Citrus Sinensis ID: 009659

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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-------53
Protein Sequence
MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMG
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccHHHHHHHHccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHcccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccccccccccccHHHHHHHcccEEEEccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mnpcipdwnfegdipisnqmkpmgqdnELVELLWQNGHVvlssqaqtqrkpslnhneprqvqkqtlrgsgscgnssnliqddetvswihcpiedsfeKDFYSQLfselppsgpmevdKHTRQLREEkmvkfdppgavtssqhpnvnhsvvpelqrnamppprfevhdaapqnknlgdlgklvnfsqstappkgelgpcsgqfdrkrsgnltqgevrecsmmtvgsshcgsnqvaydldmsrasssglnddvrkvispsergktetieptvtsssggsgssfnrtskqstgdnslkrksrdavdsecqseaagfesgagnktaqrsgscrrSRAAEVHNLSERRRRDRINEKMRALQELIphcnktdkaSMLDEAIEYLKSLQLQLQVMWMgsgmaplmfpgmqhymsrmgmgmgppplpsvtnpmhfsrvplvdqsmSMAQAQNRAVMCQasvlnpvnyqnqmqnsnFTEQYARymgfhpmqansqpmnmfrfgsptmqnqivslpssscvpfsggaatdnsplsgkmg
Flexible Loop (DISEMBL)
mnpcipdwnfegdipISNQMKPMGQDNELVELLWQNGHVVLSSQaqtqrkpslnhneprqvqkqtlrgsgscgnssnliqddetVSWIHCPIEDSFEKDFYSQLFSelppsgpmeVDKHTRQLREEKMVKFDPpgavtssqhpnvnHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQstappkgelgpcsgqfdrkrsgnltqGEVRECSMMTVGSSHCGSNQVAYDLDMSRasssglnddvrkvispsergktetieptvtsssggsgssfnrtskqstgdnslkrksrdaVDSECQSeaagfesgagnktaqrsgscrrsraaevhnlserrrrdrINEKMRALqeliphcnktdKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSsscvpfsggaatdnsplsgkmg
Low Complexity Region (SEG)
MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTsssggsgssFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRmgmgmgpppLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMG
Disordered region (IsUnstruct)
******DWNFEGDI*************ELVELLWQNGHVVL***************************************DDETVSWIHCPIEDSFEKDFYSQLF************************************************************************************************************************************************************************************************************************************************************LIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHY****************************************AVMCQASVLNPVNYQ*******FTEQYARYMGF***************************************************
Disordered Region (DISOPRED)
***CIPD*NFEGD**************ELVELLWQ**********************************************DETVSWIHCPIEDSFEKDFY******************************************************************************************************************************************************************************************************************************************************INEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMF**********************************************************************************************************************************
Disordered Region (DISEMBL)
MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLS*******************************NSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPS*********************************************************************************SERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATD*********
Disordered Region (DISPRO)
**********EGDIPISNQMKPMGQDNELVELLWQNGHVVLSS**********************************LIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGP**************************************************************************************************************************************************************************************************************************************RRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSP*********************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKMG
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	529	2.2.26 [Sep-21-2011]
Q84LH8	444	Transcription factor PIF5	yes	no	0.495	0.590	0.445	3e-46
Q8W2F3	430	Transcription factor PIF4	no	no	0.523	0.644	0.413	7e-43
Q8GZM7	478	Transcription factor PIF1	no	no	0.776	0.859	0.323	3e-41
O80536	524	Transcription factor PIF3	no	no	0.684	0.690	0.364	7e-39
Q9SVU6	413	Transcription factor bHLH	no	no	0.614	0.786	0.336	6e-33
Q8L5W8	416	Transcription factor PIL1	no	no	0.257	0.326	0.448	2e-24
Q9SVU7	445	Putative transcription fa	no	no	0.274	0.325	0.409	3e-23
Q9FUA4	373	Transcription factor SPAT	no	no	0.183	0.260	0.582	2e-22
Q7XHI7	307	Transcription factor bHLH	no	no	0.279	0.482	0.394	8e-21
Q9FHA2	210	Transcription factor ALC	no	no	0.149	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 (473), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 142/319 (44%), Positives = 190/319 (59%), Gaps = 57/319 (17%)

Query: 219 SMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSG 278
           S++TVG SHCGSNQ           S+ ++      +S S+R K    E   TSS G SG
Sbjct: 146 SVITVGPSHCGSNQ-----------STNIHQATTLPVSMSDRSKN-VEERLDTSSGGSSG 193

Query: 279 SSFNRTSKQSTGDNS--LKRKSRDAVDSECQSEA---AGFESG----AGNKTAQRSGSCR 329
            S+ R +K++    S  + RK +  +D++ +S +    G  S      GNK++QRSGS R
Sbjct: 194 CSYGRNNKETVSGTSVTIDRKRKHVMDADQESVSQSDIGLTSTDDQTMGNKSSQRSGSTR 253

Query: 330 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMW 389
           RSRAAEVHNLSERRRRDRINE+M+ALQELIPHC++TDKAS+LDEAI+YLKSLQ+QLQVMW
Sbjct: 254 RSRAAEVHNLSERRRRDRINERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQLQVMW 313

Query: 390 MGSGM--------APLMFPGMQH--YMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSM 439
           MGSGM        +P+MFPG+Q   Y+++M M           + M  S+ P++++S   
Sbjct: 314 MGSGMAAAAAAAASPMMFPGVQSSPYINQMAM----------QSQMQLSQFPVMNRS--- 360

Query: 440 AQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHP--------MQ-ANSQPMNM 490
           A   +  ++CQ    NPV  Q Q QN   +EQ ARYMG  P        MQ    QP +M
Sbjct: 361 APQNHPGLVCQ----NPVQLQLQAQNQILSEQLARYMGGIPQMPPAGNQMQTVQQQPADM 416

Query: 491 FRFGSPTMQNQIVSLPSSS 509
             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 (444), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 134/324 (41%), Positives = 177/324 (54%), Gaps = 47/324 (14%)

Query: 207 SGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETI 266
           S  + + E+ + S+ TVG SHCGSN    DLD+S +     N  + + ++P+    +   
Sbjct: 145 SSGIRETEMEQYSVTTVGPSHCGSNPSQNDLDVSMSHDRSKN--IEEKLNPNASSSSGGS 202

Query: 267 EPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSG 326
                       +S     +  T D   KRK  +  D     E+       GNK+ QRSG
Sbjct: 203 SGCSFGKDIKEMAS----GRCITTDR--KRKRINHTD-----ESVSLSDAIGNKSNQRSG 251

Query: 327 SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQ 386
           S RRSRAAEVHNLSERRRRDRINE+M+ALQELIPHC+KTDKAS+LDEAI+YLKSLQLQLQ
Sbjct: 252 SNRRSRAAEVHNLSERRRRDRINERMKALQELIPHCSKTDKASILDEAIDYLKSLQLQLQ 311

Query: 387 VMW------MGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMA 440
           VMW        +  AP+MFPG+Q              +  + +P+   R P++DQS   A
Sbjct: 312 VMWMGSGMAAAAASAPMMFPGVQPQQF----------IRQIQSPVQLPRFPVMDQS---A 358

Query: 441 QAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHP-MQANS--QPMNMFRFGSPT 497
              N  ++CQ    NPV      QN   ++++ARY+G  P MQA +  QPM M RF SP 
Sbjct: 359 IQNNPGLVCQ----NPV------QNQIISDRFARYIGGFPHMQAATQMQPMEMLRFSSPA 408

Query: 498 MQNQIVSLPSSSCVPFSGGAATDN 521
            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 =  170 bits (430), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 167/517 (32%), Positives = 239/517 (46%), Gaps = 106/517 (20%)

Query: 1   MNPCIPDWNFEGDIPISNQ-----------MKPMGQDNELVELLWQNGHVVLSSQAQTQR 49
           M+  +PD++ + D  ++N            +  MG+D++L+ELLWQNG VV+ +Q    +
Sbjct: 1   MHHFVPDFDTDDDY-VNNHNSSLNHLPRKSITTMGEDDDLMELLWQNGQVVVQNQRLHTK 59

Query: 50  KPSLNHNEPRQVQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELP 109
           KPS   + P ++            + +  IQ+DE  SW+H P+ D    DF S L     
Sbjct: 60  KPS---SSPPKLLPSMDPQQQPSSDQNLFIQEDEMTSWLHYPLRDD---DFCSDLLFS-- 111

Query: 110 PSGPMEVDKHTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAA 169
                     T      ++    PP + T+   P V         RN M           
Sbjct: 112 -----AAPTATATATVSQVTAARPPVSSTNESRPPV---------RNFM----------- 146

Query: 170 PQNKNLGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGN----LTQGEVRECSMMT--- 222
                        NFS+             G F+  R G     L++  VRE + ++   
Sbjct: 147 -------------NFSR-----------LRGDFNNGRGGESGPLLSKAVVRESTQVSPSA 182

Query: 223 ---VGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGS 279
                +S  G  +     D S  +  G  +   K ++ +       IE T TSSS  S S
Sbjct: 183 TPSAAASESGLTRRTDGTDSSAVAGGGAYNRKGKAVAMT----APAIEITGTSSSVVSKS 238

Query: 280 SFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNL 339
                  + T  +  KRK R+A  ++ ++E+   E+     +   + S +RSRAAEVHNL
Sbjct: 239 EIE---PEKTNVDDRKRKEREATTTD-ETESRSEETKQARVS---TTSTKRSRAAEVHNL 291

Query: 340 SERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMF 399
           SER+RRDRINE+M+ALQELIP CNK+DKASMLDEAIEY+KSLQLQ+Q+M MG GM P+M+
Sbjct: 292 SERKRRDRINERMKALQELIPRCNKSDKASMLDEAIEYMKSLQLQIQMMSMGCGMMPMMY 351

Query: 400 PGMQHYMSRMGMGMG-----PPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVL 454
           PGMQ YM  M MGMG     PPP       M  ++ PL  Q+          V   AS  
Sbjct: 352 PGMQQYMPHMAMGMGMNQPIPPPSFMPFPNMLAAQRPLPTQTHMAGSGPQYPV--HASDP 409

Query: 455 NPVNYQNQMQN---------SNFTEQYARYMGFHPMQ 482
           + V   NQ  +         + +T+ Y ++ G HP Q
Sbjct: 410 SRVFVPNQQYDPTSGQPQYPAGYTDPYQQFRGLHPTQ 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 =  162 bits (409), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 150/411 (36%), Positives = 205/411 (49%), Gaps = 49/411 (11%)

Query: 27  NELVELLWQNGHVVLSSQAQTQRK---PSLNHNEPRQVQKQTLRGSGSCGNS-------- 75
           +E+VEL+W+NG +   SQ+   R    P  N +  R++      G+GS            
Sbjct: 27  DEVVELVWENGQISTQSQSSRSRNIPPPQANSSRAREI------GNGSKTTMVDEIPMSV 80

Query: 76  ----SNLIQDDETVSWI-HCPIEDSFEKDFYSQLFSELPPS---GPMEVDKHTRQLREEK 127
               + L QDD+ V W+ H P  D +  DF   + S +  +     M V++    L + +
Sbjct: 81  PSLMTGLSQDDDFVPWLNHHPSLDGYCSDFLRDVSSPVTVNEQESDMAVNQTAFPLFQRR 140

Query: 128 MVKFDPPGAVTSSQHPNV-NHSVVPELQRNAMP-----PPRFEVHDAAPQNKNLGDLGKL 181
               +   A +SSQ+    +HS+    +   +P     P RF          N      L
Sbjct: 141 KDGNESAPAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNKP---SL 197

Query: 182 VNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSR 241
           VNFS    P        +   D K     +   V +  ++    S    ++V   L+ S 
Sbjct: 198 VNFSHFLRPATFAKTTNNNLHDTKEKSPQSPPNVFQTRVLGAKDSE---DKV---LNESV 251

Query: 242 ASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDA 301
           AS++  ++    +IS     K +  E  V  SS GSG+S +  S+  +   SLKRK  + 
Sbjct: 252 ASATPKDNQKACLISEDSCRKDQESEKAVVCSSVGSGNSLDGPSESPSL--SLKRKHSNI 309

