Citrus Sinensis ID: 042904

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320
Protein Sequence
MGGVGDDTLSEYFFDEGETNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKATNNNSVEPSPCSSSTSSIDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKVTKL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccEEEccccEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEccccEEEEEEEEEEEEc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHcHcccccccccccHHHHHHcHHccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccEEEEEEEEcccEEEEEEcccccHHHHHHHHHHHHcccEEEEEEEEEcccEEEEEEEEEEEEc
Coil and Loop (DISEMBL)
mggvgddtlseyffdegetnlaedDLFAIFEsldsvtpldeAATAVSEARLVsqkstsssilqesdetdqltetlpknkrqktaatsavnssdeanntdgqqRMSHITVERNRRKQMNENLSVLRSlmpcfyvkrgdqasiIGGVVDYINELQQVLQSLEAKKQRKVYCEvlsprlvssprpsplsprkpplsprlnlpisprtpqpgspykprlqqqgylsptkatnnnsvepspcssstssIDSINELVANsksaiadvevkfsgpnlllktvspripgQAVKIISALEDLAFEILHVNIstvdetmhnsftikvtkl
Flexible Loop (DISEMBL)
MGGVGDDTLSEYFFDEGETNLAEDDLFAIFESLDSVTPLDEAATAVsearlvsqkstsssilqesdetdqltetlpknkrqktaatsavnssdeanntdgqqrmshitvernrrkQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLsprlvssprpsplsprkpplsprlnlPISPRTPQPGSPYKPRLQQQGYLsptkatnnnsvepspcssSTSSIDSINELVANSKSAIADVEVKFSgpnlllktvspripGQAVKIISALEDLAFEILHVNistvdetmhnsftikvtkl
Low Complexity Region (SEG)
MGGVGDDTLSEYFFDEGETNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVlsprlvssprpsplsprkpplsprlnlpISPRTPQPGSPYKPRLQQQGYLSPTKATnnnsvepspcssstssidsineLVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKVTKL
Disordered region (IsUnstruct)
**********EYFFDEGETNLAEDDLFAIFESLDSV************************************************************************************LSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVL************************************************************************************AIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTI*****
Disordered Region (DISOPRED)
*******TLSEYFFDEGETNLAEDDLFA**********************************************************************************RNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQ***************************************************************************************************NSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKVTKL
Disordered Region (DISEMBL)
MGGVGDDTLSEYFFDEGETNLAEDDLFAIFESLDSVTPLDEAA**********************************************************QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLSPRL***************LSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKA*****************IDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKVTKL
Disordered Region (DISPRO)
**GVGDDTLSEYFFDEGETNLAEDDLFAIFESLDSVT*******************************************************************SHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQR*******************************************************************************DSINEL**NSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKVTKL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGGVGDDTLSEYFFDEGETNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGxxxxxxxxxxxxxxxxxxxxxKVYCEVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKATNNNSVEPSPCSSSTSSIDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKVTKL
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	320	2.2.26 [Sep-21-2011]
Q700C7	364	Transcription factor SPEE	yes	no	0.953	0.837	0.534	2e-75
Q9M8K6	202	Transcription factor MUTE	no	no	0.506	0.801	0.404	4e-38
Q56YJ8	414	Transcription factor FAMA	no	no	0.653	0.504	0.384	4e-36
Q9SK91	304	Transcription factor bHLH	no	no	0.2	0.210	0.671	1e-20
Q9M128	315	Transcription factor bHLH	no	no	0.215	0.219	0.630	1e-20
Q9C7T4	320	Transcription factor bHLH	no	no	0.184	0.184	0.694	1e-19
Q56XR0	327	Transcription factor bHLH	no	no	0.215	0.211	0.602	7e-19
O81037	371	Transcription factor bHLH	no	no	0.181	0.156	0.619	1e-17
Q700E4	358	Transcription factor bHLH	no	no	0.196	0.175	0.571	3e-17
Q9FKQ6	296	Transcription factor bHLH	no	no	0.190	0.206	0.622	7e-15

>sp|Q700C7|SPCH_ARATH Transcription factor SPEECHLESS OS=Arabidopsis thaliana GN=SPCH PE=1 SV=1

 Score =  282 bits (722), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 180/337 (53%), Positives = 208/337 (61%), Gaps = 32/337 (9%)

Query: 13  FFDEGE---TNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESDETD 69
           F +E E   T+LA DDLFAI ESL+    +   A +  +    S K        E+    
Sbjct: 8   FLEECEFVDTSLAGDDLFAILESLEGAGEISPTAASTPKDGTTSSKELVKDQDYENSSPK 67

Query: 70  QLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMP 129
           +  + L   K +          ++E N  DGQQ+MSH+TVERNRRKQMNE+L+VLRSLMP
Sbjct: 68  RKKQRLETRKEEDEEEEDGDGEAEEDNKQDGQQKMSHVTVERNRRKQMNEHLTVLRSLMP 127

