Citrus Sinensis ID: 007797

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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-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------59
Protein Sequence
MQQIFVSSAMNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMVGERRRLIKWLWSPIFIMGRSQEGESCSSWRIFGPFLSCIAYDINALSIAWL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccHHHHHHHHccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHccccccccccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccEEEEccccccccccccEEEcccHHHHHHcccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEccccccccccccccccccccccccccccccHHHHHHHcccEEEEccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccEEEEcccccccccccHHHccHHHHHHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
MQQIFVSsamnpcipdwnfegdipisnqmkpmgqdnELVELLWQNGHVvlssqaqtqrkpslnhneprqvqkqtlrgsgscgnssnliqddetvswihcpiedsfeKDFYSQLfselppsgpmevdKHTRQLREEkmvkfdppgavtssqhpnvnhsvvpelqrnamppprfevhdaapqnknlgdlgklvnfsqstappkgelgpcsgqfdrkrsgnltqgevrecsmmtvgsshcgsnqvaydldmsrasssglnddvrkvispsergktetieptvtsssggsgssfnrtskqstgdnslkrksrdavdsecqseaagfesgagnktaqrsgscrrSRAAEVHNLSERRRRDRINEKMRALQELIphcnktdkaSMLDEAIEYLKSLQLQLQVMWMgsgmaplmfpgmqhymsrmgmgmgppplpsvtnpmhfsrvplvdqsmSMAQAQNRAVMCQasvlnpvnyqnqmqnsnFTEQYARymgfhpmqansqpmnmfrfgsptmqnqivslpssscvpfsggaatdnsplsgkmVGERRRLIKWLWspifimgrsqegescsswrifgpflSCIAYDINALSIAWL
Flexible Loop (DISEMBL)
MQQIFVSSAMNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQaqtqrkpslnhneprqvqkqtlrgsgscgnssnliqddetVSWIHCPIEDSFEKDFYSQLFSelppsgpmeVDKHTRQLREEKMVKFDPpgavtssqhpnvnHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQstappkgelgpcsgqfdrkrsgnltqGEVRECSMMTVGSSHCGSNQVAYDLDMSRasssglnddvrkvispsergktetieptvtsssggsgssfnrtskqstgdnslkrksrdaVDSECQSeaagfesgagnktaqrsgscrrsraaevhnlserrrrdrINEKMRALqeliphcnktdKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGgaatdnsplsgkmVGERRRLIKWLWSPIFIMGRSQEGESCSSWRIFGPFLSCIAYDINALSIAWL
Low Complexity Region (SEG)
MQQIFVSSAMNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTsssggsgssFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRmgmgmgpppLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMVGERRRLIKWLWSPIFIMGRSQEGESCSSWRIFGPFLSCIAYDINALSIAWL
Disordered region (IsUnstruct)
*****VSSAMNPCIPDWNFEGDIPIS*********NELVELLWQNGHVVL***************************************DDETVSWIHCPIEDSFEKDFYSQLF************************************************************************************************************************************************************************************************************************************************************LIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHY****************************************AVMCQASVLNPVNYQ*******FTEQYARYMGF**************************************************VGERRRLIKWLWSPIFIMGRSQEGESCSSWRIFGPFLSCIAYDINALSIAW*
Disordered Region (DISOPRED)
****FVS*AMNPCIPDWNF******************LVELLWQ**********************************************DETVSWIHCPIEDSFEKDF********************************************************************************************************************************************************************************************************************************************************NEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLM****************************************************************************************************************************************LIKWLWSPIFIM*********SSWRIFGPFLSCIAYDINALSIAWL
Disordered Region (DISEMBL)
********AMNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLS*******************************NSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPS*********************************************************************************SERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMVGERRRLIKWLWSPIFIMGRSQEGESCSSWRIFGPFLSCIAYDINALSIAWL
Disordered Region (DISPRO)
*QQIFVSSAMNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSS**********************************LIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGP**************************************************************************************************************************************************************************************************************************************RRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPT********************************GERRRLIKWLWSPIFIMGRS***ESCSSWRIFGPFLSCIAYDINALSIAWL
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQQIFVSSAMNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMVGERRRLIKWLWSPIFIMGRSQEGESCSSWRIFGPFLSCIAYDINALSIAWL
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	589	2.2.26 [Sep-21-2011]
Q84LH8	444	Transcription factor PIF5	yes	no	0.444	0.590	0.445	5e-46
Q8W2F3	430	Transcription factor PIF4	no	no	0.470	0.644	0.413	9e-43
Q8GZM7	478	Transcription factor PIF1	no	no	0.697	0.859	0.323	4e-41
O80536	524	Transcription factor PIF3	no	no	0.614	0.690	0.367	1e-38
Q9SVU6	413	Transcription factor bHLH	no	no	0.551	0.786	0.336	6e-33
Q8L5W8	416	Transcription factor PIL1	no	no	0.230	0.326	0.448	2e-24
Q9SVU7	445	Putative transcription fa	no	no	0.246	0.325	0.409	3e-23
Q9FUA4	373	Transcription factor SPAT	no	no	0.164	0.260	0.582	2e-22
Q7XHI7	307	Transcription factor bHLH	no	no	0.251	0.482	0.394	7e-21
Q9FHA2	210	Transcription factor ALC	no	no	0.134	0.376	0.592	2e-20

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

 Score =  186 bits (472), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 142/319 (44%), Positives = 190/319 (59%), Gaps = 57/319 (17%)

Query: 228 SMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSG 287
           S++TVG SHCGSNQ           S+ ++      +S S+R K    E   TSS G SG
Sbjct: 146 SVITVGPSHCGSNQ-----------STNIHQATTLPVSMSDRSKN-VEERLDTSSGGSSG 193

Query: 288 SSFNRTSKQSTGDNS--LKRKSRDAVDSECQSEA---AGFESG----AGNKTAQRSGSCR 338
            S+ R +K++    S  + RK +  +D++ +S +    G  S      GNK++QRSGS R
Sbjct: 194 CSYGRNNKETVSGTSVTIDRKRKHVMDADQESVSQSDIGLTSTDDQTMGNKSSQRSGSTR 253

Query: 339 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMW 398
           RSRAAEVHNLSERRRRDRINE+M+ALQELIPHC++TDKAS+LDEAI+YLKSLQ+QLQVMW
Sbjct: 254 RSRAAEVHNLSERRRRDRINERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQLQVMW 313

Query: 399 MGSGM--------APLMFPGMQH--YMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSM 448
           MGSGM        +P+MFPG+Q   Y+++M M           + M  S+ P++++S   
Sbjct: 314 MGSGMAAAAAAAASPMMFPGVQSSPYINQMAM----------QSQMQLSQFPVMNRS--- 360

Query: 449 AQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHP--------MQ-ANSQPMNM 499
           A   +  ++CQ    NPV  Q Q QN   +EQ ARYMG  P        MQ    QP +M
Sbjct: 361 APQNHPGLVCQ----NPVQLQLQAQNQILSEQLARYMGGIPQMPPAGNQMQTVQQQPADM 416

Query: 500 FRFGSPTMQNQIVSLPSSS 518
             FGSP      +S P+++
Sbjct: 417 LGFGSPAGPQSQLSAPATT 435

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|Q8W2F3|PIF4_ARATH Transcription factor PIF4 OS=Arabidopsis thaliana GN=PIF4 PE=1 SV=1

 Score =  175 bits (443), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 134/324 (41%), Positives = 177/324 (54%), Gaps = 47/324 (14%)

Query: 216 SGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETI 275
           S  + + E+ + S+ TVG SHCGSN    DLD+S +     N  + + ++P+    +   
Sbjct: 145 SSGIRETEMEQYSVTTVGPSHCGSNPSQNDLDVSMSHDRSKN--IEEKLNPNASSSSGGS 202

Query: 276 EPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSG 335
                       +S     +  T D   KRK  +  D     E+       GNK+ QRSG
Sbjct: 203 SGCSFGKDIKEMAS----GRCITTDR--KRKRINHTD-----ESVSLSDAIGNKSNQRSG 251

Query: 336 SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQ 395
           S RRSRAAEVHNLSERRRRDRINE+M+ALQELIPHC+KTDKAS+LDEAI+YLKSLQLQLQ
Sbjct: 252 SNRRSRAAEVHNLSERRRRDRINERMKALQELIPHCSKTDKASILDEAIDYLKSLQLQLQ 311

Query: 396 VMW------MGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMA 449
           VMW        +  AP+MFPG+Q              +  + +P+   R P++DQS   A
Sbjct: 312 VMWMGSGMAAAAASAPMMFPGVQPQQF----------IRQIQSPVQLPRFPVMDQS---A 358

Query: 450 QAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHP-MQANS--QPMNMFRFGSPT 506
              N  ++CQ    NPV      QN   ++++ARY+G  P MQA +  QPM M RF SP 
Sbjct: 359 IQNNPGLVCQ----NPV------QNQIISDRFARYIGGFPHMQAATQMQPMEMLRFSSPA 408

Query: 507 MQNQIVSLPSSSCVPFSGGAATDN 530
            Q      PSS     + G+  D+
Sbjct: 409 GQQS--QQPSSVPTKTTDGSRLDH 430

Transcription factor acting negatively in the phytochrome B signaling pathway. May regulate the expression of a subset of genes involved in cell expansion by binding to the G-box motif.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  169 bits (429), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 167/517 (32%), Positives = 241/517 (46%), Gaps = 106/517 (20%)

Query: 10  MNPCIPDWNFEGDIPISNQ-----------MKPMGQDNELVELLWQNGHVVLSSQAQTQR 58
           M+  +PD++ + D  ++N            +  MG+D++L+ELLWQNG VV+ +Q    +
Sbjct: 1   MHHFVPDFDTDDDY-VNNHNSSLNHLPRKSITTMGEDDDLMELLWQNGQVVVQNQRLHTK 59

Query: 59  KPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQL-FSEL 117
           KPS   + P ++            + +  IQ+DE  SW+H P+ D    DF S L FS  
Sbjct: 60  KPS---SSPPKLLPSMDPQQQPSSDQNLFIQEDEMTSWLHYPLRDD---DFCSDLLFSA- 112

Query: 118 PPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDA 177
                      T      ++    PP + T+   P V         RN M          
Sbjct: 113 -------APTATATATVSQVTAARPPVSSTNESRPPV---------RNFM---------- 146

Query: 178 APQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGN----LTQGEVRECSMMT-- 231
                         NFS+             G F+  R G     L++  VRE + ++  
Sbjct: 147 --------------NFSR-----------LRGDFNNGRGGESGPLLSKAVVRESTQVSPS 181

Query: 232 ----VGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSG 287
                 +S  G  +     D S  +  G  +   K ++ +       IE T TSSS  S 
Sbjct: 182 ATPSAAASESGLTRRTDGTDSSAVAGGGAYNRKGKAVAMT----APAIEITGTSSSVVSK 237

Query: 288 SSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHN 347
           S       + T  +  KRK R+A  ++ ++E+   E+     +   + S +RSRAAEVHN
Sbjct: 238 SEIE---PEKTNVDDRKRKEREATTTD-ETESRSEETKQARVS---TTSTKRSRAAEVHN 290

Query: 348 LSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLM 407
           LSER+RRDRINE+M+ALQELIP CNK+DKASMLDEAIEY+KSLQLQ+Q+M MG GM P+M
Sbjct: 291 LSERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQLQIQMMSMGCGMMPMM 350

Query: 408 FPGMQHYMSRMGMGMG-----PPPLPSVTNPMHFSRVPLVDQS--------MSMAQAQNR 454
           +PGMQ YM  M MGMG     PPP       M  ++ PL  Q+          +  +   
Sbjct: 351 YPGMQQYMPHMAMGMGMNQPIPPPSFMPFPNMLAAQRPLPTQTHMAGSGPQYPVHASDPS 410

Query: 455 AVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQ 491
            V       +P + Q Q   + +T+ Y ++ G HP Q
Sbjct: 411 RVFVPNQQYDPTSGQPQYP-AGYTDPYQQFRGLHPTQ 446

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

 Score =  161 bits (408), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 151/411 (36%), Positives = 207/411 (50%), Gaps = 49/411 (11%)

Query: 36  NELVELLWQNGHVVLSSQAQTQRK---PSLNHNEPRQVQKQTLRGSGSCGNS-------- 84
           +E+VEL+W+NG +   SQ+   R    P  N +  R++      G+GS            
Sbjct: 27  DEVVELVWENGQISTQSQSSRSRNIPPPQANSSRAREI------GNGSKTTMVDEIPMSV 80

Query: 85  ----SNLIQDDETVSWI-HCPIEDSFEKDFYSQLFSELPPS---GPMEVDKHTRQLREEK 136
               + L QDD+ V W+ H P  D +  DF   + S +  +     M V++    L + +
Sbjct: 81  PSLMTGLSQDDDFVPWLNHHPSLDGYCSDFLRDVSSPVTVNEQESDMAVNQTAFPLFQRR 140

Query: 137 MVKFDPPGAVTSSQHPNV-NHSVVPELQRNAMP-----PPRFEVHDAAPQNKNLGDLGKL 190
               +   A +SSQ+    +HS+    +   +P     P RF          N      L
Sbjct: 141 KDGNESAPAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNKP---SL 197