Query: 302 VDSECQSEAAGFESGAGNKTA--QRSG-SCRRSRAAEVHNLSERRRRDRINEKMRALQEL 358
            D +C SE    ESG G K A   R+G   +RSR+AEVHNLSERRRRDRINEKMRALQEL
Sbjct: 310 QDIDCHSEDVEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDRINEKMRALQEL 369

Query: 359 IPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMA---PLMF-PGMQHY 405
           IP+CNK DKASMLDEAIEYLKSLQLQ+Q+M M SG      +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 (358), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 144/428 (33%), Positives = 191/428 (44%), Gaps = 103/428 (24%)

Query: 16  ISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQVQKQTLRGSGSCGNS 75
           IS +   MG+D+ +VELL ++  VV SSQ QT   PS +   P  +    LRGSGS    
Sbjct: 15  ISPEKYIMGEDD-IVELLGKSSQVVTSSQTQT---PSCD---PPLI----LRGSGSGDGE 63

Query: 76  SN----------------LIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKH 119
            N                 IQ+DE  SW+H P    +       L+S+L  SG       
Sbjct: 64  GNGPLPQPPPPLYHQQSLFIQEDEMASWLHQPNRQDY-------LYSQLLYSG------- 109

Query: 120 TRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAA--PQNKNLGD 177
                              +S HP    S+ P       PPPR +   AA  P    L +
Sbjct: 110 ------------------VASTHPQSLASLEPP------PPPRAQYILAADRPTGHILAE 145

Query: 178 LGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVREC-SMMTVGSSHCGSNQVAYD 236
             +  NF                   R+R GN+  G V    S  T+ SS   S    + 
Sbjct: 146 R-RAENFMN---------------ISRQR-GNIFLGGVEAVPSNSTLLSSATESIPATHG 188

Query: 237 LDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSL-- 294
            + SRA+ +G       V     RGK   IE   T S G   +      +Q   +  +  
Sbjct: 189 TE-SRATVTGGVSRTFAVPGLGPRGKAVAIETAGTQSWGLCKAETEPVQRQPATETDITD 247

Query: 295 --KRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKM 352
             KRK+R+  + E Q          G + A+ S S +RSRAA +H LSERRRR +INE M
Sbjct: 248 ERKRKTREETNVENQ----------GTEEARDSTSSKRSRAAIMHKLSERRRRQKINEMM 297

Query: 353 RALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMA-PLMFPG--MQHYMSRM 409
           +ALQEL+P C KTD++SMLD+ IEY+KSLQ Q+Q+  MG  M  P+M+ G   Q YM  M
Sbjct: 298 KALQELLPRCTKTDRSSMLDDVIEYVKSLQSQIQMFSMGHVMIPPMMYAGNIQQQYMPHM 357

Query: 410 GMGMGPPP 417
            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 (284), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 65/145 (44%), Positives = 90/145 (62%), Gaps = 9/145 (6%)

Query: 276 GSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQ-----RSGSCRR 330
            S S F+R + +     SLKRK  D  + E    +   +  + +   Q     R    +R
Sbjct: 168 ASSSKFSRGTSRDLSCCSLKRKYGDIEEEESTYLSNNSDDESDDAKTQVHARTRKPVTKR 227

Query: 331 SRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWM 390
            R+ EVH L ER+RRD  N+KMRALQ+L+P+C K DKAS+LDEAI+Y+++LQLQ+Q+M M
Sbjct: 228 KRSTEVHKLYERKRRDEFNKKMRALQDLLPNCYKDDKASLLDEAIKYMRTLQLQVQMMSM 287

Query: 391 GSGMA--PLMFPGMQHYMSRMGMGM 413
           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: 260 RGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGN 319
           +GK   +E   T SSG   +       Q   ++ LK +                E   G 
Sbjct: 199 KGKAVAVEAAGTPSSGVCKAETEPVQIQPATESKLKAR----------------EETHGT 242

Query: 320 KTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLK 379
           + A+ S S +RSR AE+HNL+ERRRR++INEKM+ LQ+LIP CNK+ K S LD+AIEY+K
Sbjct: 243 EEARGSTSRKRSRTAEMHNLAERRRREKINEKMKTLQQLIPRCNKSTKVSTLDDAIEYVK 302

Query: 380 SLQLQLQVMWMGSGMAPLMFPG-MQHYMSRMGMGMGPP----PLPSVTNPM 425
           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 (267), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 60/103 (58%), Positives = 73/103 (70%), Gaps = 6/103 (5%)

Query: 305 ECQSEAAGF----ESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIP 360
           +C+SE  G     E+ +         S +R RAAEVHNLSE+RRR RINEKM+ALQ LIP
Sbjct: 166 DCESEEGGEAVVDEAPSSKSGPSSRSSSKRCRAAEVHNLSEKRRRSRINEKMKALQSLIP 225

Query: 361 HCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSG--MAPLMFPG 401
           + 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 (254), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 69/175 (39%), Positives = 96/175 (54%), Gaps = 27/175 (15%)

Query: 318 GNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEY 377
           G + A+ S S +RSRAAE+HNL+ERRRR++INE+M+ LQ+LIP CNK+ K SML++ IEY
Sbjct: 136 GTEEARGSTSRKRSRAAEMHNLAERRRREKINERMKTLQQLIPRCNKSTKVSMLEDVIEY 195

Query: 378 LKSLQLQLQV----MWMGSGMAPLMFP-GMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPL 432
           +KSL++Q+      M MG    P   P   Q +M+ +G    PP  P       F  +  
Sbjct: 196 VKSLEMQINQFMPHMAMGMNQPPAYIPFPSQAHMAGVGPSYPPPRYP-------FPNIQT 248

Query: 433 VDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQP 487
            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 =  100 bits (250), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 48/81 (59%), Positives = 64/81 (79%), Gaps = 2/81 (2%)

Query: 322 AQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSL 381
           A++  S +R+  A+ HNLSE++RR +INEKM+ALQ+LIP+ NKTDKASMLDEAIEYLK L
Sbjct: 83  AKQRNSLKRNIDAQFHNLSEKKRRSKINEKMKALQKLIPNSNKTDKASMLDEAIEYLKQL 142

Query: 382 QLQLQVMWM--GSGMAPLMFP 400
           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	529
449463597	550	PREDICTED: transcription factor PIF5-lik	0.979	0.941	0.593	1e-160
225446765	531	PREDICTED: transcription factor PIF5-lik	0.971	0.967	0.585	1e-160
302143504	544	unnamed protein product [Vitis vinifera]	0.954	0.928	0.589	1e-159
356553623	562	PREDICTED: transcription factor PIF5-lik	0.990	0.932	0.516	1e-126
356501423	562	PREDICTED: transcription factor PIF4-lik	0.988	0.930	0.513	1e-124
224082612	380	predicted protein [Populus trichocarpa]	0.684	0.952	0.641	1e-109
356567480	397	PREDICTED: transcription factor PIF5-lik	0.699	0.931	0.549	6e-97
224066527	233	predicted protein [Populus trichocarpa]	0.432	0.982	0.751	2e-85
356526934	266	PREDICTED: transcription factor PIF5-lik	0.497	0.988	0.624	1e-71
115489518	445	Os12g0610200 [Oryza sativa Japonica Grou	0.655	0.779	0.402	1e-61

>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 =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 333/561 (59%), Positives = 398/561 (70%), Gaps = 43/561 (7%)

Query: 1   MNPCIPDWNFEGDIPISNQMKPMG-QDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPR 59
           MN C PDWNFEGDIP +   K MG + ++LVELLW+NG VVL  Q+Q  RK SL  NE R
Sbjct: 1   MNYCFPDWNFEGDIPPAK--KSMGPEHDDLVELLWRNGQVVL--QSQKARKSSLIANEVR 56

Query: 60  QVQKQT---LRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEV 116
           Q QKQ     R + SCGNSSNLIQDDETVSWI  P++DSFEK+F S  FSELPP+ P+E+
Sbjct: 57  QFQKQNQPLYRSNVSCGNSSNLIQDDETVSWIQDPLDDSFEKEFCSNFFSELPPADPIEI 116

Query: 117 DKH-TRQLREEKMVKFDPPGAVTSSQHPNVNHSV---------VPELQRNAMPPPRFEVH 166
            K   +  +++K  +F   GA  ++ H    + V         + E   N MPPPRF+  
Sbjct: 117 VKQPIKHFQDDKQTRF---GAFDTATHVTFGNFVKKNSKPPASLAEFPMNTMPPPRFQFQ 173

Query: 167 DAAPQNKNLGDLGKLVNFSQSTAPP-KGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGS 225
           D++ QNK+LGDLGKLVNFSQ   PP KG+LG  +G    + SGNL QGE R+CS MTVGS
Sbjct: 174 DSSRQNKDLGDLGKLVNFSQVPVPPLKGDLGSSNG---GRESGNLIQGEGRDCSGMTVGS 230

Query: 226 SHCGSNQVAY--DLDMSRASSSGL----------NDDVRKVISPSERGKTETIEPTVTSS 273
           SHCGSNQV    DLD+SR S+SG            +D RK+++  ER KTET++PT TSS
Sbjct: 231 SHCGSNQVPNPNDLDLSRVSTSGFGNAGLSAGFSKEDNRKMVAQGERDKTETMDPTATSS 290

Query: 274 SGGSGSSFNR--TSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRS 331
           SGGSGSS +R  T  QSTG N  KRK RD  +SECQSE A  ES  GNKTA RSGS RR+
Sbjct: 291 SGGSGSSMDRSRTIGQSTGGNGNKRKGRDGEESECQSETAELESAEGNKTAPRSGSSRRT 350

Query: 332 RAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMG 391
           RAAEVHNLSERRRR+RINEKM+ALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMG
Sbjct: 351 RAAEVHNLSERRRRERINEKMKALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMG 410

Query: 392 SGMAPLMFPGMQHYMSR--MGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMC 449
           SGMAP+MFPG+QHYMSR  MGMGM  P +PS+ NPM   RVP+VDQS+S+A   N+ +MC
Sbjct: 411 SGMAPMMFPGVQHYMSRVAMGMGMAQPSMPSIHNPMQLPRVPIVDQSVSVAPTPNQPMMC 470

Query: 450 QASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFG-SPTMQNQIVSLPSS 508
           Q  + NP+NYQNQMQN    EQYAR MGFH MQ  SQP+N+FRF  S  +Q+Q  + P  
Sbjct: 471 QPQMFNPMNYQNQMQNPALQEQYARLMGFHHMQPTSQPINVFRFCPSAVLQSQPAAAPGP 530

Query: 509 SCVPFSGGAATDNSPLSGKMG 529
           +  P +GG+ T N  ++G +G
Sbjct: 531 ASGPTAGGSIT-NDIVNGNLG 550

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  572 bits (1474), Expect = e-160,   Method: Compositional matrix adjust.
 Identities = 318/543 (58%), Positives = 386/543 (71%), Gaps = 29/543 (5%)

Query: 2   NPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQV 61
           +P +PDWN EGD+P++NQ KPMGQ++ELVELLW+NG VVL SQ  TQRK  L  NE +QV
Sbjct: 3   HPLLPDWNIEGDVPVTNQKKPMGQEHELVELLWRNGQVVLHSQ--TQRKSGLAPNESKQV 60

Query: 62  QKQ---TLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDK 118
           QK     LR  GSCGN SNLIQD+E++SWI  P++DS +K+F S LF ELPP+ P++ +K
Sbjct: 61  QKHDQTMLRNGGSCGNWSNLIQDEESISWIQYPLDDSLDKEFCSNLFMELPPNDPVQPEK 120

Query: 119 HTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDL 178
             R   +EK        +V SSQ P   H   PE   N MPPP+F+V  +  QN + G  
Sbjct: 121 PVRHSEQEK--------SVPSSQQPIFKHLGSPEFPGNPMPPPKFQVPGSVQQNCSSGGF 172

Query: 179 GKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQG-EVRECSMMTVGSSHCGSNQVAYDL 237
           GK+VNF   + P +  LG    Q   K SGN+ QG + +E S+MTVG SHCGSNQV  + 
Sbjct: 173 GKIVNFPNFSFPGRSNLGSSKAQLGGKGSGNMAQGGDAKEGSVMTVGLSHCGSNQVVNEA 232

