Citrus Sinensis ID: 038084

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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--
Protein Sequence
MAWFLVIFFDDNGHCHIIMACAAQNNLRVNSSFDVSGGDSGSEEIRLEIMKRPDNSRTHSPTTAKMETTPAEAEEQARAQVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
Secondary Structure (PSIPRED)
cccEEEEEEEcccccEEEEEccccccccccccccccccccccHHHHHHHccccccccccccccccccccccHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccEEEEEEcccEEEEEEccccccHHHHHHHHHHccccEEEEEEEEEcccEEEEEEEEc
Secondary Structure Prediction (SSPRO)
cEEEEEEEEcccccccEEEEEEHcccccccccEEEcccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHcHHHcccccccccccccccccccccccccccHHHccccccccEEEEEEcccEEEEEEcccccHHHHHHHHHHHHcccEEEEEEEEcccccEEEEEEcc
Coil and Loop (DISEMBL)
MAWFLVIFFDDNGHCHIIMACAaqnnlrvnssfdvsggdsgseEIRLEImkrpdnsrthspttakmettpaEAEEQARAQVgkkrsgngkavsggeseheMHILTERERRKKMRNMFSNLHAllphlppkadkstiVDEAVKYIKTLQHTHQTLEKQKfekvqgattvdheqsiiaSPLEAVVESREAYLADhlgssvpknlSMAANIhhslqvpsdcfqtwfspnvvvnmcgddaqisvcsprkpglLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
Flexible Loop (DISEMBL)
MAWFLVIFFDDNGHCHIIMACAAQNNLRVNSSFDVSGGDSGSEEIRLEimkrpdnsrthspttakmettpaeAEEQAraqvgkkrsgngkavsggesehemhILTERERRKKMRNMFSNLHallphlppkaDKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGattvdheqsiiaSPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
Low Complexity Region (SEG)
MAWFLVIFFDDNGHCHIIMACAAQNNLRVNssfdvsggdsgsEEIRLEIMKRPDNSRTHSPTTAKMETTPAEAEEQARAQVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNlhallphlppKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
Disordered region (IsUnstruct)
*AWFLVIFFDDNGHCHIIMACAAQNNLRV*******************************************************************************************HALL**********TIVDEAVKYIKTLQHTHQTLE***F**VQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMY*****
Disordered Region (DISOPRED)
*AWFLVIFFDDNGHCHIIMACAAQNNL********************************************************************************ERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQH****************************************************************************NVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
Disordered Region (DISEMBL)
MAWFLVIFFDDNGHCHIIMACAAQNNLRVNSSF*********EEIRLEIMKRP***********************************************MHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
Disordered Region (DISPRO)
MAWFLVIFFDDNGHCHIIMACAAQNNLRVNSSFDVSG***************************************************************MHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEK****************************************************VPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAWFLVIFFDDNGHCHIIMACAAQNNLRVNSSFDVSGGDSGSEEIRLEIMKRPDNSRTHSPTTAKMETTPAEAEEQARAQVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH
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	282	2.2.26 [Sep-21-2011]
Q9FXA3	308	Transcription factor bHLH	yes	no	0.812	0.743	0.405	4e-39
Q56YJ8	414	Transcription factor FAMA	no	no	0.666	0.454	0.244	1e-08
Q8S3F1	320	Transcription factor NAI1	no	no	0.599	0.528	0.305	1e-06
Q1PF16	295	Transcription factor bHLH	no	no	0.198	0.189	0.491	1e-06
Q9T072	328	Transcription factor bHLH	no	no	0.301	0.259	0.360	2e-06
Q9M8K6	202	Transcription factor MUTE	no	no	0.574	0.801	0.265	5e-06
Q1PF17	305	Transcription factor bHLH	no	no	0.265	0.245	0.342	2e-05
Q9CAD0	596	Transcription factor EGL1	no	no	0.553	0.261	0.230	3e-05
P13027	612	Anthocyanin regulatory R-	N/A	no	0.563	0.259	0.254	3e-05
P13526	610	Anthocyanin regulatory Lc	N/A	no	0.613	0.283	0.243	3e-05

>sp|Q9FXA3|BH095_ARATH Transcription factor bHLH95 OS=Arabidopsis thaliana GN=BHLH95 PE=2 SV=2

 Score =  162 bits (409), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 109/269 (40%), Positives = 148/269 (55%), Gaps = 40/269 (14%)

Query: 39  DSGSEEIRLEIMKRPDNSRTHSPTTAKMETTPAEAEEQARAQVGKKRSG-NGKAVSGGES 97
           DSG    R+E  K P  S    P+     TT          + GKKR+  N K       
Sbjct: 21  DSGGGCKRIE--KEPLPSHPSHPSPEIQTTT---------VKKGKKRTKRNDKNHEEESP 69

Query: 98  EHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQ 157
           +HE+HI TERERRKKMR+MFS LHALLP LPPKADKSTIVDEAV  IK+L+ T Q LE Q
Sbjct: 70  DHEIHIWTERERRKKMRDMFSKLHALLPQLPPKADKSTIVDEAVSSIKSLEQTLQKLEMQ 129

Query: 158 KFEKVQGATTVDHEQS--------------------IIASPLEAVVES---REAYLADHL 194
           K EK+Q ++   +                       I   P++A       R A+LAD  
Sbjct: 130 KLEKLQYSSASTNTTPTTTFAYAPSSSSSPTALLTPISNHPIDATATDSYPRAAFLADQ- 188

Query: 195 GSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPR-KPGLLTTIF 253
              V  + + AAN+ +    P   F TW S NVV+ +CG++A  ++C P+ KPG+ T++ 
Sbjct: 189 ---VSSSSAAAANLPYPCNDPIVNFDTWSSRNVVLTICGNEAFFNLCVPKHKPGVFTSVC 245

Query: 254 YILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
           Y+ EK+N++V+ A+VSS+ + S Y+I A 
Sbjct: 246 YLFEKYNMEVLFANVSSNVFWSTYVIQAQ 274

Controls embryo growth.
Arabidopsis thaliana (taxid: 3702)

>sp|Q56YJ8|FAMA_ARATH Transcription factor FAMA OS=Arabidopsis thaliana GN=FMA PE=1 SV=1

 Score = 60.5 bits (145), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 48/196 (24%), Positives = 85/196 (43%), Gaps = 8/196 (4%)

Query: 83  KKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNLHALLP-HLPPKADKSTIVDEAV 141
           +KR+   K     ES+   HI  ER RRK+M      L +L+P     + D+++I+  A+
Sbjct: 180 RKRARTSKTSEEVESQRMTHIAVERNRRKQMNEHLRVLRSLMPGSYVQRGDQASIIGGAI 239

Query: 142 KYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKN 201
           ++++ L+   Q LE QK  ++ G T  D   +  +S       + +A      G+     
Sbjct: 240 EFVRELEQLLQCLESQKRRRILGETGRDMTTTTTSSSSPITTVANQAQPLIITGNVTE-- 297

Query: 202 LSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNL 261
           L     +         C       +V V + G DA I + S R+PG L      LE  +L
Sbjct: 298 LEGGGGLREETAENKSCL-----ADVEVKLLGFDAMIKILSRRRPGQLIKTIAALEDLHL 352

Query: 262 DVVSAHVSSDRYRSMY 277
            ++  ++++     +Y
Sbjct: 353 SILHTNITTMEQTVLY 368

Transcription activator. Together with SPCH and MUTE, regulates the stomata formation. Required to promote differentiation and morphogenesis of stomatal guard cells and to halt proliferative divisions in their immediate precursors. Mediates the formation of stomata.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8S3F1|BH020_ARATH Transcription factor NAI1 OS=Arabidopsis thaliana GN=NAI1 PE=2 SV=1

 Score = 54.3 bits (129), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/190 (30%), Positives = 91/190 (47%), Gaps = 21/190 (11%)

Query: 80  QVGKKRSGNGKAVSGGESEHEM---HILTERERRKKMRNMFSNLHALLPHLPPKADKSTI 136
           +VG KR       +GG  E  +   H+L ER+RR+K+      L ALLP L  K DK+T+
Sbjct: 110 KVGSKRKDC--VNNGGRREPHLLKEHVLAERKRRQKLNERLIALSALLPGLK-KTDKATV 166

Query: 137 VDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGS 196
           +++A+K++K LQ   + LE+++        T   +QSII      +V+  + YL D   S
Sbjct: 167 LEDAIKHLKQLQERVKKLEEER------VVTKKMDQSII------LVKRSQVYLDDDSSS 214

Query: 197 SVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYIL 256
                 + +     S +V S   QT   P +   +   D  I V   +  G +  I   L
Sbjct: 215 YSSTCSAASPLSSSSDEV-SIFKQTM--PMIEARVSDRDLLIRVHCEKNKGCMIKILSSL 271

Query: 257 EKHNLDVVSA 266
           EK  L+VV++
Sbjct: 272 EKFRLEVVNS 281

Transcription activator that regulates the expression of at least NAI2, PYK10 and PBP1. Required for and mediates the formation of endoplasmic reticulum bodies (ER bodies). Involved in the symbiotic interactions with the endophytes of the Sebacinaceae fungus family, such as Piriformospora indica and Sebacina.

Arabidopsis thaliana (taxid: 3702)

>sp|Q1PF16|BH019_ARATH Transcription factor bHLH19 OS=Arabidopsis thaliana GN=BHLH19 PE=2 SV=1

 Score = 53.9 bits (128), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 40/57 (70%), Gaps = 1/57 (1%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
           H+L ER+RR+K+   F  L ALLP L  KADK TI+D+A+  +K LQ   +TL+++K
Sbjct: 120 HVLAERKRREKLSEKFIALSALLPGLK-KADKVTILDDAISRMKQLQEQLRTLKEEK 175

Arabidopsis thaliana (taxid: 3702)

>sp|Q9T072|BH025_ARATH Transcription factor bHLH25 OS=Arabidopsis thaliana GN=BHLH25 PE=2 SV=2

 Score = 53.1 bits (126), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 51/86 (59%), Gaps = 1/86 (1%)

Query: 76  QARAQVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKST 135
           Q   +  +K +   +  S  +S  + HI+ ER+RR+K+   F  L AL+P L  K DK++
Sbjct: 127 QKSDEFNRKGTKRAQPFSRNQSNAQDHIIAERKRREKLTQRFVALSALVPGL-KKMDKAS 185

Query: 136 IVDEAVKYIKTLQHTHQTLEKQKFEK 161
           ++ +A+K+IK LQ     LE+QK E+
Sbjct: 186 VLGDALKHIKYLQERVGELEEQKKER 211

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M8K6|MUTE_ARATH Transcription factor MUTE OS=Arabidopsis thaliana GN=MUTE PE=2 SV=1

 Score = 52.0 bits (123), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 81/181 (44%), Gaps = 19/181 (10%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPK-ADKSTIVDEAVKYIKTLQHTHQTLEKQKFE 160
           HI  ER RR++M     +L +L P    K  D+++I+   +++IK LQ   Q LE +K  
Sbjct: 3   HIAVERNRRRQMNEHLKSLRSLTPCFYIKRGDQASIIGGVIEFIKELQQLVQVLESKKRR 62

Query: 161 KVQGATTVDHE-QSIIASPLEAVVESREAY--LADHLGSSVPKNLSMAANIHHSLQVPSD 217
           K     +  ++ Q+I  S L A   +R  +  + + + +S  K +    N  H+      
Sbjct: 63  KTLNRPSFPYDHQTIEPSSLGAAT-TRVPFSRIENVMTTSTFKEVGACCNSPHA------ 115

Query: 218 CFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMY 277
                   NV   + G +  + V S R  G L  I  +LEK +  V+  ++SS     +Y
Sbjct: 116 --------NVEAKISGSNVVLRVVSRRIVGQLVKIISVLEKLSFQVLHLNISSMEETVLY 167

Query: 278 M 278
            
Sbjct: 168 F 168

Transcription factor. Together with FMA and SPCH, regulates the stomata formation. Required for the differentiation of stomatal guard cells, by promoting successive asymmetric cell divisions and the formation of guard mother cells. Promotes the conversion of the leaf epidermis into stomata.

Arabidopsis thaliana (taxid: 3702)

>sp|Q1PF17|BH018_ARATH Transcription factor bHLH18 OS=Arabidopsis thaliana GN=BHLH18 PE=2 SV=1

 Score = 49.7 bits (117), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 75  EQARAQVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKS 134
           E  +A++  + +   ++++  +S  + HIL ER+RR+K+   F  L AL+P L  K DK+
Sbjct: 100 EHKKAELIIRGTKRAQSLTRSQSNAQDHILAERKRREKLTQRFVALSALIPGL-KKMDKA 158

Query: 135 TIVDEAVKYIKTLQHT 150
           +++ +A+K+IK LQ +
Sbjct: 159 SVLGDAIKHIKYLQES 174

Arabidopsis thaliana (taxid: 3702)

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

 Score = 49.7 bits (117), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 39/169 (23%), Positives = 78/169 (46%), Gaps = 13/169 (7%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEK 161
           H L+E++RR+K+   F  L +++P +  K DK +I+D+ ++Y++ LQ   Q LE  +   
Sbjct: 406 HALSEKKRREKLNERFMTLRSIIPSI-SKIDKVSILDDTIEYLQDLQKRVQELESCR--- 461

Query: 162 VQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQT 221
                + D E  I     +   +  E   A+ + S         ++++     P+D    
Sbjct: 462 ----ESADTETRITMMKRKKPDDEEERASANCMNSK-----RKGSDVNVGEDEPADIGYA 512

Query: 222 WFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS 270
             + N+ ++  G++  I +    + G+L  I  ++   NLD  S   S+
Sbjct: 513 GLTDNLRISSLGNEVVIELRCAWREGILLEIMDVISDLNLDSHSVQSST 561

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

Arabidopsis thaliana (taxid: 3702)

>sp|P13027|ARRS_MAIZE Anthocyanin regulatory R-S protein OS=Zea mays GN=R-S PE=2 SV=1

 Score = 49.7 bits (117), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/169 (25%), Positives = 79/169 (46%), Gaps = 10/169 (5%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEK 161
           H+++ER+RR+K+  MF  L +LLP +  + +K++I+ E + Y+K LQ   Q LE  +   
Sbjct: 419 HVMSERKRREKLNEMFLVLKSLLPSI-HRVNKASILAETIAYLKELQRRVQELESSREPA 477

Query: 162 VQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQT 221
            + + T      +I  P      + E+   +    S  K+  +       ++ P      
Sbjct: 478 SRPSETTTR---LITRPSRG---NNESVRKEVCAGSKRKSPELG---RDDVERPPVLTMD 528

Query: 222 WFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS 270
             S NV V +   D  + V    +  L+T +F  ++  +LDV+S   S+
Sbjct: 529 AGSSNVTVTVSDKDVLLEVQCRWEELLMTRVFDAIKSLHLDVLSVQASA 577

Putative transcriptional activator. Control tissue-specific synthesis of anthocyanin pigments in various parts of the maize plant.

Zea mays (taxid: 4577)

>sp|P13526|ARLC_MAIZE Anthocyanin regulatory Lc protein OS=Zea mays GN=LC PE=2 SV=1

 Score = 49.3 bits (116), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 45/185 (24%), Positives = 88/185 (47%), Gaps = 12/185 (6%)

Query: 86  SGNGKAVSGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIK 145
           +G  + +SG  +++  H+++ER+RR+K+  MF  L +LLP +  + +K++I+ E + Y+K
Sbjct: 403 TGAAQEMSGTGTKN--HVMSERKRREKLNEMFLVLKSLLPSI-HRVNKASILAETIAYLK 459

Query: 146 TLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMA 205
            LQ   Q LE  +    + + T      +I  P      + E+   +    S  K+  + 
Sbjct: 460 ELQRRVQELESSREPASRPSETTTR---LITRPSRG---NNESVRKEVCAGSKRKSPELG 513

Query: 206 ANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVS 265
                 ++ P        + NV V +   D  + V    +  L+T +F  ++  +LDV+S
Sbjct: 514 ---RDDVERPPVLTMDAGTSNVTVTVSDKDVLLEVQCRWEELLMTRVFDAIKSLHLDVLS 570

Query: 266 AHVSS 270
              S+
Sbjct: 571 VQASA 575

Putative transcriptional activator. Control tissue-specific synthesis of anthocyanin pigments in various parts of the maize plant.