Query: 191 VNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSR 250
           VNFS    P        +   D K     +   V +  ++    S    ++V   L+ S 
Sbjct: 198 VNFSHFLRPATFAKTTNNNLHDTKEKSPQSPPNVFQTRVLGAKDSE---DKV---LNESV 251

Query: 251 ASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDA 310
           AS++  ++    +IS     K +  E  V  SS GSG+S +  S+  +   SLKRK  + 
Sbjct: 252 ASATPKDNQKACLISEDSCRKDQESEKAVVCSSVGSGNSLDGPSESPSL--SLKRKHSNI 309

Query: 311 VDSECQSEAAGFESGAGNKTA--QRSG-SCRRSRAAEVHNLSERRRRDRINEKMRALQEL 367
            D +C SE    ESG G K A   R+G   +RSR+AEVHNLSERRRRDRINEKMRALQEL
Sbjct: 310 QDIDCHSEDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDRINEKMRALQEL 369

Query: 368 IPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSG--MAP-LMF-PGMQHY 414
           IP+CNK DKASMLDEAIEYLKSLQLQ+Q+M M SG  + P +MF PGM HY
Sbjct: 370 IPNCNKVDKASMLDEAIEYLKSLQLQVQIMSMASGYYLPPAVMFPPGMGHY 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|Q9SVU6|BH023_ARATH Transcription factor bHLH23 OS=Arabidopsis thaliana GN=BHLH23 PE=2 SV=1

 Score =  142 bits (359), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 144/428 (33%), Positives = 191/428 (44%), Gaps = 103/428 (24%)

Query: 25  ISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNS 84
           IS +   MG+D+ +VELL ++  VV SSQ QT   PS +   P  +    LRGSGS    
Sbjct: 15  ISPEKYIMGEDD-IVELLGKSSQVVTSSQTQT---PSCD---PPLI----LRGSGSGDGE 63

Query: 85  SN----------------LIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKH 128
            N                 IQ+DE  SW+H P    +       L+S+L  SG       
Sbjct: 64  GNGPLPQPPPPLYHQQSLFIQEDEMASWLHQPNRQDY-------LYSQLLYSG------- 109

Query: 129 TRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAA--PQNKNLGD 186
                              +S HP    S+ P       PPPR +   AA  P    L +
Sbjct: 110 ------------------VASTHPQSLASLEPP------PPPRAQYILAADRPTGHILAE 145

Query: 187 LGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVREC-SMMTVGSSHCGSNQVAYD 245
             +  NF                   R+R GN+  G V    S  T+ SS   S    + 
Sbjct: 146 R-RAENFMN---------------ISRQR-GNIFLGGVEAVPSNSTLLSSATESIPATHG 188

Query: 246 LDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSL-- 303
            + SRA+ +G       V     RGK   IE   T S G   +      +Q   +  +  
Sbjct: 189 TE-SRATVTGGVSRTFAVPGLGPRGKAVAIETAGTQSWGLCKAETEPVQRQPATETDITD 247

Query: 304 --KRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKM 361
             KRK+R+  + E Q          G + A+ S S +RSRAA +H LSERRRR +INE M
Sbjct: 248 ERKRKTREETNVENQ----------GTEEARDSTSSKRSRAAIMHKLSERRRRQKINEMM 297

Query: 362 RALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMA-PLMFPG--MQHYMSRM 418
           +ALQEL+P C KTD++SMLD+ IEY+KSLQ Q+Q+  MG  M  P+M+ G   Q YM  M
Sbjct: 298 KALQELLPRCTKTDRSSMLDDVIEYVKSLQSQIQMFSMGHVMIPPMMYAGNIQQQYMPHM 357

Query: 419 GMGMGPPP 426
            MGM  PP
Sbjct: 358 AMGMNRPP 365

Arabidopsis thaliana (taxid: 3702)

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

 Score =  114 bits (285), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 65/145 (44%), Positives = 90/145 (62%), Gaps = 9/145 (6%)

Query: 285 GSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQ-----RSGSCRR 339
            S S F+R + +     SLKRK  D  + E    +   +  + +   Q     R    +R
Sbjct: 168 ASSSKFSRGTSRDLSCCSLKRKYGDIEEEESTYLSNNSDDESDDAKTQVHARTRKPVTKR 227

Query: 340 SRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWM 399
            R+ EVH L ER+RRD  N+KMRALQ+L+P+C K DKAS+LDEAI+Y+++LQLQ+Q+M M
Sbjct: 228 KRSTEVHKLYERKRRDEFNKKMRALQDLLPNCYKDDKASLLDEAIKYMRTLQLQVQMMSM 287

Query: 400 GSGMA--PLMFPGMQHYMSRMGMGM 422
           G+G+   P M P M HY S MG+GM
Sbjct: 288 GNGLIRPPTMLP-MGHY-SPMGLGM 310

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  110 bits (275), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 70/171 (40%), Positives = 93/171 (54%), Gaps = 26/171 (15%)

Query: 269 RGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGN 328
           +GK   +E   T SSG   +       Q   ++ LK +                E   G 
Sbjct: 199 KGKAVAVEAAGTPSSGVCKAETEPVQIQPATESKLKAR----------------EETHGT 242

Query: 329 KTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLK 388
           + A+ S S +RSR AE+HNL+ERRRR++INEKM+ LQ+LIP CNK+ K S LD+AIEY+K
Sbjct: 243 EEARGSTSRKRSRTAEMHNLAERRRREKINEKMKTLQQLIPRCNKSTKVSTLDDAIEYVK 302

Query: 389 SLQLQLQVMWMGSGMAPLMFPG-MQHYMSRMGMGMGPP----PLPSVTNPM 434
           SLQ Q+Q M     M+P+M  G  Q +M  M M M  P    P P  + PM
Sbjct: 303 SLQSQIQGM-----MSPMMNAGNTQQFMPHMAMDMNRPPPFIPFPGTSFPM 348

Arabidopsis thaliana (taxid: 3702)

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

 Score =  107 bits (268), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 60/103 (58%), Positives = 73/103 (70%), Gaps = 6/103 (5%)

Query: 314 ECQSEAAGF----ESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIP 369
           +C+SE  G     E+ +         S +R RAAEVHNLSE+RRR RINEKM+ALQ LIP
Sbjct: 166 DCESEEGGEAVVDEAPSSKSGPSSRSSSKRCRAAEVHNLSEKRRRSRINEKMKALQSLIP 225

Query: 370 HCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSG--MAPLMFPG 410
           + NKTDKASMLDEAIEYLK LQLQ+Q++ M +G  + PL  PG
Sbjct: 226 NSNKTDKASMLDEAIEYLKQLQLQVQMLTMRNGINLHPLCLPG 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 =  102 bits (255), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 69/175 (39%), Positives = 96/175 (54%), Gaps = 27/175 (15%)

Query: 327 GNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEY 386
           G + A+ S S +RSRAAE+HNL+ERRRR++INE+M+ LQ+LIP CNK+ K SML++ IEY
Sbjct: 136 GTEEARGSTSRKRSRAAEMHNLAERRRREKINERMKTLQQLIPRCNKSTKVSMLEDVIEY 195

Query: 387 LKSLQLQLQV----MWMGSGMAPLMFP-GMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPL 441
           +KSL++Q+      M MG    P   P   Q +M+ +G    PP  P       F  +  
Sbjct: 196 VKSLEMQINQFMPHMAMGMNQPPAYIPFPSQAHMAGVGPSYPPPRYP-------FPNIQT 248

Query: 442 VDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQP 496
            D S          V  Q+   NPV+ Q QM        Y +++G H MQ +  P
Sbjct: 249 FDPS---------RVWLQSPQPNPVSNQPQM------NPYGQFVGHHQMQQSLPP 288

Arabidopsis thaliana (taxid: 3702)

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

 Score =  101 bits (251), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/81 (59%), Positives = 64/81 (79%), Gaps = 2/81 (2%)

Query: 331 AQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSL 390
           A++  S +R+  A+ HNLSE++RR +INEKM+ALQ+LIP+ NKTDKASMLDEAIEYLK L
Sbjct: 83  AKQRNSLKRNIDAQFHNLSEKKRRSKINEKMKALQKLIPNSNKTDKASMLDEAIEYLKQL 142

Query: 391 QLQLQVMWM--GSGMAPLMFP 409
           QLQ+Q + +  G G+ P+  P
Sbjct: 143 QLQVQTLAVMNGLGLNPMRLP 163

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

Arabidopsis thaliana (taxid: 3702)

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	589
225446765	531	PREDICTED: transcription factor PIF5-lik	0.867	0.962	0.586	1e-160
449463597	550	PREDICTED: transcription factor PIF5-lik	0.867	0.929	0.596	1e-159
302143504	544	unnamed protein product [Vitis vinifera]	0.825	0.893	0.606	1e-158
356553623	562	PREDICTED: transcription factor PIF5-lik	0.886	0.928	0.516	1e-125
356501423	562	PREDICTED: transcription factor PIF4-lik	0.877	0.919	0.512	1e-123
224082612	380	predicted protein [Populus trichocarpa]	0.612	0.95	0.640	1e-109
356567480	397	PREDICTED: transcription factor PIF5-lik	0.626	0.929	0.548	3e-96
224066527	233	predicted protein [Populus trichocarpa]	0.385	0.974	0.753	9e-85
356526934	266	PREDICTED: transcription factor PIF5-lik	0.444	0.984	0.622	7e-71
108862947	446	Helix-loop-helix DNA-binding domain cont	0.589	0.778	0.402	3e-61

>gi|225446765|ref|XP_002278399.1| PREDICTED: transcription factor PIF5-like [Vitis vinifera]

 Score =  571 bits (1471), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 316/539 (58%), Positives = 383/539 (71%), Gaps = 28/539 (5%)

Query: 11  NPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQV 70
           +P +PDWN EGD+P++NQ KPMGQ++ELVELLW+NG VVL SQ  TQRK  L  NE +QV
Sbjct: 3   HPLLPDWNIEGDVPVTNQKKPMGQEHELVELLWRNGQVVLHSQ--TQRKSGLAPNESKQV 60

Query: 71  QKQT---LRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDK 127
           QK     LR  GSCGN SNLIQD+E++SWI  P++DS +K+F S LF ELPP+ P++ +K
Sbjct: 61  QKHDQTMLRNGGSCGNWSNLIQDEESISWIQYPLDDSLDKEFCSNLFMELPPNDPVQPEK 120

Query: 128 HTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDL 187
             R   +EK        +V SSQ P   H   PE   N MPPP+F+V  +  QN + G  
Sbjct: 121 PVRHSEQEK--------SVPSSQQPIFKHLGSPEFPGNPMPPPKFQVPGSVQQNCSSGGF 172

Query: 188 GKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQG-EVRECSMMTVGSSHCGSNQVAYDL 246
           GK+VNF   + P +  LG    Q   K SGN+ QG + +E S+MTVG SHCGSNQV  + 
Sbjct: 173 GKIVNFPNFSFPGRSNLGSSKAQLGGKGSGNMAQGGDAKEGSVMTVGLSHCGSNQVVNEA 232

Query: 247 DMSRASSSGL----------NDDVRKVISPSERGKTETIEPTVTSSSGGSGSS-FNRTSK 295
           D+SR SSSG+           ++V +++S  +R +TET+EPTVTSSSGG   S F RT K
Sbjct: 233 DLSRFSSSGVGTGCLSSGHVKENVMRIVSQGDRRQTETLEPTVTSSSGGGSGSSFGRTYK 292

Query: 296 QSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRD 355
           QST  NS KRK R+A +SECQSEAA  ES A NK +QRSGS RRSRAAEVHNLSERRRRD
Sbjct: 293 QSTDTNSHKRKGREAEESECQSEAAEHESAARNKASQRSGSTRRSRAAEVHNLSERRRRD 352

Query: 356 RINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYM 415
           RINEKM+ALQELIPH NK+DKASMLDEAIEYLKSLQLQLQ+MWMG G+AP+MFPG+QHYM
Sbjct: 353 RINEKMKALQELIPHSNKSDKASMLDEAIEYLKSLQLQLQLMWMGGGVAPMMFPGVQHYM 412

Query: 416 SRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNS 475
           +RMGMGM PPPLPS+ NPMH  RV LVDQS S     N+  +CQ  VLNPVNYQNQM N 
Sbjct: 413 ARMGMGMCPPPLPSIHNPMHLPRVQLVDQSTSAVPPSNQPPICQTPVLNPVNYQNQMPNP 472

Query: 476 NFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLS 534
           NF EQ+A YMGFHPMQ  SQPMN+F FGS   Q+  ++ P+++    +  AA D +P S
Sbjct: 473 NFPEQFAHYMGFHPMQTPSQPMNVFSFGS---QSHPMASPATTGGTPTAAAAVDGAPGS 528

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463597|ref|XP_004149520.1| PREDICTED: transcription factor PIF5-like [Cucumis sativus] gi|449505798|ref|XP_004162571.1| PREDICTED: transcription factor PIF5-like [Cucumis sativus]

 Score =  569 bits (1467), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 330/553 (59%), Positives = 394/553 (71%), Gaps = 42/553 (7%)

Query: 10  MNPCIPDWNFEGDIPISNQMKPMG-QDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPR 68
           MN C PDWNFEGDIP +   K MG + ++LVELLW+NG VVL  Q+Q  RK SL  NE R
Sbjct: 1   MNYCFPDWNFEGDIPPAK--KSMGPEHDDLVELLWRNGQVVL--QSQKARKSSLIANEVR 56