Query: 238 DMSRASSSGL----------NDDVRKVISPSERGKTETIEPTVTSSSGGSGSS-FNRTSK 286
           D+SR SSSG+           ++V +++S  +R +TET+EPTVTSSSGG   S F RT K
Sbjct: 233 DLSRFSSSGVGTGCLSSGHVKENVMRIVSQGDRRQTETLEPTVTSSSGGGSGSSFGRTYK 292

Query: 287 QSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRD 346
           QST  NS KRK R+A +SECQSEAA  ES A NK +QRSGS RRSRAAEVHNLSERRRRD
Sbjct: 293 QSTDTNSHKRKGREAEESECQSEAAEHESAARNKASQRSGSTRRSRAAEVHNLSERRRRD 352

Query: 347 RINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYM 406
           RINEKM+ALQELIPH NK+DKASMLDEAIEYLKSLQLQLQ+MWMG G+AP+MFPG+QHYM
Sbjct: 353 RINEKMKALQELIPHSNKSDKASMLDEAIEYLKSLQLQLQLMWMGGGVAPMMFPGVQHYM 412

Query: 407 SRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNS 466
           +RMGMGM PPPLPS+ NPMH  RV LVDQS S     N+  +CQ  VLNPVNYQNQM N 
Sbjct: 413 ARMGMGMCPPPLPSIHNPMHLPRVQLVDQSTSAVPPSNQPPICQTPVLNPVNYQNQMPNP 472

Query: 467 NFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSG 526
           NF EQ+A YMGFHPMQ  SQPMN+F FGS   Q+  ++ P+++    +  AA D +P S 
Sbjct: 473 NFPEQFAHYMGFHPMQTPSQPMNVFSFGS---QSHPMASPATTGGTPTAAAAVDGAPGS- 528

Query: 527 KMG 529
           K+G
Sbjct: 529 KLG 531

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  566 bits (1459), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 314/533 (58%), Positives = 377/533 (70%), Gaps = 28/533 (5%)

Query: 2   NPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQV 61
           +P +PDWN EGD+P++NQ KPMGQ++ELVELLW+NG VVL SQ  TQRK  L  NE +QV
Sbjct: 3   HPLLPDWNIEGDVPVTNQKKPMGQEHELVELLWRNGQVVLHSQ--TQRKSGLAPNESKQV 60

Query: 62  QKQ---TLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDK 118
           QK     LR  GSCGN SNLIQD+E++SWI  P++DS +K+F S LF ELPP+ P++ +K
Sbjct: 61  QKHDQTMLRNGGSCGNWSNLIQDEESISWIQYPLDDSLDKEFCSNLFMELPPNDPVQPEK 120

Query: 119 HTRQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDL 178
             R   +EK        +V SSQ P   H   PE   N MPPP+F+V  +  QN + G  
Sbjct: 121 PVRHSEQEK--------SVPSSQQPIFKHLGSPEFPGNPMPPPKFQVPGSVQQNCSSGGF 172

Query: 179 GKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQG-EVRECSMMTVGSSHCGSNQVAYDL 237
           GK+VNF   + P +  LG    Q   K SGN+ QG + +E S+MTVG SHCGSNQV  + 
Sbjct: 173 GKIVNFPNFSFPGRSNLGSSKAQLGGKGSGNMAQGGDAKEGSVMTVGLSHCGSNQVVNEA 232

Query: 238 DMSRASSSGL----------NDDVRKVISPSERGKTETIEPTVTSSSGGSGSS-FNRTSK 286
           D+SR SSSG+           ++V +++S  +R +TET+EPTVTSSSGG   S F RT K
Sbjct: 233 DLSRFSSSGVGTGCLSSGHVKENVMRIVSQGDRRQTETLEPTVTSSSGGGSGSSFGRTYK 292

Query: 287 QSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRD 346
           QST  NS KRK R+A +SECQSEAA  ES A NK +QRSGS RRSRAAEVHNLSERRRRD
Sbjct: 293 QSTDTNSHKRKGREAEESECQSEAAEHESAARNKASQRSGSTRRSRAAEVHNLSERRRRD 352

Query: 347 RINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYM 406
           RINEKM+ALQELIPH NK+DKASMLDEAIEYLKSLQLQLQ+MWMG G+AP+MFPG+QHYM
Sbjct: 353 RINEKMKALQELIPHSNKSDKASMLDEAIEYLKSLQLQLQLMWMGGGVAPMMFPGVQHYM 412

Query: 407 SRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNS 466
           +RMGMGM PPPLPS+ NPMH  RV LVDQS S     N+  +CQ  VLNPVNYQNQM N 
Sbjct: 413 ARMGMGMCPPPLPSIHNPMHLPRVQLVDQSTSAVPPSNQPPICQTPVLNPVNYQNQMPNP 472

Query: 467 NFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAAT 519
           NF EQ+A YMGFHPMQ  SQPMN+F FGS   Q   V+    +C   + G+ T
Sbjct: 473 NFPEQFAHYMGFHPMQTPSQPMNVFSFGS---QTSWVNTSGYACCSNAFGSIT 522

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 =  459 bits (1180), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 290/562 (51%), Positives = 361/562 (64%), Gaps = 38/562 (6%)

Query: 1   MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQ 60
           M   IP  +FE D  ++NQ K +G D ELVELLWQNG VV     QT RKP  N +  RQ
Sbjct: 1   MKNSIPGLDFESDACLTNQRKLIGPDQELVELLWQNGQVV--RHNQTHRKPLGNSSNLRQ 58

Query: 61  VQK---QTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVD 117
            QK    TLR SG  GNSSNL Q++ T  WI  P+ED  E+DF S L SELPP+   E  
Sbjct: 59  AQKTDHSTLRSSGPYGNSSNLDQEEAT-PWIQFPLEDPLEQDFCSNLLSELPPTCEFESY 117

Query: 118 KHTRQLREEKMVKF----DPPGAVTSSQHP---NVNHSVVPELQRNA--MPPPRFEVHDA 168
           K  +QL E+K   F     P    TSS  P   N+  S V  +Q N   MP PRF V D+
Sbjct: 118 KPIKQLEEDKFTNFFASSTPHHPTTSSSKPLPPNMTSSWVQRIQGNPNPMPAPRFHVPDS 177

Query: 169 APQNKNLGDLGKLVNFSQSTAPPKG-ELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSH 227
           + ++ +LG   K++NF   + P       P S QF  K + NL+Q E RE S++TVGSSH
Sbjct: 178 SQKDNDLGASRKVLNFPHFSTPRNNVSSAPGSTQFREKTTANLSQSEAREYSVITVGSSH 237

Query: 228 CGSNQVAYDLDMSRASSSGL----------------NDDVRKVISP-SERGKTETIEPTV 270
           CGS+ +  + D+SR SSS +                 D V++ I P S++GK+E IEPTV
Sbjct: 238 CGSSHIPQEKDVSRVSSSAVWATNNNNSLSAEPEAVRDCVQRPICPRSDKGKSEMIEPTV 297

Query: 271 TSSSGGSGSSFN-RTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCR 329
           TSSSGGSGS+   RT   ST D+  KRK  +   SE QSEA   +S  GNK +QR+GS +
Sbjct: 298 TSSSGGSGSTGIGRTCSLSTRDHGQKRKGTEEEASEEQSEATELKSADGNKASQRTGSSK 357

Query: 330 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMW 389
           R+RAAEVHN SERRRRDRINEKMR LQ+LIP+ NKTDKASML+EAIEYLKSLQ QLQVMW
Sbjct: 358 RNRAAEVHNQSERRRRDRINEKMRTLQQLIPNSNKTDKASMLEEAIEYLKSLQFQLQVMW 417

Query: 390 MGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMC 449
           MGSGM P+MFPG+QHYMS+MGMGMG P LPS+ NPM   +VP  DQ+MS+ Q  N+ +MC
Sbjct: 418 MGSGMTPVMFPGIQHYMSQMGMGMGAPSLPSIYNPMQLPKVPH-DQAMSVPQMPNQNLMC 476

Query: 450 QASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQ--IVSLPS 507
           Q  VL   NYQ  MQN    EQYA YMG+H M++ SQPMN+FR+GS  +Q+   +++  +
Sbjct: 477 QNQVLGAFNYQTHMQNPCLPEQYAPYMGYHFMRSASQPMNVFRYGSQAVQHSQTMIAPGN 536

Query: 508 SSCVPFSGGAATDNSPLSGKMG 529
           +S  P SG A  D++ +SGK G
Sbjct: 537 NSSGPMSGTANIDDA-VSGKAG 557

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 =  451 bits (1161), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 289/563 (51%), Positives = 356/563 (63%), Gaps = 40/563 (7%)

Query: 1   MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQ 60
           MN  IP W+FE D  ++NQ K +G D ELVELLW+NG VV+ +Q  T RK   N +  RQ
Sbjct: 1   MNNSIPGWDFESDTCLTNQRKLIGPDQELVELLWKNGQVVMHNQ--THRKTLGNSSNLRQ 58

Query: 61  VQKQ---TLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVD 117
           VQK     LR SG  GNSSNL Q+D    W+  P+ED  E+DF S L SELP +   E  
Sbjct: 59  VQKSDQSVLRSSGPYGNSSNLDQED-AAPWVQFPLEDPLEQDFCSNLLSELP-TCEFESY 116

Query: 118 KHTRQLREEKMVKFDPPGA----VTSSQHP---NVNHSVVPELQRNA--MPPPRFEVHDA 168
           K  RQL EEK  KF   G      TSS  P   N+  S +  LQ N   MP PRF   D+
Sbjct: 117 KPIRQLEEEKFAKFFASGTPHHPTTSSSQPLPPNMKPSCIQGLQGNPIPMPAPRFHGPDS 176

Query: 169 APQNKNLGDLGKLVNFSQSTAPPKG-ELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSH 227
           + +  + G   K++NF Q + P       P   QF  K + N++Q E RE S++TVGSSH
Sbjct: 177 SQKIHDFGASRKVLNFPQFSTPRNNVPSAPGITQFREKTTANMSQSEAREYSVITVGSSH 236

Query: 228 CGSNQVAYDLDMSRASSSGL-----------------NDDVRKVISP-SERGKTETIEPT 269
           CGSN +  + D+SR SS+G+                  D V++ I P S +GK+E IE T
Sbjct: 237 CGSNHIPQEQDVSRISSTGVWATTNNNTTLSAEPEAVRDYVQRPICPKSGQGKSEMIELT 296

Query: 270 VTSSSGGSGSSFN-RTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSC 328
           VTSSSGGSGS+   RT   ST D+  KRK  +    E QSE    +S  GNK +QR+ S 
Sbjct: 297 VTSSSGGSGSTGIGRTCSLSTRDHGQKRKGTEEEALEEQSEDTELKSADGNKASQRTRSS 356

Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVM 388
           RR+RAAEVHN SERRRRDRINEKMR LQ+LIP+ NKTDKASML+EAIEYLKSLQ QLQVM
Sbjct: 357 RRNRAAEVHNQSERRRRDRINEKMRTLQQLIPNSNKTDKASMLEEAIEYLKSLQFQLQVM 416

Query: 389 WMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVM 448
           WMG GM P+MFPG+QHYMS+MGMGMG P LPS+ NPM   +VP  DQ+MS+ Q  N+ +M
Sbjct: 417 WMGGGMTPVMFPGIQHYMSQMGMGMGAPSLPSIHNPMQLPKVPH-DQAMSVLQIPNQNLM 475

Query: 449 CQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQNQ--IVSLP 506
           CQ  VL   NYQNQMQN    EQYARYMG+H MQ  SQPMN+FR+GS  +Q+   +++  
Sbjct: 476 CQNPVLGAFNYQNQMQNPCLPEQYARYMGYHLMQNASQPMNVFRYGSQAVQHSQTMIAPG 535

Query: 507 SSSCVPFSGGAATDNSPLSGKMG 529
           ++S  P SG A  D++  SGK G
Sbjct: 536 NNSSGPMSGTANIDDAD-SGKAG 557

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 =  403 bits (1036), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 250/390 (64%), Positives = 290/390 (74%), Gaps = 28/390 (7%)

Query: 158 MPPPRFEVHDAAPQNKNLGDLGKLVN--FSQSTAPPKG-ELGPCSGQFDRKRSGNLTQGE 214
           MPPPR +V +    +  +G  G+ VN  FSQ +AP KG +    SGQF  + SGN  QGE
Sbjct: 1   MPPPRIQVPEK--NHAGVGGFGEAVNANFSQFSAPFKGGDFRTSSGQFGGQGSGNSPQGE 58

