--~K~DKASIL~eAIeYIK~LQ~q  381 (423)
                      +-.|++.||+|-..+|+.|..||.++|..  .|+.|.-.|.-|..||.+|-.-
T Consensus        79 rv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v  131 (173)
T KOG4447|consen   79 RVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV  131 (173)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence            34599999999999999999999999965  6999999999999999999653

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=91.46  E-value=0.17  Score=55.19  Aligned_cols=39  Identities=38%  Similarity=0.658  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHhccCC----CCCCchhhhHHHHHHHHHH
Q 014485          339 RRRRDRINEKMRALQELIPR----CNKSDKASMLDEAIEYLKS  377 (423)
Q Consensus       339 RrRRdrINe~~~~Lr~LVP~----~~K~DKASIL~eAIeYIK~  377 (423)
                      ||-|||+|..++.|.+|+|-    .+|+||.+||.-+|-||+-
T Consensus        34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~   76 (712)
T KOG3560|consen   34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV   76 (712)
T ss_pred             hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence            67799999999999999995    4799999999999999973

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

Probab=89.70  E-value=0.37  Score=53.79  Aligned_cols=44  Identities=34%  Similarity=0.496  Sum_probs=37.7

Q ss_pred             cchHHHHHHHHHHHHHHHHHhccCCC----CCCchhhhHHHHHHHHHH
Q 014485          334 HNLSERRRRDRINEKMRALQELIPRC----NKSDKASMLDEAIEYLKS  377 (423)
Q Consensus       334 H~~~ERrRRdrINe~~~~Lr~LVP~~----~K~DKASIL~eAIeYIK~  377 (423)
                      ..-+.|-||-|-|+-|.+|..+||--    ..+|||+|+.-||-|+|.
T Consensus        50 SRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   50 SRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            33456899999999999999999943    478999999999999983

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

Probab=86.56  E-value=1.1  Score=44.53  Aligned_cols=50  Identities=32%  Similarity=0.410  Sum_probs=43.3

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHH
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQL  380 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~  380 (423)
                      +..=|..||+|=-.+|+.|+.||++||..   .|+.|...|.-|-.||..|++
T Consensus        73 R~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~  125 (254)
T KOG3898|consen   73 RLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE  125 (254)
T ss_pred             cccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence            34457789999899999999999999953   588999999999999999875

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

Probab=84.75  E-value=1.5  Score=43.96  Aligned_cols=55  Identities=25%  Similarity=0.338  Sum_probs=47.4

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHHHHHH
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQLQVQM  384 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~qvq~  384 (423)
                      ++..-+..||+|=..+|..|+.|+..||..   .|+.|-..|.+|-.||--|-..++.
T Consensus       174 rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~~  231 (285)
T KOG4395|consen  174 RRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLDL  231 (285)
T ss_pred             hhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhcC
Confidence            345678899999999999999999999976   4889999999999999988765543

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=81.40  E-value=1.5  Score=46.71  Aligned_cols=42  Identities=33%  Similarity=0.510  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHhccCCC----CCCchhhhHHHHHHHHHHH
Q 014485          337 SERRRRDRINEKMRALQELIPRC----NKSDKASMLDEAIEYLKSL  378 (423)
Q Consensus       337 ~ERrRRdrINe~~~~Lr~LVP~~----~K~DKASIL~eAIeYIK~L  378 (423)
                      ..|.||++-|-.|.+|..|+|-.    +.+||++|+.-|..|||.-
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            34889999999999999999965    3689999999999999953

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	423
4ati_A	118	Mitf:m-Box Complex Length = 118		5e-05
4f3l_B	387	Crystal Structure Of The Heterodimeric Clock:bmal1		5e-04

>pdb|4ATI|A Chain A, Mitf:m-Box Complex Length = 118

Iteration: 1
 Score = 45.4 bits (106), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 309 ELESADAKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCNKSD----K 364
           EL +     +S     AK  +  + HNL ERRRR  IN++++ L  LIP+ N  D    K
Sbjct: 6   ELTACIFPTESEARALAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNK 65
Query: 365 ASMLDEAIEYLKSLQLQVQ 383
            ++L  +++Y++ LQ + Q
Sbjct: 66  GTILKASVDYIRKLQREQQ 84