Query: 69  QVQKQT---LRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEV 125
           Q QKQ     R + SCGNSSNLIQDDETVSWI  P++DSFEK+F S  FSELPP+ P+E+
Sbjct: 57  QFQKQNQPLYRSNVSCGNSSNLIQDDETVSWIQDPLDDSFEKEFCSNFFSELPPADPIEI 116

Query: 126 DKH-TRQLREEKMVKFDPPGAVTSSQHPNVNHSV---------VPELQRNAMPPPRFEVH 175
            K   +  +++K  +F   GA  ++ H    + V         + E   N MPPPRF+  
Sbjct: 117 VKQPIKHFQDDKQTRF---GAFDTATHVTFGNFVKKNSKPPASLAEFPMNTMPPPRFQFQ 173

Query: 176 DAAPQNKNLGDLGKLVNFSQSTAPP-KGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGS 234
           D++ QNK+LGDLGKLVNFSQ   PP KG+LG  +G    + SGNL QGE R+CS MTVGS
Sbjct: 174 DSSRQNKDLGDLGKLVNFSQVPVPPLKGDLGSSNG---GRESGNLIQGEGRDCSGMTVGS 230

Query: 235 SHCGSNQVAY--DLDMSRASSSGL----------NDDVRKVISPSERGKTETIEPTVTSS 282
           SHCGSNQV    DLD+SR S+SG            +D RK+++  ER KTET++PT TSS
Sbjct: 231 SHCGSNQVPNPNDLDLSRVSTSGFGNAGLSAGFSKEDNRKMVAQGERDKTETMDPTATSS 290

Query: 283 SGGSGSSFNR--TSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRS 340
           SGGSGSS +R  T  QSTG N  KRK RD  +SECQSE A  ES  GNKTA RSGS RR+
Sbjct: 291 SGGSGSSMDRSRTIGQSTGGNGNKRKGRDGEESECQSETAELESAEGNKTAPRSGSSRRT 350

Query: 341 RAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMG 400
           RAAEVHNLSERRRR+RINEKM+ALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMG
Sbjct: 351 RAAEVHNLSERRRRERINEKMKALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMG 410

Query: 401 SGMAPLMFPGMQHYMSR--MGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMC 458
           SGMAP+MFPG+QHYMSR  MGMGM  P +PS+ NPM   RVP+VDQS+S+A   N+ +MC
Sbjct: 411 SGMAPMMFPGVQHYMSRVAMGMGMAQPSMPSIHNPMQLPRVPIVDQSVSVAPTPNQPMMC 470

Query: 459 QASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRF-GSPTMQNQIVSLPSS 517
           Q  + NP+NYQNQMQN    EQYAR MGFH MQ  SQP+N+FRF  S  +Q+Q  + P  
Sbjct: 471 QPQMFNPMNYQNQMQNPALQEQYARLMGFHHMQPTSQPINVFRFCPSAVLQSQPAAAPGP 530

Query: 518 SCVPFSGGAATDN 530
           +  P +GG+ T++
Sbjct: 531 ASGPTAGGSITND 543

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302143504|emb|CBI22065.3| unnamed protein product [Vitis vinifera]

 Score =  565 bits (1457), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 310/511 (60%), Positives = 369/511 (72%), Gaps = 25/511 (4%)

Query: 11  NPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQV 70
           +P +PDWN EGD+P++NQ KPMGQ++ELVELLW+NG VVL SQ  TQRK  L  NE +QV
Sbjct: 3   HPLLPDWNIEGDVPVTNQKKPMGQEHELVELLWRNGQVVLHSQ--TQRKSGLAPNESKQV 60

Query: 71  QKQT---LRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDK 127
           QK     LR  GSCGN SNLIQD+E++SWI  P++DS +K+F S LF ELPP+ P++ +K
Sbjct: 61  QKHDQTMLRNGGSCGNWSNLIQDEESISWIQYPLDDSLDKEFCSNLFMELPPNDPVQPEK 120

Query: 128 HTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDL 187
             R   +EK        +V SSQ P   H   PE   N MPPP+F+V  +  QN + G  
Sbjct: 121 PVRHSEQEK--------SVPSSQQPIFKHLGSPEFPGNPMPPPKFQVPGSVQQNCSSGGF 172

Query: 188 GKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQG-EVRECSMMTVGSSHCGSNQVAYDL 246
           GK+VNF   + P +  LG    Q   K SGN+ QG + +E S+MTVG SHCGSNQV  + 
Sbjct: 173 GKIVNFPNFSFPGRSNLGSSKAQLGGKGSGNMAQGGDAKEGSVMTVGLSHCGSNQVVNEA 232

Query: 247 DMSRASSSGL----------NDDVRKVISPSERGKTETIEPTVTSSSGGSGSS-FNRTSK 295
           D+SR SSSG+           ++V +++S  +R +TET+EPTVTSSSGG   S F RT K
Sbjct: 233 DLSRFSSSGVGTGCLSSGHVKENVMRIVSQGDRRQTETLEPTVTSSSGGGSGSSFGRTYK 292

Query: 296 QSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRD 355
           QST  NS KRK R+A +SECQSEAA  ES A NK +QRSGS RRSRAAEVHNLSERRRRD
Sbjct: 293 QSTDTNSHKRKGREAEESECQSEAAEHESAARNKASQRSGSTRRSRAAEVHNLSERRRRD 352

Query: 356 RINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYM 415
           RINEKM+ALQELIPH NK+DKASMLDEAIEYLKSLQLQLQ+MWMG G+AP+MFPG+QHYM
Sbjct: 353 RINEKMKALQELIPHSNKSDKASMLDEAIEYLKSLQLQLQLMWMGGGVAPMMFPGVQHYM 412

Query: 416 SRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNS 475
           +RMGMGM PPPLPS+ NPMH  RV LVDQS S     N+  +CQ  VLNPVNYQNQM N 
Sbjct: 413 ARMGMGMCPPPLPSIHNPMHLPRVQLVDQSTSAVPPSNQPPICQTPVLNPVNYQNQMPNP 472

Query: 476 NFTEQYARYMGFHPMQANSQPMNMFRFGSPT 506
           NF EQ+A YMGFHPMQ  SQPMN+F FGS T
Sbjct: 473 NFPEQFAHYMGFHPMQTPSQPMNVFSFGSQT 503

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356553623|ref|XP_003545154.1| PREDICTED: transcription factor PIF5-like [Glycine max]

 Score =  456 bits (1173), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 289/560 (51%), Positives = 359/560 (64%), Gaps = 38/560 (6%)

Query: 10  MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQ 69
           M   IP  +FE D  ++NQ K +G D ELVELLWQNG VV     QT RKP  N +  RQ
Sbjct: 1   MKNSIPGLDFESDACLTNQRKLIGPDQELVELLWQNGQVV--RHNQTHRKPLGNSSNLRQ 58

Query: 70  VQK---QTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVD 126
            QK    TLR SG  GNSSNL Q+ E   WI  P+ED  E+DF S L SELPP+   E  
Sbjct: 59  AQKTDHSTLRSSGPYGNSSNLDQE-EATPWIQFPLEDPLEQDFCSNLLSELPPTCEFESY 117

Query: 127 KHTRQLREEKMVKF----DPPGAVTSSQHP---NVNHSVVPELQRNA--MPPPRFEVHDA 177
           K  +QL E+K   F     P    TSS  P   N+  S V  +Q N   MP PRF V D+
Sbjct: 118 KPIKQLEEDKFTNFFASSTPHHPTTSSSKPLPPNMTSSWVQRIQGNPNPMPAPRFHVPDS 177

Query: 178 APQNKNLGDLGKLVNFSQSTAPPKG-ELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSH 236
           + ++ +LG   K++NF   + P       P S QF  K + NL+Q E RE S++TVGSSH
Sbjct: 178 SQKDNDLGASRKVLNFPHFSTPRNNVSSAPGSTQFREKTTANLSQSEAREYSVITVGSSH 237

Query: 237 CGSNQVAYDLDMSRASSSGL----------------NDDVRKVISP-SERGKTETIEPTV 279
           CGS+ +  + D+SR SSS +                 D V++ I P S++GK+E IEPTV
Sbjct: 238 CGSSHIPQEKDVSRVSSSAVWATNNNNSLSAEPEAVRDCVQRPICPRSDKGKSEMIEPTV 297

Query: 280 TSSSGGSGSSFN-RTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCR 338
           TSSSGGSGS+   RT   ST D+  KRK  +   SE QSEA   +S  GNK +QR+GS +
Sbjct: 298 TSSSGGSGSTGIGRTCSLSTRDHGQKRKGTEEEASEEQSEATELKSADGNKASQRTGSSK 357

Query: 339 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMW 398
           R+RAAEVHN SERRRRDRINEKMR LQ+LIP+ NKTDKASML+EAIEYLKSLQ QLQVMW
Sbjct: 358 RNRAAEVHNQSERRRRDRINEKMRTLQQLIPNSNKTDKASMLEEAIEYLKSLQFQLQVMW 417

Query: 399 MGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMC 458
           MGSGM P+MFPG+QHYMS+MGMGMG P LPS+ NPM   +VP  DQ+MS+ Q  N+ +MC
Sbjct: 418 MGSGMTPVMFPGIQHYMSQMGMGMGAPSLPSIYNPMQLPKVPH-DQAMSVPQMPNQNLMC 476

Query: 459 QASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQ--IVSLPS 516
           Q  VL   NYQ  MQN    EQYA YMG+H M++ SQPMN+FR+GS  +Q+   +++  +
Sbjct: 477 QNQVLGAFNYQTHMQNPCLPEQYAPYMGYHFMRSASQPMNVFRYGSQAVQHSQTMIAPGN 536

Query: 517 SSCVPFSGGAATDNSPLSGK 536
           +S  P SG A  D++ +SGK
Sbjct: 537 NSSGPMSGTANIDDA-VSGK 555

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356501423|ref|XP_003519524.1| PREDICTED: transcription factor PIF4-like [Glycine max]

 Score =  448 bits (1152), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 285/556 (51%), Positives = 352/556 (63%), Gaps = 39/556 (7%)

Query: 10  MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQ 69
           MN  IP W+FE D  ++NQ K +G D ELVELLW+NG VV+ +Q  T RK   N +  RQ
Sbjct: 1   MNNSIPGWDFESDTCLTNQRKLIGPDQELVELLWKNGQVVMHNQ--THRKTLGNSSNLRQ 58

Query: 70  VQKQ---TLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVD 126
           VQK     LR SG  GNSSNL Q+D    W+  P+ED  E+DF S L SELP +   E  
Sbjct: 59  VQKSDQSVLRSSGPYGNSSNLDQED-AAPWVQFPLEDPLEQDFCSNLLSELP-TCEFESY 116

Query: 127 KHTRQLREEKMVKF----DPPGAVTSSQHP---NVNHSVVPELQRNA--MPPPRFEVHDA 177
           K  RQL EEK  KF     P    TSS  P   N+  S +  LQ N   MP PRF   D+
Sbjct: 117 KPIRQLEEEKFAKFFASGTPHHPTTSSSQPLPPNMKPSCIQGLQGNPIPMPAPRFHGPDS 176

Query: 178 APQNKNLGDLGKLVNFSQSTAPPKG-ELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSH 236
           + +  + G   K++NF Q + P       P   QF  K + N++Q E RE S++TVGSSH
Sbjct: 177 SQKIHDFGASRKVLNFPQFSTPRNNVPSAPGITQFREKTTANMSQSEAREYSVITVGSSH 236

Query: 237 CGSNQVAYDLDMSRASSSGL-----------------NDDVRKVISP-SERGKTETIEPT 278
           CGSN +  + D+SR SS+G+                  D V++ I P S +GK+E IE T
Sbjct: 237 CGSNHIPQEQDVSRISSTGVWATTNNNTTLSAEPEAVRDYVQRPICPKSGQGKSEMIELT 296

Query: 279 VTSSSGGSGSSFN-RTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSC 337
           VTSSSGGSGS+   RT   ST D+  KRK  +    E QSE    +S  GNK +QR+ S 
Sbjct: 297 VTSSSGGSGSTGIGRTCSLSTRDHGQKRKGTEEEALEEQSEDTELKSADGNKASQRTRSS 356

Query: 338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVM 397
           RR+RAAEVHN SERRRRDRINEKMR LQ+LIP+ NKTDKASML+EAIEYLKSLQ QLQVM
Sbjct: 357 RRNRAAEVHNQSERRRRDRINEKMRTLQQLIPNSNKTDKASMLEEAIEYLKSLQFQLQVM 416

Query: 398 WMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVM 457
           WMG GM P+MFPG+QHYMS+MGMGMG P LPS+ NPM   +VP  DQ+MS+ Q  N+ +M
Sbjct: 417 WMGGGMTPVMFPGIQHYMSQMGMGMGAPSLPSIHNPMQLPKVPH-DQAMSVLQIPNQNLM 475

Query: 458 CQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQ--IVSLP 515
           CQ  VL   NYQNQMQN    EQYARYMG+H MQ  SQPMN+FR+GS  +Q+   +++  
Sbjct: 476 CQNPVLGAFNYQNQMQNPCLPEQYARYMGYHLMQNASQPMNVFRYGSQAVQHSQTMIAPG 535