Query: 215 VRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLN-----------DDVRKVISPSERGKT 263
           VRECS++TVGSS    NQ+ +D DMSRASS+ +            DD RK++S SERGKT
Sbjct: 59  VRECSVVTVGSS----NQIPHDRDMSRASSNAMGTSTAFSTGPSMDDPRKIVSQSERGKT 114

Query: 264 ETIEPTVTSSSGGSGSSFNRTSKQSTG-DNSLKRKSRDAVDSECQSEAA--GFESGAGNK 320
           ET+E T+T+SSGGSGSSF RT KQS G  +S KRK+ D  DSE QSEAA    +S AGN 
Sbjct: 115 ETLEATLTTSSGGSGSSFGRTCKQSAGPSSSQKRKTIDTEDSEYQSEAAELDLDSMAGNN 174

Query: 321 TAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKS 380
             +RSGS RRSRAAEVHNLSERRRRDRINEKMRALQELIPHC KTDKASMLDEAIEYLKS
Sbjct: 175 PTKRSGSTRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCYKTDKASMLDEAIEYLKS 234

Query: 381 LQLQLQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMA 440
           LQLQLQVMWMG GMAP++FPG+QH+MSRMGMG   PPLPS+ NPMH  RV L+DQS+SMA
Sbjct: 235 LQLQLQVMWMGGGMAPMLFPGVQHFMSRMGMG---PPLPSMQNPMHLPRVQLIDQSISMA 291

Query: 441 QAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTM-Q 499
             QN  VMCQA VLNPVN+ NQMQN  F +QYAR+MGFH MQA SQPMNMFRFGS T+ Q
Sbjct: 292 PTQNSGVMCQAPVLNPVNFHNQMQNPAFADQYARFMGFH-MQAASQPMNMFRFGSQTVQQ 350

Query: 500 NQIVSLPSSSCVPFSGGAATDNSPLSGKMG 529
           NQ+++  SS   P S G A  ++P S K+G
Sbjct: 351 NQMMAPTSSVGGPLSAGTAVSDAPPSDKVG 380

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 =  361 bits (926), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 212/386 (54%), Positives = 267/386 (69%), Gaps = 16/386 (4%)

Query: 158 MPPPRFEVHDAAPQNKN-LGDLGKLVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVR 216
           +P PRF V D+  +N N LG   K+ NFS  +AP        +  F  K +GN+++ E+R
Sbjct: 14  IPAPRFHVSDSPQKNNNDLGGSCKVQNFSHFSAPLNVSSASANAHFRDKITGNMSKNEIR 73

Query: 217 ECSMMTVGSSHCGSNQVAYDLDMSRASSSGL------------NDDVRKVISPSERGKTE 264
           ECS+MTVGSS+CGSN +  D D SRASS+G+             D V +    +E+GK+E
Sbjct: 74  ECSLMTVGSSYCGSNHIPQDPDASRASSNGVWTTTLSAEPEAVRDHVPRTSPQNEKGKSE 133

Query: 265 TIEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQR 324
            +EPT TSSSGGSGSS  +    ST +   KRK  D  +SE QSE    +S  GNK++QR
Sbjct: 134 MLEPTTTSSSGGSGSSLGKNCSLSTRNQGQKRKGIDVEESEEQSEDTELKSALGNKSSQR 193

Query: 325 SGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQ 384
           +G  RR+RAAEVHNLSERRRRDRINEKM+ALQ+LIPH +KTDKASML+EAIEYLKSLQLQ
Sbjct: 194 AGLARRNRAAEVHNLSERRRRDRINEKMKALQQLIPHSSKTDKASMLEEAIEYLKSLQLQ 253

Query: 385 LQVMWMGSGMAPLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQN 444
           LQ+MWMGSGMAP+MFPG+QHYMS+MGMGM  PP P + NPM   R+PL DQS+S +Q  N
Sbjct: 254 LQLMWMGSGMAPIMFPGIQHYMSQMGMGMATPPFPPIHNPMQLPRLPL-DQSVSASQTPN 312

Query: 445 RAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQN-QIV 503
           + +M Q  +L   NY NQMQN   +EQYARYMG+H MQ  SQPMN+FR+G   +++ Q +
Sbjct: 313 QTLMSQNPILGAFNYHNQMQNPALSEQYARYMGYHLMQNASQPMNVFRYGPQGVRHSQTM 372

Query: 504 SLPSSSCVPFSGGAATDNSPLSGKMG 529
             PS+S    SG A  D + +SGKMG
Sbjct: 373 ITPSNSSGNMSGAANIDEA-VSGKMG 397

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 =  323 bits (827), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 175/233 (75%), Positives = 196/233 (84%), Gaps = 4/233 (1%)

Query: 300 DAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELI 359
           DA +SECQSE A  +S   NK A+RSGS RRSRAAEVHNLSERRRRDRINEKMRALQELI
Sbjct: 2   DAEESECQSEDAELDSAVANKPAKRSGSTRRSRAAEVHNLSERRRRDRINEKMRALQELI 61

Query: 360 PHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSR--MGMGMGPPP 417
           PHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSG+ P+MFPG+QH+MSR  MGMGMGPPP
Sbjct: 62  PHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGIVPVMFPGVQHFMSRMGMGMGMGPPP 121

Query: 418 LPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMG 477
           LPS+ NPMH  RVPLVDQS+SM   QN+AV+CQ  VLNPVNYQNQMQN  F++QYAR+MG
Sbjct: 122 LPSMQNPMHLPRVPLVDQSISMTPTQNQAVICQTPVLNPVNYQNQMQNPTFSDQYARFMG 181

Query: 478 FHPMQANSQPMNMFRFGSPTM-QNQIVSLPSSSCVPFSGGAATDNSPLSGKMG 529
           FH MQA SQPMNMFRFGS T+ QNQ+++ P+S   P S G A  ++P SGK G
Sbjct: 182 FH-MQAASQPMNMFRFGSQTVQQNQMMAPPNSGGGPLSAGTAASDAPPSGKTG 233

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 =  277 bits (708), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 166/266 (62%), Positives = 200/266 (75%), Gaps = 3/266 (1%)

Query: 266 IEPTVTSSSGGSGSSFNRTSKQSTGDNSLKRKSRDAVDSECQSEAAGFESGAGNKTAQRS 325
           +EP VTSSSGGSGSS  +T   ST +   KRK  D  +SE QSE    +S  GNK++QR+
Sbjct: 2   LEPAVTSSSGGSGSSLGKTCSLSTRNQGQKRKGIDVEESEEQSEDTELKSALGNKSSQRT 61

Query: 326 GSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQL 385
           GS RR+RAAEVHNLSERRRRDRINEKM+ALQ+LIPH +KTDKASML+EAIEYLKSLQLQL
Sbjct: 62  GSARRNRAAEVHNLSERRRRDRINEKMKALQQLIPHSSKTDKASMLEEAIEYLKSLQLQL 121

Query: 386 QVMWMGSGMAPLMFPGMQHYMSRMGMGMG-PPPLPSVTNPMHFSRVPLVDQSMSMAQAQN 444
           Q+MWMGSGMAP+MFPG+QHYMS+MGMGM  PP  P + NPM   RVPL D+S+S +Q  N
Sbjct: 122 QLMWMGSGMAPIMFPGIQHYMSQMGMGMARPPFPPPIHNPMQLPRVPL-DKSVSASQTPN 180

Query: 445 RAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPMQANSQPMNMFRFGSPTMQN-QIV 503
           + +MCQ  +L   NYQNQMQN   +EQY RYMG+H MQ  SQPMN+FR+G   +Q+ Q +
Sbjct: 181 QTLMCQNPILGAFNYQNQMQNPALSEQYVRYMGYHLMQNASQPMNVFRYGPQGVQHSQTM 240

Query: 504 SLPSSSCVPFSGGAATDNSPLSGKMG 529
             PSS+      GAA  +  +SGKMG
Sbjct: 241 ITPSSNSSGNMSGAANIDEAVSGKMG 266

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|115489518|ref|NP_001067246.1| Os12g0610200 [Oryza sativa Japonica Group] gi|77556567|gb|ABA99363.1| Helix-loop-helix DNA-binding domain containing protein, expressed [Oryza sativa Japonica Group] gi|108862946|gb|ABA99364.2| Helix-loop-helix DNA-binding domain containing protein, expressed [Oryza sativa Japonica Group] gi|113649753|dbj|BAF30265.1| Os12g0610200 [Oryza sativa Japonica Group] gi|125537356|gb|EAY83844.1| hypothetical protein OsI_39060 [Oryza sativa Indica Group] gi|215694924|dbj|BAG90115.1| unnamed protein product [Oryza sativa Japonica Group]

 Score =  243 bits (621), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 176/437 (40%), Positives = 224/437 (51%), Gaps = 90/437 (20%)

Query: 1   MNPCIPDWNFEGDIPISNQMKPMGQDNELVELLWQNGHVVLSSQAQTQRKPSLNHNEPRQ 60
           MN  +PDWN      + +   P+G+D+ LVELLW NGHVV+ SQA   RKP      PR 
Sbjct: 1   MNQFVPDWN---TTSMGDGFAPLGEDDGLVELLWCNGHVVMQSQAP--RKP------PRP 49

Query: 61  VQKQTLRGSGSCGNSSNLIQDDETVSWIHCPIEDSFEKDFYSQLFSELPPSGPMEVDKHT 120
            +K T         ++  + +DE+ SW   P++D  EKD +++LF E+  +G    D   
Sbjct: 50  -EKTTA-------AAAAAMAEDESASWFQYPVDDVLEKDLFTELFGEMTAAGGGGGDVRR 101

Query: 121 RQLREEKMVKFDPPGAVTSSQHPNVNHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGK 180
              +EE+       GAV +              Q   MPPP       A      GD+  
Sbjct: 102 AACKEER-------GAVAA-------------FQSRMMPPPW-----PARGKAEFGDVDD 136

Query: 181 LVNFSQSTAPPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQV------A 234
           +   S+                  K  G      V E SM+T+GSS CGSN V       
Sbjct: 137 VCGVSEVVMA--------------KMDGAAAAETVGESSMLTIGSSICGSNHVQTPPVGN 182

Query: 235 YDLDMSRASSSGLNDDVRKVISPSERGK--TETIEPTVTSSSGGSGSSFNRTSKQSTGDN 292
                  A ++    D   V S S R +  T   EP   +++G  G              
Sbjct: 183 GKAGAGTAGAARRAHDTATVASSSMRSRSCTAKAEPRDVAAAGVGG-------------- 228

Query: 293 SLKRKSRD--AVDSECQSEAAGFESGAGNKT-AQRSGSCRRSRAAEVHNLSERRRRDRIN 349
             KRK R   A++S   SE   FES A   + AQ++ + +R RAAEVHNLSERRRRDRIN
Sbjct: 229 --KRKQRGGAAMESGSPSEDVEFESAAATCSPAQKTTTAKRRRAAEVHNLSERRRRDRIN 286

Query: 350 EKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAP--LMFP--GMQHY 405
           EKM+ALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQ+MWMG GMAP  +MFP  G+  Y
Sbjct: 287 EKMKALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQMMWMGGGMAPPAVMFPAAGVHQY 346

Query: 406 MSRMG-MGMGPPPLPSV 421
           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	529
TAIR|locus:2053733	430	PIF4 "AT2G43010" [Arabidopsis	0.551	0.679	0.412	1.4e-64
TAIR|locus:2077680	444	PIL6 "AT3G59060" [Arabidopsis	0.495	0.590	0.423	6.1e-64
TAIR|locus:2061634	478	PIL5 "phytochrome interacting	0.548	0.606	0.368	1.1e-48
UNIPROTKB|Q8GRJ1	417	OJ1343_B12.103 "Transcription	0.510	0.647	0.374	4.1e-43
TAIR|locus:2012345	524	PIF3 "AT1G09530" [Arabidopsis	0.727	0.734	0.346	6.6e-42
TAIR|locus:4010713915	544	AT4G28811 [Arabidopsis thalian	0.332	0.323	0.398	1.7e-28
UNIPROTKB|Q5NAE0	565	P0498A12.33 "Putative BP-5 pro	0.223	0.208	0.578	3.3e-28
UNIPROTKB|Q7FA23	181	OSJNBa0058K23.6 "Os04g0618600	0.160	0.469	0.705	3.7e-27
TAIR|locus:2117773	413	AT4G28790 [Arabidopsis thalian	0.361	0.462	0.380	7.1e-27
TAIR|locus:4010713916	307	AT4G28815 [Arabidopsis thalian	0.164	0.283	0.516	1.2e-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:   190 PPKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLND 249
             PP   + P   +     SG + + E+ + S+ TVG SHCGSN    DLD+S      ++ 
Sbjct:   129 PPPQVMPPPKFRLTNSSSG-IRETEMEQYSVTTVGPSHCGSNPSQNDLDVS------MSH 181