Query: 130 CFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVL--SPRLVSSPRPSPLSP 187
           CFYVKRGDQASIIGGVV+YI+ELQQVLQSLEAKKQRK Y EVL         P P  LSP
Sbjct: 128 CFYVKRGDQASIIGGVVEYISELQQVLQSLEAKKQRKTYAEVLSPRVVPSPRPSPPVLSP 187

Query: 188 RKPPLSPRLNL----------PISPRTPQPGSPYKP-----------------RLQQQGY 220
           RKPPLSPR+N           PISPRTPQP SPY+                   L     
Sbjct: 188 RKPPLSPRINHHQIHHHLLLPPISPRTPQPTSPYRAIPPQLPLIPQPPLRSYSSLASCSS 247

Query: 221 LSPTKATNNNSVEPSPCSSSTSSIDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIP 280
           L      +  S   SP  SS      INELVANSKSA+ADVEVKFSG N+LLKTVS +IP
Sbjct: 248 LGDPPPYSPASSSSSPSVSSNHESSVINELVANSKSALADVEVKFSGANVLLKTVSHKIP 307

Query: 281 GQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV 317
           GQ +KII+ALEDLA EIL VNI+TVDETM NSFTIK+
Sbjct: 308 GQVMKIIAALEDLALEILQVNINTVDETMLNSFTIKI 344

Transcription factor. Together with FMA and MUTE, regulates the stomata formation. Required for the initiation and the formation of stomata, by promoting the first asymmetric cell divisions.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  158 bits (400), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 126/225 (56%), Gaps = 63/225 (28%)

Query: 104 MSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKK 163
           MSHI VERNRR+QMNE+L  LRSL PCFY+KRGDQASIIGGV+++I ELQQ++Q LE+KK
Sbjct: 1   MSHIAVERNRRRQMNEHLKSLRSLTPCFYIKRGDQASIIGGVIEFIKELQQLVQVLESKK 60

Query: 164 QRKVYCEVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSP 223
           +RK                             LN        +P  PY            
Sbjct: 61  RRKT----------------------------LN--------RPSFPY------------ 72

Query: 224 TKATNNNSVEPSPCSSSTSSI-----------DSINELVANSKSAIADVEVKFSGPNLLL 272
               ++ ++EPS   ++T+ +            +  E+ A   S  A+VE K SG N++L
Sbjct: 73  ----DHQTIEPSSLGAATTRVPFSRIENVMTTSTFKEVGACCNSPHANVEAKISGSNVVL 128

Query: 273 KTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV 317
           + VS RI GQ VKIIS LE L+F++LH+NIS+++ET+   F +K+
Sbjct: 129 RVVSRRIVGQLVKIISVLEKLSFQVLHLNISSMEETVLYFFVVKI 173

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

 Score =  152 bits (383), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 100/260 (38%), Positives = 142/260 (54%), Gaps = 51/260 (19%)

Query: 63  QESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLS 122
           +E  E   +T+   K+KR K A TS  +   E+      QRM+HI VERNRRKQMNE+L 
Sbjct: 163 EEDRENKNVTKKEVKSKR-KRARTSKTSEEVES------QRMTHIAVERNRRKQMNEHLR 215

Query: 123 VLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCE----VLSPRLVS 178
           VLRSLMP  YV+RGDQASIIGG ++++ EL+Q+LQ LE++K+R++  E    + +    S
Sbjct: 216 VLRSLMPGSYVQRGDQASIIGGAIEFVRELEQLLQCLESQKRRRILGETGRDMTTTTTSS 275

Query: 179 SPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKATNNNSVEPSPCS 238
           S   + ++ +  PL    N+                L+  G L    A N          
Sbjct: 276 SSPITTVANQAQPLIITGNV--------------TELEGGGGLREETAEN---------- 311

Query: 239 SSTSSIDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEIL 298
                           KS +ADVEVK  G + ++K +S R PGQ +K I+ALEDL   IL
Sbjct: 312 ----------------KSCLADVEVKLLGFDAMIKILSRRRPGQLIKTIAALEDLHLSIL 355

Query: 299 HVNISTVDETMHNSFTIKVT 318
           H NI+T+++T+  SF +K+T
Sbjct: 356 HTNITTMEQTVLYSFNVKIT 375

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|Q9SK91|BH094_ARATH Transcription factor bHLH94 OS=Arabidopsis thaliana GN=BHLH94 PE=2 SV=2

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 43/64 (67%), Positives = 54/64 (84%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEA 161
           QRM+HI VERNRRKQMNE L+VLRSLMP  Y +RGDQASI+GG ++Y+ EL+ +LQS+E 
Sbjct: 113 QRMTHIAVERNRRKQMNEYLAVLRSLMPSSYAQRGDQASIVGGAINYVKELEHILQSMEP 172

Query: 162 KKQR 165
           K+ R
Sbjct: 173 KRTR 176

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M128|BH057_ARATH Transcription factor bHLH57 OS=Arabidopsis thaliana GN=BHLH57 PE=2 SV=1