Zea mays (taxid: 4577)

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	282
255538252	247	conserved hypothetical protein [Ricinus	0.723	0.825	0.655	2e-69
147845459	333	hypothetical protein VITISV_042279 [Viti	0.787	0.666	0.6	2e-66
302142295	291	unnamed protein product [Vitis vinifera]	0.787	0.762	0.595	6e-66
225428845	305	PREDICTED: transcription factor bHLH95 [	0.890	0.822	0.513	3e-64
224137578	291	predicted protein [Populus trichocarpa]	0.776	0.752	0.642	6e-61
255555415	278	conserved hypothetical protein [Ricinus	0.641	0.651	0.619	3e-49
449495725	253	PREDICTED: transcription factor bHLH95-l	0.712	0.794	0.497	2e-48
449438671	297	PREDICTED: transcription factor bHLH95-l	0.705	0.670	0.493	5e-48
116783198	297	unknown [Picea sitchensis]	0.677	0.643	0.448	3e-44
357475305	305	Transcription factor bHLH95 [Medicago tr	0.758	0.701	0.467	1e-41

>gi|255538252|ref|XP_002510191.1| conserved hypothetical protein [Ricinus communis] gi|223550892|gb|EEF52378.1| conserved hypothetical protein [Ricinus communis]

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 143/218 (65%), Positives = 165/218 (75%), Gaps = 14/218 (6%)

Query: 75  EQARAQVGKKRSGNGKA-------VSGGESEHEMHILTERERRKKMRNMFSNLHALLPHL 127
           E + AQ+G+KR+  G A        S GESEHE HILTERERRKKMR MF+NLHALLP L
Sbjct: 2   EASVAQMGQKRNRKGAAKNLETSVTSSGESEHEAHILTERERRKKMRTMFTNLHALLPQL 61

Query: 128 PPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVD-HEQSIIASPLEAVVESR 186
           P KADKSTIVDEA+KY++TL+ T QTLEKQ+ EK+QGAT  D  E S+I    EA VESR
Sbjct: 62  PAKADKSTIVDEAIKYVRTLEETLQTLEKQRQEKLQGATFADSSEPSVITVQTEA-VESR 120

Query: 187 EAYLADHLGSSVPKNLSMAANIHHSLQVP--SDCFQTWFSPNVVVNMCGDDAQISVCSPR 244
           EA+LA   G S  KN   A  + H L V     CFQTWFSPNVV+NMCGDDAQISVCS +
Sbjct: 121 EAFLAIQ-GPS--KNYPRATKMPHMLPVSLTPACFQTWFSPNVVMNMCGDDAQISVCSVK 177

Query: 245 KPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
           KPGLLT+I YIL+KH LDVVSAH+SSD++RS+YMIHAH
Sbjct: 178 KPGLLTSIVYILQKHKLDVVSAHISSDQFRSIYMIHAH 215

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147845459|emb|CAN83348.1| hypothetical protein VITISV_042279 [Vitis vinifera]

 Score =  258 bits (659), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 144/240 (60%), Positives = 168/240 (70%), Gaps = 18/240 (7%)

Query: 48  EIMKRPDNSRTHSPTTAKMETTPAEAEEQARAQVGKKRSGNGKAV--SGGESEHEMHILT 105
           ++ ++P +S ++SP   +          Q  A VG+KR    KA    GGESEHE HI T
Sbjct: 74  KLGEKPPDSSSNSPVENR----------QGMALVGRKRGRRAKASDGGGGESEHETHIWT 123

Query: 106 ERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGA 165
           ERERRKKMRNMFS+LHALLP LPPKADKSTIVDEAV YIKTLQ++   L+KQ+ E  QGA
Sbjct: 124 ERERRKKMRNMFSSLHALLPQLPPKADKSTIVDEAVNYIKTLQNSLIKLQKQRHEMQQGA 183

Query: 166 TTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKN-LSMAANIHHSLQVPSD--CFQTW 222
           T VD EQSII S   A  ++RE  L    G    KN  S+  N  + L VPS   CFQTW
Sbjct: 184 TAVDCEQSIITSQALA-PDTRETSLP--AGDRSLKNYFSLPTNKPNLLSVPSSSLCFQTW 240

Query: 223 FSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
           FSPNVVV+MCG+DA ISVCS RKPGLL TIFYILEKH LDV+SAH+SS + RS+YMIHAH
Sbjct: 241 FSPNVVVSMCGNDAHISVCSSRKPGLLATIFYILEKHKLDVLSAHISSTQQRSIYMIHAH 300

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302142295|emb|CBI19498.3| unnamed protein product [Vitis vinifera]

 Score =  256 bits (655), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 143/240 (59%), Positives = 167/240 (69%), Gaps = 18/240 (7%)

Query: 48  EIMKRPDNSRTHSPTTAKMETTPAEAEEQARAQVGKKRSGNGKAV--SGGESEHEMHILT 105
           ++ ++P +S ++SP   +          Q  A VG+KR    KA    GGESEHE HI T
Sbjct: 32  KLGEKPPDSSSNSPVENR----------QGMALVGRKRGRRAKASDGGGGESEHETHIWT 81

Query: 106 ERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGA 165
           ERERRKKMRNMFS+LHALLP LPPKADKSTIVDEAV YIKTLQ++   L+KQ+ E  QGA
Sbjct: 82  ERERRKKMRNMFSSLHALLPQLPPKADKSTIVDEAVNYIKTLQNSLTKLQKQRHEMQQGA 141

Query: 166 TTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKN-LSMAANIHHSLQVPSD--CFQTW 222
           T VD EQSII S   A  ++RE  L    G    KN  S+  N  + L  PS   CFQTW
Sbjct: 142 TAVDCEQSIITSQALA-PDTRETSLP--AGDRSLKNYFSLPTNKPNLLSAPSSSLCFQTW 198

Query: 223 FSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
           FSPNVVV+MCG+DA ISVCS RKPGLL TIFYILEKH LDV+SAH+SS + RS+YMIHAH
Sbjct: 199 FSPNVVVSMCGNDAHISVCSSRKPGLLATIFYILEKHKLDVLSAHISSTQQRSIYMIHAH 258

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428845|ref|XP_002282369.1| PREDICTED: transcription factor bHLH95 [Vitis vinifera] gi|147766738|emb|CAN74162.1| hypothetical protein VITISV_026442 [Vitis vinifera] gi|297741258|emb|CBI32389.3| unnamed protein product [Vitis vinifera]

 Score =  251 bits (641), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 138/269 (51%), Positives = 177/269 (65%), Gaps = 18/269 (6%)

Query: 27  LRVNSSFDVSGGDSGSEEIRLEIMKRPDNSRTHSPTTAKMETTPAEAEEQARAQVGKKRS 86
           L  N S+  S  D+     +    K+P ++         M+  P + +      +   ++
Sbjct: 11  LWENQSWGFSNSDNSGGSDKKSGEKQPGSASNSQTAATGMDLVPPDKKRGRGGAIKNGKN 70

Query: 87  GNGKAVSGGE---------SEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIV 137
           G G                S+HE+HI TERERRKKMRNMFS+LHALLP LPPKADKSTIV
Sbjct: 71  GKGSGEGNEGKSGGGGGGESDHEIHIWTERERRKKMRNMFSSLHALLPQLPPKADKSTIV 130

Query: 138 DEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSS 197
           DEAV YIKTLQHT Q L+KQK E++QGATTV++E SII S  +   +SREA+LAD   SS
Sbjct: 131 DEAVNYIKTLQHTLQKLQKQKLERLQGATTVNYEPSIITSQ-KLAFDSREAFLADQGSSS 189

Query: 198 VPKNLSMA-ANIHHSL---QVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIF 253
              NL++  +N  +SL   +VP+  FQ+W SPNV +N+CG++AQISVCSP+KPGLLTTI 
Sbjct: 190 ---NLAITPSNSSNSLSVARVPA-VFQSWTSPNVTLNVCGNEAQISVCSPKKPGLLTTIC 245

Query: 254 YILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
           Y+LEKH L+V+SAHVSSD  RSMYMI  +
Sbjct: 246 YVLEKHKLEVISAHVSSDYNRSMYMIQTN 274

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224137578|ref|XP_002327161.1| predicted protein [Populus trichocarpa] gi|222835476|gb|EEE73911.1| predicted protein [Populus trichocarpa]

 Score =  240 bits (612), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 149/232 (64%), Positives = 171/232 (73%), Gaps = 13/232 (5%)

Query: 59  HSPTTAKMET-TPAEA--EEQARAQVGKKRSGNGKAVSGG---ESEHEMHILTERERRKK 112
           +S T++ M+T  PA A    Q R++ G   + N K V+GG   ESEHE+HI TERERRKK
Sbjct: 33  YSATSSLMDTEIPAVAVVPGQKRSRKGGD-ARNKKVVNGGGSGESEHEIHIWTERERRKK 91

Query: 113 MRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQ 172
           MRNMFS+LHALLP LP KADKS+IVDEAVKYIKTLQ T QTL+KQK EK QGA  +D E 
Sbjct: 92  MRNMFSSLHALLPQLPAKADKSSIVDEAVKYIKTLQQTLQTLQKQKVEKFQGAI-IDFEP 150

Query: 173 SIIASPLEAVVESREAYLADHLGSS--VPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVN 230
           S+I S L   V SREA  A  LG S   P    M+ N   S+ +   CFQTWFSPNVV+N
Sbjct: 151 SVITS-LTDTVGSREASFA-ALGPSKNSPLTSKMSQN-SFSVSLSPACFQTWFSPNVVMN 207

Query: 231 MCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
           MCGDDAQ S+CS RKPGLL TI YILEKHNLDVVSAH+SSD+YRS+YMIHAH
Sbjct: 208 MCGDDAQFSLCSTRKPGLLATILYILEKHNLDVVSAHISSDQYRSIYMIHAH 259

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255555415|ref|XP_002518744.1| conserved hypothetical protein [Ricinus communis] gi|223542125|gb|EEF43669.1| conserved hypothetical protein [Ricinus communis]

 Score =  201 bits (511), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 119/192 (61%), Positives = 144/192 (75%), Gaps = 11/192 (5%)

Query: 97  SEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEK 156
           S+HE+HI TERERRKKMRNMF+NLHALLP LPPKADKSTIVDEAV YIKTLQ T Q L+K
Sbjct: 88  SDHEIHIWTERERRKKMRNMFANLHALLPQLPPKADKSTIVDEAVNYIKTLQQTLQKLQK 147

Query: 157 QKFEKVQ-GATTVDHEQSIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVP 215
           QK E++Q GA T  +E S++    + + +SREA++AD  GSS   NLS       S  VP
Sbjct: 148 QKLERLQGGAATFCYEPSLVTP--QKIADSREAFMADQ-GSS-NNNLS-NVTTRSSNNVP 202

Query: 216 SD-----CFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS 270
           S       FQTW S NVV+N+CGD+AQIS+CS +KPGL TTI Y+LEKHN++++SAHVSS
Sbjct: 203 SIPRYPVLFQTWTSSNVVLNICGDEAQISICSSKKPGLFTTICYVLEKHNIEMLSAHVSS 262

Query: 271 DRYRSMYMIHAH 282
           D  R+ YMI AH
Sbjct: 263 DSNRNTYMIQAH 274

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449495725|ref|XP_004159926.1| PREDICTED: transcription factor bHLH95-like [Cucumis sativus]

 Score =  198 bits (503), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 111/223 (49%), Positives = 144/223 (64%), Gaps = 22/223 (9%)

Query: 80  QVGKKRSGNGKAVSGGESE---HEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTI 136
           Q GKKR    +  S G +E   H++HI TERERRKKMRNMFSNLHALLPHLPPKADKS+I
Sbjct: 2   QAGKKRELETEGKSAGATESSDHDIHIWTERERRKKMRNMFSNLHALLPHLPPKADKSSI 61

Query: 137 VDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPL--EAVVESREAYLADHL 194
           VDEAV YIKTLQ T Q L KQK EK+      ++  S+  S +    +  +REA+LAD  
Sbjct: 62  VDEAVNYIKTLQETFQRLHKQKVEKLNNNNNNNNNPSMGCSKIVHHPLPTTREAFLADQA 121

Query: 195 GSSVPKNLSMAA-------------NIHHSLQVPS--DCFQTWFSPNVVVNMCGDDAQIS 239
            S+   ++S +A             N+  +L +PS    FQTW S N+V+++CG  A   
Sbjct: 122 SSN--DDMSSSATLLSHLSTTITPENVLSNLPLPSPPSAFQTWTSSNLVLSVCGRHAHFC 179

Query: 240 VCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
           VCS +KPGL   + Y+L+K+ +DVVSAHVSSD ++S +MI AH
Sbjct: 180 VCSAKKPGLFAALCYVLDKYRIDVVSAHVSSDVHQSFFMIQAH 222

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449438671|ref|XP_004137111.1| PREDICTED: transcription factor bHLH95-like [Cucumis sativus]

 Score =  197 bits (501), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 111/225 (49%), Positives = 144/225 (64%), Gaps = 26/225 (11%)

Query: 80  QVGKKRSGNGKAVSGGESE---HEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTI 136
           Q GKKR    +  S G +E   H++HI TERERRKKMRNMFSNLHALLPHLPPKADKS+I
Sbjct: 46  QAGKKRELETEGKSAGATESSDHDIHIWTERERRKKMRNMFSNLHALLPHLPPKADKSSI 105

Query: 137 VDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPL--EAVVESREAYLAD-- 192
           VDEAV YIKTLQ T Q L KQK EK+      ++  S+  S +    +  +REA+LAD  
Sbjct: 106 VDEAVNYIKTLQETFQRLHKQKVEKLNNNNNNNNNPSMGCSKIVHHPLPTTREAFLADQA 165

Query: 193 --------------HLGSSV-PKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQ 237
                         HL +++ P+N+   +N+   L  P   FQTW S N+V+++CG  A 
Sbjct: 166 SSNDDMSSSATLLSHLSTTITPENV--LSNL--PLPSPPSAFQTWTSSNLVLSVCGRHAH 221

Query: 238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHAH 282
             VCS +KPGL   + Y+L+K+ +DVVSAHVSSD ++S +MI AH
Sbjct: 222 FCVCSAKKPGLFAALCYVLDKYRIDVVSAHVSSDVHQSFFMIQAH 266

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|116783198|gb|ABK22833.1| unknown [Picea sitchensis]

 Score =  184 bits (467), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 104/232 (44%), Positives = 138/232 (59%), Gaps = 41/232 (17%)

Query: 80  QVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDE 139
           ++G+   GN    S    +  +HI TERERRKKMR+MFSNLH+LLPHLP KADKSTIV+E
Sbjct: 42  KLGELGLGNSLMKSIEPEDQGIHIWTERERRKKMRSMFSNLHSLLPHLPAKADKSTIVEE 101

Query: 140 AVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIASPLEAVVESREAYLADHLGSSVP 199
           A+ YIKTLQ +   LE Q+ +K + A+T++ E S     ++            H+ ++  
Sbjct: 102 AISYIKTLQQSLHVLENQRLDKARAASTLEFELSSTFHEMQQ---------QHHVSTATM 152