Query:   250 DVRKVISPSERGKTETIEPTVTXXXXXXXX-XFNRTSKQSTGDNSLKR-KSRDAVDSECQ 307
             D  K I        E + P  +          F +  K+      +   + R  ++    
Sbjct:   182 DRSKNIE-------EKLNPNASSSSGGSSGCSFGKDIKEMASGRCITTDRKRKRINHT-- 232

Query:   308 SEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDK 367
              E+       GNK+ QRSGS RRSRAAEVHNLSERRRRDRINE+M+ALQELIPHC+KTDK
Sbjct:   233 DESVSLSDAIGNKSNQRSGSNRRSRAAEVHNLSERRRRDRINERMKALQELIPHCSKTDK 292

Query:   368 ASMLDEAIEYLKSLQLQLQVMWMGSGMA------PLMFPGMQHYMSRXXXXXXXXXLPSV 421
             AS+LDEAI+YLKSLQLQLQVMWMGSGMA      P+MFPG+Q              +  +
Sbjct:   293 ASILDEAIDYLKSLQLQLQVMWMGSGMAAAAASAPMMFPGVQPQQ----------FIRQI 342

Query:   422 TNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHPM 481
              +P+   R P++DQS   A   N  ++CQ    NPV  QNQ+ +  F        GF  M
Sbjct:   343 QSPVQLPRFPVMDQS---AIQNNPGLVCQ----NPV--QNQIISDRFARYIG---GFPHM 390

Query:   482 QANSQ--PMNMFRFGSPTMQNQIVSLPSSSCVPFSGGAATDN 521
             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:   219 SMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTXXXXXXX 278
             S++TVG SHCGSNQ           S+ ++      +S S+R K    E   T       
Sbjct:   146 SVITVGPSHCGSNQ-----------STNIHQATTLPVSMSDRSKNVE-ERLDTSSGGSSG 193

Query:   279 XXFNRTSKQSTGDNS--LKRKSRDAVDSECQSEAA---GFESG----AGNKTAQRSGSCR 329
               + R +K++    S  + RK +  +D++ +S +    G  S      GNK++QRSGS R
Sbjct:   194 CSYGRNNKETVSGTSVTIDRKRKHVMDADQESVSQSDIGLTSTDDQTMGNKSSQRSGSTR 253

Query:   330 RSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMW 389
             RSRAAEVHNLSERRRRDRINE+M+ALQELIPHC++TDKAS+LDEAI+YLKSLQ+QLQVMW
Sbjct:   254 RSRAAEVHNLSERRRRDRINERMKALQELIPHCSRTDKASILDEAIDYLKSLQMQLQVMW 313

Query:   390 MGSGMA--------PLMFPGMQH--YMSRXXXXXXXXXLPSVTNPMHFSRVPLVDQSMSM 439
             MGSGMA        P+MFPG+Q   Y+++           ++ + M  S+ P++++S   
Sbjct:   314 MGSGMAAAAAAAASPMMFPGVQSSPYINQM----------AMQSQMQLSQFPVMNRS--- 360

Query:   440 AQAQNRAVMCQASVLNPVNYQNQMQNSNFTEQYARYMGFHP--------MQA-NSQPMNM 490
             A   +  ++CQ    NPV  Q Q QN   +EQ ARYMG  P        MQ    QP +M
Sbjct:   361 APQNHPGLVCQ----NPVQLQLQAQNQILSEQLARYMGGIPQMPPAGNQMQTVQQQPADM 416

Query:   491 FRFGSPTMQNQIVSLPSSS 509
               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 = 1.1e-48, Sum P(2) = 1.1e-48
 Identities = 125/339 (36%), Positives = 170/339 (50%)

Query:   200 GQFDRKRSGN----LTQGEVRECSMMT------VGSSHCGSNQVAYDLDMSRASSSGLND 249
             G F+  R G     L++  VRE + ++        +S  G  +     D S  +  G  +
Sbjct:   153 GDFNNGRGGESGPLLSKAVVRESTQVSPSATPSAAASESGLTRRTDGTDSSAVAGGGAYN 212

Query:   250 DVRKVISPSERGKTETIEPTVTXXXXXXXXXFNRTSKQSTGDNSLKRKSRDAVDSECQSE 309
                K ++ +       IE T T          +    + T  +  KRK R+A  ++ ++E
Sbjct:   213 RKGKAVAMT----APAIEITGTSSSVVSK---SEIEPEKTNVDDRKRKEREATTTD-ETE 264

Query:   310 AAGFESGAGNKTAQRSG-SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKA 368
             +   E+    K A+ S  S +RSRAAEVHNLSER+RRDRINE+M+ALQELIP CNK+DKA
Sbjct:   265 SRSEET----KQARVSTTSTKRSRAAEVHNLSERKRRDRINERMKALQELIPRCNKSDKA 320

Query:   369 SMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQHYMSRXXXXXXXXXL---PS-VTNP 424
             SMLDEAIEY+KSLQLQ+Q+M MG GM P+M+PGMQ YM               PS +  P
Sbjct:   321 SMLDEAIEYMKSLQLQIQMMSMGCGMMPMMYPGMQQYMPHMAMGMGMNQPIPPPSFMPFP 380

Query:   425 -MHFSRVPLVDQSMSMAQAQNRAVMCQ--ASVLNPVNYQ-----NQMQN-SNFTEQYARY 475
              M  ++ PL  Q+          V     + V  P N Q      Q Q  + +T+ Y ++
Sbjct:   381 NMLAAQRPLPTQTHMAGSGPQYPVHASDPSRVFVP-NQQYDPTSGQPQYPAGYTDPYQQF 439

Query:   476 MGFHPMQANSQPMNMFRFGSPTMQNQIVSLPSSSCVPFS 514
              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 = 4.1e-43, Sum P(2) = 4.1e-43
 Identities = 110/294 (37%), Positives = 152/294 (51%)

Query:   226 SHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTXXXXXXXXXFNRTS 285
             S CGSN V     ++ A  +  +DD+    +P E  + E   P                S
Sbjct:   137 SICGSNAV-----VAPALPADDDDDI-DAAAPREEEEEEEEGPGAARAAGASSSG---GS 187

Query:   286 KQSTGDNSL-KRKSRDAVDSECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRR 344
                +G   L KR   + VDS   SE A  E+    + ++R  + RR+RAAEVHNLSERRR
Sbjct:   188 GSGSGSYPLFKRGREELVDS--LSEVAD-ET----RPSKRPAAKRRTRAAEVHNLSERRR 240

Query:   345 RDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMAPLMFPGMQH 404
             RDRINEK+RALQEL+PHCNKTDKAS+LDEAIEYLKSLQ+Q+Q+MWM +G+ P+MFPG   
Sbjct:   241 RDRINEKLRALQELVPHCNKTDKASILDEAIEYLKSLQMQVQIMWMTTGIVPMMFPGTHQ 300

Query:   405 YMSRXXXXXXXXXLPSVTNPMHFSRVPLVDQSMSMAQAQNRAVMCQASVLNPVNYQNQMQ 464
              M           +P        +++      M+ +   N+     +  +N  +  + MQ
Sbjct:   301 LMPPMGMGLNTACMPGA-QAQGLNQMQRTTYYMNNS-LPNQMPQIPSPAMNAPSVPDDMQ 358

Query:   465 NSNFTEQYARYMGFH---PMQANSQPMNMFRFGSPTM-QNQIVSLPSSSCVPFS 514
             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:    27 NELVELLWQNGHVVLSSQAQTQRK---PSLNHNEPRQV---QKQTLRGSGSCGNSS---N 77
             +E+VEL+W+NG +   SQ+   R    P  N +  R++    K T+         S    
Sbjct:    27 DEVVELVWENGQISTQSQSSRSRNIPPPQANSSRAREIGNGSKTTMVDEIPMSVPSLMTG 86

Query:    78 LIQDDETVSWI-HCPIEDSFEKDFYSQLFSELPPS---GPMEVDKHTRQLREEKMVKFDP 133
             L QDD+ V W+ H P  D +  DF   + S +  +     M V++    L + +    + 
Sbjct:    87 LSQDDDFVPWLNHHPSLDGYCSDFLRDVSSPVTVNEQESDMAVNQTAFPLFQRRKDGNES 146

Query:   134 PGAVTSSQHPNV-NHSVVPELQRNAMPPPRFEVHDAAPQNKNLGDLGK--LVNFSQSTAP 190
               A +SSQ+    +HS+    +   +P  +          + L    K  LVNFS    P
Sbjct:   147 APAASSSQYNGFQSHSLYGSDRARDLPSQQTNPDRFTQTQEPLITSNKPSLVNFSHFLRP 206

Query:   191 PKGELGPCSGQFDRKRSGNLTQGEVRECSMMTVGSSHCGSNQVAYDLDMSRASSSGLNDD 250
                     +   D K     +   V +  ++    S    ++V   L+ S AS++  ++ 
Sbjct:   207 ATFAKTTNNNLHDTKEKSPQSPPNVFQTRVLGAKDSE---DKV---LNESVASATPKDNQ 260

Query:   251 VRKVISPSERGKTETIEPTVTXXXXXXXXXFNRTSKQSTGDNSLKRKSRDAVDSECQSEA 310
                +IS     K +  E  V           +  S+  +   SLKRK  +  D +C SE 
Sbjct:   261 KACLISEDSCRKDQESEKAVVCSSVGSGNSLDGPSESPS--LSLKRKHSNIQDIDCHSED 318

Query:   311 AGFESGAGNKTA--QRSG-SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDK 367
                ESG G K A   R+G   +RSR+AEVHNLSERRRRDRINEKMRALQELIP+CNK DK
Sbjct:   319 VEEESGDGRKEAGPSRTGLGSKRSRSAEVHNLSERRRRDRINEKMRALQELIPNCNKVDK 378

Query:   368 ASMLDEAIEYLKSLQLQLQVMWMGSG--MAP-LMFP-GMQHYMSRXXXXXXXXXLP 419
             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 = 1.7e-28, Sum P(2) = 1.7e-28
 Identities = 79/198 (39%), Positives = 108/198 (54%)

Query:   318 GNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEY 377
             G + A  S S +RSRAA++HNLSERRRR+RINE+M+ LQEL+P C KTDK SML++ IEY
Sbjct:   343 GTEEAHGSTSRKRSRAADMHNLSERRRRERINERMKTLQELLPRCRKTDKVSMLEDVIEY 402

Query:   378 LKSLQLQLQVMWMGSGMAP-LMFPG-MQHYMSRXXXXXXXXXLP---------SVTNPMH 426
             +KSLQLQ+Q+M MG GM P +M  G  Q +M            P         +   P H
Sbjct:   403 VKSLQLQIQMMSMGHGMMPPMMHEGNTQQFMPHMAMGMKGMNRPPPFVPFPGKTFPRPGH 462

Query:   427 FSRV----PLVDQSMSMAQAQNRAVMCQASV-LNPVNYQNQMQNSNFTEQYARYMGFHPM 481
              + V    P +       QA + + +   S+  NPV   NQ +   +   Y++++G H M
Sbjct:   463 MAGVGPSYPALRYPFPDTQASDLSRVHVPSLHSNPV--PNQPRFPAYINPYSQFVGLHQM 520

Query:   482 QANSQPMNMFRFGSPTMQ 499
             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 = 3.3e-28, Sum P(2) = 3.3e-28
 Identities = 74/128 (57%), Positives = 88/128 (68%)