 Score =  100 bits (249), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 46/73 (63%), Positives = 61/73 (83%), Gaps = 4/73 (5%)

Query: 93  DEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINEL 152
           DE  N    QRM+HI VERNRR+QMNE+L+ LRSLMP  +++RGDQASI+GG +D+I EL
Sbjct: 108 DEVEN----QRMTHIAVERNRRRQMNEHLNSLRSLMPPSFLQRGDQASIVGGAIDFIKEL 163

Query: 153 QQVLQSLEAKKQR 165
           +Q+LQSLEA+K++
Sbjct: 164 EQLLQSLEAEKRK 176

Arabidopsis thaliana (taxid: 3702)

>sp|Q9C7T4|BH096_ARATH Transcription factor bHLH96 OS=Arabidopsis thaliana GN=BHLH96 PE=2 SV=1

 Score = 97.4 bits (241), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 41/59 (69%), Positives = 51/59 (86%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLE 160
           QRM+HI VERNRRKQMNE L+VLRSLMP +Y +RGDQASI+GG ++Y+ EL+  LQS+E
Sbjct: 123 QRMTHIAVERNRRKQMNEYLAVLRSLMPPYYAQRGDQASIVGGAINYLKELEHHLQSME 181

Arabidopsis thaliana (taxid: 3702)

>sp|Q56XR0|BH071_ARATH Transcription factor bHLH71 OS=Arabidopsis thaliana GN=BHLH71 PE=1 SV=1

 Score = 94.7 bits (234), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 44/73 (60%), Positives = 56/73 (76%), Gaps = 4/73 (5%)

Query: 93  DEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINEL 152
           +EA N    QRM+HI VERNRR+QMN++LSVLRSLMP  +  +GDQASI+GG +D+I EL
Sbjct: 81  EEAEN----QRMTHIAVERNRRRQMNQHLSVLRSLMPQPFAHKGDQASIVGGAIDFIKEL 136

Query: 153 QQVLQSLEAKKQR 165
           +  L SLEA+K  
Sbjct: 137 EHKLLSLEAQKHH 149

Transcription factor. May be involved in the differentiation of stomatal guard cells.

Arabidopsis thaliana (taxid: 3702)

>sp|O81037|BH070_ARATH Transcription factor bHLH70 OS=Arabidopsis thaliana GN=BHLH70 PE=2 SV=1

 Score = 90.9 bits (224), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 39/63 (61%), Positives = 54/63 (85%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEA 161
           QRM+HI VERNRR+QMN +L+ LRS++P  Y++RGDQASI+GG +D++  L+Q LQSLEA
Sbjct: 191 QRMTHIAVERNRRRQMNVHLNSLRSIIPSSYIQRGDQASIVGGAIDFVKILEQQLQSLEA 250

Query: 162 KKQ 164
           +K+
Sbjct: 251 QKR 253

Arabidopsis thaliana (taxid: 3702)

>sp|Q700E4|BH067_ARATH Transcription factor bHLH67 OS=Arabidopsis thaliana GN=BHLH67 PE=2 SV=1

 Score = 89.7 bits (221), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 36/63 (57%), Positives = 56/63 (88%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEA 161
           QR++HI VERNRR+QMNE+++ LR+L+P  Y++RGDQASI+GG ++Y+  L+Q++QSLE+
Sbjct: 176 QRINHIAVERNRRRQMNEHINSLRALLPPSYIQRGDQASIVGGAINYVKVLEQIIQSLES 235

Query: 162 KKQ 164
           +K+
Sbjct: 236 QKR 238

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKQ6|BH099_ARATH Transcription factor bHLH99 OS=Arabidopsis thaliana GN=BHLH99 PE=2 SV=1

 Score = 81.6 bits (200), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 38/61 (62%), Positives = 48/61 (78%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEA 161
           QRM+HI VERNRRKQMN  LS+L+S+MP  Y +  DQASII G + Y+ +L+Q LQSLEA
Sbjct: 100 QRMNHIAVERNRRKQMNHFLSILKSMMPLSYSQPNDQASIIEGTISYLKKLEQRLQSLEA 159

Query: 162 K 162
           +
Sbjct: 160 Q 160

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	320
255545056	336	DNA binding protein, putative [Ricinus c	0.937	0.892	0.744	1e-111
224118162	323	predicted protein [Populus trichocarpa]	0.918	0.910	0.745	1e-104
356518615	349	PREDICTED: transcription factor SPEECHLE	0.95	0.871	0.687	1e-102
356509301	344	PREDICTED: transcription factor SPEECHLE	0.943	0.877	0.693	1e-101
225462721	338	PREDICTED: transcription factor SPEECHLE	0.931	0.881	0.685	3e-96
357463825	329	Transcription factor SPEECHLESS [Medicag	0.925	0.899	0.691	1e-94
224116902	303	predicted protein [Populus trichocarpa]	0.837	0.884	0.678	2e-93
449463493	376	PREDICTED: transcription factor SPEECHLE	0.928	0.789	0.585	2e-93
356546430	328	PREDICTED: transcription factor SPEECHLE	0.915	0.893	0.638	2e-89
312282859	368	unnamed protein product [Thellungiella h	0.915	0.796	0.546	9e-84