Query: 516 SSSCVPFSGGAATDNS 531
           ++S  P SG A  D++
Sbjct: 536 NNSSGPMSGTANIDDA 551

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224082612|ref|XP_002306764.1| predicted protein [Populus trichocarpa] gi|222856213|gb|EEE93760.1| predicted protein [Populus trichocarpa]

 Score =  401 bits (1031), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 249/389 (64%), Positives = 289/389 (74%), Gaps = 28/389 (7%)

Query: 167 MPPPRFEVHDAAPQNKNLGDLGKLVN--FSQSTAPPKG-ELGPCSGQFDRKRSGNLTQGE 223
           MPPPR +V +    +  +G  G+ VN  FSQ +AP KG +    SGQF  + SGN  QGE
Sbjct: 1   MPPPRIQVPEK--NHAGVGGFGEAVNANFSQFSAPFKGGDFRTSSGQFGGQGSGNSPQGE 58

Query: 224 VRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLN-----------DDVRKVISPSERGKT 272
           VRECS++TVGSS    NQ+ +D DMSRASS+ +            DD RK++S SERGKT
Sbjct: 59  VRECSVVTVGSS----NQIPHDRDMSRASSNAMGTSTAFSTGPSMDDPRKIVSQSERGKT 114

Query: 273 ETIEPTVTSSSGGSGSSFNRTSKQSTG-DNSLKRKSRDAVDSECQSEAA--GFESGAGNK 329
           ET+E T+T+SSGGSGSSF RT KQS G  +S KRK+ D  DSE QSEAA    +S AGN 
Sbjct: 115 ETLEATLTTSSGGSGSSFGRTCKQSAGPSSSQKRKTIDTEDSEYQSEAAELDLDSMAGNN 174

Query: 330 TAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKS 389
             +RSGS RRSRAAEVHNLSERRRRDRINEKMRALQELIPHC KTDKASMLDEAIEYLKS
Sbjct: 175 PTKRSGSTRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCYKTDKASMLDEAIEYLKS 234

Query: 390 LQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMA 449
           LQLQLQVMWMG GMAP++FPG+QH+MSRMGMG   PPLPS+ NPMH  RV L+DQS+SMA
Sbjct: 235 LQLQLQVMWMGGGMAPMLFPGVQHFMSRMGMG---PPLPSMQNPMHLPRVQLIDQSISMA 291

Query: 450 QAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTM-Q 508
             QN  VMCQA VLNPVN+ NQMQN  F +QYAR+MGFH MQA SQPMNMFRFGS T+ Q
Sbjct: 292 PTQNSGVMCQAPVLNPVNFHNQMQNPAFADQYARFMGFH-MQAASQPMNMFRFGSQTVQQ 350

Query: 509 NQIVSLPSSSCVPFSGGAATDNSPLSGKM 537
           NQ+++  SS   P S G A  ++P S K+
Sbjct: 351 NQMMAPTSSVGGPLSAGTAVSDAPPSDKV 379

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356567480|ref|XP_003551947.1| PREDICTED: transcription factor PIF5-like [Glycine max]

 Score =  359 bits (921), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 211/385 (54%), Positives = 266/385 (69%), Gaps = 16/385 (4%)

Query: 167 MPPPRFEVHDAAPQNKN-LGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVR 225
           +P PRF V D+  +N N LG   K+ NFS  +AP        +  F  K +GN+++ E+R
Sbjct: 14  IPAPRFHVSDSPQKNNNDLGGSCKVQNFSHFSAPLNVSSASANAHFRDKITGNMSKNEIR 73

Query: 226 ECSMMTVGSSHCGSNQVAYDLDMSRASSSGL------------NDDVRKVISPSERGKTE 273
           ECS+MTVGSS+CGSN +  D D SRASS+G+             D V +    +E+GK+E
Sbjct: 74  ECSLMTVGSSYCGSNHIPQDPDASRASSNGVWTTTLSAEPEAVRDHVPRTSPQNEKGKSE 133

Query: 274 TIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQR 333
            +EPT TSSSGGSGSS  +    ST +   KRK  D  +SE QSE    +S  GNK++QR
Sbjct: 134 MLEPTTTSSSGGSGSSLGKNCSLSTRNQGQKRKGIDVEESEEQSEDTELKSALGNKSSQR 193

Query: 334 SGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQ 393
           +G  RR+RAAEVHNLSERRRRDRINEKM+ALQ+LIPH +KTDKASML+EAIEYLKSLQLQ
Sbjct: 194 AGLARRNRAAEVHNLSERRRRDRINEKMKALQQLIPHSSKTDKASMLEEAIEYLKSLQLQ 253

Query: 394 LQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQN 453
           LQ+MWMGSGMAP+MFPG+QHYMS+MGMGM  PP P + NPM   R+PL DQS+S +Q  N
Sbjct: 254 LQLMWMGSGMAPIMFPGIQHYMSQMGMGMATPPFPPIHNPMQLPRLPL-DQSVSASQTPN 312

Query: 454 RAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQN-QIV 512
           + +M Q  +L   NY NQMQN   +EQYARYMG+H MQ  SQPMN+FR+G   +++ Q +
Sbjct: 313 QTLMSQNPILGAFNYHNQMQNPALSEQYARYMGYHLMQNASQPMNVFRYGPQGVRHSQTM 372

Query: 513 SLPSSSCVPFSGGAATDNSPLSGKM 537
             PS+S    SG A  D + +SGKM
Sbjct: 373 ITPSNSSGNMSGAANIDEA-VSGKM 396

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224066527|ref|XP_002302124.1| predicted protein [Populus trichocarpa] gi|222843850|gb|EEE81397.1| predicted protein [Populus trichocarpa]

 Score =  321 bits (822), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 174/231 (75%), Positives = 195/231 (84%), Gaps = 4/231 (1%)

Query: 309 DAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELI 368
           DA +SECQSE A  +S   NK A+RSGS RRSRAAEVHNLSERRRRDRINEKMRALQELI
Sbjct: 2   DAEESECQSEDAELDSAVANKPAKRSGSTRRSRAAEVHNLSERRRRDRINEKMRALQELI 61

Query: 369 PHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSR--MGMGMGPPP 426
           PHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSG+ P+MFPG+QH+MSR  MGMGMGPPP
Sbjct: 62  PHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGIVPVMFPGVQHFMSRMGMGMGMGPPP 121

Query: 427 LPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMG 486
           LPS+ NPMH  RVPLVDQS+SM   QN+AV+CQ  VLNPVNYQNQMQN  F++QYAR+MG
Sbjct: 122 LPSMQNPMHLPRVPLVDQSISMTPTQNQAVICQTPVLNPVNYQNQMQNPTFSDQYARFMG 181

Query: 487 FHPMQANSQPMNMFRFGSPTM-QNQIVSLPSSSCVPFSGGAATDNSPLSGK 536
           FH MQA SQPMNMFRFGS T+ QNQ+++ P+S   P S G A  ++P SGK
Sbjct: 182 FH-MQAASQPMNMFRFGSQTVQQNQMMAPPNSGGGPLSAGTAASDAPPSGK 231

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356526934|ref|XP_003532070.1| PREDICTED: transcription factor PIF5-like [Glycine max]

 Score =  275 bits (702), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 165/265 (62%), Positives = 199/265 (75%), Gaps = 3/265 (1%)

Query: 275 IEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRS 334
           +EP VTSSSGGSGSS  +T   ST +   KRK  D  +SE QSE    +S  GNK++QR+
Sbjct: 2   LEPAVTSSSGGSGSSLGKTCSLSTRNQGQKRKGIDVEESEEQSEDTELKSALGNKSSQRT 61

Query: 335 GSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQL 394
           GS RR+RAAEVHNLSERRRRDRINEKM+ALQ+LIPH +KTDKASML+EAIEYLKSLQLQL
Sbjct: 62  GSARRNRAAEVHNLSERRRRDRINEKMKALQQLIPHSSKTDKASMLEEAIEYLKSLQLQL 121

Query: 395 QVMWMGSGMAPLMFPGMQHYMSRMGMGMG-PPPLPSVTNPMHFSRVPLVDQSMSMAQAQN 453
           Q+MWMGSGMAP+MFPG+QHYMS+MGMGM  PP  P + NPM   RVPL D+S+S +Q  N
Sbjct: 122 QLMWMGSGMAPIMFPGIQHYMSQMGMGMARPPFPPPIHNPMQLPRVPL-DKSVSASQTPN 180

Query: 454 RAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQN-QIV 512
           + +MCQ  +L   NYQNQMQN   +EQY RYMG+H MQ  SQPMN+FR+G   +Q+ Q +
Sbjct: 181 QTLMCQNPILGAFNYQNQMQNPALSEQYVRYMGYHLMQNASQPMNVFRYGPQGVQHSQTM 240

Query: 513 SLPSSSCVPFSGGAATDNSPLSGKM 537
             PSS+      GAA  +  +SGKM
Sbjct: 241 ITPSSNSSGNMSGAANIDEAVSGKM 265

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|108862947|gb|ABA99362.2| Helix-loop-helix DNA-binding domain containing protein, expressed [Oryza sativa Japonica Group]

 Score =  242 bits (618), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 176/437 (40%), Positives = 224/437 (51%), Gaps = 90/437 (20%)

Query: 10  MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQ 69
           MN  +PDWN      + +   P+G+D+ LVELLW NGHVV+ SQA   RKP      PR 
Sbjct: 1   MNQFVPDWN---TTSMGDGFAPLGEDDGLVELLWCNGHVVMQSQAP--RKP------PRP 49

Query: 70  VQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHT 129
            +K T         ++  + +DE+ SW   P++D  EKD +++LF E+  +G    D   
Sbjct: 50  -EKTTA-------AAAAAMAEDESASWFQYPVDDVLEKDLFTELFGEMTAAGGGGGDVRR 101

Query: 130 RQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGK 189
              +EE+       GAV +              Q   MPPP       A      GD+  
Sbjct: 102 AACKEER-------GAVAA-------------FQSRMMPPPW-----PARGKAEFGDVDD 136

Query: 190 LVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQV------A 243
           +   S+                  K  G      V E SM+T+GSS CGSN V       
Sbjct: 137 VCGVSEVVMA--------------KMDGAAAAETVGESSMLTIGSSICGSNHVQTPPVGN 182

Query: 244 YDLDMSRASSSGLNDDVRKVISPSERGK--TETIEPTVTSSSGGSGSSFNRTSKQSTGDN 301
                  A ++    D   V S S R +  T   EP   +++G  G              
Sbjct: 183 GKAGAGTAGAARRAHDTATVASSSMRSRSCTAKAEPRDVAAAGVGG-------------- 228

Query: 302 SLKRKSRD--AVDSECQSEAAGFESGAGNKT-AQRSGSCRRSRAAEVHNLSERRRRDRIN 358
             KRK R   A++S   SE   FES A   + AQ++ + +R RAAEVHNLSERRRRDRIN
Sbjct: 229 --KRKQRGGAAMESGSPSEDVEFESAAATCSPAQKTTTAKRRRAAEVHNLSERRRRDRIN 286

Query: 359 EKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAP--LMFP--GMQHY 414
           EKM+ALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQ+MWMG GMAP  +MFP  G+  Y
Sbjct: 287 EKMKALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQMMWMGGGMAPPAVMFPAAGVHQY 346

Query: 415 MSRMG-MGMGPPPLPSV 430
           M RMG +GMGPP + S+
Sbjct: 347 MQRMGAVGMGPPHMASL 363

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	589
TAIR|locus:2053733	430	PIF4 "AT2G43010" [Arabidopsis	0.495	0.679	0.412	1.4e-64
TAIR|locus:2077680	444	PIL6 "AT3G59060" [Arabidopsis	0.444	0.590	0.423	6.1e-64
TAIR|locus:2061634	478	PIL5 "phytochrome interacting	0.492	0.606	0.368	3.4e-48
UNIPROTKB|Q8GRJ1	417	OJ1343_B12.103 "Transcription	0.458	0.647	0.374	8.1e-43
TAIR|locus:2012345	524	PIF3 "AT1G09530" [Arabidopsis	0.653	0.734	0.346	6.6e-42
TAIR|locus:4010713915	544	AT4G28811 [Arabidopsis thalian	0.298	0.323	0.398	4e-28
UNIPROTKB|Q5NAE0	565	P0498A12.33 "Putative BP-5 pro	0.200	0.208	0.578	1e-27
UNIPROTKB|Q7FA23	181	OSJNBa0058K23.6 "Os04g0618600	0.144	0.469	0.705	6.1e-27
TAIR|locus:2117773	413	AT4G28790 [Arabidopsis thalian	0.324	0.462	0.380	1.4e-26
TAIR|locus:4010713916	307	AT4G28815 [Arabidopsis thalian	0.147	0.283	0.516	2.5e-26

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

 Score = 511 (184.9 bits), Expect = 1.4e-64, Sum P(2) = 1.4e-64
 Identities = 141/342 (41%), Positives = 182/342 (53%)

Query:   199 PPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLND 258
             PP   + P   +     SG + + E+ + S+ TVG SHCGSN    DLD+S      ++ 
Sbjct:   129 PPPQVMPPPKFRLTNSSSG-IRETEMEQYSVTTVGPSHCGSNPSQNDLDVS------MSH 181