Query:   285 SKQSTGDNSLKR--KSRDAVDSEC---QSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNL 339
             S    G + L R  K +    +EC   Q +    E G   K+  RS   +RSR AEVHNL
Sbjct:   262 SGNGAGSDELWRQQKRKCQAQAECSASQDDDLDDEPGVLRKSGTRS--TKRSRTAEVHNL 319

Query:   340 SERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSLQLQLQVMWMGSGMA--PL 397
             SERRRRDRINEKMRALQELIP+CNK DKASMLDEAIEYLK+LQLQ+Q+M MG+G+   P+
Sbjct:   320 SERRRRDRINEKMRALQELIPNCNKIDKASMLDEAIEYLKTLQLQVQMMSMGTGLCIPPM 379

Query:   398 MFP-GMQH 404
             + 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 = 3.7e-27, P = 3.7e-27
 Identities = 60/85 (70%), Positives = 72/85 (84%)

Query:   322 AQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLKSL 381
             A+R    RRSR+AE HN SERRRRDRINEK++ALQEL+P+C KTDK SMLDEAI+YLKSL
Sbjct:     3 ARRPTPTRRSRSAEFHNFSERRRRDRINEKLKALQELLPNCTKTDKVSMLDEAIDYLKSL 62

Query:   382 QLQLQVMWMGSGMAPLMFPGMQHYM 406
             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 = 7.1e-27, Sum P(2) = 7.1e-27
 Identities = 80/210 (38%), Positives = 109/210 (51%)

Query:   205 KRSGNLTQGEVREC-SMMTVGSSHCGSNQVAYDLDMSRASSSGLNDDVRKVISPSERGKT 263
             ++ GN+  G V    S  T+ SS   S    +  + SRA+ +G       V     RGK 
Sbjct:   156 RQRGNIFLGGVEAVPSNSTLLSSATESIPATHGTE-SRATVTGGVSRTFAVPGLGPRGKA 214

Query:   264 ETIEPTVTXXXXXXXXXFNRTSKQSTGDNSL----KRKSRDAVDSECQSEAAGFESGAGN 319
               IE   T              +Q   +  +    KRK+R+  + E Q          G 
Sbjct:   215 VAIETAGTQSWGLCKAETEPVQRQPATETDITDERKRKTREETNVENQ----------GT 264

Query:   320 KTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEYLK 379
             + A+ S S +RSRAA +H LSERRRR +INE M+ALQEL+P C KTD++SMLD+ IEY+K
Sbjct:   265 EEARDSTSSKRSRAAIMHKLSERRRRQKINEMMKALQELLPRCTKTDRSSMLDDVIEYVK 324

Query:   380 SLQLQLQVMWMGSGMAP-LMFPG--MQHYM 406
             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 = 1.2e-26, Sum P(3) = 1.2e-26
 Identities = 48/93 (51%), Positives = 66/93 (70%)

Query:   318 GNKTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCNKTDKASMLDEAIEY 377
             G + A+ S S +RSRAAE+HNL+ERRRR++INE+M+ LQ+LIP CNK+ K SML++ IEY
Sbjct:   136 GTEEARGSTSRKRSRAAEMHNLAERRRREKINERMKTLQQLIPRCNKSTKVSMLEDVIEY 195

Query:   378 LKSLQLQLQV----MWMGSGMAP--LMFPGMQH 404
             +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

Your Input: GSVIVG00018844001 SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (437 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	529
smart00353	53	smart00353, HLH, helix loop helix domain	3e-17
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	5e-17
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	2e-15

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

 Score = 75.3 bits (186), Expect = 3e-17
 Identities = 26/52 (50%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 338 NLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQ 386
           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 = 74.6 bits (184), Expect = 5e-17
 Identities = 27/55 (49%), Positives = 36/55 (65%), Gaps = 3/55 (5%)

Query: 335 EVHNLSERRRRDRINEKMRALQELIP---HCNKTDKASMLDEAIEYLKSLQLQLQ 386
           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 = 2e-15
 Identities = 26/50 (52%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 335 EVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQ 382
           + 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	529
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.38
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.36
smart00353	53	HLH helix loop helix domain.	99.28
KOG1318	411	consensus Helix loop helix transcription factor EB	99.23
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.95
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.86
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.53
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.01
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	97.98
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.95
KOG0561	373	consensus bHLH transcription factor [Transcription	97.53
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.52
PLN03217	93	transcription factor ATBS1; Provisional	97.22
KOG3910	632	consensus Helix loop helix transcription factor [T	96.99
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	94.98
KOG3898	254	consensus Transcription factor NeuroD and related	94.31
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	94.18
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	91.07
KOG4395	285	consensus Transcription factor Atonal, contains HT	88.0
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	86.52

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

Probab=99.38  E-value=6.9e-13  Score=103.64  Aligned_cols=54  Identities=50%  Similarity=0.773  Sum_probs=50.2

Q ss_pred             hhhccchhHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHH
Q 009659          333 AAEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQ  386 (529)
Q Consensus       333 ~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~qv~  386 (529)
                      .+..|+..||+||++||+.|..|+.+||.+   .|++|++||..||+||+.|+.+++
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   799999999999999999998763

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=99.36  E-value=7.4e-13  Score=103.01  Aligned_cols=49  Identities=55%  Similarity=0.889  Sum_probs=46.3

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC-----CCCchhhHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC-----NKTDKASMLDEAIEYLKSLQ  382 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~-----~K~dKAsIL~~AI~YIk~Lq  382 (529)
                      +..|+..||+||++||+.|.+|+.+||.+     .|++|++||+.||+||++||
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            45799999999999999999999999998     48999999999999999997

; 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=99.28  E-value=7.6e-12  Score=96.02  Aligned_cols=49  Identities=53%  Similarity=0.736  Sum_probs=45.5

Q ss_pred             chhHHHHHHHHHHHHHHHHhhCCC---CCCCchhhHHHHHHHHHHHHHHHHH
Q 009659          338 NLSERRRRDRINEKMRALQELIPH---CNKTDKASMLDEAIEYLKSLQLQLQ  386 (529)
Q Consensus       338 ~~~ERrRRerIN~~~~~Lr~LVP~---~~K~dKAsIL~~AI~YIk~Lq~qv~  386 (529)
                      +..||+||++||+.|..|+.+||.   ..|++|++||.+||+||++|+.+++
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   5589999999999999999999875

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

Probab=99.23  E-value=7.4e-12  Score=132.55  Aligned_cols=60  Identities=42%  Similarity=0.758  Sum_probs=53.9

Q ss_pred             CcccchhhhccchhHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHH
Q 009659          327 SCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQLQ  386 (529)
Q Consensus       327 ~~rr~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq~qv~  386 (529)
                      ..|.+++|+.||++|||||++||++|++|..|||.|+    |..|..||..+++||+.||+..+
T Consensus       227 ~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q  290 (411)
T KOG1318|consen  227 LERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ  290 (411)
T ss_pred             hHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence            3455566779999999999999999999999999995    67899999999999999998776

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.95  E-value=4.6e-10  Score=107.69  Aligned_cols=63  Identities=35%  Similarity=0.527  Sum_probs=53.5

Q ss_pred             CCCcccchhhhccchhHHHHHHHHHHHHHHHHhhCCCCC-------CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          325 SGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN-------KTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       325 ~~~~rr~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~-------K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +.+.||++   .|..+||+||+-||..+..|+.|||.|.       |+.||.||.++|+||.+|++++...+.
T Consensus        57 syk~rrr~---aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~  126 (229)
T KOG1319|consen   57 SYKDRRRR---AHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEE  126 (229)
T ss_pred             hHHHHHHH---HHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34444443   6999999999999999999999999883       889999999999999999887766553

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

Probab=98.86  E-value=1.2e-09  Score=110.06  Aligned_cols=54  Identities=35%  Similarity=0.531  Sum_probs=47.9

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC--------CCCchhhHHHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC--------NKTDKASMLDEAIEYLKSLQLQLQV  387 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--------~K~dKAsIL~~AI~YIk~Lq~qv~~  387 (529)
                      +..|.++|||||+|||+.|.+|++||+.+        .|++||.||+.||+|||.|+.....
T Consensus        33 k~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   33 KVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             hhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            44689999999999999999999999965        5789999999999999999975443

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

Probab=98.53  E-value=1e-07  Score=108.54  Aligned_cols=51  Identities=33%  Similarity=0.531  Sum_probs=48.1

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQ  384 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq~q  384 (529)
                      +++|+.+||||||++|..|.+|.+|||.|.    |+||..||++||.+||.+++.
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            568999999999999999999999999986    999999999999999998874

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.01  E-value=2.4e-06  Score=98.06  Aligned_cols=58  Identities=34%  Similarity=0.549  Sum_probs=52.0

Q ss_pred             hhhhccchhHHHHHHHHHHHHHHHHhhCCCCC-CCchhhHHHHHHHHHHHHHHHHHHHh
Q 009659          332 RAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVMW  389 (529)
Q Consensus       332 ~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~-K~dKAsIL~~AI~YIk~Lq~qv~~L~  389 (529)
                      .+|.+||++|||.|..||++|.+|+.+||+.. |+.|..+|..||+||++|+...+.+-
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk  333 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLK  333 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccc
Confidence            34568999999999999999999999999875 99999999999999999998766554

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

Probab=97.98  E-value=1.8e-05  Score=79.33  Aligned_cols=54  Identities=30%  Similarity=0.483  Sum_probs=46.6

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCCC--CCc-hhhHHHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHCN--KTD-KASMLDEAIEYLKSLQLQLQV  387 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~--K~d-KAsIL~~AI~YIk~Lq~qv~~  387 (529)
                      +..||..||+||+.|.+.|..|+.+||...  |.. .++||++|++||+.|+.+...
T Consensus        60 R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~  116 (232)
T KOG2483|consen   60 RAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSAT  116 (232)
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHH
Confidence            457999999999999999999999999764  333 799999999999999875443

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

Probab=97.95  E-value=1.8e-05  Score=79.54  Aligned_cols=54  Identities=31%  Similarity=0.423  Sum_probs=46.2

Q ss_pred             cchhHHHHHHHHHHHHHHHHhh-CCCCC-CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          337 HNLSERRRRDRINEKMRALQEL-IPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       337 H~~~ERrRRerIN~~~~~Lr~L-VP~~~-K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      -.+.||||=.|+||.|.+|+.- +++-+ .+-|..||..||+||+.||.-++.+..
T Consensus       122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~  177 (284)
T KOG3960|consen  122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQ  177 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            3689999999999999999875 34433 689999999999999999998888754

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.53  E-value=8.5e-05  Score=76.43  Aligned_cols=52  Identities=33%  Similarity=0.556  Sum_probs=46.4

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQL  385 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~qv  385 (529)
                      ++.-|--||||=.-||..|..||.|||..  .|++||.||+.+.+||.+|+.+.
T Consensus        61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~K  114 (373)
T KOG0561|consen   61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHK  114 (373)
T ss_pred             HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcc
Confidence            45667889999999999999999999975  59999999999999999997643

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

Probab=97.52  E-value=8e-05  Score=73.93  Aligned_cols=55  Identities=27%  Similarity=0.378  Sum_probs=48.9

Q ss_pred             ccchhHHHHHHHHHHHHHHHHhhCCC----CCCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          336 VHNLSERRRRDRINEKMRALQELIPH----CNKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       336 ~H~~~ERrRRerIN~~~~~Lr~LVP~----~~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      .+|..||.|=..+|..|..||.+||.    -+|+.|..+|..||+||++|+.-++.-+.
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            46778999999999999999999995    35899999999999999999987776654

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.22  E-value=0.00069  Score=58.26  Aligned_cols=46  Identities=26%  Similarity=0.507  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHHhhCCCC------CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          345 RDRINEKMRALQELIPHC------NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       345 RerIN~~~~~Lr~LVP~~------~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      -|.||+.+..|+.|+|..      .|..-+-||++|+.||+.|+.+|..|+.
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSe   70 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSE   70 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999964      4678889999999999999999999974

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.99  E-value=0.001  Score=72.45  Aligned_cols=57  Identities=26%  Similarity=0.307  Sum_probs=48.6

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCCCCC----chhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHCNKT----DKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~K~----dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +...|..||.|-..||+.|++|..+.-..-|.    -|..||..||..|-.|++||.+--+
T Consensus       527 R~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERNL  587 (632)
T KOG3910|consen  527 RMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERNL  587 (632)
T ss_pred             HhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHccC
Confidence            34678999999999999999999987655443    4999999999999999999997643