>gi|255545056|ref|XP_002513589.1| DNA binding protein, putative [Ricinus communis] gi|223547497|gb|EEF48992.1| DNA binding protein, putative [Ricinus communis]

 Score =  406 bits (1043), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 242/325 (74%), Positives = 269/325 (82%), Gaps = 25/325 (7%)

Query: 7   DTLSEYFFDE--GETNLAEDDLFAIFESLDSVT------PLDEAATAVSEA-----RLVS 53
           D++S++F +   G+  L  +DLFAIFE+LDSVT      P +E      +      RLVS
Sbjct: 3   DSVSDFFEEHEFGDNTLDGEDLFAIFETLDSVTQFPPVTPSNEVVVISKDGGEETTRLVS 62

Query: 54  QKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNR 113
           QKSTSSS + ES ET+   ET PKNKRQKT   S+     E  N DGQQRMSHITVERNR
Sbjct: 63  QKSTSSSAILES-ETE--LETSPKNKRQKTGIASS-----EEINPDGQQRMSHITVERNR 114

Query: 114 RKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLS 173
           RKQMNE+LSVLRSLMPCFYVKRGDQASIIGGVV+YINELQQVLQ+LEAKKQRKVY EVLS
Sbjct: 115 RKQMNEHLSVLRSLMPCFYVKRGDQASIIGGVVNYINELQQVLQALEAKKQRKVYSEVLS 174

Query: 174 PRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKATNNNSVE 233
           PR+ SSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPY+PRLQQQGYLSPT A+   S+E
Sbjct: 175 PRIASSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYRPRLQQQGYLSPTVAS---SLE 231

Query: 234 PSPCSSSTSSI-DSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALED 292
           PSP +SS+SSI D+INELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQA KIISALE+
Sbjct: 232 PSPTTSSSSSINDNINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQATKIISALEE 291

Query: 293 LAFEILHVNISTVDETMHNSFTIKV 317
           L+ EILHVN+STVDETM NSFTIK+
Sbjct: 292 LSLEILHVNVSTVDETMLNSFTIKI 316

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224118162|ref|XP_002317746.1| predicted protein [Populus trichocarpa] gi|222858419|gb|EEE95966.1| predicted protein [Populus trichocarpa]

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 234/314 (74%), Positives = 257/314 (81%), Gaps = 20/314 (6%)

Query: 7   DTLSEYFFDEGETNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESD 66
           D L E   + G+T    DDLFAIFESLDSVT                  S+SS+ L + D
Sbjct: 7   DFLEEVQPEFGDTAFDADDLFAIFESLDSVTDFP--------------PSSSSNALHDFD 52

Query: 67  ETDQLTETLPKNKRQKTAATSAVNSS-DEANNTDGQQRMSHITVERNRRKQMNENLSVLR 125
           ET+   ET PK+KRQK +A++A  +S D+  N DGQQRMSHITVERNRRKQMNE+LSVLR
Sbjct: 53  ETNNELETSPKSKRQKISASAAATASSDQEVNPDGQQRMSHITVERNRRKQMNEHLSVLR 112

Query: 126 SLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLSPRLVSSPRPSPL 185
           SLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKK+RKVY EVLSPR+VSSPRPSPL
Sbjct: 113 SLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKKRKVYSEVLSPRIVSSPRPSPL 172

Query: 186 SPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKATNNNSVEPSPCSSSTSSI- 244
           SPRKPPLSPRLNLPISPRTPQP SPYKPR+ QQGYLSPT A   NS+E SP  SS+SSI 
Sbjct: 173 SPRKPPLSPRLNLPISPRTPQPCSPYKPRILQQGYLSPTMA---NSLESSPSPSSSSSIN 229

Query: 245 DSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNIST 304
           D+INELVANSKSAIADVEVKFSGPN+LLKTVSP+IPGQAVKIISALEDLA EILHV+IS 
Sbjct: 230 DNINELVANSKSAIADVEVKFSGPNVLLKTVSPQIPGQAVKIISALEDLALEILHVSISI 289

Query: 305 VD-ETMHNSFTIKV 317
           VD ETM NSFTIK+
Sbjct: 290 VDHETMLNSFTIKI 303

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356518615|ref|XP_003527974.1| PREDICTED: transcription factor SPEECHLESS-like [Glycine max]

 Score =  377 bits (967), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 233/339 (68%), Positives = 266/339 (78%), Gaps = 35/339 (10%)

Query: 4   VGDDTLSEYFFDE--GETNLAEDDLFAIFESLDS-----VTPL--DEA--ATAVSE---- 48
           + D++L + F D+  G  +   DDLFAI ESL+S       PL  +EA  A AVS+    
Sbjct: 1   MDDNSLCDIFDDKEFGSDHFGGDDLFAILESLESDFTTDFPPLINEEAVVAAAVSKDINN 60