Query:   259 DVRKVISPSERGKTETIEPTVTXXXXXXXX-XFNRTSKQSTGDNSLKR-KSRDAVDSECQ 316
             D  K I        E + P  +          F +  K+      +   + R  ++    
Sbjct:   182 DRSKNIE-------EKLNPNASSSSGGSSGCSFGKDIKEMASGRCITTDRKRKRINHT-- 232

Query:   317 SEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDK 376
              E+       GNK+ QRSGS RRSRAAEVHNLSERRRRDRINE+M+ALQELIPHC+KTDK
Sbjct:   233 DESVSLSDAIGNKSNQRSGSNRRSRAAEVHNLSERRRRDRINERMKALQELIPHCSKTDK 292

Query:   377 ASMLDEAIEYLKSLQLQLQVMWMGSGMA------PLMFPGMQHYMSRXXXXXXXXXLPSV 430
             AS+LDEAI+YLKSLQLQLQVMWMGSGMA      P+MFPG+Q              +  +
Sbjct:   293 ASILDEAIDYLKSLQLQLQVMWMGSGMAAAAASAPMMFPGVQPQQ----------FIRQI 342

Query:   431 TNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPM 490
              +P+   R P++DQS   A   N  ++CQ    NPV  QNQ+ +  F        GF  M
Sbjct:   343 QSPVQLPRFPVMDQS---AIQNNPGLVCQ----NPV--QNQIISDRFARYIG---GFPHM 390

Query:   491 QANSQ--PMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDN 530
             QA +Q  PM M RF SP  Q      PSS     + G+  D+
Sbjct:   391 QAATQMQPMEMLRFSSPAGQQS--QQPSSVPTKTTDGSRLDH 430

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 = 500 (181.1 bits), Expect = 6.1e-64, Sum P(2) = 6.1e-64
 Identities = 135/319 (42%), Positives = 184/319 (57%)

Query:   228 SMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTXXXXXXX 287
             S++TVG SHCGSNQ           S+ ++      +S S+R K    E   T       
Sbjct:   146 SVITVGPSHCGSNQ-----------STNIHQATTLPVSMSDRSKNVE-ERLDTSSGGSSG 193

Query:   288 XXFNRTSKQSTGDNS--LKRKSRDAVDSECQSEAA---GFESG----AGNKTAQRSGSCR 338
               + R +K++    S  + RK +  +D++ +S +    G  S      GNK++QRSGS R
Sbjct:   194 CSYGRNNKETVSGTSVTIDRKRKHVMDADQESVSQSDIGLTSTDDQTMGNKSSQRSGSTR 253

Query:   339 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMW 398
             RSRAAEVHNLSERRRRDRINE+M+ALQELIPHC++TDKAS+LDEAI+YLKSLQ+QLQVMW
Sbjct:   254 RSRAAEVHNLSERRRRDRINERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQLQVMW 313

Query:   399 MGSGMA--------PLMFPGMQH--YMSRXXXXXXXXXLPSVTNPMHFSRVPLVDQSMSM 448
             MGSGMA        P+MFPG+Q   Y+++           ++ + M  S+ P++++S   
Sbjct:   314 MGSGMAAAAAAAASPMMFPGVQSSPYINQM----------AMQSQMQLSQFPVMNRS--- 360

Query:   449 AQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHP--------MQA-NSQPMNM 499
             A   +  ++CQ    NPV  Q Q QN   +EQ ARYMG  P        MQ    QP +M
Sbjct:   361 APQNHPGLVCQ----NPVQLQLQAQNQILSEQLARYMGGIPQMPPAGNQMQTVQQQPADM 416

Query:   500 FRFGSPTMQNQIVSLPSSS 518
               FGSP      +S P+++
Sbjct:   417 LGFGSPAGPQSQLSAPATT 435

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

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

 Score = 377 (137.8 bits), Expect = 3.4e-48, Sum P(2) = 3.4e-48
 Identities = 125/339 (36%), Positives = 170/339 (50%)

Query:   209 GQFDRKRSGN----LTQGEVRECSMMT------VGSSHCGSNQVAYDLDMSRASSSGLND 258
             G F+  R G     L++  VRE + ++        +S  G  +     D S  +  G  +
Sbjct:   153 GDFNNGRGGESGPLLSKAVVRESTQVSPSATPSAAASESGLTRRTDGTDSSAVAGGGAYN 212

Query:   259 DVRKVISPSERGKTETIEPTVTXXXXXXXXXFNRTSKQSTGDNSLKRKSRDAVDSECQSE 318
                K ++ +       IE T T          +    + T  +  KRK R+A  ++ ++E
Sbjct:   213 RKGKAVAMT----APAIEITGTSSSVVSK---SEIEPEKTNVDDRKRKEREATTTD-ETE 264

Query:   319 AAGFESGAGNKTAQRSG-SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKA 377
             +   E+    K A+ S  S +RSRAAEVHNLSER+RRDRINE+M+ALQELIP CNK+DKA
Sbjct:   265 SRSEET----KQARVSTTSTKRSRAAEVHNLSERKRRDRINERMKALQELIPRCNKSDKA 320

Query:   378 SMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRXXXXXXXXXL---PS-VTNP 433
             SMLDEAIEY+KSLQLQ+Q+M MG GM P+M+PGMQ YM               PS +  P
Sbjct:   321 SMLDEAIEYMKSLQLQIQMMSMGCGMMPMMYPGMQQYMPHMAMGMGMNQPIPPPSFMPFP 380

Query:   434 -MHFSRVPLVDQSMSMAQAQNRAVMCQ--ASVLNPVNYQ-----NQMQN-SNFTEQYARY 484
              M  ++ PL  Q+          V     + V  P N Q      Q Q  + +T+ Y ++
Sbjct:   381 NMLAAQRPLPTQTHMAGSGPQYPVHASDPSRVFVP-NQQYDPTSGQPQYPAGYTDPYQQF 439

Query:   485 MGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFS 523
              G HP    +QP        P  QNQ  S PSSS V  S
Sbjct:   440 RGLHP----TQP--------PQFQNQATSYPSSSRVSSS 466

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0015995 "chlorophyll biosynthetic process" evidence=IMP

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

GO:0010313 "phytochrome binding" evidence=IDA

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

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

GO:0010099 "regulation of photomorphogenesis" evidence=TAS

GO:0003677 "DNA binding" evidence=IDA

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

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

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

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

GO:0006783 "heme biosynthetic process" evidence=IMP

GO:0042802 "identical protein binding" evidence=IPI

GO:0009686 "gibberellin biosynthetic process" evidence=RCA

GO:0009845 "seed germination" evidence=RCA

GO:0048608 "reproductive structure development" evidence=RCA

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

 Score = 386 (140.9 bits), Expect = 8.1e-43, Sum P(2) = 8.1e-43
 Identities = 110/294 (37%), Positives = 152/294 (51%)

Query:   235 SHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTXXXXXXXXXFNRTS 294
             S CGSN V     ++ A  +  +DD+    +P E  + E   P                S
Sbjct:   137 SICGSNAV-----VAPALPADDDDDI-DAAAPREEEEEEEEGPGAARAAGASSSG---GS 187

Query:   295 KQSTGDNSL-KRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRR 353
                +G   L KR   + VDS   SE A  E+    + ++R  + RR+RAAEVHNLSERRR
Sbjct:   188 GSGSGSYPLFKRGREELVDS--LSEVAD-ET----RPSKRPAAKRRTRAAEVHNLSERRR 240

Query:   354 RDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQH 413
             RDRINEK+RALQEL+PHCNKTDKAS+LDEAIEYLKSLQ+Q+Q+MWM +G+ P+MFPG   
Sbjct:   241 RDRINEKLRALQELVPHCNKTDKASILDEAIEYLKSLQMQVQIMWMTTGIVPMMFPGTHQ 300

Query:   414 YMSRXXXXXXXXXLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQ 473
              M           +P        +++      M+ +   N+     +  +N  +  + MQ
Sbjct:   301 LMPPMGMGLNTACMPGA-QAQGLNQMQRTTYYMNNS-LPNQMPQIPSPAMNAPSVPDDMQ 358

Query:   474 NSNFTEQYARYMGFH---PMQANSQPMNMFRFGSPTM-QNQIVSLPSSSCVPFS 523
             N N      R    H    + A +Q   +F +GS    QN+I  L S + +P S
Sbjct:   359 NDNRIRG-PRNPFLHCNDTLTATAQVPGLFTYGSQIAEQNEIQELLSGAVIPSS 411

GO:0005634 "nucleus" evidence=IC

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

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 144/416 (34%), Positives = 202/416 (48%)

Query:    36 NELVELLWQNGHVVLSSQAQTQRK---PSLNHNEPRQV---QKQTLRGSGSCGNSS---N 86
             +E+VEL+W+NG +   SQ+   R    P  N +  R++    K T+         S    
Sbjct:    27 DEVVELVWENGQISTQSQSSRSRNIPPPQANSSRAREIGNGSKTTMVDEIPMSVPSLMTG 86

Query:    87 LIQDDETVSWI-HCPIEDSFEKDFYSQLFSELPPS---GPMEVDKHTRQLREEKMVKFDP 142
             L QDD+ V W+ H P  D +  DF   + S +  +     M V++    L + +    + 
Sbjct:    87 LSQDDDFVPWLNHHPSLDGYCSDFLRDVSSPVTVNEQESDMAVNQTAFPLFQRRKDGNES 146

Query:   143 PGAVTSSQHPNV-NHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGK--LVNFSQSTAP 199
               A +SSQ+    +HS+    +   +P  +          + L    K  LVNFS    P
Sbjct:   147 APAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNKPSLVNFSHFLRP 206

Query:   200 PKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDD 259
                     +   D K     +   V +  ++    S    ++V   L+ S AS++  ++ 
Sbjct:   207 ATFAKTTNNNLHDTKEKSPQSPPNVFQTRVLGAKDSE---DKV---LNESVASATPKDNQ 260

Query:   260 VRKVISPSERGKTETIEPTVTXXXXXXXXXFNRTSKQSTGDNSLKRKSRDAVDSECQSEA 319
                +IS     K +  E  V           +  S+  +   SLKRK  +  D +C SE 
Sbjct:   261 KACLISEDSCRKDQESEKAVVCSSVGSGNSLDGPSESPS--LSLKRKHSNIQDIDCHSED 318

Query:   320 AGFESGAGNKTA--QRSG-SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDK 376
                ESG G K A   R+G   +RSR+AEVHNLSERRRRDRINEKMRALQELIP+CNK DK
Sbjct:   319 VEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDRINEKMRALQELIPNCNKVDK 378

Query:   377 ASMLDEAIEYLKSLQLQLQVMWMGSG--MAP-LMFP-GMQHYMSRXXXXXXXXXLP 428
             ASMLDEAIEYLKSLQLQ+Q+M M SG  + P +MFP GM HY +          +P
Sbjct:   379 ASMLDEAIEYLKSLQLQVQIMSMASGYYLPPAVMFPPGMGHYPAAAAAMAMGMGMP 434

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:4010713915 AT4G28811 [Arabidopsis thaliana (taxid:3702)]

 Score = 296 (109.3 bits), Expect = 4.0e-28, Sum P(2) = 4.0e-28
 Identities = 79/198 (39%), Positives = 108/198 (54%)

Query:   327 GNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEY 386
             G + A  S S +RSRAA++HNLSERRRR+RINE+M+ LQEL+P C KTDK SML++ IEY
Sbjct:   343 GTEEAHGSTSRKRSRAADMHNLSERRRRERINERMKTLQELLPRCRKTDKVSMLEDVIEY 402

Query:   387 LKSLQLQLQVMWMGSGMAP-LMFPG-MQHYMSRXXXXXXXXXLP---------SVTNPMH 435
             +KSLQLQ+Q+M MG GM P +M  G  Q +M            P         +   P H
Sbjct:   403 VKSLQLQIQMMSMGHGMMPPMMHEGNTQQFMPHMAMGMKGMNRPPPFVPFPGKTFPRPGH 462

Query:   436 FSRV----PLVDQSMSMAQAQNRAVMCQASV-LNPVNYQNQMQNSNFTEQYARYMGFHPM 490
              + V    P +       QA + + +   S+  NPV   NQ +   +   Y++++G H M
Sbjct:   463 MAGVGPSYPALRYPFPDTQASDLSRVHVPSLHSNPV--PNQPRFPAYINPYSQFVGLHQM 520

Query:   491 QANSQPMNMFRFGSPTMQ 508
             Q    P+     G PT Q
Sbjct:   521 QQPPLPLQ----GQPTSQ 534

GO:0005634 "nucleus" evidence=ISM

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

 Score = 318 (117.0 bits), Expect = 1.0e-27, Sum P(2) = 1.0e-27
 Identities = 74/128 (57%), Positives = 88/128 (68%)

Query:   294 SKQSTGDNSLKR--KSRDAVDSEC---QSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNL 348
             S    G + L R  K +    +EC   Q +    E G   K+  RS   +RSR AEVHNL
Sbjct:   262 SGNGAGSDELWRQQKRKCQAQAECSASQDDDLDDEPGVLRKSGTRS--TKRSRTAEVHNL 319