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=94.98  E-value=0.012  Score=55.78  Aligned_cols=50  Identities=32%  Similarity=0.471  Sum_probs=45.7

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQL  383 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~  383 (529)
                      +--||+.||+|-..+|+.|.+||.+||..  .|++|+-.|+.|..||-+|=+
T Consensus        79 rv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~  130 (173)
T KOG4447|consen   79 RVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ  130 (173)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence            34699999999999999999999999975  699999999999999998864

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

Probab=94.31  E-value=0.09  Score=53.66  Aligned_cols=48  Identities=35%  Similarity=0.486  Sum_probs=42.4

Q ss_pred             ccchhHHHHHHHHHHHHHHHHhhCCC---CCCCchhhHHHHHHHHHHHHHH
Q 009659          336 VHNLSERRRRDRINEKMRALQELIPH---CNKTDKASMLDEAIEYLKSLQL  383 (529)
Q Consensus       336 ~H~~~ERrRRerIN~~~~~Lr~LVP~---~~K~dKAsIL~~AI~YIk~Lq~  383 (529)
                      .=|..||+|=-.+|+.|+.||++||.   ..|+.|+..|.-|-.||..|++
T Consensus        75 kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~  125 (254)
T KOG3898|consen   75 KANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE  125 (254)
T ss_pred             cccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence            35677998889999999999999994   3489999999999999999985

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=94.18  E-value=0.04  Score=61.10  Aligned_cols=39  Identities=38%  Similarity=0.692  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHHHHHHhhCCC----CCCCchhhHHHHHHHHHHH
Q 009659          342 RRRRDRINEKMRALQELIPH----CNKTDKASMLDEAIEYLKS  380 (529)
Q Consensus       342 RrRRerIN~~~~~Lr~LVP~----~~K~dKAsIL~~AI~YIk~  380 (529)
                      ||-|||+|..++.|..|+|-    ++|+||.+||.-+|.||+.
T Consensus        34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~   76 (712)
T KOG3560|consen   34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV   76 (712)
T ss_pred             hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence            67899999999999999995    4799999999999999874

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

Probab=91.07  E-value=0.16  Score=57.83  Aligned_cols=44  Identities=34%  Similarity=0.505  Sum_probs=38.1

Q ss_pred             cchhHHHHHHHHHHHHHHHHhhCCCC----CCCchhhHHHHHHHHHHH
Q 009659          337 HNLSERRRRDRINEKMRALQELIPHC----NKTDKASMLDEAIEYLKS  380 (529)
Q Consensus       337 H~~~ERrRRerIN~~~~~Lr~LVP~~----~K~dKAsIL~~AI~YIk~  380 (529)
                      -.-+.|-||-|-|+-|.+|..+||--    .-+|||+|+.-||-|+|-
T Consensus        50 SRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   50 SRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence            34567999999999999999999932    368999999999999984

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

Probab=88.00  E-value=0.75  Score=47.11  Aligned_cols=51  Identities=29%  Similarity=0.405  Sum_probs=45.2

Q ss_pred             ccchhHHHHHHHHHHHHHHHHhhCCCCC---CCchhhHHHHHHHHHHHHHHHHH
Q 009659          336 VHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQ  386 (529)
Q Consensus       336 ~H~~~ERrRRerIN~~~~~Lr~LVP~~~---K~dKAsIL~~AI~YIk~Lq~qv~  386 (529)
                      .-|..||||=..+|..|+.||.+||..+   |++|-..|..|-.||--|-..+.
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            5688999999999999999999999764   89999999999999998866543

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=86.52  E-value=0.63  Score=50.53  Aligned_cols=43  Identities=33%  Similarity=0.512  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHH
Q 009659          340 SERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQ  382 (529)
Q Consensus       340 ~ERrRRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq  382 (529)
                      ..|.||++-|-.|.+|..++|-..    .+||++|+.-|..|||.-.
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr~   54 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMRN   54 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHHH
Confidence            458999999999999999999653    6899999999999999543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	529
4f3l_B	387	Crystal Structure Of The Heterodimeric Clock:bmal1		3e-04
4ati_A	118	Mitf:m-Box Complex Length = 118		5e-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: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQ 382
           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 = 42.7 bits (99), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 337 HNLSERRRRDRINEKMRALQELIPHCNKTD----KASMLDEAIEYLKSLQLQLQ 386
           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	529
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	3e-20
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	4e-16
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	5e-14
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	2e-13
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	7e-13
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	6e-09
1a0a_A	63	BHLH, protein (phosphate system positive regulator	8e-09
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;	7e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-04

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

 Score = 84.4 bits (209), Expect = 3e-20
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQV 387
            R      HN  E+R R  IN+K+  L++L+     K +K+++L +AI+Y++ LQ   Q 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 388 M 388
           +
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 = 72.0 bits (177), Expect = 4e-16
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQ 382
            + RA   HN  ERRRRD+IN  +  L ++IP  +         K  +L +A +Y++ L+
Sbjct: 3   EKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Query: 383 LQLQ 386
               
Sbjct: 61  QSNH 64

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

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 335 EVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQVM 388
             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: 335 EVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQVM 388
             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 = 63.5 bits (155), Expect = 7e-13
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 335 EVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQVM 388
             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 = 52.1 bits (125), Expect = 6e-09
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 335 EVHNLSERRRRDRINEKMRALQELIP---HCNKTDKASMLDEAIEYLKSLQLQLQVM 388
             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 = 51.0 bits (122), Expect = 8e-09
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 7/55 (12%)

Query: 335 EVHNLSERRRRDRINEKMRALQELIPHCNKTD-------KASMLDEAIEYLKSLQ 382
           E H  +E+ RR+R+   +  L  LIP   K         KA+ ++ A  Y++ LQ
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQ 58

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

 Score = 48.5 bits (115), Expect = 3e-06
 Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 328 CRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQL 383
            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 = 47.6 bits (113), Expect = 5e-06
 Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHC-NKTDKASMLDEAIEYLKSLQLQLQV 387
           +  R +   N SE++RRD+ N  ++ L  ++P    K DK+++L ++I++L+  +     
Sbjct: 10  KAKRVS--RNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQ 67

Query: 388 M 388
            
Sbjct: 68  S 68

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

 Score = 40.3 bits (94), Expect = 7e-05
 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 326 GSCRRSRAAEVHNLSERRRRDRINEKMRAL-QELIPHCNKTDKAS---MLDEAIEYLKSL 381
           G+ +R+     HN  ER+RR  INE  R L +    H       +   +L +A++ +  L
Sbjct: 2   GADKRA----HHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGL 57

Query: 382 QLQLQ 386
           + Q++
Sbjct: 58  EQQVR 62

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

 Score = 41.4 bits (96), Expect = 8e-04
 Identities = 38/337 (11%), Positives = 93/337 (27%), Gaps = 80/337 (23%)

Query: 236 DLDMSRASSSGLNDDVRKVISPSERGKTETIEPTVTSSSGGSGSSFNRTSKQSTGDNSLK 295
           + D          D  + ++S  E      I+  + S    SG+     +  S  +  ++
Sbjct: 32  NFDCKDVQ-----DMPKSILSKEE------IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQ 80

Query: 296 RKSRDAVD-------SECQSEAAGFESGAGNKTAQRSGSCRRSRAAEVHNLSERRRRDRI 348
           +   + +        S  ++E             QR      ++    +N+S   R    
Sbjct: 81  KFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS---RLQPY 137

Query: 349 NEKMRALQELIPH----------CNKTDKASMLDEAIEYLKSLQLQL----QVMWMGSGM 394
            +  +AL EL P             K    + +  A++   S ++Q     ++ W+    
Sbjct: 138 LKLRQALLELRPAKNVLIDGVLGSGK----TWV--ALDVCLSYKVQCKMDFKIFWLNLKN 191

Query: 395 ---APLMFPGMQHYMSRMGMGMGPPPLPSVTNPMHFSRVPLVDQSMSMAQAQNRA--VM- 448
                 +   +Q  + ++          S    +    +    + +  ++       V+ 
Sbjct: 192 CNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL 251

Query: 449 --CQASVLNPVNYQNQM----QNSNFTEQYA-----------RYMGFHPMQANSQPMNMF 491
               A   N  N   ++    +    T+  +             M   P +      ++ 
Sbjct: 252 NVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV----KSLL 307

Query: 492 RFGSPTMQNQIVSLPSSSCVPFSGGAATDNSPLSGKM 528
                 +  +   LP               +P    +
Sbjct: 308 ---LKYLDCRPQDLPREVL---------TTNPRRLSI 332

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	529
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.6
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.58
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.56
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.55
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.55
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.54
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.45
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.45
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.41
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.38
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.31
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.11
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.07
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.01
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.93
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.67
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.64
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.18

>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=99.60  E-value=7.4e-16  Score=129.07  Aligned_cols=59  Identities=32%  Similarity=0.467  Sum_probs=55.5

Q ss_pred             hhhhccchhHHHHHHHHHHHHHHHHhhCCCC-CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          332 RAAEVHNLSERRRRDRINEKMRALQELIPHC-NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       332 ~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~-~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      ..+..|+++||+||++||++|.+|+.|||.+ .|++|++||.+||+||++||.+++.|..
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            4567899999999999999999999999998 7999999999999999999999999875

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

Probab=99.58  E-value=2e-15  Score=123.68  Aligned_cols=59  Identities=25%  Similarity=0.419  Sum_probs=53.9

Q ss_pred             chhhhccchhHHHHHHHHHHHHHHHHhhCCCC-CCCchhhHHHHHHHHHHHHHHHHHHHh
Q 009659          331 SRAAEVHNLSERRRRDRINEKMRALQELIPHC-NKTDKASMLDEAIEYLKSLQLQLQVMW  389 (529)
Q Consensus       331 ~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~-~K~dKAsIL~~AI~YIk~Lq~qv~~L~  389 (529)
                      ...+.+|+++||+||++||++|.+|+.|||.+ .|+||++||++||+||+.||.++.-|+
T Consensus         6 ~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            6 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            34567899999999999999999999999975 599999999999999999999988775

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

Probab=99.56  E-value=3.8e-15  Score=132.76  Aligned_cols=62  Identities=34%  Similarity=0.580  Sum_probs=50.8

Q ss_pred             ccchhhhccchhHHHHHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       329 rr~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      ++++++..|+++||+||++||++|.+|+.|||.|.    |++|++||++||+||++||.+++.|..
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            34445678999999999999999999999999985    678999999999999999999999864

>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=99.55  E-value=1.5e-15  Score=121.52  Aligned_cols=53  Identities=30%  Similarity=0.476  Sum_probs=48.2

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC-------CCCchhhHHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC-------NKTDKASMLDEAIEYLKSLQLQLQ  386 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~-------~K~dKAsIL~~AI~YIk~Lq~qv~  386 (529)
                      +.+|+++||+||++||..|.+|+.|||.+       .|++||+||++||+||+.||++++
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            45899999999999999999999999976       467899999999999999998753

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

Probab=99.55  E-value=1.4e-15  Score=125.13  Aligned_cols=55  Identities=38%  Similarity=0.619  Sum_probs=50.5

Q ss_pred             ccchhhhccchhHHHHHHHHHHHHHHHHhhCCCC----CCCchhhHHHHHHHHHHHHHH
Q 009659          329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHC----NKTDKASMLDEAIEYLKSLQL  383 (529)
Q Consensus       329 rr~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~----~K~dKAsIL~~AI~YIk~Lq~  383 (529)
                      +.++++..|+++||+||++||+.|.+|+.|||.|    .|+|||+||+.||+|||.|+.
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=99.54  E-value=1.3e-15  Score=121.90  Aligned_cols=52  Identities=35%  Similarity=0.570  Sum_probs=48.6

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCCC------CCchhhHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQLQL  385 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~------K~dKAsIL~~AI~YIk~Lq~qv  385 (529)
                      +..|+++||+||++||+.|.+|+.|||.|.      |++|++||++||+||++||+++
T Consensus         6 r~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            458999999999999999999999999986      7899999999999999999865

>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=99.45  E-value=6.7e-14  Score=116.38  Aligned_cols=58  Identities=29%  Similarity=0.521  Sum_probs=54.2