Query: 200 KNLSMAANIHHSLQVPSDC-----------------------------FQTWFSPNVVVN 230
           ++ S A   +H L   ++C                             FQTW SPNVV++
Sbjct: 153 RSASEAPAFYHPLT--AECSASSGFEPWISRQYSRTISTGSPAIDHCFFQTWSSPNVVLS 210

Query: 231 MCGDDAQISVC-SPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA 281
           +CGDDA + +C SP K GLLTTIFY LEKH +DVV+AH+SSD  RSMYMIHA
Sbjct: 211 VCGDDAHMMICSSPPKQGLLTTIFYTLEKHKVDVVTAHISSDSCRSMYMIHA 262

Source: Picea sitchensis

Species: Picea sitchensis

Genus: Picea

Family: Pinaceae

Order: Coniferales

Class: Coniferopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357475305|ref|XP_003607938.1| Transcription factor bHLH95 [Medicago truncatula] gi|355508993|gb|AES90135.1| Transcription factor bHLH95 [Medicago truncatula]

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 114/244 (46%), Positives = 147/244 (60%), Gaps = 30/244 (12%)

Query: 65  KMETTPAEAEE---QARAQVGKKRSGNG------KAVSGGES--------EHEMHILTER 107
           +++T P    E   +A A V KKR+  G        ++ GE         +HEMHILTER
Sbjct: 39  RVDTKPLNQNEGINEAEAPVSKKRNWGGVVIRSENNITTGEEKDKKYRDFDHEMHILTER 98

Query: 108 ERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATT 167
           ERRKKMRNMF +LHALLP LP KADKSTIVD AVK+IK L+   + LEK+K E ++  + 
Sbjct: 99  ERRKKMRNMFDSLHALLPELPSKADKSTIVDAAVKHIKNLEEIKEKLEKKKQEMLKSVSP 158

Query: 168 VDHEQSIIASPLEAVVESREAYLADH---------LGSSVPKNLSMAANIHHSLQVPSDC 218
           +  E S+I S      ESREA+LAD            + V  N S A +I    QV    
Sbjct: 159 LGSESSVINSQWHP-YESREAFLADQGSSSYNNNLSNAIVTSNPSNAFSISPPQQV---G 214

Query: 219 FQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYM 278
           FQTW S NVV+N+CG +AQ  +CS +KPGLLTTI  +LEKH +DV+SA++  +   + YM
Sbjct: 215 FQTWSSQNVVLNICGGEAQFCICSTKKPGLLTTIALVLEKHKIDVISANIMCNANGNFYM 274

Query: 279 IHAH 282
           I AH
Sbjct: 275 IMAH 278

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	282
TAIR|locus:2012146	308	RGE1 "AT1G49770" [Arabidopsis	0.333	0.305	0.505	1.3e-34
UNIPROTKB|Q6YYG9	327	OSJNBa0051E21.18 "Putative unc	0.535	0.461	0.331	7.8e-16
UNIPROTKB|Q7XT88	239	OSJNBa0042L16.11 "OSJNBa0042L1	0.241	0.284	0.347	2.3e-08
UNIPROTKB|Q6YYG5	365	OSJNBa0051E21.28 "Putative unc	0.315	0.243	0.322	1e-07
TAIR|locus:2093746	414	FMA "AT3G24140" [Arabidopsis t	0.659	0.449	0.232	3.8e-07
TAIR|locus:2062235	320	NAI1 "AT2G22770" [Arabidopsis	0.666	0.587	0.275	3.8e-07
TAIR|locus:2062225	305	AT2G22750 "AT2G22750" [Arabido	0.354	0.327	0.267	3.2e-06
UNIPROTKB|Q2QLR0	338	LOC_Os12g43620 "Helix-loop-hel	0.319	0.266	0.383	1.9e-05
TAIR|locus:2137574	328	AT4G37850 "AT4G37850" [Arabido	0.379	0.326	0.312	4e-05
UNIPROTKB|Q5JNS0	379	P0706B05.43 "Os01g0293100 prot	0.677	0.503	0.247	8.9e-05

TAIR|locus:2012146 RGE1 "AT1G49770" [Arabidopsis thaliana (taxid:3702)]

 Score = 203 (76.5 bits), Expect = 1.3e-34, Sum P(2) = 1.3e-34
 Identities = 48/95 (50%), Positives = 58/95 (61%)

Query:    70 PAEAEEQARAQVGKKRSG-NGKAVSGGESEHEMHILTERERRKKMRNMFSNXXXXXXXXX 128
             P+   +    + GKKR+  N K       +HE+HI TERERRKKMR+MFS          
Sbjct:    41 PSPEIQTTTVKKGKKRTKRNDKNHEEESPDHEIHIWTERERRKKMRDMFSKLHALLPQLP 100

Query:   129 XKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQ 163
              KADKSTIVDEAV  IK+L+ T Q LE QK EK+Q
Sbjct:   101 PKADKSTIVDEAVSSIKSLEQTLQKLEMQKLEKLQ 135

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009790 "embryo development" evidence=IMP

UNIPROTKB|Q6YYG9 OSJNBa0051E21.18 "Putative uncharacterized protein OSJNBa0051E21.18" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 200 (75.5 bits), Expect = 7.8e-16, P = 7.8e-16
 Identities = 53/160 (33%), Positives = 84/160 (52%)

Query:   130 KADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATT-----VDHEQSIIASPLE---A 181
             +ADK+TIV EA+ +I++L+ T   LE++K E+   A       +    S  A P     A
Sbjct:   134 QADKATIVGEAISFIRSLEETVADLERRKRERNSLAARCARLGLGGSSSSSAPPPPPPPA 193

Query:   182 VVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCG-DDAQISV 240
               +   A +        P   ++ A    +          W  P+VV+N+CG D A I+V
Sbjct:   194 AADDTAAVMPPAPAVPPPDAAAVTAGPEPAPAPAPGTLMVWSGPSVVLNLCGGDQAFINV 253

Query:   241 CSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIH 280
                R+PG+LT I  +LE+H++DVV+A ++SD  RS++ IH
Sbjct:   254 SVARRPGVLTMIVDVLERHSIDVVTAQIASDLSRSLFTIH 293

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q7XT88 OSJNBa0042L16.11 "OSJNBa0042L16.11 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 118 (46.6 bits), Expect = 2.3e-08, Sum P(2) = 2.3e-08
 Identities = 25/72 (34%), Positives = 43/72 (59%)

Query:   215 PSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPG---LLTTIFYILEKHNLDVVSAHVS-S 270
             P+   QTW  PN+  ++ GDD  I++  P + G   L+     +LE+H++DVV+A VS S
Sbjct:   137 PAASLQTWTGPNMTASLTGDDGFITLSLPHQGGQKNLVAGAVSVLERHHIDVVTATVSAS 196

Query:   271 DRYRSMYMIHAH 282
             ++  ++  +H H
Sbjct:   197 EQGDNLISLHCH 208

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q6YYG5 OSJNBa0051E21.28 "Putative uncharacterized protein OSJNBa0051E21.28" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 107 (42.7 bits), Expect = 1.0e-07, Sum P(2) = 1.0e-07
 Identities = 30/93 (32%), Positives = 44/93 (47%)

Query:    72 EAEEQARAQVGKKRSGNGKAV----SGGESEHEMHILTERERRKKMRNMFSNXXXXXXXX 127
             + EE+ R   G     +  AV     GG +   M  + ERERR++M +MF+         
Sbjct:    58 DGEEEGRGSQGGDDDDDVVAVHGGGGGGGNRACMFAVRERERRRRMNDMFAGIRRLVPNL 117

Query:   128 XXKADKSTIVDEAVKYIKTLQHTHQTLEKQKFE 160
               K+ +  I+D A+ YIK LQ     +E QK E
Sbjct:   118 PEKSSRVEIIDGAIAYIKMLQGEEVRMEAQKQE 150

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2093746 FMA "AT3G24140" [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 3.8e-07, P = 3.8e-07
 Identities = 46/198 (23%), Positives = 84/198 (42%)

Query:    83 KKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNXXXXX-XXXXXKADKSTIVDEAV 141
             +KR+   K     ES+   HI  ER RRK+M                 + D+++I+  A+
Sbjct:   180 RKRARTSKTSEEVESQRMTHIAVERNRRKQMNEHLRVLRSLMPGSYVQRGDQASIIGGAI 239

Query:   142 KYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSIIAS--PLEAVVESREAYLADHLGSSVP 199
             ++++ L+   Q LE QK  ++ G T  D   +  +S  P+  V    +  +   +  +V 
Sbjct:   240 EFVRELEQLLQCLESQKRRRILGETGRDMTTTTTSSSSPITTVANQAQPLI---ITGNVT 296

Query:   200 KNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCSPRKPGLLTTIFYILEKH 259
             + L     +         C       +V V + G DA I + S R+PG L      LE  
Sbjct:   297 E-LEGGGGLREETAENKSCLA-----DVEVKLLGFDAMIKILSRRRPGQLIKTIAALEDL 350

Query:   260 NLDVVSAHVSSDRYRSMY 277
             +L ++  ++++     +Y
Sbjct:   351 HLSILHTNITTMEQTVLY 368

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0010052 "guard cell differentiation" evidence=IMP

GO:0045597 "positive regulation of cell differentiation" evidence=IMP

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

GO:0051782 "negative regulation of cell division" evidence=IMP

GO:0000165 "MAPK cascade" evidence=RCA

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

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

GO:0009617 "response to bacterium" evidence=RCA

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

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

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

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

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

GO:0030154 "cell differentiation" evidence=RCA

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

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

TAIR|locus:2062235 NAI1 "AT2G22770" [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 3.8e-07, P = 3.8e-07
 Identities = 59/214 (27%), Positives = 92/214 (42%)

Query:    60 SPTTAKMETTPAEAEEQARAQVGKKRSGNGKAV----SGGESEHEM---HILTERERRKK 112
             SP T   +T P E       QV   +    K      +GG  E  +   H+L ER+RR+K
Sbjct:    87 SPDT---KTNPVETSLNFSNQVSMDQKVGSKRKDCVNNGGRREPHLLKEHVLAERKRRQK 143

Query:   113 MRNMFSNXXXXXXXXXXKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQ 172
             +                K DK+T++++A+K++K LQ   + LE+++        T   +Q
Sbjct:   144 LNERLI-ALSALLPGLKKTDKATVLEDAIKHLKQLQERVKKLEEER------VVTKKMDQ 196

Query:   173 SIIASPLEAVVESREAYLADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMC 232
             SII      +V+  + YL D   SS     S A+ +  S    S   QT   P +   + 
Sbjct:   197 SII------LVKRSQVYLDDD-SSSYSSTCSAASPLSSSSDEVSIFKQTM--PMIEARVS 247

Query:   233 GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSA 266
               D  I V   +  G +  I   LEK  L+VV++
Sbjct:   248 DRDLLIRVHCEKNKGCMIKILSSLEKFRLEVVNS 281

GO:0003677 "DNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0007029 "endoplasmic reticulum organization" evidence=IMP

TAIR|locus:2062225 AT2G22750 "AT2G22750" [Arabidopsis thaliana (taxid:3702)]

 Score = 118 (46.6 bits), Expect = 3.2e-06, Sum P(2) = 3.2e-06
 Identities = 27/101 (26%), Positives = 56/101 (55%)

Query:    75 EQARAQVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNXXXXXXXXXXKADKS 134
             E  +A++  + +   ++++  +S  + HIL ER+RR+K+   F            K DK+
Sbjct:   100 EHKKAELIIRGTKRAQSLTRSQSNAQDHILAERKRREKLTQRFV-ALSALIPGLKKMDKA 158

Query:   135 TIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTVDHEQSII 175
             +++ +A+K+IK LQ + +  E+QK EK   +  +  + S++
Sbjct:   159 SVLGDAIKHIKYLQESVKEYEEQKKEKTMESVVLVKKSSLV 199

GO:0003677 "DNA binding" evidence=ISS

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

UNIPROTKB|Q2QLR0 LOC_Os12g43620 "Helix-loop-helix DNA-binding domain containing protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 125 (49.1 bits), Expect = 1.9e-05, P = 1.9e-05
 Identities = 38/99 (38%), Positives = 52/99 (52%)

Query:    60 SPTTAKMETTPAEAEEQARAQVGKKRSGNGKAVSGGESEH-EMHILTERERRKKMRNMFS 118
             +P  A METT       ARA V KK  G G + S     + + HI+ ER RR+K+   F 
Sbjct:   132 APLQA-METTAT-----ARAAV-KKGGGGGSSSSAAAPGYVQDHIIAERRRREKINQRFI 184

Query:   119 NXXXXXXXXXXKADKSTIVDEAVKYIKTLQHTHQTLEKQ 157
                        K DK+TI+ +AVKY+K LQ   +TLE++
Sbjct:   185 ELSTVIPGLK-KMDKATILGDAVKYVKELQEKVKTLEEE 222

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2137574 AT4G37850 "AT4G37850" [Arabidopsis thaliana (taxid:3702)]

 Score = 115 (45.5 bits), Expect = 4.0e-05, Sum P(2) = 4.0e-05
 Identities = 35/112 (31%), Positives = 56/112 (50%)

Query:    54 DNSRTHSPTTAKMETTPA-EAEEQARAQVGK-KRSGNGKA--VSGGESEHEMHILTERER 109
             D    +SPT      +P  EA+ Q   +  +  R G  +A   S  +S  + HI+ ER+R
Sbjct:   101 DMEHEYSPTYLNSIFSPKLEAQVQPHQKSDEFNRKGTKRAQPFSRNQSNAQDHIIAERKR 160

Query:   110 RKKMRNMFSNXXXXXXXXXXKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEK 161
             R+K+   F            K DK++++ +A+K+IK LQ     LE+QK E+
Sbjct:   161 REKLTQRFV-ALSALVPGLKKMDKASVLGDALKHIKYLQERVGELEEQKKER 211

GO:0003677 "DNA binding" evidence=ISS

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

UNIPROTKB|Q5JNS0 P0706B05.43 "Os01g0293100 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 120 (47.3 bits), Expect = 8.9e-05, P = 8.9e-05
 Identities = 52/210 (24%), Positives = 93/210 (44%)

Query:    70 PAEAEEQARAQVGKKRSGNGKAVSGGESEHEMHILTERERRKKMRNMFSNXXXXXXXXXX 129
             P E+    R+  G+KRS       GG   + +    E++RR ++   + N          
Sbjct:   147 PFESSPTPRSGGGRKRSRATAGFHGGGPANGVE-KKEKQRRLRLTEKY-NALMLLIPNRT 204

Query:   130 KADKSTIVDEAVKYIKTLQHTHQTL-----EKQKFEKVQGATTVDHEQSIIASPLEAVVE 184
             K D++T++ +A++YI+ L  T + L     +K++  ++QG   VD   S + + ++   E
Sbjct:   205 KEDRATVISDAIEYIQELGRTVEELTLLVEKKRRRREMQG-DVVDAATSSVVAGMDQAAE 263

Query:   185 SREAYL--ADHLGSSVPKNLSMAANIHHSLQVPSDCFQTWFSPNVVVNMCGDDAQISVCS 242
             S E  +  A  +G+  P      A I  S  +     +T+    V V +  DD  I +  
Sbjct:   264 SSEGEVMAAAAMGAVAPP--PRQAPIR-STYIQRRSKETF----VDVRIVEDDVNIKLTK 316

Query:   243 PRKPGLLTTIFYILEKHNLDVVSAHVSSDR 272
              R+ G L      L+   LD+V  H+S  +
Sbjct:   317 RRRDGCLAAASRALDDLRLDLV--HLSGGK 344

GO:0005634 "nucleus" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	282
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	5e-12
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	1e-11
smart00353	53	smart00353, HLH, helix loop helix domain	6e-09
cd04873	70	cd04873, ACT_UUR-ACR-like, ACT domains of the bact	8e-05
cd04899	70	cd04899, ACT_ACR-UUR-like_2, C-terminal ACT domain	6e-04
cd02116	60	cd02116, ACT, ACT domains are commonly involved in	0.004