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 35/54 (64%), Gaps = 4/54 (7%)
Query: 330 AAEVHNLSERRRRDRINEKMRALQELIPRCN----KSDKASMLDEAIEYLKSLQ 379
           A E H+  E+RRRD++N  +  L  L+P CN    K DK ++L  A++++K+L+
Sbjct: 13  AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	423
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	8e-21
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	3e-16
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-14
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	9e-14
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-13
1a0a_A	63	BHLH, protein (phosphate system positive regulator	3e-09
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	5e-09
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	9e-07
4f3l_A	361	Mclock, circadian locomoter output cycles protein	3e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	4e-04

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

 Score = 85.1 bits (211), Expect = 8e-21
 Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 326 KRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN-KSDKASMLDEAIEYLKSLQLQVQM 384
            R      HN  E+R R  IN+K+  L++L+     K +K+++L +AI+Y++ LQ   Q 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 385 MSM 387
           +  
Sbjct: 62  LKQ 64

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

 Score = 72.0 bits (177), Expect = 3e-16
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 326 KRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN------KSDKASMLDEAIEYLKSLQ 379
           ++ RA   HN  ERRRRD+IN  +  L ++IP  +         K  +L +A +Y++ L+
Sbjct: 3   EKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Query: 380 LQVQ 383
               
Sbjct: 61  QSNH 64

>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 = 66.2 bits (162), Expect = 4e-14
 Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 319 SRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN--KSDKASMLDEAIEYLK 376
           +        +     HN  ER+RRD I +   +L++ +P     K+ +A +LD+A EY++
Sbjct: 1   NDDIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 60

Query: 377 SLQLQVQMM 385
            ++ +    
Sbjct: 61  YMRRKNHTH 69

>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 = 65.8 bits (161), Expect = 9e-14
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 7/68 (10%)

Query: 321 GSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN---KSDKASMLDEAIEYLKS 377
           G  + KR      HN+ ER+RR+ +     AL++ IP      K+ K  +L +A  Y+ S
Sbjct: 1   GHMNVKRR----THNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILS 56

Query: 378 LQLQVQMM 385
           +Q + Q +
Sbjct: 57  VQAEEQKL 64

>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 = 64.3 bits (157), Expect = 2e-13
 Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 332 EVHNLSERRRRDRINEKMRALQELIPRCN--KSDKASMLDEAIEYLKSLQLQVQMM 385
             HN  ER+RRD I +   +L++ +P     K+ +A +LD+A EY++ ++ +    
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTH 59

>1a0a_A BHLH, protein (phosphate system positive regulatory protein PHO4); transcription factor, basic helix loop helix; HET: DNA; 2.80A {Saccharomyces cerevisiae} SCOP: a.38.1.1 Length = 63

 Score = 51.7 bits (124), Expect = 3e-09
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 7/58 (12%)

Query: 332 EVHNLSERRRRDRINEKMRALQELIPRCNKSD-------KASMLDEAIEYLKSLQLQV 382
           E H  +E+ RR+R+   +  L  LIP   K         KA+ ++ A  Y++ LQ   
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

>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 = 51.8 bits (124), Expect = 5e-09
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 332 EVHNLSERRRRDRINEKMRALQELIP---RCNKSDKASMLDEAIEYLKSLQLQVQMM 385
             HN  E+ RR  +   +  L+ L+P     ++    S+L +A  ++K L+   +  
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKA 59

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

 Score = 49.6 bits (118), Expect = 9e-07
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 8/70 (11%)

Query: 315 AKKQSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN----KSDKASMLDE 370
              + +G     R    E H+  E+RRRD++N  +  L  L+P CN    K DK ++L  
Sbjct: 2   EYAEHQGRIKNAR----EAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRM 57