Query:   349 SERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMA--PL 406
             SERRRRDRINEKMRALQELIP+CNK DKASMLDEAIEYLK+LQLQ+Q+M MG+G+   P+
Sbjct:   320 SERRRRDRINEKMRALQELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMSMGTGLCIPPM 379

Query:   407 MFP-GMQH 413
             + P  MQH
Sbjct:   380 LLPTAMQH 387

GO:0005634 "nucleus" evidence=IC

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

 Score = 309 (113.8 bits), Expect = 6.1e-27, P = 6.1e-27
 Identities = 60/85 (70%), Positives = 72/85 (84%)

Query:   331 AQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSL 390
             A+R    RRSR+AE HN SERRRRDRINEK++ALQEL+P+C KTDK SMLDEAI+YLKSL
Sbjct:     3 ARRPTPTRRSRSAEFHNFSERRRRDRINEKLKALQELLPNCTKTDKVSMLDEAIDYLKSL 62

Query:   391 QLQLQVMWMGSGMAPLMFPGMQHYM 415
             QLQLQ++ MG GMAP++ P +Q YM
Sbjct:    63 QLQLQMLVMGKGMAPVVPPELQQYM 87

GO:0005634 "nucleus" evidence=IC

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

 Score = 269 (99.8 bits), Expect = 1.4e-26, Sum P(2) = 1.4e-26
 Identities = 80/210 (38%), Positives = 109/210 (51%)

Query:   214 KRSGNLTQGEVREC-SMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKT 272
             ++ GN+  G V    S  T+ SS   S    +  + SRA+ +G       V     RGK 
Sbjct:   156 RQRGNIFLGGVEAVPSNSTLLSSATESIPATHGTE-SRATVTGGVSRTFAVPGLGPRGKA 214

Query:   273 ETIEPTVTXXXXXXXXXFNRTSKQSTGDNSL----KRKSRDAVDSECQSEAAGFESGAGN 328
               IE   T              +Q   +  +    KRK+R+  + E Q          G 
Sbjct:   215 VAIETAGTQSWGLCKAETEPVQRQPATETDITDERKRKTREETNVENQ----------GT 264

Query:   329 KTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLK 388
             + A+ S S +RSRAA +H LSERRRR +INE M+ALQEL+P C KTD++SMLD+ IEY+K
Sbjct:   265 EEARDSTSSKRSRAAIMHKLSERRRRQKINEMMKALQELLPRCTKTDRSSMLDDVIEYVK 324

Query:   389 SLQLQLQVMWMGSGMAP-LMFPG--MQHYM 415
             SLQ Q+Q+  MG  M P +M+ G   Q YM
Sbjct:   325 SLQSQIQMFSMGHVMIPPMMYAGNIQQQYM 354

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 = 233 (87.1 bits), Expect = 2.5e-26, Sum P(3) = 2.5e-26
 Identities = 48/93 (51%), Positives = 66/93 (70%)

Query:   327 GNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEY 386
             G + A+ S S +RSRAAE+HNL+ERRRR++INE+M+ LQ+LIP CNK+ K SML++ IEY
Sbjct:   136 GTEEARGSTSRKRSRAAEMHNLAERRRREKINERMKTLQQLIPRCNKSTKVSMLEDVIEY 195

Query:   387 LKSLQLQLQV----MWMGSGMAP--LMFPGMQH 413
             +KSL++Q+      M MG    P  + FP   H
Sbjct:   196 VKSLEMQINQFMPHMAMGMNQPPAYIPFPSQAH 228

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	589
smart00353	53	smart00353, HLH, helix loop helix domain	4e-17
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	5e-17
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	3e-15

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

 Score = 74.9 bits (185), Expect = 4e-17
 Identities = 26/52 (50%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 347 NLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQ 395
           N  ERRRR +INE    L+ L+P      K  KA +L  AIEY+KSLQ +LQ
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 = 74.9 bits (185), Expect = 5e-17
 Identities = 27/55 (49%), Positives = 36/55 (65%), Gaps = 3/55 (5%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIP---HCNKTDKASMLDEAIEYLKSLQLQLQ 395
           E HNL ERRRR+RIN+    L+ L+P      K  KA +L +A++Y+KSLQ  LQ
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 = 69.8 bits (172), Expect = 3e-15
 Identities = 26/50 (52%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQ 391
           + HN  ERRRRDRIN+    L+EL+P     K  KA +L  AIEY+K LQ
Sbjct: 3   KAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	589
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.35
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.33
smart00353	53	HLH helix loop helix domain.	99.25
KOG1318	411	consensus Helix loop helix transcription factor EB	99.2
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.91
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.75
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.48
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	97.99
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.97
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.86
KOG0561	373	consensus bHLH transcription factor [Transcription	97.38
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.32
PLN03217	93	transcription factor ATBS1; Provisional	97.17
KOG3910	632	consensus Helix loop helix transcription factor [T	96.84
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	94.33
KOG3898	254	consensus Transcription factor NeuroD and related	93.93
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	92.69
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	88.73
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	82.26
KOG4395	285	consensus Transcription factor Atonal, contains HT	81.13

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

Probab=99.35  E-value=1.3e-12  Score=103.11  Aligned_cols=54  Identities=50%  Similarity=0.773  Sum_probs=50.2

Q ss_pred             hhhhcchhHHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHHHHH
Q 007797          342 AAEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       342 a~~~Hn~~ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      .+..|+..||+||++||+.|..|+.+||.+   .|++|++||+.||+||+.|+.+++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            355799999999999999999999999998   789999999999999999998863

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=99.33  E-value=1.7e-12  Score=102.11  Aligned_cols=49  Identities=55%  Similarity=0.889  Sum_probs=46.2

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC-----CCcchhhHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC-----NKTDKASMLDEAIEYLKSLQ  391 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~-----~K~dKAsIL~~AI~YIK~LQ  391 (589)
                      +..|+..||+||++||+.|..|+++||.+     .|++|++||+.||+||+.||
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            45799999999999999999999999988     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=99.25  E-value=1.4e-11  Score=95.53  Aligned_cols=49  Identities=53%  Similarity=0.736  Sum_probs=45.6

Q ss_pred             chhHHHHHHHHHHHHHHHHhhCCC---CCCcchhhHHHHHHHHHHHHHHHHH
Q 007797          347 NLSERRRRDRINEKMRALQELIPH---CNKTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       347 n~~ERrRRerINe~~~~Lr~LVP~---~~K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      +..||+||++||+.|..|+.+||.   ..|++|++||.+||+||+.|+.+++
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   5689999999999999999999876

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

Probab=99.20  E-value=1.2e-11  Score=132.36  Aligned_cols=61  Identities=41%  Similarity=0.735  Sum_probs=54.3

Q ss_pred             CccccchhhhcchhHHHHHHHHHHHHHHHHhhCCCCC----CcchhhHHHHHHHHHHHHHHHHHH
Q 007797          336 SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQLQV  396 (589)
Q Consensus       336 ~~rr~ra~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIK~LQ~qvq~  396 (589)
                      ..|.+++++.||++|||||++||++|++|..|||.|+    |..|..||..+++||+.||+..+.
T Consensus       227 ~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~  291 (411)
T KOG1318|consen  227 LERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQR  291 (411)
T ss_pred             hHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHH
Confidence            3455566789999999999999999999999999995    677999999999999999987773

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.91  E-value=7.4e-10  Score=107.78  Aligned_cols=55  Identities=33%  Similarity=0.564  Sum_probs=49.6

Q ss_pred             hhcchhHHHHHHHHHHHHHHHHhhCCCCC-------CcchhhHHHHHHHHHHHHHHHHHHHh
Q 007797          344 EVHNLSERRRRDRINEKMRALQELIPHCN-------KTDKASMLDEAIEYLKSLQLQLQVMW  398 (589)
Q Consensus       344 ~~Hn~~ERrRRerINe~~~~Lr~LVP~~~-------K~dKAsIL~~AI~YIK~LQ~qvq~L~  398 (589)
                      +.|...||+||+.||.++..|+.|||.|.       |+.||.||.++|+||.+|+++...-+
T Consensus        64 ~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe  125 (229)
T KOG1319|consen   64 RAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQE  125 (229)
T ss_pred             HHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36999999999999999999999999774       88999999999999999988765544

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

Probab=98.75  E-value=6.4e-09  Score=105.96  Aligned_cols=53  Identities=36%  Similarity=0.543  Sum_probs=47.2

Q ss_pred             hhcchhHHHHHHHHHHHHHHHHhhCCCC--------CCcchhhHHHHHHHHHHHHHHHHHH
Q 007797          344 EVHNLSERRRRDRINEKMRALQELIPHC--------NKTDKASMLDEAIEYLKSLQLQLQV  396 (589)
Q Consensus       344 ~~Hn~~ERrRRerINe~~~~Lr~LVP~~--------~K~dKAsIL~~AI~YIK~LQ~qvq~  396 (589)
                      ..|-++|||||+|||+.|.+|++||+.+        .|++||.||+.|++|+|.|+...+.
T Consensus        34 ~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   34 VRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             hcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            3688999999999999999999999954        5789999999999999999876543

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

Probab=98.48  E-value=1.5e-07  Score=108.47  Aligned_cols=51  Identities=33%  Similarity=0.531  Sum_probs=48.0

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCCC----CcchhhHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQ  393 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIK~LQ~q  393 (589)
                      +++|+.+||||||++|..|.+|.+|||.|.    |+||-+||++||++||.+++.
T Consensus        21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~   75 (803)
T KOG3561|consen   21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ   75 (803)
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence            568999999999999999999999999885    999999999999999988875

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

Probab=97.99  E-value=1.6e-05  Score=80.59  Aligned_cols=53  Identities=30%  Similarity=0.489  Sum_probs=46.0

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCCC--Cc-chhhHHHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHCN--KT-DKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~--K~-dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      +..||..||+||+.|.++|..|+.+||...  |. ..++||++|++||+.|+.+..
T Consensus        60 R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~  115 (232)
T KOG2483|consen   60 RAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSA  115 (232)
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHH
Confidence            457999999999999999999999999775  22 379999999999999986543

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.97  E-value=3.1e-06  Score=98.24  Aligned_cols=58  Identities=34%  Similarity=0.563  Sum_probs=52.2

Q ss_pred             hhhhcchhHHHHHHHHHHHHHHHHhhCCCCC-CcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          342 AAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       342 a~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~-K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      .+.+||++|||.|..||++|.+|+.+||+.. |+.|..+|.+||+||++|+...+.+..
T Consensus       276 kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~  334 (953)
T KOG2588|consen  276 KRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKL  334 (953)
T ss_pred             ccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccch
Confidence            3558999999999999999999999999775 999999999999999999987766543

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

Probab=97.86  E-value=3e-05  Score=79.07  Aligned_cols=54  Identities=31%  Similarity=0.423  Sum_probs=47.2

Q ss_pred             cchhHHHHHHHHHHHHHHHHhh-CCCCC-CcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          346 HNLSERRRRDRINEKMRALQEL-IPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       346 Hn~~ERrRRerINe~~~~Lr~L-VP~~~-K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      -.+.||||=.|+||.|.+|+.- .++-+ .+-|..||..||+||+.||.-++.+..
T Consensus       122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~  177 (284)
T KOG3960|consen  122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQ  177 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3689999999999999999875 55554 689999999999999999999988764

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.38  E-value=0.00017  Score=75.24  Aligned_cols=52  Identities=33%  Similarity=0.556  Sum_probs=46.5

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC--CCcchhhHHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQL  394 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIK~LQ~qv  394 (589)
                      ++.-|.-||||=.-||-.|..||.|+|.-  .|++||.||+.+.+||.+|+.+.
T Consensus        61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~K  114 (373)
T KOG0561|consen   61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHK  114 (373)
T ss_pred             HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcc
Confidence            45678889999999999999999999965  59999999999999999997643

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

Probab=97.32  E-value=0.00019  Score=72.00  Aligned_cols=55  Identities=27%  Similarity=0.378  Sum_probs=49.1

Q ss_pred             hcchhHHHHHHHHHHHHHHHHhhCCC----CCCcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          345 VHNLSERRRRDRINEKMRALQELIPH----CNKTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       345 ~Hn~~ERrRRerINe~~~~Lr~LVP~----~~K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      .+|..||.|=..+|..|..||.+||.    .+|+.|..+|..||.||++|++-++.-+.
T Consensus       112 ~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~  170 (228)
T KOG4029|consen  112 ARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA  170 (228)
T ss_pred             hhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence            46778999999999999999999993    56899999999999999999998876553

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.17  E-value=0.00083  Score=58.74  Aligned_cols=47  Identities=26%  Similarity=0.490  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHhhCCCC------CCcchhhHHHHHHHHHHHHHHHHHHHhcC
Q 007797          354 RDRINEKMRALQELIPHC------NKTDKASMLDEAIEYLKSLQLQLQVMWMG  400 (589)
Q Consensus       354 RerINe~~~~Lr~LVP~~------~K~dKAsIL~~AI~YIK~LQ~qvq~L~~~  400 (589)
                      -|.||+-+..||.|+|..      .|..-+-||++|+.||+.|+.+|..|+..
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSer   71 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSER   71 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999954      36778889999999999999999999853

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.84  E-value=0.0016  Score=71.90  Aligned_cols=56  Identities=27%  Similarity=0.296  Sum_probs=48.0