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

 Score = 59.4 bits (145), Expect = 5e-12
 Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQ 148
           + H   ER RR ++ + F  L  LLP  P  K  K+ I+  A++YIK LQ
Sbjct: 3   KAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

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

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 26/56 (46%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 96  ESEHEMHILTERERRKKMRNMFSNLHALLPHLPP--KADKSTIVDEAVKYIKTLQH 149
           +S  E H L ER RR+++ + F  L +LLP LPP  K  K+ I+ +AV YIK+LQ 
Sbjct: 2   KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQE 57

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

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

 Score = 50.7 bits (122), Expect = 6e-09
 Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 2/50 (4%)

Query: 106 ERERRKKMRNMFSNLHALLPHLPP--KADKSTIVDEAVKYIKTLQHTHQT 153
           ER RR+K+   F  L +LLP LP   K  K+ I+  A++YIK+LQ   Q 
Sbjct: 4   ERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

>gnl|CDD|153145 cd04873, ACT_UUR-ACR-like, ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD

 Score = 39.8 bits (94), Expect = 8e-05
 Identities = 12/40 (30%), Positives = 22/40 (55%)

Query: 237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSM 276
            + V +P +PGLL  I  +L    L++  A +S+   R++
Sbjct: 2   VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERAL 41

This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains. Length = 70

>gnl|CDD|153171 cd04899, ACT_ACR-UUR-like_2, C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains

 Score = 37.0 bits (87), Expect = 6e-04
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVS 269
           + + +  +PGLL  +  +L +  L++ SA ++
Sbjct: 3   LELTALDRPGLLADVTRVLAELGLNIHSAKIA 34

This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains. Length = 70

>gnl|CDD|153139 cd02116, ACT, ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme

 Score = 34.6 bits (80), Expect = 0.004
 Identities = 9/42 (21%), Positives = 19/42 (45%)

Query: 238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI 279
           ++V  P +PGLL  +  +L +  +++ S    +        I
Sbjct: 1   LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADI 42

Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times. Length = 60

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	282
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.45
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.44
smart00353	53	HLH helix loop helix domain.	99.35
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.13
KOG1318	411	consensus Helix loop helix transcription factor EB	98.97
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.7
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.64
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.53
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.51
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.39
KOG0561	373	consensus bHLH transcription factor [Transcription	98.21
KOG4029	228	consensus Transcription factor HAND2/Transcription	98.06
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	97.95
PLN03217	93	transcription factor ATBS1; Provisional	97.93
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	97.86
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	97.85
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.69
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.68
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	97.47
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.24
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	97.22
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.19
KOG3898	254	consensus Transcription factor NeuroD and related	96.94
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	96.93
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	96.88
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	96.57
KOG3910	632	consensus Helix loop helix transcription factor [T	96.42
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	96.23
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	95.84
PRK05007	884	PII uridylyl-transferase; Provisional	95.83
KOG4395	285	consensus Transcription factor Atonal, contains HT	95.69
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	95.55
PRK00275	895	glnD PII uridylyl-transferase; Provisional	95.43
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	95.27
PRK03381	774	PII uridylyl-transferase; Provisional	95.01
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.93
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	94.93
PRK04374	869	PII uridylyl-transferase; Provisional	94.93
PRK05092	931	PII uridylyl-transferase; Provisional	94.87
PRK00194	90	hypothetical protein; Validated	94.85
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	94.78
PRK03059	856	PII uridylyl-transferase; Provisional	94.7
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	94.63
PRK03381	774	PII uridylyl-transferase; Provisional	94.38
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	94.21
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.11
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	94.09
PRK01759	854	glnD PII uridylyl-transferase; Provisional	94.08
PRK00275	895	glnD PII uridylyl-transferase; Provisional	93.82
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	93.81
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	93.74
PRK03059	856	PII uridylyl-transferase; Provisional	93.71
PRK05007	884	PII uridylyl-transferase; Provisional	93.69
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	92.97
cd02116	60	ACT ACT domains are commonly involved in specifica	92.93
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	92.88
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	92.86
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	92.85
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	92.85
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	92.84
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	92.69
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	92.54
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	92.45
PRK05092	931	PII uridylyl-transferase; Provisional	92.42
PRK04374	869	PII uridylyl-transferase; Provisional	92.34
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	92.3
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	92.29
KOG3582	856	consensus Mlx interactors and related transcriptio	92.0
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	91.79
PRK04435	147	hypothetical protein; Provisional	91.65
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	91.55
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	91.47
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	89.94
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	89.66
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	89.19
PRK08577	136	hypothetical protein; Provisional	88.74
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	88.3
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	87.8
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	87.46
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	86.9
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	86.13
PRK07334	403	threonine dehydratase; Provisional	84.09
PRK11152	76	ilvM acetolactate synthase 2 regulatory subunit; P	83.74
cd04901	69	ACT_3PGDH C-terminal ACT (regulatory) domain of D-	80.96

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

Probab=99.45  E-value=1.2e-13  Score=97.23  Aligned_cols=51  Identities=37%  Similarity=0.636  Sum_probs=47.8

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCC----CCCCChhhHHHHHHHHHHHHH
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHL----PPKADKSTIVDEAVKYIKTLQ  148 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~----~~K~~k~~iL~~ai~YIk~Lq  148 (282)
                      +|..|+..||+||++||+.|..|+.+||..    ..|++|++||..||+||++||
T Consensus         1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            468899999999999999999999999986    378999999999999999997

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

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

Probab=99.44  E-value=2.1e-13  Score=96.87  Aligned_cols=55  Identities=45%  Similarity=0.727  Sum_probs=51.4

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTH  151 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~  151 (282)
                      ..+..|+..||+||++||..|..|+++||...  .|++|++||..||+||+.|+.++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999999999999984  89999999999999999999875

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

>smart00353 HLH helix loop helix domain

Probab=99.35  E-value=2.6e-12  Score=89.35  Aligned_cols=50  Identities=42%  Similarity=0.634  Sum_probs=45.7

Q ss_pred             cHHHHHHHHHHHHHHHHHHhhCCCC--CCCCChhhHHHHHHHHHHHHHHHHH
Q 038084          103 ILTERERRKKMRNMFSNLHALLPHL--PPKADKSTIVDEAVKYIKTLQHTHQ  152 (282)
Q Consensus       103 ~~~ER~RR~~in~~~~~Lr~lvP~~--~~K~~k~~iL~~ai~YIk~Lq~~~~  152 (282)
                      +..||+||++||+.|..|+++||..  ..|++|++||.+||+||+.|+.+++
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            4679999999999999999999974  3789999999999999999998875

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.13  E-value=2.1e-11  Score=104.67  Aligned_cols=75  Identities=20%  Similarity=0.380  Sum_probs=66.0

Q ss_pred             CCCCccccccHHHHHHHHHHHHHHHHHHhhCCCCC------CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhccccc
Q 038084           94 GGESEHEMHILTERERRKKMRNMFSNLHALLPHLP------PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATT  167 (282)
Q Consensus        94 ~~~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~------~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~~~~  167 (282)
                      .++.+|..|..+||+||+.||..++.|+.|||.+.      .|++|+-||.++|+||.+|++++.+.+++...|+..++.
T Consensus        58 yk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtA  137 (229)
T KOG1319|consen   58 YKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTA  137 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44457899999999999999999999999999864      388999999999999999999999999998888766554


Q ss_pred             c
Q 038084          168 V  168 (282)
Q Consensus       168 ~  168 (282)
                      +
T Consensus       138 L  138 (229)
T KOG1319|consen  138 L  138 (229)
T ss_pred             H
Confidence            3

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

Probab=98.97  E-value=8.5e-10  Score=105.85  Aligned_cols=63  Identities=29%  Similarity=0.452  Sum_probs=55.5

Q ss_pred             CCCCCccccccHHHHHHHHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHH
Q 038084           93 SGGESEHEMHILTERERRKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKTLQHTHQTLE  155 (282)
Q Consensus        93 ~~~~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~Lq~~~~~L~  155 (282)
                      .++..+|..||.+||+||++||+++.+|..|||.+.   .|..|..||..+++||++||+..++..
T Consensus       228 ~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~  293 (411)
T KOG1318|consen  228 ERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR  293 (411)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence            345568899999999999999999999999999974   477799999999999999999887433

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

Probab=98.70  E-value=7.1e-08  Score=86.74  Aligned_cols=69  Identities=23%  Similarity=0.370  Sum_probs=58.2

Q ss_pred             CCCCCccccccHHHHHHHHHHHHHHHHHHhhCCCCCCCCC--hhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038084           93 SGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKAD--KSTIVDEAVKYIKTLQHTHQTLEKQKFEK  161 (282)
Q Consensus        93 ~~~~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~~K~~--k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l  161 (282)
                      ......|..||..||+||..|++.|..|+.+||.+.....  .+.||+.|+.||+.|+.+.....+.+++|
T Consensus        54 ~~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l  124 (232)
T KOG2483|consen   54 SSAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDL  124 (232)
T ss_pred             CCCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHH
Confidence            4455689999999999999999999999999999864333  58999999999999998877776655554

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

Probab=98.64  E-value=1.4e-08  Score=92.42  Aligned_cols=58  Identities=24%  Similarity=0.414  Sum_probs=49.7

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC-------CCCChhhHHHHHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP-------PKADKSTIVDEAVKYIKTLQHTHQTL  154 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-------~K~~k~~iL~~ai~YIk~Lq~~~~~L  154 (282)
                      .++..|-++||+||.+||+.|.+|++|||...       .|++|++||..|++|++.|+.....-
T Consensus        31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~~   95 (250)
T KOG4304|consen   31 YRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQAA   95 (250)
T ss_pred             HhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccccc
Confidence            35567779999999999999999999999642       58899999999999999999765443

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.53  E-value=1e-07  Score=98.70  Aligned_cols=67  Identities=24%  Similarity=0.379  Sum_probs=62.9

Q ss_pred             CCccccccHHHHHHHHHHHHHHHHHHhhCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 038084           96 ESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKV  162 (282)
Q Consensus        96 ~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~  162 (282)
                      ..+|.+||.+|||.|..||+++.+|+.+||+...|+.|..+|..||+||++|+...+.+..++..++
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~  340 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR  340 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence            5789999999999999999999999999999889999999999999999999999999988777654

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

Probab=98.51  E-value=1.1e-07  Score=98.12  Aligned_cols=52  Identities=25%  Similarity=0.401  Sum_probs=49.3

Q ss_pred             cccccHHHHHHHHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHHHHHH
Q 038084           99 HEMHILTERERRKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKTLQHT  150 (282)
Q Consensus        99 r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~Lq~~  150 (282)
                      |+.|+.+||+||++||..+.+|.+|||.+.   -|+||.+||.+||.+|+.+++.
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            688999999999999999999999999986   7999999999999999999985

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

Probab=98.39  E-value=1.1e-06  Score=78.99  Aligned_cols=66  Identities=23%  Similarity=0.299  Sum_probs=57.1

Q ss_pred             CCccccccHHHHHHHHHHHHHHHHHHhh-CCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038084           96 ESEHEMHILTERERRKKMRNMFSNLHAL-LPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEK  161 (282)
Q Consensus        96 ~~~r~~h~~~ER~RR~~in~~~~~Lr~l-vP~~~~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l  161 (282)
                      ..+|..-.++||+|-+|+|+.|..|+.- +++-..++.|++||..||+||..||.-++++.+....+
T Consensus       116 vDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  116 VDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            3577888899999999999999999854 45555899999999999999999999999888777655

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.21  E-value=8.7e-07  Score=81.50  Aligned_cols=63  Identities=30%  Similarity=0.418  Sum_probs=54.3

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFE  160 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~  160 (282)
                      +|+.-|.-||+|...||..|..||+|+|.-. .|++|+.||+.+.+||..|+.+.-+|-.++.+
T Consensus        60 RReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ll~qn~e  123 (373)
T KOG0561|consen   60 RREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTELLPQNGE  123 (373)
T ss_pred             HHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccccccccch
Confidence            5677788899999999999999999999754 69999999999999999999887777654433

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

Probab=98.06  E-value=4.3e-06  Score=75.21  Aligned_cols=65  Identities=29%  Similarity=0.390  Sum_probs=55.7

Q ss_pred             CCCCCccccccHHHHHHHHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 038084           93 SGGESEHEMHILTERERRKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKTLQHTHQTLEKQ  157 (282)
Q Consensus        93 ~~~~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~  157 (282)
                      .....++..+|.+||+|-..+|..|..||.+||..+   +|.+|+++|..||.||.+|++-++.-...
T Consensus       104 ~~~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  104 SQTSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             cchhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            345567888999999999999999999999999865   58999999999999999999766655543

>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.95  E-value=4.1e-05  Score=56.97  Aligned_cols=45  Identities=33%  Similarity=0.404  Sum_probs=42.9

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .|+|.++.|||+|.+|.++|.++||+|..|.|++.++++..+|+.
T Consensus         3 viev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV   47 (72)
T cd04895           3 LVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHV   47 (72)
T ss_pred             EEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEE
Confidence            588999999999999999999999999999999999999999875

This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.93  E-value=2.7e-05  Score=59.10  Aligned_cols=54  Identities=20%  Similarity=0.449  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHHHhhCCCCC-----CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 038084          110 RKKMRNMFSNLHALLPHLP-----PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQ  163 (282)
Q Consensus       110 R~~in~~~~~Lr~lvP~~~-----~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~  163 (282)
                      -++|++.+..|+.|+|...     .|.+-+.+|++|.+||+.|+.++..|.+.+.+|..
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~   77 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLA   77 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3689999999999999853     35566799999999999999999999999998874

>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.86  E-value=7.1e-05  Score=55.93  Aligned_cols=46  Identities=17%  Similarity=0.247  Sum_probs=42.6

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEe
Q 038084          236 AQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS-DRYRSMYMIHA  281 (282)
Q Consensus       236 ~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~-~~~~~~~~i~a  281 (282)
                      +.|+|.|+.|+|+|.+|..+|..+||+|+.|.|.+ .++.++.+|+.
T Consensus         1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V   47 (76)
T cd04927           1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFI   47 (76)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEE
Confidence            46899999999999999999999999999999996 88999988875

This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.85  E-value=7.3e-05  Score=56.08  Aligned_cols=45  Identities=18%  Similarity=0.194  Sum_probs=42.6

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .|+|.|+.|||||.+|..+|-++|++|.+|.|++.++++.-+|+.
T Consensus         3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV   47 (75)
T cd04897           3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYI   47 (75)
T ss_pred             EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEE
Confidence            488999999999999999999999999999999999999988874

This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.69  E-value=0.00017  Score=54.10  Aligned_cols=45  Identities=18%  Similarity=0.287  Sum_probs=42.4

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE--eeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVS--SDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs--~~~~~~~~~i~a  281 (282)
                      .|.|.|+.|||||.+|.++|..+||+|..|.|+  +.++++..+|+.
T Consensus         2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv   48 (75)
T cd04896           2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV   48 (75)
T ss_pred             EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE
Confidence            488999999999999999999999999999999  999999988874

This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains

Probab=97.68  E-value=0.00022  Score=52.47  Aligned_cols=45  Identities=18%  Similarity=0.373  Sum_probs=40.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD-RYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~-~~~~~~~i~a  281 (282)
                      .|.|.|+.++|+|.+|..+|..+||+|+.|.+.+. ++.++.+|+.
T Consensus         3 ~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v   48 (73)
T cd04900           3 EVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVV   48 (73)
T ss_pred             EEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEE
Confidence            58899999999999999999999999999999876 6888888764

This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.47  E-value=0.00064  Score=50.34  Aligned_cols=45  Identities=27%  Similarity=0.425  Sum_probs=42.2