Query: 371 AIEYLKSLQL 380
           A++++K+L+ 
Sbjct: 58  AVQHMKTLRG 67

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

 Score = 48.0 bits (114), Expect = 3e-06
 Identities = 16/57 (28%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 326 KRSRAAEVHNLSERRRRDRINEKMRALQELIPRC-NKSDKASMLDEAIEYLKSLQLQ 381
           K        N SE++RRD+ N  ++ L  ++P    K DK+++L ++I++L+  +  
Sbjct: 8   KDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET 64

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

 Score = 45.2 bits (106), Expect = 4e-05
 Identities = 20/116 (17%), Positives = 36/116 (31%), Gaps = 34/116 (29%)

Query: 10  FDDDHSIPTSSVLNRPRKSAMAEEDVMELLWQNGP-----VVLHNQNQRSLKKSQPSFPA 64
           F     IP                 ++ L+W +       VV++  ++ SL         
Sbjct: 381 FPPSAHIP---------------TILLSLIWFDVIKSDVMVVVNKLHKYSL--------V 417

Query: 65  DQSAPREIPSSHHHQQEQQDHLFMQEDEMASWLHYPLNDT-NFDSDFCTDLLYPAP 119
           ++       S      E    L ++ +   + LH  + D  N    F +D L P  
Sbjct: 418 EKQPKESTISIPSIYLE----LKVKLENEYA-LHRSIVDHYNIPKTFDSDDLIPPY 468

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

 Score = 41.0 bits (95), Expect = 8e-04
 Identities = 31/199 (15%), Positives = 51/199 (25%), Gaps = 69/199 (34%)

Query: 27  KSAMA-----EEDVMELL-----W-----QNGPVVLHNQNQRSLKKSQPSFPADQSAPRE 71
           K+ +A        V   +     W      N P  +    Q+ L +  P++ +       
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222

Query: 72  IPSSHHHQQEQQDHLFMQEDEMASWLHYP-----LNDTN-------FDSDFCTDLLYPAP 119
           I    H  Q +   L   +        Y      L +         F+   C  LL    
Sbjct: 223 IKLRIHSIQAELRRLLKSKP-------YENCLLVLLNVQNAKAWNAFNLS-CKILL---- 270

Query: 120 CITSTTTTTATATATPPVRATRVRDSRPQLNTATTVASAPPLRPPIPPPPRRTENFGLFA 179
               TT              T +          +    +  L P         E   L  
Sbjct: 271 ----TTRFKQVTDFLSAATTTHI----------SLDHHSMTLTPD--------EVKSLLL 308

Query: 180 RHM-------PREVASG-P 190
           +++       PREV +  P
Sbjct: 309 KYLDCRPQDLPREVLTTNP 327

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

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 7/64 (10%)

Query: 324 SAKRSRAAEVHNLSERRRRDRINEKMRAL-QELIPRCNKSDKAS---MLDEAIEYLKSLQ 379
            A +      HN  ER+RR  INE  R L +            +   +L +A++ +  L+
Sbjct: 2   GADKRAH---HNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLE 58

Query: 380 LQVQ 383
            QV+
Sbjct: 59  QQVR 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	423
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.61
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.57
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.55
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.54
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.53
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.52
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.46
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.46
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.42
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.37
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.29
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	99.26
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.18
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.08
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.05
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.62
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.54
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.04

>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

Probab=99.61  E-value=5.8e-16  Score=126.01  Aligned_cols=61  Identities=31%  Similarity=0.473  Sum_probs=56.7

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHHhccCCC-CCCchhhhHHHHHHHHHHHHHHHHHhccC
Q 014485          328 SRAAEVHNLSERRRRDRINEKMRALQELIPRC-NKSDKASMLDEAIEYLKSLQLQVQMMSMG  388 (423)
Q Consensus       328 ~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~-~K~DKASIL~eAIeYIK~LQ~qvq~Ls~~  388 (423)
                      ..++..|+.+||+||++||++|.+|++|||.+ .|+||++||.+||+||++||.+++.|..+
T Consensus         4 ~~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e   65 (82)
T 1am9_A            4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE   65 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34567899999999999999999999999998 79999999999999999999999999864

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

Probab=99.57  E-value=2.7e-15  Score=119.87  Aligned_cols=60  Identities=25%  Similarity=0.449  Sum_probs=54.4