Q ss_pred             hhhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          333 AAEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       333 ~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      .+..|+..||+||++||+.|..|+.+||.+  .|++|++||..||+||+.|+.+++.|..
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  5999999999999999999999999864

>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=99.45  E-value=7.6e-14  Score=116.63  Aligned_cols=57  Identities=30%  Similarity=0.532  Sum_probs=53.0

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +..|+..||+||++||+.|..|+.+||.+  .|++|++||.+||+||+.|+.+++.|+.
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  6999999999999999999999888764

>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=99.41  E-value=1.7e-13  Score=116.38  Aligned_cols=56  Identities=32%  Similarity=0.503  Sum_probs=52.0

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHHHh
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMW  389 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~qv~~L~  389 (529)
                      +..||..||+||++||++|..|+.+||.+   .|++|++||.+||+||++|+.+++.|.
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   599999999999999999999988765

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

Probab=99.38  E-value=2.6e-13  Score=112.43  Aligned_cols=57  Identities=30%  Similarity=0.426  Sum_probs=50.0

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCC---CCCC-chhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPH---CNKT-DKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~---~~K~-dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +..||..||+||++||++|.+|+.+||.   ..|. +|+.||..||+||++|++++++++.
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   3465 7999999999999999999999874

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

Probab=99.31  E-value=2.6e-12  Score=107.28  Aligned_cols=57  Identities=23%  Similarity=0.277  Sum_probs=52.0

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +..||..||+||+.||++|..|+++||.+   .|++|+.||.+||+||+.|+++.+.|..
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~   61 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH   61 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34799999999999999999999999965   5899999999999999999999887753

>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=99.11  E-value=4.2e-11  Score=97.25  Aligned_cols=52  Identities=29%  Similarity=0.481  Sum_probs=48.0

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQL  385 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~qv  385 (529)
                      +..||..||+|+..||+.|..||.+||..  .|++|+.||..||+||++|++.+
T Consensus        13 R~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           13 RKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            45799999999999999999999999975  58999999999999999999765

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

Probab=99.07  E-value=1.2e-10  Score=92.30  Aligned_cols=52  Identities=27%  Similarity=0.355  Sum_probs=47.6

Q ss_pred             hccchhHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHH
Q 009659          335 EVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQ  386 (529)
Q Consensus       335 ~~H~~~ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~qv~  386 (529)
                      ..||..||+|+..||+.|..||.+||..   .|++|+.||..||+||+.|++.++
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            4689999999999999999999999975   489999999999999999998653

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

Probab=99.01  E-value=2.2e-10  Score=117.24  Aligned_cols=53  Identities=28%  Similarity=0.539  Sum_probs=42.9

Q ss_pred             hhhccchhHHHHHHHHHHHHHHHHhhCC-CCCCCchhhHHHHHHHHHHHHHHHH
Q 009659          333 AAEVHNLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEYLKSLQLQL  385 (529)
Q Consensus       333 ~~~~H~~~ERrRRerIN~~~~~Lr~LVP-~~~K~dKAsIL~~AI~YIk~Lq~qv  385 (529)
                      ++..|+++||+||++||+.|.+|+.||| ...|+||++||+.||+|||.|+...
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            3457999999999999999999999999 5569999999999999999998643

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

Probab=98.93  E-value=5.5e-10  Score=115.72  Aligned_cols=54  Identities=35%  Similarity=0.525  Sum_probs=48.7

Q ss_pred             cchhhhccchhHHHHHHHHHHHHHHHHhhCC----CCCCCchhhHHHHHHHHHHHHHH
Q 009659          330 RSRAAEVHNLSERRRRDRINEKMRALQELIP----HCNKTDKASMLDEAIEYLKSLQL  383 (529)
Q Consensus       330 r~~~~~~H~~~ERrRRerIN~~~~~Lr~LVP----~~~K~dKAsIL~~AI~YIk~Lq~  383 (529)
                      .+.++++|+.+||+||+|||+.|.+|+.|||    ...|+||++||+.||+|||.|+.
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            3455779999999999999999999999999    45799999999999999999984

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

Probab=98.67  E-value=7e-09  Score=84.09  Aligned_cols=46  Identities=24%  Similarity=0.397  Sum_probs=42.1

Q ss_pred             chhHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHH
Q 009659          338 NLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQL  383 (529)
Q Consensus       338 ~~~ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~  383 (529)
                      +..||+|+..||+.|..||.+||..   .|++|..||..||+||+.||.
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            4568999999999999999999976   589999999999999999984

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

Probab=98.64  E-value=3.3e-08  Score=83.04  Aligned_cols=45  Identities=31%  Similarity=0.584  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHHHhhCCCCC----CCchhhHHHHHHHHHHHHHHHHHHH
Q 009659          344 RRDRINEKMRALQELIPHCN----KTDKASMLDEAIEYLKSLQLQLQVM  388 (529)
Q Consensus       344 RRerIN~~~~~Lr~LVP~~~----K~dKAsIL~~AI~YIk~Lq~qv~~L  388 (529)
                      -|++||++|.+|..|||.+.    |.+|++||.+||+||++||++++.+
T Consensus         3 ~R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~   51 (83)
T 4ath_A            3 MRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRA   51 (83)
T ss_dssp             CHHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHH
T ss_pred             chhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            38999999999999999874    6899999999999999998876655

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

Probab=98.18  E-value=2.9e-06  Score=73.27  Aligned_cols=50  Identities=26%  Similarity=0.396  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          341 ERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       341 ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      ||.|-..||+.|..||.+||..   .|+.|..+|..||+||+.|++.++.-..
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~~   85 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHLK   85 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            4677788999999999999965   4899999999999999999998876554

---

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	529
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	8e-16
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	4e-15
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	8e-15
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	8e-15
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	1e-14
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-14
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	2e-14
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	2e-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 = 70.3 bits (172), Expect = 8e-16
 Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 337 HNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQVM 388
           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 = 67.5 bits (165), Expect = 4e-15
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 8/64 (12%)

Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQ 382
            + RA   HN  ERRRRD+IN  +  L ++IP  +         K  +L +A +Y++ L+
Sbjct: 3   EKRRAQ--HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELR 60

Query: 383 LQLQ 386
               
Sbjct: 61  QSNH 64

>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 = 66.8 bits (163), Expect = 8e-15
 Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)

Query: 320 KTAQRSGSCRRSRAAEVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEY 377
           +  +++ +  R +A     + ERRR  ++NE    L+         +  K  +L  AI Y
Sbjct: 2   ELKRKTTNADRRKA---ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRY 58

Query: 378 LKSLQLQLQ 386
           ++ 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: 335 EVHNLSERRRRDRINEKMRALQELIPHCN-------KTDKASMLDEAIEYLKSLQLQLQ 386
           E H  +E+ RR+R+   +  L  LIP             KA+ ++ A  Y++ LQ    
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS 62

>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 = 67.3 bits (164), Expect = 1e-14
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 329 RRSRAAEVHNLSERRRRDRINEKMRALQELIP-HCNKTDKASMLDEAIEYLKSLQLQLQV 387
            R      HN  E+R R  IN+K+  L++L+     K +K+++L +AI+Y++ LQ   Q 
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQK 61

Query: 388 M 388
           +
Sbjct: 62  L 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 = 66.3 bits (162), Expect = 1e-14
 Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)

Query: 345 RDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVM 388
           R  IN+K+  L++L+   + K  K+ +L +AI+Y+K LQ     +
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKL 45

>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 = 66.9 bits (163), Expect = 2e-14
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 335 EVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQVM 388
             HN+ ER+RR+ +     AL++ IP      K  K  +L +A  Y+ S+Q + Q +
Sbjct: 8   RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKL 64

>d1nlwa_ a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [TaxId: 9606]} Length = 79

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

 Score = 66.5 bits (162), Expect = 2e-14
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 331 SRAAEVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQV 387
           SR+   HN  E+ RR  +   +  L+ L+P      +    S+L +A  ++K L+   + 
Sbjct: 1   SRST--HNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRK 58

Query: 388 M 388
            
Sbjct: 59  A 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	529
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.5
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.5
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.47
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.43
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.4
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.39
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.38
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.25

>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=99.50  E-value=9e-15  Score=119.67  Aligned_cols=59  Identities=32%  Similarity=0.473  Sum_probs=54.4

Q ss_pred             hhhhccchhHHHHHHHHHHHHHHHHhhCCCCC-CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          332 RAAEVHNLSERRRRDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       332 ~~~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~-K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      ..+..|+.+||+||++||+.|.+|++|||.+. |++|++||.+||+||+.|+.+++.|..
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~   64 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQ   64 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34568999999999999999999999999875 899999999999999999999998864

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

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

Probab=99.50  E-value=6.1e-15  Score=115.72  Aligned_cols=52  Identities=31%  Similarity=0.484  Sum_probs=47.6

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC-------CCCchhhHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC-------NKTDKASMLDEAIEYLKSLQLQL  385 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~-------~K~dKAsIL~~AI~YIk~Lq~qv  385 (529)
                      +..|+++||+||++||+.|.+|+.|||.+       .|++|+.||++||+||++||++|
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            34799999999999999999999999953       58999999999999999999765

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

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

Probab=99.47  E-value=1.2e-14  Score=115.78  Aligned_cols=53  Identities=28%  Similarity=0.471  Sum_probs=49.1

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCCC--CCchhhHHHHHHHHHHHHHHHHH
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHCN--KTDKASMLDEAIEYLKSLQLQLQ  386 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~--K~dKAsIL~~AI~YIk~Lq~qv~  386 (529)
                      +..|++.||+||++||+.|..|+.|||.+.  |++|++||..||+||++||+.|+
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            457999999999999999999999999874  89999999999999999998764

>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=99.43  E-value=8.2e-14  Score=113.33  Aligned_cols=57  Identities=23%  Similarity=0.267  Sum_probs=52.4

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCCC---CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHCN---KTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~~---K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +..|+.+||+||++||+.|.+|+++||.+.   |++|++||.+||+||+.|+.+++.|..
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   899999999999999999999988754

>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=99.40  E-value=1.2e-13  Score=113.29  Aligned_cols=57  Identities=30%  Similarity=0.532  Sum_probs=52.5

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC--CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC--NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~--~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +..|+.+||+||++||+.|.+|++|||.+  .|++|++||..||+||+.|+.+++.|..
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            45899999999999999999999999975  5899999999999999999999888764

>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=99.39  E-value=1.5e-13  Score=113.82  Aligned_cols=57  Identities=32%  Similarity=0.486  Sum_probs=52.6

Q ss_pred             hhccchhHHHHHHHHHHHHHHHHhhCCCC---CCCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          334 AEVHNLSERRRRDRINEKMRALQELIPHC---NKTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       334 ~~~H~~~ERrRRerIN~~~~~Lr~LVP~~---~K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      +..|+.+||+||++||+.|..|+++||.+   .|++|++||..||+||+.|+.+++.|..
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            45799999999999999999999999975   4799999999999999999999988864

>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=99.38  E-value=4.8e-14  Score=111.18  Aligned_cols=51  Identities=35%  Similarity=0.585  Sum_probs=47.1

Q ss_pred             hccchhHHHHHHHHHHHHHHHHhhCCCCC------CCchhhHHHHHHHHHHHHHHHH
Q 009659          335 EVHNLSERRRRDRINEKMRALQELIPHCN------KTDKASMLDEAIEYLKSLQLQL  385 (529)
Q Consensus       335 ~~H~~~ERrRRerIN~~~~~Lr~LVP~~~------K~dKAsIL~~AI~YIk~Lq~qv  385 (529)
                      ..|+.+||+||++||+.|.+|+.|||.+.      |++|+.||..||+||+.||++.
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            47999999999999999999999999763      8999999999999999999754

>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=99.25  E-value=1.2e-12  Score=102.05  Aligned_cols=46  Identities=33%  Similarity=0.490  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHHHhhCCCCC-CCchhhHHHHHHHHHHHHHHHHHHHhc
Q 009659          345 RDRINEKMRALQELIPHCN-KTDKASMLDEAIEYLKSLQLQLQVMWM  390 (529)
Q Consensus       345 RerIN~~~~~Lr~LVP~~~-K~dKAsIL~~AI~YIk~Lq~qv~~L~~  390 (529)
                      |++||++|.+|++|||++. |+|||+||.+||+||+.||++++.|+.
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            6789999999999999975 999999999999999999999999975