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .|+|.++.++|+|.+|..+|.++|++|+.|.+.+.++.++.+|+.
T Consensus         2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V   46 (74)
T cd04925           2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYV   46 (74)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEE
Confidence            488999999999999999999999999999999999999988875

This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains

Probab=97.24  E-value=0.0017  Score=46.60  Aligned_cols=45  Identities=20%  Similarity=0.333  Sum_probs=41.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .|.|.++.++|+|.+|+.+|.+++++|+++.+.+.++..+.+|++
T Consensus         2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i   46 (70)
T cd04899           2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYV   46 (70)
T ss_pred             EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEE
Confidence            478899999999999999999999999999999988888888875

This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04928 ACT_TyrKc Uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains

Probab=97.22  E-value=0.002  Score=47.47  Aligned_cols=45  Identities=24%  Similarity=0.355  Sum_probs=40.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS-DRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~-~~~~~~~~i~a  281 (282)
                      .|-|.++.++|+|..|..+|..+||+|+.|.+.+ .++.++.+|.+
T Consensus         3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V   48 (68)
T cd04928           3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVV   48 (68)
T ss_pred             EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEE
Confidence            5788999999999999999999999999999976 57888888865

This CD includes a novel, yet uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04926 ACT_ACR_4 C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=97.19  E-value=0.002  Score=47.36  Aligned_cols=45  Identities=16%  Similarity=0.321  Sum_probs=40.6

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .|.|.++.++|+|.+|..+|.++|++|+++.+.+.++..+.+|+.
T Consensus         3 ri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v   47 (72)
T cd04926           3 RLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYV   47 (72)
T ss_pred             EEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEE
Confidence            477889999999999999999999999999999887888888764

This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=96.94  E-value=0.00066  Score=62.24  Aligned_cols=56  Identities=23%  Similarity=0.301  Sum_probs=50.2

Q ss_pred             CCCCccccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHH
Q 038084           94 GGESEHEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQH  149 (282)
Q Consensus        94 ~~~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~  149 (282)
                      ....+|.+-|..||+|...+|+.|+.||.++|...  .|+.|+..|..|-+||..|++
T Consensus        68 ~~~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~  125 (254)
T KOG3898|consen   68 ALTLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE  125 (254)
T ss_pred             hhhhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence            35567889999999999999999999999999633  799999999999999999985

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=96.93  E-value=0.00045  Score=58.05  Aligned_cols=54  Identities=28%  Similarity=0.492  Sum_probs=50.1

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC-CCCChhhHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHT  150 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-~K~~k~~iL~~ai~YIk~Lq~~  150 (282)
                      .++.-|++.||+|=..+|+.|..||.++|.++ .|.+|.-.|+-|..||.+|-+-
T Consensus        77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v  131 (173)
T KOG4447|consen   77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV  131 (173)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence            37889999999999999999999999999987 7999999999999999999753

>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold

Probab=96.88  E-value=0.0071  Score=42.44  Aligned_cols=37  Identities=32%  Similarity=0.580  Sum_probs=34.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCC
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRY  273 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~  273 (282)
                      .|.|.|+.+||+|.+|..+|.++|++|.++.+....+
T Consensus         2 ~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~   38 (66)
T PF01842_consen    2 RVRVIVPDRPGILADVTEILADHGINIDSISQSSDKD   38 (66)
T ss_dssp             EEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence            5889999999999999999999999999999999766

ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....

>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD

Probab=96.57  E-value=0.014  Score=41.31  Aligned_cols=45  Identities=27%  Similarity=0.482  Sum_probs=39.7

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .|.|.|+.++|+|.+|+.+|.++++.|.++.+.+.++.....|++
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v   46 (70)
T cd04873           2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYV   46 (70)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence            477899999999999999999999999999998876677777664

This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=96.42  E-value=0.0019  Score=63.42  Aligned_cols=60  Identities=20%  Similarity=0.233  Sum_probs=49.7

Q ss_pred             CCCccccccHHHHHHHHHHHHHHHHHHhhCCC-CC--CCCChhhHHHHHHHHHHHHHHHHHHH
Q 038084           95 GESEHEMHILTERERRKKMRNMFSNLHALLPH-LP--PKADKSTIVDEAVKYIKTLQHTHQTL  154 (282)
Q Consensus        95 ~~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~-~~--~K~~k~~iL~~ai~YIk~Lq~~~~~L  154 (282)
                      +..+|+..|.+||-|-..||+.|.+|-.+.-. +.  ....|.-||..||..|-.|++||.+-
T Consensus       523 EkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER  585 (632)
T KOG3910|consen  523 EKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER  585 (632)
T ss_pred             HHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence            44688999999999999999999999988642 21  23467899999999999999998764

>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A

Probab=96.23  E-value=0.03  Score=41.50  Aligned_cols=47  Identities=17%  Similarity=0.337  Sum_probs=39.6

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .+.|.|.++.|||++..|..+|.++|.+|+.++.+..++.....+.+
T Consensus         2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v   48 (76)
T PF13740_consen    2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLV   48 (76)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEE
T ss_pred             EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEE
Confidence            46799999999999999999999999999999999998887776654

>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains

Probab=95.84  E-value=0.043  Score=40.76  Aligned_cols=45  Identities=11%  Similarity=0.198  Sum_probs=39.6

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEE
Q 038084          236 AQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIH  280 (282)
Q Consensus       236 ~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~  280 (282)
                      +.|.+.|+.++|+...|...|.++|.+|+.++....++..++.+.
T Consensus         2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~   46 (77)
T cd04893           2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTML   46 (77)
T ss_pred             EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEE
Confidence            568999999999999999999999999999999987776655543

This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.83  E-value=0.023  Score=60.74  Aligned_cols=49  Identities=14%  Similarity=0.207  Sum_probs=45.6

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          233 GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       233 g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      ++.-.|.|.+..|||||.+|.++|.++||+|.+|-|++.++++..+|+.
T Consensus       806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV  854 (884)
T PRK05007        806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFIL  854 (884)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEE
Confidence            4556799999999999999999999999999999999999999999875

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

Probab=95.69  E-value=0.02  Score=52.00  Aligned_cols=54  Identities=22%  Similarity=0.228  Sum_probs=47.7

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHH
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTH  151 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~  151 (282)
                      +|..-+..||+|...+|..|+.||..||...  .|++|-..|+.|-.||--|-..+
T Consensus       174 rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l  229 (285)
T KOG4395|consen  174 RRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL  229 (285)
T ss_pred             hhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence            5567788999999999999999999999864  68999999999999999887544

>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A

Probab=95.55  E-value=0.087  Score=38.94  Aligned_cols=46  Identities=13%  Similarity=0.332  Sum_probs=36.6

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEE
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD--RYRSMYMIH  280 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~--~~~~~~~i~  280 (282)
                      .+.|+|.+..++|+|.+|..+|.+.|+.|.++++...  ++.....|.
T Consensus         6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~   53 (80)
T PF13291_consen    6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLT   53 (80)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEE
T ss_pred             EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEE
Confidence            4679999999999999999999999999999999985  455555443

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=95.43  E-value=0.069  Score=57.16  Aligned_cols=57  Identities=19%  Similarity=0.275  Sum_probs=48.6

Q ss_pred             CeEEEEEE--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          225 PNVVVNMC--GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       225 ~~V~V~i~--g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      +.|.+.-.  ++...|.|++..+||||.+|..+|..+||+|+.|.|++.+++++.+|+.
T Consensus       802 ~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V  860 (895)
T PRK00275        802 TQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFI  860 (895)
T ss_pred             CEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEE
Confidence            34444433  3456799999999999999999999999999999999999999999975

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=95.27  E-value=0.019  Score=57.18  Aligned_cols=41  Identities=24%  Similarity=0.513  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHH
Q 038084          106 ERERRKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKT  146 (282)
Q Consensus       106 ER~RR~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~  146 (282)
                      -|+-|+++|..++.|.+|+|.-.   +|+||.+||.-+|.|++-
T Consensus        33 SKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~   76 (712)
T KOG3560|consen   33 SKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV   76 (712)
T ss_pred             chhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence            45569999999999999999743   799999999999999863

>PRK03381 PII uridylyl-transferase; Provisional

Probab=95.01  E-value=0.096  Score=55.23  Aligned_cols=48  Identities=25%  Similarity=0.323  Sum_probs=44.9

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      +...|.|.++.+||+|.+|..+|..+|++|++|.|++.++.++.+|+.
T Consensus       706 ~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V  753 (774)
T PRK03381        706 DATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYV  753 (774)
T ss_pred             CeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEE
Confidence            347899999999999999999999999999999999999999998875

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=94.93  E-value=0.065  Score=57.08  Aligned_cols=49  Identities=12%  Similarity=0.293  Sum_probs=45.3

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          233 GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       233 g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      ++-..|.|.+..|||||.+|.++|.++||+|..|-|++.++++..+|+.
T Consensus       781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv  829 (854)
T PRK01759        781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFIL  829 (854)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEE
Confidence            3456799999999999999999999999999999999999999998875

>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains

Probab=94.93  E-value=0.12  Score=38.00  Aligned_cols=35  Identities=14%  Similarity=0.393  Sum_probs=32.9

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR  272 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~  272 (282)
                      |.|.|+.++|++.+|-+.|.++|++|...+..+.+
T Consensus         2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~   36 (81)
T cd04869           2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS   36 (81)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence            67999999999999999999999999999998865

This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in

>PRK04374 PII uridylyl-transferase; Provisional

Probab=94.93  E-value=0.12  Score=55.28  Aligned_cols=57  Identities=26%  Similarity=0.428  Sum_probs=49.3

Q ss_pred             CeEEEEEE--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          225 PNVVVNMC--GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       225 ~~V~V~i~--g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      +.|.+.-.  ++-..|.|.+..+||||.+|..+|..+||+|+.|.|++.+++++.+|+.
T Consensus       784 ~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V  842 (869)
T PRK04374        784 PRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQI  842 (869)
T ss_pred             CeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEE
Confidence            45555442  3457799999999999999999999999999999999999999999875

>PRK05092 PII uridylyl-transferase; Provisional

Probab=94.87  E-value=0.12  Score=55.58  Aligned_cols=57  Identities=26%  Similarity=0.370  Sum_probs=48.8

Q ss_pred             CeEEEEEE--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          225 PNVVVNMC--GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       225 ~~V~V~i~--g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      +.|.+.-.  +....|.|.++.+||+|.+|..+|.++||+|..|.|.+.++++..+|++
T Consensus       831 ~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v  889 (931)
T PRK05092        831 PRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYV  889 (931)
T ss_pred             CEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEE
Confidence            45555432  3456799999999999999999999999999999999999999998876

>PRK00194 hypothetical protein; Validated

Probab=94.85  E-value=0.059  Score=40.84  Aligned_cols=43  Identities=16%  Similarity=0.187  Sum_probs=37.2

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEE
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMY  277 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~  277 (282)
                      .+.|.|.|+.+||++..|...|-++|++|+..+..+.++..+.
T Consensus         3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~   45 (90)
T PRK00194          3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTM   45 (90)
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEE
Confidence            4679999999999999999999999999999988776554444

>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein

Probab=94.78  E-value=0.065  Score=40.61  Aligned_cols=44  Identities=14%  Similarity=0.178  Sum_probs=37.9

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          236 AQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       236 ~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      +.|.+.|+.+||++..|...|-++|++|++.+..+.++..+..+
T Consensus         2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~   45 (88)
T cd04872           2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIM   45 (88)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEE
Confidence            56899999999999999999999999999999888666544443

This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK03059 PII uridylyl-transferase; Provisional

Probab=94.70  E-value=0.11  Score=55.51  Aligned_cols=48  Identities=25%  Similarity=0.301  Sum_probs=44.9

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      +...|.|.++.+||+|.+|..+|..+||+|+.|.|++.++.++.+|+.
T Consensus       785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V  832 (856)
T PRK03059        785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI  832 (856)
T ss_pred             CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence            456799999999999999999999999999999999999999999875

>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase)

Probab=94.63  E-value=0.11  Score=37.81  Aligned_cols=33  Identities=18%  Similarity=0.465  Sum_probs=31.5

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS  270 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~  270 (282)
                      |.|.|+.++|++.+|...|-++|++|+.....+
T Consensus         2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~   34 (74)
T cd04875           2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFV   34 (74)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeee
Confidence            789999999999999999999999999998886

This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK03381 PII uridylyl-transferase; Provisional

Probab=94.38  E-value=0.13  Score=54.23  Aligned_cols=48  Identities=27%  Similarity=0.325  Sum_probs=44.4

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      +...|.|+|+.|||+|.+|..+|..+|++|+.|.+.+.++.++.+|.+
T Consensus       598 ~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V  645 (774)
T PRK03381        598 HMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVV  645 (774)
T ss_pred             CeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEE
Confidence            567899999999999999999999999999999999988888888865

>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains

Probab=94.21  E-value=0.21  Score=35.06  Aligned_cols=34  Identities=15%  Similarity=0.421  Sum_probs=30.2

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      |.|.++.+||.|.+|+.+|.+.|++|++.+....
T Consensus         1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~   34 (73)
T cd04886           1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRA   34 (73)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEec
Confidence            4578899999999999999999999998887654

This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.11  E-value=0.13  Score=54.77  Aligned_cols=48  Identities=21%  Similarity=0.266  Sum_probs=44.5

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      +...|.|.|..|||+|.+|.++|.++|++|.++.|++.++++..+|++
T Consensus       778 ~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v  825 (850)
T TIGR01693       778 KATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYV  825 (850)
T ss_pred             CeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEE
Confidence            457799999999999999999999999999999999999988888875

This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=94.09  E-value=0.16  Score=54.07  Aligned_cols=48  Identities=19%  Similarity=0.303  Sum_probs=43.5

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE-eeCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVS-SDRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs-~~~~~~~~~i~a  281 (282)
                      +...|.|.++.++|+|.+|..+|..+||+|+.|.|. +.++.++.+|+.
T Consensus       667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V  715 (850)
T TIGR01693       667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVV  715 (850)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEE
Confidence            456799999999999999999999999999999998 678888888875

This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=94.08  E-value=0.18  Score=53.74  Aligned_cols=57  Identities=9%  Similarity=0.092  Sum_probs=47.9

Q ss_pred             CeEEEEEE--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEe
Q 038084          225 PNVVVNMC--GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS-DRYRSMYMIHA  281 (282)
Q Consensus       225 ~~V~V~i~--g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~-~~~~~~~~i~a  281 (282)
                      +.|.+.-.  .+...|.|.++.++|+|.+|..+|..+||+|+.|.|.+ .++.++.+|++
T Consensus       665 ~~V~i~~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V  724 (854)
T PRK01759        665 LLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIV  724 (854)
T ss_pred             CEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEE
Confidence            44555432  35567999999999999999999999999999999977 78999988875

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=93.82  E-value=0.18  Score=54.01  Aligned_cols=48  Identities=15%  Similarity=0.265  Sum_probs=42.8

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEE-EeeCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHV-SSDRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~v-s~~~~~~~~~i~a  281 (282)
                      +...|.|.|+.++|+|.+|..+|..+||+|+.|.| ++.++.++-+|++
T Consensus       703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V  751 (895)
T PRK00275        703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIV  751 (895)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEE
Confidence            45779999999999999999999999999999998 5567888888875

>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein

Probab=93.81  E-value=0.26  Score=35.95  Aligned_cols=42  Identities=14%  Similarity=0.337  Sum_probs=35.6

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      .|+|.+..++|+|.+|+.+|.++++++...++... +.+.+.|
T Consensus         2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~i~l~i   43 (74)
T cd04877           2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GRIYLNF   43 (74)
T ss_pred             EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-CeEEEEe
Confidence            47899999999999999999999999999999775 4444444

ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence

>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains

Probab=93.74  E-value=0.41  Score=34.42  Aligned_cols=41  Identities=12%  Similarity=0.213  Sum_probs=34.5

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEE
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR-YRSMYM  278 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~-~~~~~~  278 (282)
                      |+|.+..++|+|.+|+.+|.+.|.+|..++..... +.....
T Consensus         2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~   43 (74)
T cd04887           2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRD   43 (74)
T ss_pred             EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEE
Confidence            78889999999999999999999999999987753 444333

The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK03059 PII uridylyl-transferase; Provisional

Probab=93.71  E-value=0.21  Score=53.37  Aligned_cols=48  Identities=17%  Similarity=0.372  Sum_probs=43.7

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEE-EeeCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHV-SSDRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~v-s~~~~~~~~~i~a  281 (282)
                      +...|.|+|+.++|+|..|..+|..+||+|+.|.| ++.++.++.+|.+
T Consensus       677 ~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V  725 (856)
T PRK03059        677 EGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQV  725 (856)
T ss_pred             CeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEE
Confidence            56789999999999999999999999999999999 4578899998875

>PRK05007 PII uridylyl-transferase; Provisional

Probab=93.69  E-value=0.24  Score=53.01  Aligned_cols=57  Identities=23%  Similarity=0.322  Sum_probs=46.1

Q ss_pred             CeEEEEEE--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEEEe
Q 038084          225 PNVVVNMC--GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD-RYRSMYMIHA  281 (282)
Q Consensus       225 ~~V~V~i~--g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~-~~~~~~~i~a  281 (282)
                      +-|.+.-.  ++...|.|+|+.++|+|..|..+|..+||+|+.|.|.+. ++.++-+|+.
T Consensus       689 p~V~i~~~~~~~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V  748 (884)
T PRK05007        689 PLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIV  748 (884)
T ss_pred             CeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEE
Confidence            34554432  356789999999999999999999999999999999775 5588777764

>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB)

Probab=92.97  E-value=0.39  Score=35.16  Aligned_cols=42  Identities=24%  Similarity=0.378  Sum_probs=35.8

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      |.|..+.|||++.+|.++|-++|++|+..+.+..++.....+
T Consensus         2 vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~   43 (75)
T cd04870           2 ITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGI   43 (75)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEE
Confidence            678899999999999999999999999998877766544433

The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme

Probab=92.93  E-value=0.56  Score=29.79  Aligned_cols=34  Identities=24%  Similarity=0.612  Sum_probs=30.6

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      |.|.++.++|.+.+|+.+|..+++.|........
T Consensus         1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~   34 (60)
T cd02116           1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTS   34 (60)
T ss_pred             CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEc
Confidence            4678888999999999999999999999998764

Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p

>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=92.88  E-value=0.23  Score=52.17  Aligned_cols=57  Identities=21%  Similarity=0.290  Sum_probs=48.3

Q ss_pred             CeEEEEEE--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          225 PNVVVNMC--GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       225 ~~V~V~i~--g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      |.|.+.-.  .+.-.++|.+..|||+|..|-.+|.+++|+|.+|.|+++|.++..+|..
T Consensus       779 p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~v  837 (867)
T COG2844         779 PRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIV  837 (867)
T ss_pred             CceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEE
Confidence            55655433  3457799999999999999999999999999999999999988777754

>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains

Probab=92.86  E-value=0.46  Score=33.75  Aligned_cols=36  Identities=25%  Similarity=0.358  Sum_probs=32.6

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          236 AQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       236 ~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      ++|.|.+..++|+|.+|+..|.+.++++...+....
T Consensus         1 ~yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~   36 (79)
T cd04881           1 YYLRLTVKDKPGVLAKITGILAEHGISIESVIQKEA   36 (79)
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEccc
Confidence            478999999999999999999999999999987654

The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH)

Probab=92.85  E-value=0.51  Score=32.71  Aligned_cols=43  Identities=14%  Similarity=0.335  Sum_probs=36.0

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC--CeEEEEEE
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR--YRSMYMIH  280 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~--~~~~~~i~  280 (282)
                      +.|....++|+|.+|+.+|.+++++|.+..+....  +...+.|.
T Consensus         2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~   46 (71)
T cd04879           2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLD   46 (71)
T ss_pred             EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEE
Confidence            56788999999999999999999999999987754  56555554

ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active

>cd04894 ACT_ACR-like_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein)

Probab=92.85  E-value=0.31  Score=35.34  Aligned_cols=43  Identities=21%  Similarity=0.314  Sum_probs=39.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      .|.|.||.+.||--++.+.+-++||.|+...+++.+...+..|
T Consensus         2 vitvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~   44 (69)
T cd04894           2 VITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVF   44 (69)
T ss_pred             EEEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEE
Confidence            4889999999999999999999999999999999987666555

This CD includes the N-terminal ACT domain of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a

Probab=92.84  E-value=0.57  Score=32.77  Aligned_cols=35  Identities=17%  Similarity=0.359  Sum_probs=31.6

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      .|.|.++.++|.|.+|+..|.+++++|...+....
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~   36 (72)
T cd04874           2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIE   36 (72)
T ss_pred             eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEecc
Confidence            37788999999999999999999999999888765

a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate

Probab=92.69  E-value=0.55  Score=32.08  Aligned_cols=43  Identities=21%  Similarity=0.347  Sum_probs=35.0

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEEEE
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR-YRSMYMIH  280 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~-~~~~~~i~  280 (282)
                      |.|..+.++|.|.+|+.+|-+.|++|....+...+ +..+..|.
T Consensus         1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~   44 (56)
T cd04889           1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLI   44 (56)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEE
Confidence            35678899999999999999999999888887754 56555554

Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A

>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit

Probab=92.54  E-value=0.6  Score=32.48  Aligned_cols=43  Identities=21%  Similarity=0.428  Sum_probs=34.5

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEE
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD--RYRSMYMIH  280 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~--~~~~~~~i~  280 (282)
                      |.|.+..++|.|.+|+..|.+++++|........  ++...+.|.
T Consensus         2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~   46 (71)
T cd04903           2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIE   46 (71)
T ss_pred             EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEE
Confidence            6778899999999999999999999999887662  344444454

The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains

Probab=92.45  E-value=0.57  Score=31.49  Aligned_cols=35  Identities=26%  Similarity=0.526  Sum_probs=30.9

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR  272 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~  272 (282)
                      |+|.+..++|.+.+|+..|.++++++....+...+
T Consensus         1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (71)
T cd04876           1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDD   35 (71)
T ss_pred             CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECC
Confidence            46778899999999999999999999999887654

ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i

>PRK05092 PII uridylyl-transferase; Provisional

Probab=92.42  E-value=0.47  Score=51.12  Aligned_cols=48  Identities=17%  Similarity=0.258  Sum_probs=42.8

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS-DRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~-~~~~~~~~i~a  281 (282)
                      +...|.|.|+.++|+|.+|..+|..+|++|+.|.|.+ .++.++.+|..
T Consensus       731 ~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V  779 (931)
T PRK05092        731 GVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWI  779 (931)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEE
Confidence            5678999999999999999999999999999999977 67887777764

>PRK04374 PII uridylyl-transferase; Provisional

Probab=92.34  E-value=0.45  Score=50.94  Aligned_cols=48  Identities=21%  Similarity=0.331  Sum_probs=43.9

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEe
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS-DRYRSMYMIHA  281 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~-~~~~~~~~i~a  281 (282)
                      +...|.|.|+.++|+|.+|..+|..+||+|+.|.|.+ .++.++.+|.+
T Consensus       689 ~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V  737 (869)
T PRK04374        689 DALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEV  737 (869)
T ss_pred             CeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEE
Confidence            5678999999999999999999999999999999977 68889888875

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

Probab=92.30  E-value=0.11  Score=53.22  Aligned_cols=47  Identities=34%  Similarity=0.541  Sum_probs=40.3

Q ss_pred             cccccHHHHHHHHHHHHHHHHHHhhCCCCC----CCCChhhHHHHHHHHHHH
Q 038084           99 HEMHILTERERRKKMRNMFSNLHALLPHLP----PKADKSTIVDEAVKYIKT  146 (282)
Q Consensus        99 r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~----~K~~k~~iL~~ai~YIk~  146 (282)
                      |++-.-+-|.||.|=|+-|.+|..+|| ++    ..+||++|+.-||.|++.
T Consensus        47 kEkSRdAARsRRsKEn~~FyeLa~~lP-lp~aisshLDkaSimRLtISyLRl   97 (768)
T KOG3558|consen   47 KEKSRDAARSRRSKENEEFYELAKLLP-LPAAISSHLDKASIMRLTISYLRL   97 (768)
T ss_pred             hhhhhhhhhhhcccchHHHHHHHHhCC-CcchhhhhhhhHHHHHHHHHHHHH
Confidence            344456689999999999999999999 44    679999999999999874

>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains

Probab=92.29  E-value=0.71  Score=32.80  Aligned_cols=40  Identities=23%  Similarity=0.359  Sum_probs=33.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEE
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSM  276 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~  276 (282)
                      .|.|..+.+||.|.+|+.+|.+.|++|.+.-+...++..+
T Consensus         3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~~~   42 (66)
T cd04908           3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEFGI   42 (66)
T ss_pred             EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCCCE
Confidence            4677889999999999999999999999998766555433

Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.

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

Probab=92.00  E-value=0.03  Score=57.27  Aligned_cols=72  Identities=19%  Similarity=0.298  Sum_probs=63.0

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC----CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccc
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP----PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGATTV  168 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~----~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~~~~~  168 (282)
                      ++...|+.+|.+||..++-.|..|-+++.+..    .|+.++.-++.++.||..++.+...+.+|...|+.++..+
T Consensus       650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr~~~s~~  725 (856)
T KOG3582|consen  650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKEISEL  725 (856)
T ss_pred             CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhhhHHH
Confidence            68899999999999999999999999997653    5788888999999999999999999998888777665533

>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a

Probab=91.79  E-value=0.73  Score=33.11  Aligned_cols=35  Identities=14%  Similarity=0.336  Sum_probs=31.4

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      .|.|.++.++|+|.+|+.+|.+++++|...+....
T Consensus         2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~   36 (76)
T cd04888           2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIP   36 (76)
T ss_pred             EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCC
Confidence            57888999999999999999999999999987553

a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK04435 hypothetical protein; Provisional

Probab=91.65  E-value=0.87  Score=38.22  Aligned_cols=49  Identities=14%  Similarity=0.235  Sum_probs=40.1

Q ss_pred             EECCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEE
Q 038084          231 MCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD-RYRSMYMI  279 (282)
Q Consensus       231 i~g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~-~~~~~~~i  279 (282)
                      ..|..+.|.+.+..++|+|.+|+.+|.++|++|+..+.+.. ++....+|
T Consensus        65 ~~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~  114 (147)
T PRK04435         65 VKGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTI  114 (147)
T ss_pred             CCCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEE
Confidence            45788999999999999999999999999999999987653 44433333

>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS)

Probab=91.55  E-value=1.1  Score=31.16  Aligned_cols=35  Identities=23%  Similarity=0.413  Sum_probs=31.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      +|.|.+..++|+|.+|+..|.+++++|...+....
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~   36 (72)
T cd04878           2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPT   36 (72)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeec
Confidence            47788899999999999999999999999988764

ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of

>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains

Probab=91.47  E-value=0.65  Score=32.18  Aligned_cols=43  Identities=21%  Similarity=0.400  Sum_probs=34.2

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC--CeEEEEEE
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR--YRSMYMIH  280 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~--~~~~~~i~  280 (282)
                      |.|.-+.++|.|.+++.+|.++|++|.+.......  +...+.|.
T Consensus         2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~   46 (65)
T cd04882           2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFR   46 (65)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEE
Confidence            56778899999999999999999999887765543  45555554

Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH)

Probab=89.94  E-value=1.4  Score=31.95  Aligned_cols=34  Identities=12%  Similarity=0.326  Sum_probs=29.1

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      |.+..+.++|.|.+|+.+|.++|+++++......
T Consensus         2 l~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~   35 (75)
T cd04880           2 LVFSLKNKPGALAKALKVFAERGINLTKIESRPS   35 (75)
T ss_pred             EEEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeec
Confidence            3455577999999999999999999999977664

ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech

>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme

Probab=89.66  E-value=1.9  Score=31.79  Aligned_cols=44  Identities=16%  Similarity=0.299  Sum_probs=34.0

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEEE
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD-RYRSMYMIH  280 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~-~~~~~~~i~  280 (282)
                      .|.+..+.++|.|.+|+..|.++|+++++...... ++...|.|+
T Consensus         3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~   47 (80)
T cd04905           3 SIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFF   47 (80)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEE
Confidence            35566678999999999999999999999987664 234445544

The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi

>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH)

Probab=89.19  E-value=2.7  Score=29.73  Aligned_cols=35  Identities=17%  Similarity=0.362  Sum_probs=30.9

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      .|.|.++.++|.|.+|+..|.++|++|........
T Consensus         3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~   37 (69)
T cd04909           3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI   37 (69)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence            47888999999999999999999999998876554

The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.

>PRK08577 hypothetical protein; Provisional

Probab=88.74  E-value=2  Score=35.29  Aligned_cols=47  Identities=17%  Similarity=0.362  Sum_probs=38.6

Q ss_pred             eEEEEEE----CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 038084          226 NVVVNMC----GDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR  272 (282)
Q Consensus       226 ~V~V~i~----g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~  272 (282)
                      +|.+.-.    .+.+.|.|.+..++|+|.+|+.+|.++++++.+.+..+..
T Consensus        43 ~~~~~~~~~~~k~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~   93 (136)
T PRK08577         43 EIHLEPIALPGKKLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELK   93 (136)
T ss_pred             EEEEEEcCCCCccEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEec
Confidence            5555432    2368899999999999999999999999999998887653

>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB

Probab=88.30  E-value=2.8  Score=29.69  Aligned_cols=44  Identities=27%  Similarity=0.452  Sum_probs=34.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEE
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD--RYRSMYMIH  280 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~--~~~~~~~i~  280 (282)
                      .|.|..+.++|.|.+|+..|.++|++|.+......  .+...+.|+
T Consensus         3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~   48 (72)
T cd04883           3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFR   48 (72)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEE
Confidence            57788899999999999999999999998865443  345445444

This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=87.80  E-value=0.61  Score=45.42  Aligned_cols=45  Identities=31%  Similarity=0.447  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHHHH
Q 038084          104 LTERERRKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKTLQ  148 (282)
Q Consensus       104 ~~ER~RR~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~Lq  148 (282)
                      ..-|.||++=|-.|.+|..++|-..   +..||++|+.-|..|||.-.
T Consensus         7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr~   54 (598)
T KOG3559|consen    7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMRN   54 (598)
T ss_pred             hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHHH
Confidence            3478899999999999999999643   67999999999999998643

>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria

Probab=87.46  E-value=2.5  Score=30.36  Aligned_cols=34  Identities=21%  Similarity=0.323  Sum_probs=30.0

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      +.|.-+.+||.|.+|+..|.++|++|++......
T Consensus         2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~   35 (72)
T cd04884           2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFE   35 (72)
T ss_pred             EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence            5677889999999999999999999999876654

This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH)

Probab=86.90  E-value=1.9  Score=30.45  Aligned_cols=44  Identities=14%  Similarity=0.332  Sum_probs=34.9

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe--eCCeEEEEEEe
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS--DRYRSMYMIHA  281 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~--~~~~~~~~i~a  281 (282)
                      +-|..+.++|.+.+|...|.++|++|.+..+..  .++...+.|..
T Consensus         2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v   47 (73)
T cd04902           2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSV   47 (73)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEe
Confidence            345778899999999999999999998887655  34666666653

The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden

>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]

Probab=86.13  E-value=1.9  Score=45.48  Aligned_cols=54  Identities=17%  Similarity=0.289  Sum_probs=46.3