Query: 49  ---ARLVSQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMS 105
              +RLVSQKSTSSS   +S ET+   ET PK KRQK   T+      E  N DGQQ+MS
Sbjct: 61  EDVSRLVSQKSTSSSAPLDS-ETE--LETSPKTKRQKLTPTTP-----EEANPDGQQKMS 112

Query: 106 HITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQR 165
           HITVERNRRKQMNE+L+VLRSLMPCFYVKRGDQASIIGGVVDYI+ELQQVLQ+LEAKKQR
Sbjct: 113 HITVERNRRKQMNEHLTVLRSLMPCFYVKRGDQASIIGGVVDYISELQQVLQALEAKKQR 172

Query: 166 KVYCEVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRL--QQQGY--- 220
           KVYCEVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPY+PRL  QQ GY   
Sbjct: 173 KVYCEVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYRPRLHQQQHGYNNI 232

Query: 221 LSPTKATNNNSVEPSPCSSSTSSI-DSINELVANSKSAIADVEVKFSGPNLLLKTVSPRI 279
           +SPT   +N S++PSP SS+ SSI D+INELVANSKS  ADVEVKFSGP++LLKTVS RI
Sbjct: 233 ISPT--ISNVSLDPSPTSSANSSINDNINELVANSKSPTADVEVKFSGPHVLLKTVSQRI 290

Query: 280 PGQAVKIISALEDLAFEILHVNIST-VDETMHNSFTIKV 317
           PGQA+KII+ALEDLA EI+HVNI+   D+TM NSFTIK+
Sbjct: 291 PGQALKIITALEDLALEIVHVNINCAADDTMLNSFTIKI 329

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509301|ref|XP_003523389.1| PREDICTED: transcription factor SPEECHLESS-like [Glycine max]

 Score =  374 bits (961), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 231/333 (69%), Positives = 263/333 (78%), Gaps = 31/333 (9%)

Query: 6   DDTLSEYFFDE--GETNLAEDDLFAIFESLDSVT-----PLDEAAT--AVSE------AR 50
           DD+L + F D+  G  +   DDLFAI ESL+S       P++E A   AVS+      +R
Sbjct: 2   DDSLCDIFDDKEFGSEHFGGDDLFAILESLESDFTDFPPPINEEAVVAAVSKDNNEDVSR 61

Query: 51  LVSQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVE 110
           LVSQKSTSSS   +S ET+   ET  K KRQK   T+      E  N DGQQ+MSHITVE
Sbjct: 62  LVSQKSTSSSAPLDS-ETE--LETSSKTKRQKLTPTTP-----EEANPDGQQKMSHITVE 113

Query: 111 RNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCE 170
           RNRRKQMNE+L+VLRSLMPCFYVKRGDQASIIGGVVDYI+ELQQVLQ+LEAKKQRKVY E
Sbjct: 114 RNRRKQMNEHLTVLRSLMPCFYVKRGDQASIIGGVVDYISELQQVLQALEAKKQRKVYSE 173

Query: 171 VLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQ-QQGY---LSPTKA 226
           VLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPY+PRLQ QQGY   +SPT +
Sbjct: 174 VLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYRPRLQAQQGYNNIISPTMS 233

Query: 227 TNNNSVEPSPCSSSTSSI-DSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVK 285
             N S++PSP SS+ SSI D+INELVANSKS  ADVEVKFSGP++LLKTVS RIPGQA+K
Sbjct: 234 --NVSLDPSPTSSANSSINDNINELVANSKSPTADVEVKFSGPHVLLKTVSQRIPGQAMK 291

Query: 286 IISALEDLAFEILHVNIST-VDETMHNSFTIKV 317
           II+ALEDLA EI+HVNI+   D+TM NSFTIK+
Sbjct: 292 IITALEDLALEIVHVNINCAADDTMLNSFTIKI 324

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225462721|ref|XP_002267745.1| PREDICTED: transcription factor SPEECHLESS [Vitis vinifera] gi|302143687|emb|CBI22548.3| unnamed protein product [Vitis vinifera]

 Score =  358 bits (918), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 224/327 (68%), Positives = 253/327 (77%), Gaps = 29/327 (8%)

Query: 7   DTLSEYFFDE----GETNLA------EDDLFAIFESLDSVT---PLDEAATAVSE----A 49
           D+LS+ FF+E    GET+L       + DLF+IFESL+ V+   PL+E      E    A
Sbjct: 3   DSLSD-FFEEPEFGGETSLTGVASPDDLDLFSIFESLEGVSEVPPLEETVLGSKEGEETA 61

Query: 50  RLVSQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITV 109
           RLVSQKSTSSS LQES ET+   E  PK KR K AA +    S E  N DGQQR+SHITV
Sbjct: 62  RLVSQKSTSSSALQES-ETE--LEASPKRKRPKLAAPT----SSEEGNPDGQQRVSHITV 114