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCCCCc----chhhHHHHHHHHHHHHHHHHHHHh
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHCNKT----DKASMLDEAIEYLKSLQLQLQVMW  398 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~K~----dKAsIL~~AI~YIK~LQ~qvq~L~  398 (589)
                      +...|..||.|-..|||.|++|-.+.-...|.    .|..||..||..|-.|++||.+-.
T Consensus       527 R~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN  586 (632)
T KOG3910|consen  527 RMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN  586 (632)
T ss_pred             HhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc
Confidence            44688999999999999999999987644443    489999999999999999998754

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=94.33  E-value=0.028  Score=54.22  Aligned_cols=51  Identities=33%  Similarity=0.482  Sum_probs=45.9

Q ss_pred             hhcchhHHHHHHHHHHHHHHHHhhCCCC--CCcchhhHHHHHHHHHHHHHHHH
Q 007797          344 EVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQL  394 (589)
Q Consensus       344 ~~Hn~~ERrRRerINe~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIK~LQ~qv  394 (589)
                      -.||+.||+|-..+|+.|.+||.+||..  .|++|.-.|+-|..||-+|=+-+
T Consensus        80 v~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   80 VMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            3699999999999999999999999955  69999999999999999886544

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

Probab=93.93  E-value=0.11  Score=53.56  Aligned_cols=50  Identities=36%  Similarity=0.484  Sum_probs=43.1

Q ss_pred             hcchhHHHHHHHHHHHHHHHHhhCCC---CCCcchhhHHHHHHHHHHHHHHHH
Q 007797          345 VHNLSERRRRDRINEKMRALQELIPH---CNKTDKASMLDEAIEYLKSLQLQL  394 (589)
Q Consensus       345 ~Hn~~ERrRRerINe~~~~Lr~LVP~---~~K~dKAsIL~~AI~YIK~LQ~qv  394 (589)
                      .=|..||+|=-.+|+.|+.||++||.   ..|+.|+..|.-|-+||..|++-+
T Consensus        75 kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~  127 (254)
T KOG3898|consen   75 KANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVL  127 (254)
T ss_pred             cccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcccc
Confidence            34678999999999999999999994   358999999999999999887543

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=92.69  E-value=0.1  Score=58.90  Aligned_cols=39  Identities=38%  Similarity=0.692  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHhhCCC----CCCcchhhHHHHHHHHHHH
Q 007797          351 RRRRDRINEKMRALQELIPH----CNKTDKASMLDEAIEYLKS  389 (589)
Q Consensus       351 RrRRerINe~~~~Lr~LVP~----~~K~dKAsIL~~AI~YIK~  389 (589)
                      ||-|||+|-.++.|.+|+|-    .+|+||.+||.-+|.|++.
T Consensus        34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~   76 (712)
T KOG3560|consen   34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV   76 (712)
T ss_pred             hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence            67799999999999999994    4699999999999999873

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

Probab=88.73  E-value=0.33  Score=56.23  Aligned_cols=44  Identities=34%  Similarity=0.505  Sum_probs=37.9

Q ss_pred             cchhHHHHHHHHHHHHHHHHhhCCCC----CCcchhhHHHHHHHHHHH
Q 007797          346 HNLSERRRRDRINEKMRALQELIPHC----NKTDKASMLDEAIEYLKS  389 (589)
Q Consensus       346 Hn~~ERrRRerINe~~~~Lr~LVP~~----~K~dKAsIL~~AI~YIK~  389 (589)
                      -.-+.|-||-|-|+-|.+|..+||--    ..+|||+|+.-||-|+|-
T Consensus        50 SRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   50 SRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            34566999999999999999999933    368999999999999983

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=82.26  E-value=1.2  Score=49.05  Aligned_cols=42  Identities=33%  Similarity=0.518  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHHHHHHHHhhCCCCC----CcchhhHHHHHHHHHHHH
Q 007797          349 SERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSL  390 (589)
Q Consensus       349 ~ERrRRerINe~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIK~L  390 (589)
                      ..|.||++-|-.|.+|..++|-..    .+||++|+.-|..|||.-
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr   53 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR   53 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence            458999999999999999999553    589999999999999953

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

Probab=81.13  E-value=2.3  Score=44.37  Aligned_cols=51  Identities=29%  Similarity=0.396  Sum_probs=44.9

Q ss_pred             hcchhHHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHHHHH
Q 007797          345 VHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       345 ~Hn~~ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      .-|..||||=..+|..|+.||.+||..   .|+.|-..|..|-.||--|-..++
T Consensus       177 aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  177 AANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             ccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            468899999999999999999999966   478999999999999998766553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	589
4f3l_B	387	Crystal Structure Of The Heterodimeric Clock:bmal1		3e-04
4ati_A	118	Mitf:m-Box Complex Length = 118		3e-04

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 4/58 (6%)
Query: 338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQ 391
           R   A E H+  E+RRRD++N  +  L  L+P CN    K DK ++L  A++++K+L+
Sbjct: 9   RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLR 66

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

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 346 HNLSERRRRDRINEKMRALQELIPHCNKTD----KASMLDEAIEYLKSLQLQLQ 395
           HNL ERRRR  IN++++ L  LIP  N  D    K ++L  +++Y++ LQ + Q
Sbjct: 31  HNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQ 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	589
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	2e-20
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	3e-16
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	4e-14
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-13
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	6e-13
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	5e-09
1a0a_A	63	BHLH, protein (phosphate system positive regulator	7e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	3e-06
4f3l_A	361	Mclock, circadian locomoter output cycles protein	5e-06
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	5e-05

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

 Score = 84.7 bits (210), Expect = 2e-20
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQV 396
            R      HN  E+R R  IN+K+  L++L+     K +K+++L +AI+Y++ LQ   Q 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 397 M 397
           +
Sbjct: 62  L 62

>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 = 72.4 bits (178), Expect = 3e-16
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQ 391
            + RA   HN  ERRRRD+IN  +  L ++IP  +         K  +L +A +Y++ L+
Sbjct: 3   EKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Query: 392 LQLQ 395
               
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 = 66.6 bits (163), Expect = 4e-14
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQVM 397
             HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY++ ++ +    
Sbjct: 14  AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTH 69

>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 = 64.7 bits (158), Expect = 2e-13
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQVM 397
             HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY++ ++ +    
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTH 59

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

 Score = 63.9 bits (156), Expect = 6e-13
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQVM 397
             HN+ ER+RR+ +     AL++ IP      K  K  +L +A  Y+ S+Q + Q +
Sbjct: 8   RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKL 64

>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 = 52.5 bits (126), Expect = 5e-09
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIP---HCNKTDKASMLDEAIEYLKSLQLQLQVM 397
             HN  E+ RR  +   +  L+ L+P     ++    S+L +A  ++K L+   +  
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKA 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 = 51.4 bits (123), Expect = 7e-09
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 7/55 (12%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIPHCNKTD-------KASMLDEAIEYLKSLQ 391
           E H  +E+ RR+R+   +  L  LIP   K         KA+ ++ A  Y++ LQ
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 58

>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 = 50.2 bits (119), Expect = 2e-06
 Identities = 51/408 (12%), Positives = 114/408 (27%), Gaps = 107/408 (26%)

Query: 245 DLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLK 304
           + D          D  + ++S  E      I+  + S    SG+     +  S  +  ++
Sbjct: 32  NFDCKDVQ-----DMPKSILSKEE------IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQ 80

Query: 305 RKSRDAVD-------SECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRI 357
           +   + +        S  ++E             QR      ++    +N+S   R    
Sbjct: 81  KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS---RLQPY 137

Query: 358 NEKMRALQELIPH----------CNKTDKASMLDEAIEYLKSLQLQL----QVMWMGSGM 403
            +  +AL EL P             K    + +  A++   S ++Q     ++ W+    
Sbjct: 138 LKLRQALLELRPAKNVLIDGVLGSGK----TWV--ALDVCLSYKVQCKMDFKIFWLNLKN 191

Query: 404 ---APLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRA--VM- 457
                 +   +Q  + ++          S    +    +    + +  ++       V+ 
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251

Query: 458 --CQASVLNPVNYQNQM----QNSNFTEQYA-----------RYMGFHPMQANSQPMNMF 500
               A   N  N   ++    +    T+  +             M   P +      ++ 
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV----KSLL 307

Query: 501 RFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMVGE--RRRLIKW-LWSPIF---- 553
                 +  +   LP               +P    ++ E  R  L  W  W  +     
Sbjct: 308 ---LKYLDCRPQDLPREVL---------TTNPRRLSIIAESIRDGLATWDNWKHVNCDKL 355

Query: 554 --IMGRSQEGESCSSWR-------IFGPFLSCIAYDIN----ALSIAW 588
             I+  S      + +R       +F P         +     LS+ W
Sbjct: 356 TTIIESSLNVLEPAEYRKMFDRLSVF-P------PSAHIPTILLSLIW 396

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

 Score = 48.9 bits (116), Expect = 3e-06
 Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 337 CRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQL 392
            R   A E H+  E+RRRD++N  +  L  L+P CN    K DK ++L  A++++K+L+ 
Sbjct: 8   GRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG 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 = 5e-06
 Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHC-NKTDKASMLDEAIEYLKSLQLQLQV 396
           +  R +   N SE++RRD+ N  ++ L  ++P    K DK+++L ++I++L+  +     
Sbjct: 10  KAKRVS--RNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQ 67

Query: 397 M---WMGSGMAPLMFPGMQH 413
                +     P      + 
Sbjct: 68  SDASEIRQDWKPTFLSNEEF 87

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

 Score = 41.0 bits (96), Expect = 5e-05
 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 335 GSCRRSRAAEVHNLSERRRRDRINEKMRAL-QELIPHCNKTDKAS---MLDEAIEYLKSL 390
           G+ +R+     HN  ER+RR  INE  R L +    H       +   +L +A++ +  L
Sbjct: 2   GADKRA----HHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGL 57

Query: 391 QLQLQ 395
           + Q++
Sbjct: 58  EQQVR 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	589
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.58
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.55
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.53
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.52
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.51
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.51
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.42
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.41
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.38
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.33
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.26
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.06
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.01
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.99
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.9
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.58
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.51
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.01

>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=99.58  E-value=1.7e-15  Score=128.45  Aligned_cols=59  Identities=32%  Similarity=0.467  Sum_probs=55.4

Q ss_pred             chhhhcchhHHHHHHHHHHHHHHHHhhCCCC-CCcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          341 RAAEVHNLSERRRRDRINEKMRALQELIPHC-NKTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       341 ra~~~Hn~~ERrRRerINe~~~~Lr~LVP~~-~K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      ..+..|+++||+||++||++|.+|++|||++ .|+||++||++||+||++||.+++.|..
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~   64 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQ   64 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3467899999999999999999999999998 7999999999999999999999999874

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

Probab=99.55  E-value=5.3e-15  Score=122.83  Aligned_cols=60  Identities=25%  Similarity=0.411  Sum_probs=54.2

Q ss_pred             ccchhhhcchhHHHHHHHHHHHHHHHHhhCCCC-CCcchhhHHHHHHHHHHHHHHHHHHHh
Q 007797          339 RSRAAEVHNLSERRRRDRINEKMRALQELIPHC-NKTDKASMLDEAIEYLKSLQLQLQVMW  398 (589)
Q Consensus       339 r~ra~~~Hn~~ERrRRerINe~~~~Lr~LVP~~-~K~dKAsIL~~AI~YIK~LQ~qvq~L~  398 (589)
                      .+..+.+|+++||+||++||++|.+|++|||.+ .|+||++||++||+||+.||.++.-|+
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=99.53  E-value=7.6e-15  Score=132.32  Aligned_cols=62  Identities=34%  Similarity=0.580  Sum_probs=50.7

Q ss_pred             cccchhhhcchhHHHHHHHHHHHHHHHHhhCCCCC----CcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       338 rr~ra~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      ++++++..|+++||+||++||++|.+|++|||.|.    |++|++||++||+||++||.+++.|..
T Consensus        23 k~~~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~   88 (118)
T 4ati_A           23 KERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKD   88 (118)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            33445678999999999999999999999999985    678999999999999999999998863

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

Probab=99.52  E-value=3.6e-15  Score=124.37  Aligned_cols=55  Identities=38%  Similarity=0.619  Sum_probs=50.5

Q ss_pred             cccchhhhcchhHHHHHHHHHHHHHHHHhhCCCC----CCcchhhHHHHHHHHHHHHHH
Q 007797          338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHC----NKTDKASMLDEAIEYLKSLQL  392 (589)
Q Consensus       338 rr~ra~~~Hn~~ERrRRerINe~~~~Lr~LVP~~----~K~dKAsIL~~AI~YIK~LQ~  392 (589)
                      +.++++++|+++||+||++||+.|.+|+.|||.|    .|+|||+||+.||+|||.|+.
T Consensus         5 k~~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            5 RIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            4556678999999999999999999999999987    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=99.51  E-value=2.7e-15  Score=121.44  Aligned_cols=53  Identities=34%  Similarity=0.567  Sum_probs=49.0

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCCC------CcchhhHHHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~------K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      +..|+++||+||++||++|.+|+.|||.+.      |++|++||++||+||++||++++
T Consensus         6 r~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            457999999999999999999999999886      78999999999999999998753

>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=99.51  E-value=2.7e-15  Score=121.68  Aligned_cols=53  Identities=30%  Similarity=0.476  Sum_probs=48.1