Q ss_pred             EEEEECCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEe
Q 038084          228 VVNMCGDDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS-DRYRSMYMIHA  281 (282)
Q Consensus       228 ~V~i~g~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~-~~~~~~~~i~a  281 (282)
                      .++.......|.|.|+.+|.+|..|..++...|++|+.|+|-+ .++..+.+|..
T Consensus       677 ~~r~~~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv  731 (867)
T COG2844         677 SVRPHSGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIV  731 (867)
T ss_pred             eecccCCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEE
Confidence            4445567788999999999999999999999999999999966 56778888853

>PRK07334 threonine dehydratase; Provisional

Probab=84.09  E-value=4.1  Score=39.56  Aligned_cols=37  Identities=14%  Similarity=0.231  Sum_probs=34.3

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      .+.|.|.+..|+|+|.+|+.+|.+.+++|.++++...
T Consensus       326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~  362 (403)
T PRK07334        326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRL  362 (403)
T ss_pred             EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEec
Confidence            4889999999999999999999999999999998764

>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional

Probab=83.74  E-value=6.7  Score=29.36  Aligned_cols=44  Identities=11%  Similarity=0.284  Sum_probs=36.1

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEE
Q 038084          236 AQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD--RYRSMYMI  279 (282)
Q Consensus       236 ~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~--~~~~~~~i  279 (282)
                      ..|.|...++||.|..|+.++...|++|.+.++...  .+..-.+|
T Consensus         4 ~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti   49 (76)
T PRK11152          4 HQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIEL   49 (76)
T ss_pred             EEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEE
Confidence            457888899999999999999999999999999884  44444444

>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria

Probab=80.96  E-value=1.4  Score=30.95  Aligned_cols=42  Identities=24%  Similarity=0.336  Sum_probs=31.9

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          238 ISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       238 I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      |-+.+..++|+|.+|+.+|.+.|+++...+....++..+..|
T Consensus         2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~   43 (69)
T cd04901           2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVI   43 (69)
T ss_pred             EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEE
Confidence            345778899999999999999999997776655444444433

The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	282
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	9e-13
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	3e-12
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	1e-11
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	3e-11
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	5e-09
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	3e-08
1a0a_A	63	BHLH, protein (phosphate system positive regulator	1e-05
4f3l_A	361	Mclock, circadian locomoter output cycles protein	7e-04

>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 = 62.0 bits (151), Expect = 9e-13
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQTLEKQ 157
             H + ER+RR +++  F  L   +P L    KA K  I+ +A  YI ++Q   Q L  +
Sbjct: 8   RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISE 67

Query: 158 K 158
           +
Sbjct: 68  E 68

>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 = 60.5 bits (147), Expect = 3e-12
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
           H   E+  R  + +    L  L+     K +KS ++ +A+ YI+ LQH++Q L+++ 
Sbjct: 10  HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN 66

>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 = 58.5 bits (142), Expect = 1e-11
 Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHL-PPKADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
           H   ER+RR  +++ F +L   +P L   KA ++ I+D+A +YI+ ++  + T ++  
Sbjct: 16  HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 73

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

 Score = 57.4 bits (139), Expect = 3e-11
 Identities = 17/60 (28%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHL-PPKADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
             H   ER+RR  +++ F +L   +P L   KA ++ I+D+A +YI+ ++  + T ++  
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 63

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

 Score = 50.8 bits (122), Expect = 5e-09
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 5/56 (8%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHL-----PPKADKSTIVDEAVKYIKTLQHTHQ 152
           H   ER RR K+ N    L  ++P            K  I+ +A  YI+ L+ ++ 
Sbjct: 9   HNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 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 = 49.4 bits (118), Expect = 3e-08
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQTLEKQ 157
             H   E+ RR  +R     L  L+P  P   +    +++ +A  +IK L+ + +    Q
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62

Query: 158 K 158
            
Sbjct: 63  I 63

>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 = 41.3 bits (97), Expect = 1e-05
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPKAD------KSTIVDEAVKYIKTLQHTHQT 153
           H   E+ RR ++      L +L+P    + +      K+T V+ A +YI+ LQ    T
Sbjct: 6   HKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST 63

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

 Score = 39.5 bits (92), Expect = 7e-04
 Identities = 12/59 (20%), Positives = 30/59 (50%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFE 160
              +E++RR +   +   L ++LP    K DKST++ +++ +++  + T    +  +  
Sbjct: 16  RNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIR 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	282
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.7
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.65
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.64
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.61
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.6
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.6
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.57
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.57
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.57
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.49
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.47
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.42
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.4
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	99.07
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.98
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.79
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.73
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.73
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	95.89
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	95.01
2nyi_A	195	Unknown protein; protein structure initiative, PSI	92.67
1u8s_A	192	Glycine cleavage system transcriptional repressor,	90.56
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	83.23

>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=99.70  E-value=2.1e-17  Score=124.93  Aligned_cols=68  Identities=24%  Similarity=0.402  Sum_probs=63.9

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQG  164 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~  164 (282)
                      .+|..|+.+||+||++||+.|.+|++|||+...|++|++||.+||+||++|+.+++.|+.++..|+..
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~~~   72 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA   72 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46789999999999999999999999999977899999999999999999999999999999888643

>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=99.65  E-value=1.9e-16  Score=119.06  Aligned_cols=66  Identities=26%  Similarity=0.461  Sum_probs=62.3

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKV  162 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~  162 (282)
                      .+|..|+.+||+||..||..|..|+++||.++ .|++|++||..||+||+.|+++++.|+.+++.|+
T Consensus        11 ~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A           11 DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999875 6999999999999999999999999999998875

>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=99.64  E-value=2.6e-16  Score=119.11  Aligned_cols=68  Identities=25%  Similarity=0.446  Sum_probs=62.5

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQGA  165 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~~  165 (282)
                      +|..|+..||+||..||+.|..|+++||.++ .|++|++||.+||+||+.|+.+++.|+.+++.|+...
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~~~~   70 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKRQN   70 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999999999864 7999999999999999999999999999998886543

>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=99.61  E-value=1e-15  Score=117.18  Aligned_cols=68  Identities=28%  Similarity=0.386  Sum_probs=61.6

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQG  164 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~  164 (282)
                      .+|..|+..||+||..||+.|..|+++||.++  .|++|++||.+||+||++|+.+.+.|..+++.|...
T Consensus         5 ~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L~~~   74 (88)
T 1nkp_A            5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKR   74 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46889999999999999999999999999874  699999999999999999999999988877766543

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

Probab=99.60  E-value=6.6e-16  Score=113.24  Aligned_cols=61  Identities=21%  Similarity=0.412  Sum_probs=55.3

Q ss_pred             CCCccccccHHHHHHHHHHHHHHHHHHhhCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHH
Q 038084           95 GESEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLE  155 (282)
Q Consensus        95 ~~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~~K~~k~~iL~~ai~YIk~Lq~~~~~L~  155 (282)
                      +..+|.+|+.+||+||++||..|.+|++|||....|++|++||.+||+||+.||.++.=|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            3457899999999999999999999999999866799999999999999999999876553

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

Probab=99.60  E-value=2.5e-15  Score=112.97  Aligned_cols=66  Identities=21%  Similarity=0.284  Sum_probs=61.1

Q ss_pred             cccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 038084           99 HEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQG  164 (282)
Q Consensus        99 r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~  164 (282)
                      |..||..||+||..||+.|..|+++||.++  .|.+|++||.+|++||+.|+++.+.|..+++.|+..
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~~e   69 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQRE   69 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999764  689999999999999999999999999999887644

>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=99.57  E-value=6.5e-16  Score=111.63  Aligned_cols=56  Identities=29%  Similarity=0.487  Sum_probs=51.1

Q ss_pred             CCccccccHHHHHHHHHHHHHHHHHHhhCCCCC-----CCCChhhHHHHHHHHHHHHHHHH
Q 038084           96 ESEHEMHILTERERRKKMRNMFSNLHALLPHLP-----PKADKSTIVDEAVKYIKTLQHTH  151 (282)
Q Consensus        96 ~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-----~K~~k~~iL~~ai~YIk~Lq~~~  151 (282)
                      ..+|..|+.+||+||++||+.|.+|++|||.+.     .|++|++||.+||+||++||++.
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            347889999999999999999999999999875     27899999999999999999764

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

Probab=99.57  E-value=3.7e-15  Score=119.91  Aligned_cols=63  Identities=29%  Similarity=0.447  Sum_probs=53.7

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFE  160 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~  160 (282)
                      ++.+|+.+||+||++||+.|.+|++|||.+.   .|++|++||.+||+||++||.+++.|..+..+
T Consensus        27 kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~~   92 (118)
T 4ati_A           27 KKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENR   92 (118)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5689999999999999999999999999873   48899999999999999999999999876543

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

Probab=99.57  E-value=9.1e-16  Score=110.29  Aligned_cols=54  Identities=30%  Similarity=0.503  Sum_probs=49.3

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCC------CCCCChhhHHHHHHHHHHHHHHHH
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHL------PPKADKSTIVDEAVKYIKTLQHTH  151 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~------~~K~~k~~iL~~ai~YIk~Lq~~~  151 (282)
                      +|.+|+.+||+||++||..|.+|++|||.+      ..|.+|++||++||+||+.||+++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            578999999999999999999999999965      257889999999999999999765

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

Probab=99.49  E-value=1.5e-14  Score=107.66  Aligned_cols=60  Identities=27%  Similarity=0.367  Sum_probs=48.6

Q ss_pred             CCccccccHHHHHHHHHHHHHHHHHHhhCCC-C-CCCC-ChhhHHHHHHHHHHHHHHHHHHHH
Q 038084           96 ESEHEMHILTERERRKKMRNMFSNLHALLPH-L-PPKA-DKSTIVDEAVKYIKTLQHTHQTLE  155 (282)
Q Consensus        96 ~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~-~-~~K~-~k~~iL~~ai~YIk~Lq~~~~~L~  155 (282)
                      ..+|..|+..||+||..||+.|.+|+.+||. . ..|. +|++||..||+||+.|++++++++
T Consensus         3 ~~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            3 ADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hhHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            4578999999999999999999999999994 2 2565 799999999999999999888764

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

Probab=99.47  E-value=1.1e-14  Score=107.57  Aligned_cols=53  Identities=36%  Similarity=0.505  Sum_probs=49.0

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKTLQH  149 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~Lq~  149 (282)
                      .+|..|+.+||+||++||+.|.+|++|||.+.   .|+||++||+.||+||+.|+.
T Consensus         8 ~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            8 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            46799999999999999999999999999753   799999999999999999974

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

Probab=99.42  E-value=1.8e-13  Score=97.24  Aligned_cols=56  Identities=23%  Similarity=0.270  Sum_probs=51.2

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQ  152 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~~  152 (282)
                      ++|..||..||+|+..||+.|..||.+||..+  .|++|++||..||+||..|++.++
T Consensus         1 ~rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            1 SRRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             CccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            36788999999999999999999999999875  699999999999999999998653

>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=99.40  E-value=2.1e-13  Score=99.30  Aligned_cols=55  Identities=25%  Similarity=0.394  Sum_probs=51.1

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC-CCCChhhHHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHTH  151 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-~K~~k~~iL~~ai~YIk~Lq~~~  151 (282)
                      .+|..|+..||+|+..||+.|..||.+||..+ .|++|++||..||+||..|++.+
T Consensus        11 ~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A           11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             hhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            47889999999999999999999999999865 69999999999999999999765

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

Probab=99.07  E-value=2.8e-11  Score=87.29  Aligned_cols=46  Identities=24%  Similarity=0.408  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHH
Q 038084          104 LTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQH  149 (282)
Q Consensus       104 ~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~  149 (282)
                      ..||+|+..||+.|..||.+||..+  .|++|++||+.||+||..||.
T Consensus        20 erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           20 EEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            4489999999999999999999876  699999999999999999984

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

Probab=98.98  E-value=4.3e-10  Score=105.40  Aligned_cols=54  Identities=22%  Similarity=0.453  Sum_probs=43.1

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCCCCCChhhHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHT  150 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~~K~~k~~iL~~ai~YIk~Lq~~  150 (282)
                      .+|.+|+.+||+||++||..|.+|++|||....|+||++||+.||+||+.|+..
T Consensus        11 ~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           11 AKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             --------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhh
Confidence            466889999999999999999999999995558999999999999999999854

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

Probab=98.79  E-value=3.3e-09  Score=100.44  Aligned_cols=54  Identities=35%  Similarity=0.533  Sum_probs=48.9

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCC---CCCCCChhhHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPH---LPPKADKSTIVDEAVKYIKTLQHT  150 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~---~~~K~~k~~iL~~ai~YIk~Lq~~  150 (282)
                      .+|.+|+.+||+||++||..|.+|+.|||.   ...|+||++||+.||+|||.|+..
T Consensus        12 ~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           12 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             hhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            467999999999999999999999999994   237999999999999999999853

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

Probab=98.73  E-value=2.2e-08  Score=77.20  Aligned_cols=47  Identities=28%  Similarity=0.455  Sum_probs=42.6

Q ss_pred             HHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHHH
Q 038084          106 ERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQ  152 (282)
Q Consensus       106 ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~~  152 (282)
                      ||.|-..||+.|..||.+||..+  .|++|.++|..||+||..|++.++
T Consensus        33 ~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~   81 (97)
T 4aya_A           33 PMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALD   81 (97)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHh
Confidence            68888999999999999999875  699999999999999999997553

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

Probab=98.73  E-value=2.9e-08  Score=74.32  Aligned_cols=52  Identities=25%  Similarity=0.408  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHHhhCCCCC---CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038084          110 RKKMRNMFSNLHALLPHLP---PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEK  161 (282)
Q Consensus       110 R~~in~~~~~Lr~lvP~~~---~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l  161 (282)
                      |..||++|.+|..|||...   .|..|.+||..||+||++||+.++.+.++..++
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r~   58 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENRQ   58 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999999999753   589999999999999999999999888766544

>1zpv_A ACT domain protein; structural genomics, PSI, protein structure INIT midwest center for structural genomics, MCSG, unknown funct; 1.90A {Streptococcus pneumoniae} SCOP: d.58.18.7

Probab=95.89  E-value=0.041  Score=40.29  Aligned_cols=45  Identities=16%  Similarity=0.124  Sum_probs=38.3

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      .+.|.|.|+.+||+|.+|..+|-++|++|++.+.....+.....|
T Consensus         5 ~~~l~v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i   49 (91)
T 1zpv_A            5 KAIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMA   49 (91)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEE
T ss_pred             eEEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEE
Confidence            467999999999999999999999999999999988765444333

>2ko1_A CTR148A, GTP pyrophosphokinase; homodimer, alpha+beta, transferase, structural genomics, PSI-2, protein structure initiative; NMR {Chlorobaculum tepidum} PDB: 3ibw_A

Probab=95.01  E-value=0.076  Score=38.28  Aligned_cols=39  Identities=15%  Similarity=0.213  Sum_probs=35.3

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCC
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRY  273 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~  273 (282)
                      .+.|.|.++.++|+|.+|..+|.+.|++|.++++...++
T Consensus         5 ~~~l~v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~   43 (88)
T 2ko1_A            5 LAGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDG   43 (88)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSS
T ss_pred             EEEEEEEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCC
Confidence            456889999999999999999999999999999987655

>2nyi_A Unknown protein; protein structure initiative, PSI, center for eukaryotic structural genomics, CESG, structural genomics; 1.80A {Galdieria sulphuraria}

Probab=92.67  E-value=0.31  Score=41.19  Aligned_cols=39  Identities=15%  Similarity=0.308  Sum_probs=35.9

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR  272 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~  272 (282)
                      ..+.|.|.|+.++|++..|..+|-++|++|+.+...+.+
T Consensus        92 ~~~iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~  130 (195)
T 2nyi_A           92 REYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLP  130 (195)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEE
T ss_pred             cEEEEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecc
Confidence            457899999999999999999999999999999998864