Query: 110 ERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYC 169
           ERNRRKQMNE+LSVLRSLMPCFYVKRGDQASIIGGVVDYI ELQQVL+SLEAKKQRKVY 
Sbjct: 115 ERNRRKQMNEHLSVLRSLMPCFYVKRGDQASIIGGVVDYIKELQQVLRSLEAKKQRKVYS 174

Query: 170 EVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKATNN 229
           EVLSPR+VSSPRP P+SPRKPPLSPR++LPISPRTPQP SPYKP   QQGYLSPT A + 
Sbjct: 175 EVLSPRVVSSPRPPPISPRKPPLSPRISLPISPRTPQPTSPYKPVRLQQGYLSPTIAPSL 234

Query: 230 NSVEPSPCSSSTSSIDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISA 289
                S  SS+    D+ NEL+ NSKSAIADVEVK+S PN++LKT S RIPGQAVKIISA
Sbjct: 235 EPSPSSSTSSN----DNANELIVNSKSAIADVEVKYSCPNVVLKTKSSRIPGQAVKIISA 290

Query: 290 LEDLAFEILHVNISTVDETMHNSFTIK 316
           LEDL+ EILHV+IS++DETM NSFTIK
Sbjct: 291 LEDLSLEILHVSISSIDETMLNSFTIK 317

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357463825|ref|XP_003602194.1| Transcription factor SPEECHLESS [Medicago truncatula] gi|355491242|gb|AES72445.1| Transcription factor SPEECHLESS [Medicago truncatula]

 Score =  352 bits (904), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 224/324 (69%), Positives = 249/324 (76%), Gaps = 28/324 (8%)

Query: 6   DDTLSEYFFDEGETNLAEDDLFAIFESLDSVT--PL---DEAAT-----AVSEARLVSQK 55
           D++L + F D  E     DDLFAI ESL+  T  PL    EAAT       S +RLVSQK
Sbjct: 2   DESLYDIFEDRTEFG-NSDDLFAILESLEDFTDFPLINQAEAATPKENEVTSTSRLVSQK 60

Query: 56  STSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRK 115
           STSS  LQ+S ET+   ET PK KRQK   T      ++ N+ DGQQR+SHITVERNRRK
Sbjct: 61  STSS--LQDS-ETE--LETEPKRKRQKLTPTLL---EEQINSVDGQQRVSHITVERNRRK 112

Query: 116 QMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLSPR 175
           QMNE+LSVLRSLMPCFYVKRGDQASIIGGVVDYI ELQQ+LQ+LEAKKQRKVY EVLSPR
Sbjct: 113 QMNEHLSVLRSLMPCFYVKRGDQASIIGGVVDYITELQQLLQALEAKKQRKVYSEVLSPR 172

Query: 176 LVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGY-LSPTKATNNNSVEP 234
           LV SPRPSPLSPRKPPLSPRLNLPISPRTPQP SPYKPR+QQ    LSP   +  +    
Sbjct: 173 LVPSPRPSPLSPRKPPLSPRLNLPISPRTPQPTSPYKPRMQQSYIALSPLDPSPTS---- 228

Query: 235 SPCSSSTSSIDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLA 294
              SS++S  D+INELVANSKS IADVEVKFSGP++LLKTVS RIPGQ +KIISALEDLA
Sbjct: 229 ---SSTSSVNDNINELVANSKSPIADVEVKFSGPHVLLKTVSQRIPGQPLKIISALEDLA 285

Query: 295 FEILHVNI-STVDETMHNSFTIKV 317
            EILHVNI ST D+TM NSFTIK+
Sbjct: 286 LEILHVNINSTSDDTMLNSFTIKI 309

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116902|ref|XP_002331842.1| predicted protein [Populus trichocarpa] gi|222875080|gb|EEF12211.1| predicted protein [Populus trichocarpa]

 Score =  348 bits (893), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 217/320 (67%), Positives = 239/320 (74%), Gaps = 52/320 (16%)

Query: 7   DTLSEYFFDEGETNLAEDDLFAIFESLDSVT------PLDEAATAVSEARLVSQKSTSSS 60
           D L E   + G+T    DDLFAIFESLDSVT      PLDE              S+SSS
Sbjct: 7   DFLEEVQPEFGDTTFDGDDLFAIFESLDSVTDFPPVIPLDEV-------------SSSSS 53

Query: 61  ILQESDETDQLTETLPKNKRQKTAATSAVNSS-DEANNTDGQQRMSHITVERNRRKQMNE 119
            LQ+ DET+   ET PK+KRQK AA++A  +S D+  N DGQQR+SHITVERNRRKQMNE
Sbjct: 54  ALQDFDETNNELETSPKSKRQKIAASAAAIASSDQEVNPDGQQRISHITVERNRRKQMNE 113

Query: 120 NLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLSPRLVSS 179
           +LSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVY EVLSPR+VSS
Sbjct: 114 HLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYSEVLSPRIVSS 173