Q ss_pred             chhhhhccchHHHHHHHHHHHHHHHHHhccCCC-CCCchhhhHHHHHHHHHHHHHHHHHhc
Q 014485          327 RSRAAEVHNLSERRRRDRINEKMRALQELIPRC-NKSDKASMLDEAIEYLKSLQLQVQMMS  386 (423)
Q Consensus       327 r~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~-~K~DKASIL~eAIeYIK~LQ~qvq~Ls  386 (423)
                      ...++.+|+++||+||++||++|.+|+.|||.+ .|+||++||++||+||++||.++.=|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            344567899999999999999999999999975 599999999999999999999987765

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

Probab=99.55  E-value=4.5e-15  Score=128.44  Aligned_cols=65  Identities=35%  Similarity=0.567  Sum_probs=51.5

Q ss_pred             cccchhhhhccchHHHHHHHHHHHHHHHHHhccCCCC----CCchhhhHHHHHHHHHHHHHHHHHhccC
Q 014485          324 SAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN----KSDKASMLDEAIEYLKSLQLQVQMMSMG  388 (423)
Q Consensus       324 ~~kr~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~----K~DKASIL~eAIeYIK~LQ~qvq~Ls~~  388 (423)
                      ..++..++..|+.+||+||++||++|.+|++|||.|.    |++|++||.+||+||++||.+++.|...
T Consensus        21 ~~k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           21 LAKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3444556778999999999999999999999999985    6789999999999999999999999853

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

Probab=99.54  E-value=2.2e-15  Score=120.86  Aligned_cols=56  Identities=36%  Similarity=0.595  Sum_probs=50.9

Q ss_pred             ccchhhhhccchHHHHHHHHHHHHHHHHHhccCCC----CCCchhhhHHHHHHHHHHHHH
Q 014485          325 AKRSRAAEVHNLSERRRRDRINEKMRALQELIPRC----NKSDKASMLDEAIEYLKSLQL  380 (423)
Q Consensus       325 ~kr~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~----~K~DKASIL~eAIeYIK~LQ~  380 (423)
                      .+...++..|+.+||+||++||+.|.+|+.|||.|    .|+|||+||++||+|||.|+.
T Consensus         4 ~k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            4 GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             -CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            34566778999999999999999999999999987    699999999999999999974

>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=99.53  E-value=1.2e-15  Score=118.52  Aligned_cols=54  Identities=33%  Similarity=0.554  Sum_probs=49.7

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCCC------CCchhhhHHHHHHHHHHHHHHHH
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRCN------KSDKASMLDEAIEYLKSLQLQVQ  383 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~------K~DKASIL~eAIeYIK~LQ~qvq  383 (423)
                      ++..|+.+||+||++||++|.+|++|||.+.      |++|++||.+||+||++||.+++
T Consensus         5 rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            5 RRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            4567999999999999999999999999986      78999999999999999998653

>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=99.52  E-value=1.9e-15  Score=117.88  Aligned_cols=53  Identities=30%  Similarity=0.486  Sum_probs=48.2

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCC-------CCCchhhhHHHHHHHHHHHHHHHH
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRC-------NKSDKASMLDEAIEYLKSLQLQVQ  383 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~-------~K~DKASIL~eAIeYIK~LQ~qvq  383 (423)
                      +.+|+++||+||++||+.|.+|+.|||.+       .|++||+||++||+||++||++++
T Consensus         3 r~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            46799999999999999999999999976       466799999999999999998753

>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=99.46  E-value=5.3e-14  Score=113.55  Aligned_cols=59  Identities=29%  Similarity=0.533  Sum_probs=55.0

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC--CCCchhhhHHHHHHHHHHHHHHHHHhccC
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC--NKSDKASMLDEAIEYLKSLQLQVQMMSMG  388 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--~K~DKASIL~eAIeYIK~LQ~qvq~Ls~~  388 (423)
                      .+..|+..||+||++||++|..|+++||.+  .|++|++||..||+||++|+.+++.|...
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e   72 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD   72 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            467799999999999999999999999987  59999999999999999999999998754