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC-------CCcchhhHHHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC-------NKTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~-------~K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      +.+|+++||+||++||..|.+|+.|||.+       .|++||+||++||+||+.||++++
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            45899999999999999999999999966       467799999999999999998763

>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=99.42  E-value=1.7e-13  Score=115.34  Aligned_cols=58  Identities=29%  Similarity=0.521  Sum_probs=54.1

Q ss_pred             hhhhcchhHHHHHHHHHHHHHHHHhhCCCC--CCcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          342 AAEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       342 a~~~Hn~~ERrRRerINe~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      .+..|+..||+||++||++|..|+.+||.+  .|++|++||..||+||+.|+.+++.|..
T Consensus        12 ~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~   71 (80)
T 1hlo_A           12 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ   71 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356899999999999999999999999987  5899999999999999999999999874

>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=99.41  E-value=1.8e-13  Score=115.70  Aligned_cols=57  Identities=30%  Similarity=0.532  Sum_probs=52.9

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC--CCcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      +..||..||+||++||+.|..|+++||.+  .|++|++||.+||+||+.|+.+++.|..
T Consensus         3 R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~   61 (83)
T 1nkp_B            3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ   61 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45899999999999999999999999985  7999999999999999999998888763

>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=99.38  E-value=3.8e-13  Score=115.56  Aligned_cols=56  Identities=32%  Similarity=0.503  Sum_probs=51.9

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHHHHHHHh
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMW  398 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~qvq~L~  398 (589)
                      +..||..||+||++||++|..|+.+||.+   .|++|++||.+||+||++|+.+.+.|.
T Consensus         7 R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~   65 (88)
T 1nkp_A            7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLI   65 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45899999999999999999999999976   599999999999999999999887765

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

Probab=99.33  E-value=7.2e-13  Score=111.25  Aligned_cols=57  Identities=30%  Similarity=0.426  Sum_probs=49.8

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCC---CCCc-chhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPH---CNKT-DKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~---~~K~-dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      +..||..||+||++||++|.+|+.+||.   ..|. +|+.||.+||+||++||+++++++.
T Consensus         6 R~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            6 RAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ---CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            3479999999999999999999999995   3455 7999999999999999999999874

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

Probab=99.26  E-value=6.8e-12  Score=106.15  Aligned_cols=56  Identities=23%  Similarity=0.290  Sum_probs=51.5

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHHHHHHHh
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMW  398 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~qvq~L~  398 (589)
                      +..||..||+||+.||++|..|+++||.+   .|++|+.||.+||+||+.|+.+.+.|.
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~   60 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAV   60 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34799999999999999999999999965   588999999999999999999988775

>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=99.06  E-value=1.2e-10  Score=95.89  Aligned_cols=53  Identities=28%  Similarity=0.481  Sum_probs=48.5

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC--CCcchhhHHHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      +..||..||+|+..||+.|..|+.+||..  .|++|+.||..||+||++|++.++
T Consensus        13 R~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             hhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            45799999999999999999999999964  589999999999999999998653

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

Probab=99.01  E-value=3.6e-10  Score=90.85  Aligned_cols=52  Identities=27%  Similarity=0.355  Sum_probs=47.8

Q ss_pred             hhcchhHHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHHHHH
Q 007797          344 EVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       344 ~~Hn~~ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      ..||..||+|+..||+.|..|+.+||..   .|++|..||..||+||+.|++.++
T Consensus         4 ~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            4 MKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            4689999999999999999999999965   489999999999999999998764

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

Probab=98.99  E-value=3.1e-10  Score=117.02  Aligned_cols=53  Identities=28%  Similarity=0.539  Sum_probs=43.1

Q ss_pred             hhhhcchhHHHHHHHHHHHHHHHHhhCC-CCCCcchhhHHHHHHHHHHHHHHHH
Q 007797          342 AAEVHNLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEYLKSLQLQL  394 (589)
Q Consensus       342 a~~~Hn~~ERrRRerINe~~~~Lr~LVP-~~~K~dKAsIL~~AI~YIK~LQ~qv  394 (589)
                      ++..|+++||+||++||+.|.+|++||| ...|+||++||+.||+|||.|+...
T Consensus        12 ~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~   65 (361)
T 4f3l_A           12 KRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETT   65 (361)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhc
Confidence            3557999999999999999999999999 5679999999999999999998653

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

Probab=98.90  E-value=7.8e-10  Score=115.48  Aligned_cols=54  Identities=35%  Similarity=0.525  Sum_probs=48.7

Q ss_pred             ccchhhhcchhHHHHHHHHHHHHHHHHhhCC----CCCCcchhhHHHHHHHHHHHHHH
Q 007797          339 RSRAAEVHNLSERRRRDRINEKMRALQELIP----HCNKTDKASMLDEAIEYLKSLQL  392 (589)
Q Consensus       339 r~ra~~~Hn~~ERrRRerINe~~~~Lr~LVP----~~~K~dKAsIL~~AI~YIK~LQ~  392 (589)
                      .+.++++|+.+||+||+|||+.|.+|+.|||    ...|+||++||+.||+|||.|+.
T Consensus        10 ~~~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           10 IKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hhhhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            3445779999999999999999999999999    55799999999999999999974

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

Probab=98.58  E-value=5.9e-08  Score=82.76  Aligned_cols=45  Identities=31%  Similarity=0.570  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHHhhCCCCC----CcchhhHHHHHHHHHHHHHHHHHHHh
Q 007797          354 RDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQLQVMW  398 (589)
Q Consensus       354 RerINe~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIK~LQ~qvq~L~  398 (589)
                      |++||++|.+|..|||.++    |.+|++||.+||+||++||++++.|.
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~   52 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAK   52 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence            8999999999999999874    68999999999999999988776553

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

Probab=98.51  E-value=3.4e-08  Score=81.36  Aligned_cols=46  Identities=24%  Similarity=0.397  Sum_probs=41.9

Q ss_pred             chhHHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHH
Q 007797          347 NLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQL  392 (589)
Q Consensus       347 n~~ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~  392 (589)
                      +..||+|+..||+.|..||.+||..   .|++|..||..||+||+.||.
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            4568999999999999999999965   589999999999999999984

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

Probab=98.01  E-value=9.9e-06  Score=70.97  Aligned_cols=51  Identities=25%  Similarity=0.378  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHHHHHHHhcC
Q 007797          350 ERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMWMG  400 (589)
Q Consensus       350 ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~qvq~L~~~  400 (589)
                      ||.|-..||+.|..||.+||..   .|+.|..+|..||+||+.|++.++.-...
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~~~   86 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLKP   86 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTTST
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence            4677789999999999999965   48999999999999999999999875543

---

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	589
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	7e-16
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	3e-15
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	6e-15
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	6e-15
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	8e-15
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	8e-15
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-14
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-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 = 7e-16
 Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 346 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQVM 397
           HN  ER+RRD I +   +L++ +P     K  +A +LD+A EY++ ++ +    
Sbjct: 6   HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTH 59

>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 = 68.3 bits (167), Expect = 3e-15
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 338 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQ 391
            + RA   HN  ERRRRD+IN  +  L ++IP  +         K  +L +A +Y++ L+
Sbjct: 3   EKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Query: 392 LQLQ 395
               
Sbjct: 61  QSNH 64

>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 = 68.0 bits (166), Expect = 6e-15
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 338 RRSRAAEVHNLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEYLKSLQLQLQV 396
            R      HN  E+R R  IN+K+  L++L+     K +K+++L +AI+Y++ LQ   Q 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 397 M 397
           +
Sbjct: 62  L 62

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

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

 Score = 67.6 bits (165), Expect = 6e-15
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 329 KTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 386
           +  +++ +  R +A     + ERRR  ++NE    L+         +  K  +L  AI Y
Sbjct: 2   ELKRKTTNADRRKA---ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRY 58

Query: 387 LKSLQLQLQ 395
           ++ LQ  L+
Sbjct: 59  IEGLQALLR 67

>d1a0aa_ a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 63

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: Pho4 B/HLH domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 66.8 bits (163), Expect = 8e-15
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 7/59 (11%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIPHCN-------KTDKASMLDEAIEYLKSLQLQLQ 395
           E H  +E+ RR+R+   +  L  LIP             KA+ ++ A  Y++ LQ    
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>d1uklc_ a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

class: All alpha proteins
fold: HLH-like
superfamily: HLH, helix-loop-helix DNA-binding domain
family: HLH, helix-loop-helix DNA-binding domain
domain: SREBP-2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.7 bits (163), Expect = 8e-15
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 354 RDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVM 397
           R  IN+K+  L++L+   + K  K+ +L +AI+Y+K LQ     +
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKL 45

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 340 SRAAEVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQV 396
           SR+   HN  E+ RR  +   +  L+ L+P      +    S+L +A  ++K L+   + 
Sbjct: 1   SRST--HNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRK 58

Query: 397 M 397
            
Sbjct: 59  A 59

>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 = 67.2 bits (164), Expect = 1e-14
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 344 EVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQVM 397
             HN+ ER+RR+ +     AL++ IP      K  K  +L +A  Y+ S+Q + Q +
Sbjct: 8   RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKL 64

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	589
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.46
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.45
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.4
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.37
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.36
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.35
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.2

>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=99.47  E-value=2.3e-14  Score=118.55  Aligned_cols=58  Identities=33%  Similarity=0.479  Sum_probs=53.8

Q ss_pred             hhhhcchhHHHHHHHHHHHHHHHHhhCCCCC-CcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          342 AAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       342 a~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~-K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      .+..|+.+||+||++||+.|..|++|||.+. |++|++||.+||+||+.|+.+++.|..
T Consensus         6 kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~   64 (80)
T d1am9a_           6 KRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQ   64 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3568999999999999999999999999875 899999999999999999999998874

>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=99.46  E-value=1.6e-14  Score=114.74  Aligned_cols=52  Identities=31%  Similarity=0.503  Sum_probs=47.6

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCC-------CCCcchhhHHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPH-------CNKTDKASMLDEAIEYLKSLQLQL  394 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~-------~~K~dKAsIL~~AI~YIK~LQ~qv  394 (589)
                      +..|+++||+||++||++|..|++|||.       ..|++|+.||++||+||++||+++
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            3479999999999999999999999995       358999999999999999999865

>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=99.45  E-value=2.4e-14  Score=115.48  Aligned_cols=53  Identities=28%  Similarity=0.471  Sum_probs=49.1

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCCC--CcchhhHHHHHHHHHHHHHHHHH
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQ  395 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~--K~dKAsIL~~AI~YIK~LQ~qvq  395 (589)
                      +..|+..||+||++||++|..|++|||.+.  |++|++||..||+||++||++|+
T Consensus        13 R~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            457999999999999999999999999864  78999999999999999998764

>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=99.40  E-value=1.7e-13  Score=112.68  Aligned_cols=57  Identities=23%  Similarity=0.267  Sum_probs=52.4

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCCC---CcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~~---K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      +..||.+||+||++||++|..|+++||.+.   |++|++||.+||+||+.|+.+++.|..
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   799999999999999999999988764

>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=99.37  E-value=2.6e-13  Score=112.53  Aligned_cols=57  Identities=30%  Similarity=0.532  Sum_probs=52.4

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC--CCcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      +..|+.+||+||++||+.|..|++|||.+  .|++|++||..||+||+.|+.+++.|..
T Consensus         3 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~   61 (83)
T d1nkpb_           3 RAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ   61 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45899999999999999999999999965  5899999999999999999999888763

>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=99.36  E-value=5.9e-14  Score=112.02  Aligned_cols=51  Identities=35%  Similarity=0.585  Sum_probs=47.2

Q ss_pred             hhcchhHHHHHHHHHHHHHHHHhhCCCCC------CcchhhHHHHHHHHHHHHHHHH
Q 007797          344 EVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQLQL  394 (589)
Q Consensus       344 ~~Hn~~ERrRRerINe~~~~Lr~LVP~~~------K~dKAsIL~~AI~YIK~LQ~qv  394 (589)
                      ..|+.+||+||++||+.|.+|++|||.+.      |++|++||.+||+||+.||++.
T Consensus         7 ~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           7 AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            46999999999999999999999999764      8999999999999999999764

>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=99.35  E-value=3.8e-13  Score=112.71  Aligned_cols=57  Identities=32%  Similarity=0.486  Sum_probs=52.4

Q ss_pred             hhhcchhHHHHHHHHHHHHHHHHhhCCCC---CCcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          343 AEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       343 ~~~Hn~~ERrRRerINe~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      +..|+.+||+||++||+.|..|+++||.+   .|++|++||..||+||+.|+.+++.|..
T Consensus         7 R~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~   66 (88)
T d1nkpa_           7 RRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS   66 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45799999999999999999999999965   4799999999999999999999988764

>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=99.20  E-value=2.6e-12  Score=101.30  Aligned_cols=46  Identities=33%  Similarity=0.490  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHhhCCCCC-CcchhhHHHHHHHHHHHHHHHHHHHhc
Q 007797          354 RDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM  399 (589)
Q Consensus       354 RerINe~~~~Lr~LVP~~~-K~dKAsIL~~AI~YIK~LQ~qvq~L~~  399 (589)
                      |++||++|.+|++|||++. |+|||+||.+||+||+.||.+++.|..
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~   47 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQ   47 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999885 999999999999999999999999974