Query: 180 PRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPRLQQQGYLSPTKATNNNSVEPSPCSS 239
           PRP PLSPRKPPLS                          Y+SPT AT   S+EPSP SS
Sbjct: 174 PRP-PLSPRKPPLS--------------------------YISPTMAT---SLEPSPTSS 203

Query: 240 STSSI-DSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEIL 298
           S+SSI D+INEL+ANSKSAIADVEVKFSGPN+LLKTVSPRIPGQAVKI+SALE LA EIL
Sbjct: 204 SSSSINDNINELIANSKSAIADVEVKFSGPNVLLKTVSPRIPGQAVKIVSALEGLALEIL 263

Query: 299 HVNISTVD-ETMHNSFTIKV 317
           HV+ISTVD ETM NSFTIK+
Sbjct: 264 HVSISTVDHETMLNSFTIKI 283

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463493|ref|XP_004149468.1| PREDICTED: transcription factor SPEECHLESS-like [Cucumis sativus] gi|449531165|ref|XP_004172558.1| PREDICTED: transcription factor SPEECHLESS-like [Cucumis sativus]

 Score =  348 bits (892), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 208/355 (58%), Positives = 243/355 (68%), Gaps = 58/355 (16%)

Query: 6   DDTLSEYFFDEGETNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQES 65
           D TL+ +F  EG      DDLF+IFESL++V         +   +    + T+S +  E+
Sbjct: 17  DHTLNPHF--EG------DDLFSIFESLENVAEFTMIEDDIEPVK--DGEETTSLVFSET 66

Query: 66  DETDQLTETLPKNKRQKT--------AATSAVNSSDEANNTDGQQRMSHITVERNRRKQM 117
           +      ET PK KR KT        A TS   SS E  N DG QRMSHITVERNRRKQM
Sbjct: 67  E-----LETSPKTKRLKTIAATSPTAAMTSTGLSSSEDPNPDGPQRMSHITVERNRRKQM 121

Query: 118 NENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRK-VYCEVLSPRL 176
           NE+L+VLRSLMPCFYVK+GDQASIIGGVV+YI ELQQVLQSLEAKKQRK VY EVLSPR+
Sbjct: 122 NEHLTVLRSLMPCFYVKKGDQASIIGGVVEYIKELQQVLQSLEAKKQRKVVYSEVLSPRV 181

Query: 177 VSSPRPS-PLSPRKPPLSPRLNLPISPRTPQPGSPYK---PRLQQ--------QGYLSP- 223
           VSSPRP+  +SPRKPPLSPRLNLPISPRTPQP SPY    PRLQQ          Y  P 
Sbjct: 182 VSSPRPNLAMSPRKPPLSPRLNLPISPRTPQPTSPYSKPPPRLQQPPSAATGGGAYNIPS 241

Query: 224 -----TKATNNNSVEPSPCSSSTSS----------------IDSINELVANSKSAIADVE 262
                T   NNNS+EPSPC+S +++                 ++ N+LVANSKSAIA+VE
Sbjct: 242 SSSSTTNMANNNSLEPSPCNSCSTTNSSIDNNNNNNNSNSNSNNNNDLVANSKSAIAEVE 301

Query: 263 VKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV 317
           VKF+GPN++LKTVSP IPGQA KIISALE L+ EILHV I+T+DETM NSFTIK+
Sbjct: 302 VKFTGPNVVLKTVSPPIPGQAFKIISALEQLSLEILHVKITTLDETMFNSFTIKI 356

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546430|ref|XP_003541629.1| PREDICTED: transcription factor SPEECHLESS-like [Glycine max]

 Score =  335 bits (859), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 208/326 (63%), Positives = 239/326 (73%), Gaps = 33/326 (10%)

Query: 6   DDTLSEYFFDE--GETNLAEDDLFAIFESLDSVTPL-----DEAATAVS------EARLV 52
           D++L + F D   G+T+    DLF+I ES+D +        +EA    +       +R+V
Sbjct: 2   DESLCDIFKDTEFGDTHFGGGDLFSILESIDDLKDFPPTNNNEAVIGRTSKENEQNSRMV 61

Query: 53  SQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERN 112
           SQK   SS   +  ET+   E  PK+KRQK  +TS           +  Q++SHITVERN
Sbjct: 62  SQKVLISSSAPQDSETEH--EISPKSKRQKLRSTSP----------EELQKVSHITVERN 109

Query: 113 RRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVL 172
           RRKQMNENL VLRSLMP FYVKRGDQASIIGGVVDYINE+QQ+LQ LEAKKQRKVY EVL
Sbjct: 110 RRKQMNENLLVLRSLMPSFYVKRGDQASIIGGVVDYINEMQQLLQCLEAKKQRKVYIEVL 169

Query: 173 SPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTP-QPGSPYKPRLQQQGYLSPTKATNNNS 231
           SPRLVSSPRPSPLSPRKPPLSPR++LPISPRTP QP SPYKPRL Q GYLSPT A +  S
Sbjct: 170 SPRLVSSPRPSPLSPRKPPLSPRISLPISPRTPQQPSSPYKPRL-QPGYLSPTIANSPTS 228