>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=99.46  E-value=5.7e-14  Score=113.81  Aligned_cols=58  Identities=29%  Similarity=0.541  Sum_probs=53.7

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC--CCCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC--NKSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--~K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      ++..|+..||+||++||+.|..|+++||.+  .|++|++||.+||+||++|+.+++.|..
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~   61 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ   61 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356799999999999999999999999986  6999999999999999999999888864

>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=99.42  E-value=1.6e-13  Score=113.24  Aligned_cols=58  Identities=31%  Similarity=0.485  Sum_probs=53.2

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      .+..|+..||+||++||++|..|+++||.+   .|++|++||.+||+||++|+.+++.|..
T Consensus         6 ~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~   66 (88)
T 1nkp_A            6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS   66 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456799999999999999999999999986   4999999999999999999999887654

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

Probab=99.37  E-value=4.2e-13  Score=108.32  Aligned_cols=58  Identities=31%  Similarity=0.443  Sum_probs=49.8

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC---CCC-chhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC---NKS-DKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~-DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      ++..|+..||+||+.||++|.+|+.+||.+   .|. .|+.||..||+||++|++++++++.
T Consensus         5 rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            456799999999999999999999999953   455 7999999999999999999999874

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

Probab=99.29  E-value=4e-12  Score=103.29  Aligned_cols=57  Identities=23%  Similarity=0.293  Sum_probs=52.3

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      +..||..||+||+.||++|..|+++||.+   .|.+|+.||.+|++||+.|+.+.+.|..
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~   61 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH   61 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45799999999999999999999999965   5889999999999999999999987764

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

Probab=99.26  E-value=2.4e-12  Score=128.31  Aligned_cols=94  Identities=26%  Similarity=0.377  Sum_probs=72.3

Q ss_pred             chhhhhccchHHHHHHHHHHHHHHHHHhccC----CCCCCchhhhHHHHHHHHHHHHHHHHHhccCCCCCCCCCc--hhh
Q 014485          327 RSRAAEVHNLSERRRRDRINEKMRALQELIP----RCNKSDKASMLDEAIEYLKSLQLQVQMMSMGCGVVPMMFP--GVQ  400 (423)
Q Consensus       327 r~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP----~~~K~DKASIL~eAIeYIK~LQ~qvq~Ls~~~~~~P~~~p--g~q  400 (423)
                      ...++++|+.+||+||++||+.|.+|+.|||    ...|+||++||..||+|||.|+......... ...|.++.  .+.
T Consensus        10 ~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~   88 (387)
T 4f3l_B           10 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGATNPYTEA-NYKPTFLSDDELK   88 (387)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC------C-CSSCTTSCHHHHH
T ss_pred             hhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhccccccccc-ccCcccCCHHHHH
Confidence            3455778999999999999999999999999    4579999999999999999998544333222 23344443  577


Q ss_pred             hcccccCCCCcccccCCcccc
Q 014485          401 QYMPNMGMGIGMGMGMGRAWI  421 (423)
Q Consensus       401 ~~m~~~g~gm~~~~g~~~~~i  421 (423)
                      +++.....||.+.+.++-|+|
T Consensus        89 ~~ll~~~~gfi~v~~~~~G~i  109 (387)
T 4f3l_B           89 HLILRAADGFLFVVGCDRGKI  109 (387)
T ss_dssp             HHHHHTCCSEEEEEETTTCBE
T ss_pred             HHHHhcCCCEEEEEecCCeEE
Confidence            888888899999988876665

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

Probab=99.18  E-value=1.6e-11  Score=120.85  Aligned_cols=94  Identities=21%  Similarity=0.322  Sum_probs=62.1