>1u8s_A Glycine cleavage system transcriptional repressor, putative; structural genomics, protein structure initiative (PSI), domain swapping; 2.45A {Vibrio cholerae} SCOP: d.58.18.5 d.58.18.5

Probab=90.56  E-value=0.63  Score=38.86  Aligned_cols=38  Identities=16%  Similarity=0.185  Sum_probs=34.6

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR  272 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~  272 (282)
                      .+.|.|.|+.++|++..|..+|-++|++|..+...+.+
T Consensus        93 ~~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~  130 (192)
T 1u8s_A           93 TVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTIS  130 (192)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC
T ss_pred             eEEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhccc
Confidence            46689999999999999999999999999999988764

>3o1l_A Formyltetrahydrofolate deformylase; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 2.20A {Pseudomonas syringae PV}

Probab=83.23  E-value=3.8  Score=37.18  Aligned_cols=37  Identities=22%  Similarity=0.355  Sum_probs=34.2

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSD  271 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~  271 (282)
                      .+.|.|.|+.|+|+...|...|-++|++|+.++-...
T Consensus        22 ~~iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d   58 (302)
T 3o1l_A           22 TFRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSD   58 (302)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEE
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEec
Confidence            4679999999999999999999999999999998864

---

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	282
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	2e-13
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	7e-13
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	1e-12
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	7e-12
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	6e-11
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	1e-10
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	4e-10
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	6e-10

>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 = 62.3 bits (151), Expect = 2e-13
 Identities = 16/57 (28%), Positives = 31/57 (54%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
           H   E+  R  + +    L  L+     K +KS ++ +A+ YI+ LQH++Q L+++ 
Sbjct: 10  HNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQEN 66

>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 = 60.7 bits (147), Expect = 7e-13
 Identities = 17/60 (28%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
             H   ER+RR  +++ F +L   +P L   KA ++ I+D+A +YI+ ++  + T ++  
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDI 63

>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 = 59.9 bits (145), Expect = 1e-12
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHLPP--KADKSTIVDEAVKYIKTLQHTHQTLEKQ 157
             H   E+ RR  +R     L  L+P  P   +    +++ +A  +IK L+ + +    Q
Sbjct: 3   STHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ 62

Query: 158 K 158
            
Sbjct: 63  I 63

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

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

 Score = 58.4 bits (141), Expect = 7e-12
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 102 HILTERERRKKMRNMFSNLHALLPHLPP--KADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
           H + ER+RR +++  F  L   +P L    KA K  I+ +A  YI ++Q   Q L  ++
Sbjct: 10  HNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEE 68

>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 = 54.7 bits (132), Expect = 6e-11
 Identities = 13/49 (26%), Positives = 23/49 (46%)

Query: 110 RKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQK 158
           R  + +    L  L+     K  KS ++ +A+ YIK LQ  +  L ++ 
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQEN 49

>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 = 54.0 bits (130), Expect = 1e-10
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 5/58 (8%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHL-----PPKADKSTIVDEAVKYIKTLQHTHQ 152
             H   ER RR K+ N    L  ++P            K  I+ +A  YI+ L+ ++ 
Sbjct: 7   AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH 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 = 53.0 bits (127), Expect = 4e-10
 Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 90  KAVSGGESEHEMHILTERERRKKMRNMFSNLHALLPHLPPK-ADKSTIVDEAVKYIKTLQ 148
           K  +      +   + ER R  K+   F  L       P +   K  I+  A++YI+ LQ
Sbjct: 4   KRKTTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQ 63

Query: 149 HTHQ 152
              +
Sbjct: 64  ALLR 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 = 52.2 bits (125), Expect = 6e-10
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 6/60 (10%)

Query: 100 EMHILTERERRKKMRNMFSNLHALLPHLP------PKADKSTIVDEAVKYIKTLQHTHQT 153
           E H   E+ RR ++      L +L+P             K+T V+ A +YI+ LQ    T
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	282
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.66
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.61
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.59
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.57
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.56
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.5
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.47
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.27
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	96.15
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	95.06
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	94.57
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	93.14
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	93.06
d2fgca2	78	Acetolactate synthase small subunit, IlvH {Thermot	83.94
d1sc6a3	84	Phosphoglycerate dehydrogenase, regulatory (C-term	80.39

>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=99.66  E-value=6.2e-17  Score=119.94  Aligned_cols=67  Identities=24%  Similarity=0.406  Sum_probs=63.0

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQ  163 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~  163 (282)
                      .+|..|+.+||+||++||+.|..|++|||+...|++|++||.+||+||+.|+.+++.|..++..|+.
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk~   71 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRT   71 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999998789999999999999999999999999999987754

>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=99.62  E-value=4.1e-16  Score=115.06  Aligned_cols=66  Identities=21%  Similarity=0.284  Sum_probs=60.7

Q ss_pred             cccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 038084           99 HEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQG  164 (282)
Q Consensus        99 r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~  164 (282)
                      |..|+.+||+||++||+.|..|+++||.++  .|++|++||..||+||+.|+.+++.|..+++.|...
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~~~   69 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQRE   69 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999999999999999864  689999999999999999999999999998877543

>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=99.61  E-value=4.2e-16  Score=116.07  Aligned_cols=66  Identities=26%  Similarity=0.466  Sum_probs=61.3

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCCC-CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQ  163 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~  163 (282)
                      +|..|+.+||+||.+||+.|..|+++||+.+ .|++|++||..||+||+.|+++++.|..+.+.+..
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~   68 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLKR   68 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6789999999999999999999999999765 68999999999999999999999999998887754

>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=99.59  E-value=8.2e-16  Score=115.68  Aligned_cols=68  Identities=28%  Similarity=0.386  Sum_probs=61.7

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP--PKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQG  164 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~--~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~~  164 (282)
                      .+|..|+.+||+||+.||+.|..|+++||+++  .|.+|++||..||+||+.|+++++.|..+++.+...
T Consensus         5 ~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~~~   74 (88)
T d1nkpa_           5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLRKR   74 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            36789999999999999999999999999764  589999999999999999999999999988877543

>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=99.57  E-value=8.2e-16  Score=108.81  Aligned_cols=54  Identities=30%  Similarity=0.503  Sum_probs=49.2

Q ss_pred             ccccccHHHHHHHHHHHHHHHHHHhhCCCC------CCCCChhhHHHHHHHHHHHHHHHH
Q 038084           98 EHEMHILTERERRKKMRNMFSNLHALLPHL------PPKADKSTIVDEAVKYIKTLQHTH  151 (282)
Q Consensus        98 ~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~------~~K~~k~~iL~~ai~YIk~Lq~~~  151 (282)
                      +|..|+.+||+||++||+.|..|++|||++      ..|++|++||++||+||++||+++
T Consensus         2 rR~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            578999999999999999999999999952      379999999999999999999764

>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=99.56  E-value=7.6e-16  Score=110.62  Aligned_cols=56  Identities=25%  Similarity=0.396  Sum_probs=51.6

Q ss_pred             CccccccHHHHHHHHHHHHHHHHHHhhCCCCC-CCCChhhHHHHHHHHHHHHHHHHH
Q 038084           97 SEHEMHILTERERRKKMRNMFSNLHALLPHLP-PKADKSTIVDEAVKYIKTLQHTHQ  152 (282)
Q Consensus        97 ~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-~K~~k~~iL~~ai~YIk~Lq~~~~  152 (282)
                      .+|..|+..||+||.+||+.|..|++|||.++ .|++|++||..||+||++||+.++
T Consensus        11 ~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_          11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            46789999999999999999999999999975 689999999999999999997654

>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=99.50  E-value=2.6e-15  Score=106.79  Aligned_cols=56  Identities=29%  Similarity=0.487  Sum_probs=50.5

Q ss_pred             CCccccccHHHHHHHHHHHHHHHHHHhhCCCCC-----CCCChhhHHHHHHHHHHHHHHHH
Q 038084           96 ESEHEMHILTERERRKKMRNMFSNLHALLPHLP-----PKADKSTIVDEAVKYIKTLQHTH  151 (282)
Q Consensus        96 ~~~r~~h~~~ER~RR~~in~~~~~Lr~lvP~~~-----~K~~k~~iL~~ai~YIk~Lq~~~  151 (282)
                      ..+|..|+.+||+||++||+.|..|++|||.+.     .|++|++||..||+||+.||++.
T Consensus         3 ~~rR~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            346789999999999999999999999999763     48999999999999999998754

>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=99.47  E-value=1.2e-14  Score=102.05  Aligned_cols=54  Identities=24%  Similarity=0.362  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHHhhCCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 038084          110 RKKMRNMFSNLHALLPHLPPKADKSTIVDEAVKYIKTLQHTHQTLEKQKFEKVQ  163 (282)
Q Consensus       110 R~~in~~~~~Lr~lvP~~~~K~~k~~iL~~ai~YIk~Lq~~~~~L~~~~~~l~~  163 (282)
                      |++||++|..|+++||++..|++|++||.+||+||+.|+.+++.|+.++..|+.
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~~   54 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLKL   54 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999998789999999999999999999999999999988753

>d1u8sa1 d.58.18.5 (A:2-87) putative transcriptional repressor VC2159 {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Glycine cleavage system transcriptional repressor
domain: putative transcriptional repressor VC2159
species: Vibrio cholerae [TaxId: 666]

Probab=96.27  E-value=0.008  Score=42.85  Aligned_cols=47  Identities=6%  Similarity=0.248  Sum_probs=41.8

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEE
Q 038084          234 DDAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIH  280 (282)
Q Consensus       234 ~~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~  280 (282)
                      ..+.|.+.|+.|||++..|..+|-++|++|+.++....++...+.+.
T Consensus         4 ~~~vitv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~   50 (86)
T d1u8sa1           4 QHLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLML   50 (86)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEE
T ss_pred             cEEEEEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEE
Confidence            35779999999999999999999999999999999998887766654

>d1zpva1 d.58.18.7 (A:1-83) UPF0237 protein SP0238 {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: SP0238-like
domain: UPF0237 protein SP0238
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=96.15  E-value=0.013  Score=41.30  Aligned_cols=44  Identities=16%  Similarity=0.123  Sum_probs=38.1

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          236 AQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       236 ~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      +.|.|.|+.|||++..|..+|-++|++|+.++-...++..+..+
T Consensus         3 ~vitv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~   46 (83)
T d1zpva1           3 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMA   46 (83)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEE
Confidence            56899999999999999999999999999999888766544443

>d2f06a2 d.58.18.11 (A:1-70) Hypothetical protein BT0572 {Bacteroides thetaiotaomicron [TaxId: 818]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: BT0572-like
domain: Hypothetical protein BT0572
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=95.06  E-value=0.043  Score=37.71  Aligned_cols=43  Identities=21%  Similarity=0.280  Sum_probs=38.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEE
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMI  279 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i  279 (282)
                      +|.|..+.+||.|.+|..+|.+.|++|...++....+..+.-|
T Consensus         5 QisV~~eNkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Ri   47 (70)
T d2f06a2           5 QLSIFLENKSGRLTEVTEVLAKENINLSALCIAENADFGILRG   47 (70)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEE
Confidence            5889999999999999999999999999999988776665544

>d2f06a1 d.58.18.11 (A:71-141) Hypothetical protein BT0572 {Bacteroides thetaiotaomicron [TaxId: 818]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: BT0572-like
domain: Hypothetical protein BT0572
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=94.57  E-value=0.07  Score=36.52  Aligned_cols=45  Identities=13%  Similarity=0.226  Sum_probs=39.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRYRSMYMIHA  281 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~~~~~~i~a  281 (282)
                      .|.|..+.+||.|.+|+++|.+.|++|....+....+..+..|.+
T Consensus         1 ViaV~v~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl~v   45 (71)
T d2f06a1           1 VVGISCPNVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVIRP   45 (71)
T ss_dssp             EEEEEEESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEE
T ss_pred             CEEEEecCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEEEE
Confidence            367888999999999999999999999999988877877766654

>d1u8sa2 d.58.18.5 (A:88-180) putative transcriptional repressor VC2159 {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Glycine cleavage system transcriptional repressor
domain: putative transcriptional repressor VC2159
species: Vibrio cholerae [TaxId: 666]

Probab=93.14  E-value=0.092  Score=37.52  Aligned_cols=36  Identities=17%  Similarity=0.232  Sum_probs=32.6

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS  270 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~  270 (282)
                      .+.|.|.|+.|||++..|...|-++|++|...+..+
T Consensus         6 tv~v~v~g~DrpGIV~~it~~la~~~~nI~~l~t~~   41 (93)
T d1u8sa2           6 TVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQT   41 (93)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEE
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHHcCCCchhhhccc
Confidence            456889999999999999999999999999988765

>d1y7pa2 d.58.18.12 (A:2-78) Hypothetical protein AF1403, N-terminal domain {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: AF1403 N-terminal domain-like
domain: Hypothetical protein AF1403, N-terminal domain
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.06  E-value=0.04  Score=38.37  Aligned_cols=34  Identities=15%  Similarity=0.214  Sum_probs=27.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe
Q 038084          237 QISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSS  270 (282)
Q Consensus       237 ~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~  270 (282)
                      -|+|.|..|+|+|.+|+.++-+++++|++++...
T Consensus         3 ~i~i~~~Dr~GlL~di~~~ia~~~~NI~~i~~~~   36 (77)
T d1y7pa2           3 GLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFL   36 (77)
T ss_dssp             EEEEEEECCTTHHHHHHHHCC----CEEEEEEEE
T ss_pred             eEEEEEecCCChHHHHHHHHHHcCCCeEEEEeec
Confidence            3889999999999999999999999999999776

>d2fgca2 d.58.18.6 (A:27-104) Acetolactate synthase small subunit, IlvH {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: IlvH-like
domain: Acetolactate synthase small subunit, IlvH
species: Thermotoga maritima [TaxId: 2336]

Probab=83.94  E-value=2.1  Score=29.45  Aligned_cols=46  Identities=17%  Similarity=0.325  Sum_probs=37.2

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC--CeEEEEEE
Q 038084          235 DAQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDR--YRSMYMIH  280 (282)
Q Consensus       235 ~~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~--~~~~~~i~  280 (282)
                      ...|.+....+||+|.+|..++...|+.+.+.++....  +..-.+|.
T Consensus         3 ~~tisvlv~n~pGvL~Ri~~lF~rRg~NI~SL~v~~te~~~iSR~tiv   50 (78)
T d2fgca2           3 EHLVSMLVHNKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIM   50 (78)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEE
T ss_pred             eEEEEEEEeCCCcHHHHHHHHHhhCCcceEEEEEeecCCCCeEEEEEE
Confidence            35688899999999999999999999999999987743  44444443

>d1sc6a3 d.58.18.1 (A:327-410) Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
domain: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
species: Escherichia coli [TaxId: 562]

Probab=80.39  E-value=2  Score=29.49  Aligned_cols=38  Identities=13%  Similarity=0.340  Sum_probs=32.4

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCC
Q 038084          236 AQISVCSPRKPGLLTTIFYILEKHNLDVVSAHVSSDRY  273 (282)
Q Consensus       236 ~~I~I~c~~r~glL~~Il~aLe~lgLdVv~a~vs~~~~  273 (282)
                      ..|.|.-..+||+|.+|..+|-+.|+.|.+......++
T Consensus        12 ~rl~i~~~d~PGvla~I~~~l~~~~iNI~~~~~~~~~~   49 (84)
T d1sc6a3          12 RRLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQ   49 (84)
T ss_dssp             EEEEEEEESCTTHHHHHHHHHHHTTCEEEEEEEEECSS
T ss_pred             eEEEEEeCCcCCHHHHHHHHHHHcCCCHHHhccccCCC
Confidence            34666668899999999999999999999998887654