Q ss_pred             chhhhhccchHHHHHHHHHHHHHHHHHhccC-CCCCCchhhhHHHHHHHHHHHHHHHHHhc---cCCCCCCCCCc--hhh
Q 014485          327 RSRAAEVHNLSERRRRDRINEKMRALQELIP-RCNKSDKASMLDEAIEYLKSLQLQVQMMS---MGCGVVPMMFP--GVQ  400 (423)
Q Consensus       327 r~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP-~~~K~DKASIL~eAIeYIK~LQ~qvq~Ls---~~~~~~P~~~p--g~q  400 (423)
                      ...++..|+.+||+||++||+.|.+|+.||| ...|+||++||.+||+|||.|+.......   ......|.++.  .+.
T Consensus         9 ~~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (361)
T 4f3l_A            9 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFT   88 (361)
T ss_dssp             ----------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHHTSCSCGGGTSCCSCTTSCHHHHH
T ss_pred             cchhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhcccccccccccccCcccccHHHHH
Confidence            3445677999999999999999999999999 56799999999999999999986543211   11123344443  456


Q ss_pred             hcccccCCCCcccccCCcccc
Q 014485          401 QYMPNMGMGIGMGMGMGRAWI  421 (423)
Q Consensus       401 ~~m~~~g~gm~~~~g~~~~~i  421 (423)
                      +++.....||.+.+..+ |+|
T Consensus        89 ~~~l~a~~~~i~v~~~~-G~i  108 (361)
T 4f3l_A           89 QLMLEALDGFFLAIMTD-GSI  108 (361)
T ss_dssp             HHHHHHTTEEEEEEETT-SBE
T ss_pred             HHHHHhcCceEEEEcCC-ccE
Confidence            77777777776666554 443

>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=99.08  E-value=8.5e-11  Score=93.03  Aligned_cols=53  Identities=26%  Similarity=0.449  Sum_probs=48.6

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC--CCCchhhhHHHHHHHHHHHHHHH
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC--NKSDKASMLDEAIEYLKSLQLQV  382 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--~K~DKASIL~eAIeYIK~LQ~qv  382 (423)
                      .+..|+..||+|+..||+.|..|+++||..  .|++|+.||..||+||++|++.+
T Consensus        12 rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           12 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            456799999999999999999999999975  59999999999999999999754

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

Probab=99.05  E-value=1.9e-10  Score=88.94  Aligned_cols=53  Identities=25%  Similarity=0.320  Sum_probs=48.1

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHHHHH
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQLQVQ  383 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~qvq  383 (423)
                      +..||..||+|+..||+.|..|+++||..   .|++|+.||..||+||++|++.++
T Consensus         3 R~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            3 RMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            45689999999999999999999999975   499999999999999999998653

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

Probab=98.62  E-value=3.9e-08  Score=80.74  Aligned_cols=46  Identities=30%  Similarity=0.582  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHhccCCCC----CCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          342 RDRINEKMRALQELIPRCN----KSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       342 RdrINe~~~~Lr~LVP~~~----K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      |..||++|.+|..|||.++    |.+|++||..||+||++||.+++.|..
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e   53 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKD   53 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999999999874    789999999999999999887776653

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

Probab=98.54  E-value=1.9e-08  Score=79.78  Aligned_cols=46  Identities=24%  Similarity=0.394  Sum_probs=41.8

Q ss_pred             chHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHH
Q 014485          335 NLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQL  380 (423)
Q Consensus       335 ~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~  380 (423)
                      +..||+|...||+.|..||++||..   .|++|..||..||+||+.||.
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            3567899999999999999999976   599999999999999999984

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

Probab=98.04  E-value=9.8e-06  Score=68.29  Aligned_cols=49  Identities=24%  Similarity=0.379  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHHHHHHhc
Q 014485          338 ERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQLQVQMMS  386 (423)
Q Consensus       338 ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~qvq~Ls  386 (423)
                      |+.|=..||+.|..||.+||..   .|+.|..+|..||+||++|+..++.-.
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            4567788999999999999965   499999999999999999999877644

---

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	423
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	5e-16
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-15
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	3e-15
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	4e-15
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	8e-15
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-14
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-14
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	8e-14

>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 = 70.7 bits (173), Expect = 5e-16
 Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 334 HNLSERRRRDRINEKMRALQELIPRCN--KSDKASMLDEAIEYLKSLQLQVQMMSM 387
           HN  ER+RRD I +   +L++ +P     K+ +A +LD+A EY++ ++ +      
Sbjct: 6   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ 61

>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 = 68.6 bits (168), Expect = 1e-15
 Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 342 RDRINEKMRALQELIPRCN-KSDKASMLDEAIEYLKSLQLQVQMMSM 387
           R  IN+K+  L++L+   + K  K+ +L +AI+Y+K LQ     +  
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQ 47

>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 = 68.4 bits (167), Expect = 3e-15
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 8/69 (11%)

Query: 318 QSRGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN-KSDKASMLDEAIEYLK 376
           QSRG    KR+     HN  E+R R  IN+K+  L++L+     K +K+++L +AI+Y++
Sbjct: 1   QSRGE---KRTA----HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIR 53

Query: 377 SLQLQVQMM 385
            LQ   Q +
Sbjct: 54  FLQHSNQKL 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 = 68.4 bits (167), Expect = 4e-15
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 7/70 (10%)

Query: 321 GSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN---KSDKASMLDEAIEYLKS 377
           G  + KR      HN+ ER+RR+ +     AL++ IP      K+ K  +L +A  Y+ S
Sbjct: 1   GHMNVKRRT----HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILS 56

Query: 378 LQLQVQMMSM 387
           +Q + Q +  
Sbjct: 57  VQAEEQKLIS 66

>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 = 66.4 bits (162), Expect = 8e-15
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 7/59 (11%)

Query: 332 EVHNLSERRRRDRINEKMRALQELIPRCN-------KSDKASMLDEAIEYLKSLQLQVQ 383
           E H  +E+ RR+R+   +  L  LIP             KA+ ++ A  Y++ LQ    
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>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 = 66.3 bits (162), Expect = 1e-14
 Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 8/64 (12%)

Query: 326 KRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN------KSDKASMLDEAIEYLKSLQ 379
           ++ RA   HN  ERRRRD+IN  +  L ++IP  +         K  +L +A +Y++ L+
Sbjct: 3   EKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Query: 380 LQVQ 383
               
Sbjct: 61  QSNH 64

>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 = 66.5 bits (162), Expect = 1e-14
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 5/63 (7%)

Query: 328 SRAAEVHNLSERRRRDRINEKMRALQELIP---RCNKSDKASMLDEAIEYLKSLQLQVQM 384
           SR+   HN  E+ RR  +   +  L+ L+P     ++    S+L +A  ++K L+   + 
Sbjct: 1   SRST--HNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRK 58

Query: 385 MSM 387
              
Sbjct: 59  AVH 61

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

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

 Score = 63.7 bits (155), Expect = 8e-14
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 320 RGSTSAKRSRAAEVHNLSERRRRDRINEKMRALQELIPRCN--KSDKASMLDEAIEYLKS 377
           R +T+A R +A     + ERRR  ++NE    L+         +  K  +L  AI Y++ 
Sbjct: 5   RKTTNADRRKA---ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEG 61

Query: 378 LQLQVQ 383
           LQ  ++
Sbjct: 62  LQALLR 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	423
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.5
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.48
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.42
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.41
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.4
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.28

>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=99.52  E-value=5.2e-15  Score=117.51  Aligned_cols=61  Identities=31%  Similarity=0.479  Sum_probs=55.4

Q ss_pred             hhhhhccchHHHHHHHHHHHHHHHHHhccCCCC-CCchhhhHHHHHHHHHHHHHHHHHhccC
Q 014485          328 SRAAEVHNLSERRRRDRINEKMRALQELIPRCN-KSDKASMLDEAIEYLKSLQLQVQMMSMG  388 (423)
Q Consensus       328 ~~~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~-K~DKASIL~eAIeYIK~LQ~qvq~Ls~~  388 (423)
                      ...+..|+.+||+||++||+.|..|++|||.+. |++|++||.+||+||++|+.+++.|...
T Consensus         4 ~~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e   65 (80)
T d1am9a_           4 GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE   65 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            344678999999999999999999999999864 9999999999999999999999988753

>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=99.50  E-value=4.8e-15  Score=113.05  Aligned_cols=52  Identities=31%  Similarity=0.494  Sum_probs=47.8

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCC-------CCCchhhhHHHHHHHHHHHHHHH
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRC-------NKSDKASMLDEAIEYLKSLQLQV  382 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~-------~K~DKASIL~eAIeYIK~LQ~qv  382 (423)
                      +..|+.+||+||++||++|.+|++|||.+       .|++|++||++||+||++||+++
T Consensus         3 R~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            45799999999999999999999999953       58999999999999999999765

>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=99.48  E-value=8.4e-15  Score=113.55  Aligned_cols=54  Identities=26%  Similarity=0.450  Sum_probs=49.5

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC--CCCchhhhHHHHHHHHHHHHHHHH
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC--NKSDKASMLDEAIEYLKSLQLQVQ  383 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--~K~DKASIL~eAIeYIK~LQ~qvq  383 (423)
                      ++..|+..||+||++||+.|..|++|||.+  .|++|++||..||+||++||+.++
T Consensus        12 rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          12 RRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            456799999999999999999999999986  488999999999999999998764

>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=99.45  E-value=5.1e-14  Score=111.10  Aligned_cols=57  Identities=23%  Similarity=0.283  Sum_probs=52.6

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCCC---CCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRCN---KSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~---K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      +..|+.+||+||++||+.|..|+++||.+.   |++|++||.+||+||+.|+.+++.|..
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~   61 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH   61 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457999999999999999999999999763   899999999999999999999988764

>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=99.42  E-value=7.7e-14  Score=111.00  Aligned_cols=58  Identities=29%  Similarity=0.541  Sum_probs=53.3

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC--CCCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC--NKSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~--~K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      ++..|+.+||+||++||+.|..|++|||.+  .|++|++||..||+||++|+.+++.|..
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~   61 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ   61 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356799999999999999999999999975  5899999999999999999999988774

>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=99.41  E-value=9.1e-14  Score=111.70  Aligned_cols=58  Identities=31%  Similarity=0.485  Sum_probs=53.4

Q ss_pred             hhhccchHHHHHHHHHHHHHHHHHhccCCC---CCCchhhhHHHHHHHHHHHHHHHHHhcc
Q 014485          330 AAEVHNLSERRRRDRINEKMRALQELIPRC---NKSDKASMLDEAIEYLKSLQLQVQMMSM  387 (423)
Q Consensus       330 ~~~~H~~~ERrRRdrINe~~~~Lr~LVP~~---~K~DKASIL~eAIeYIK~LQ~qvq~Ls~  387 (423)
                      ++..|+.+||+||++||+.|..|+++||++   .|++|++||..||+||++|+.+++.|..
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~   66 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS   66 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            456799999999999999999999999976   4789999999999999999999988865

>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=99.40  E-value=2.3e-14  Score=109.82  Aligned_cols=52  Identities=35%  Similarity=0.572  Sum_probs=47.8

Q ss_pred             hhccchHHHHHHHHHHHHHHHHHhccCCCC------CCchhhhHHHHHHHHHHHHHHH
Q 014485          331 AEVHNLSERRRRDRINEKMRALQELIPRCN------KSDKASMLDEAIEYLKSLQLQV  382 (423)
Q Consensus       331 ~~~H~~~ERrRRdrINe~~~~Lr~LVP~~~------K~DKASIL~eAIeYIK~LQ~qv  382 (423)
                      +..|+.+||+||++||+.|.+|++|||.+.      |++|++||.+||+||++||++.
T Consensus         6 R~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            456999999999999999999999999763      8999999999999999999764

>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=99.28  E-value=6e-13  Score=100.86  Aligned_cols=47  Identities=32%  Similarity=0.489  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHhccCCCC-CCchhhhHHHHHHHHHHHHHHHHHhccC
Q 014485          342 RDRINEKMRALQELIPRCN-KSDKASMLDEAIEYLKSLQLQVQMMSMG  388 (423)
Q Consensus       342 RdrINe~~~~Lr~LVP~~~-K~DKASIL~eAIeYIK~LQ~qvq~Ls~~  388 (423)
                      |++||++|.+|++|||++. |+|||+||.+||+||++||.+++.|..+
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e   48 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQE   48 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999975 9999999999999999999999999754