Query: 232 VEPSPCSSSTSSIDSINELVANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALE 291
              S  +      D+INELVANSKS IADVEVKFSGP++LLKTVSP IPGQA++IISALE
Sbjct: 229 SASSSIN------DNINELVANSKSIIADVEVKFSGPHVLLKTVSPPIPGQAMRIISALE 282

Query: 292 DLAFEILHVNISTVDETMHNSFTIKV 317
           DLA EILHVNIST DETM NSFTIK+
Sbjct: 283 DLALEILHVNISTADETMLNSFTIKI 308

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312282859|dbj|BAJ34295.1| unnamed protein product [Thellungiella halophila]

 Score =  316 bits (810), Expect = 9e-84,   Method: Compositional matrix adjust.
 Identities = 193/353 (54%), Positives = 226/353 (64%), Gaps = 60/353 (16%)

Query: 13  FFDEGE---TNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESDETD 69
           F +E E   T+LA DDLFAI ESL+    +  AA +  +       +TSS  L +    D
Sbjct: 8   FLEECELVDTSLAGDDLFAILESLEGAGEISPAAASTPK-----DGTTSSKELVKDQNYD 62

Query: 70  QLTETLPKNKRQK------------TAATSAVNSSDEANNTDGQQRMSHITVERNRRKQM 117
             +   PK KRQ+                      +E N  DGQQ+MSH+TVERNRRKQM
Sbjct: 63  TSS---PKRKRQRLETEKEEDEDEEDGEGEGEGEGEEENKQDGQQKMSHVTVERNRRKQM 119

Query: 118 NENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVLSPRLV 177
           NE+L+VLRSLMPCFYVKRGDQASIIGGVV+YI+ELQQVLQSLEAKKQRK Y EVLSPRLV
Sbjct: 120 NEHLTVLRSLMPCFYVKRGDQASIIGGVVEYISELQQVLQSLEAKKQRKTYAEVLSPRLV 179

Query: 178 SSPRPSP--LSPRKPPLSPRLN----------LPISPRTPQPGSPYKPRLQQQGYLSPTK 225
            SPRPSP  LSPRK PLSPR+N           PISPRTPQP SPY+    Q   +    
Sbjct: 180 PSPRPSPPILSPRKLPLSPRINNHQIHHHLLLPPISPRTPQPTSPYRAHPPQLPLIPQPP 239

Query: 226 ATNNNSVEPSPCSS---------------------STSSIDSINELVANSKSAIADVEVK 264
             + +S+  + CSS                       SS+  INELVANSKSA+ADVEVK
Sbjct: 240 LRSYSSL--AGCSSLGDPPPYSPASSSSSPSVSSNHESSV--INELVANSKSALADVEVK 295

Query: 265 FSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV 317
           FSG N+LLKT+S +IPGQ +KII+ALEDLA EIL VNI+TVDETM NSFTIK+
Sbjct: 296 FSGANVLLKTISHKIPGQVMKIIAALEDLALEILQVNINTVDETMLNSFTIKI 348

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

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	320
TAIR|locus:2154197	364	SPCH "AT5G53210" [Arabidopsis	0.481	0.423	0.551	2.2e-69
UNIPROTKB|Q6ETQ5	415	P0613F08.25 "Basic helix-loop-	0.425	0.327	0.537	2.9e-50
UNIPROTKB|Q653A4	396	OSJNBa0043B22.14 "Basic helix-	0.278	0.224	0.706	6.8e-49
TAIR|locus:2093746	414	FMA "AT3G24140" [Arabidopsis t	0.315	0.243	0.537	1.5e-38
TAIR|locus:2082400	202	MUTE "AT3G06120" [Arabidopsis	0.196	0.311	0.746	6.4e-37
UNIPROTKB|Q5KQG3	227	OSJNBb0086G17.12 "Putative unc	0.196	0.277	0.730	2.4e-35
UNIPROTKB|Q8H7N8	329	OJ1217B09.8 "BHLH transcriptio	0.381	0.370	0.433	2e-30
UNIPROTKB|Q6ZGS3	373	OJ1148_D05.9 "Putative basic-h	0.893	0.766	0.300	3e-30
UNIPROTKB|Q7XLY9	362	OSJNBa0086O06.20 "OSJNBa0086O0	0.293	0.259	0.525	6.8e-30
TAIR|locus:2009537	304	AT1G22490 "AT1G22490" [Arabido	0.268	0.282	0.544	1.8e-29

TAIR|locus:2154197 SPCH "AT5G53210" [Arabidopsis thaliana (taxid:3702)]

 Score = 407 (148.3 bits), Expect = 2.2e-69, Sum P(3) = 2.2e-69
 Identities = 85/154 (55%), Positives = 103/154 (66%)

Query:    18 ETNLAEDDLFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESDETDQLTETLPK 77
             +T+LA DDLFAI ESL+    +   A +  +    S K        E+    +  + L  
Sbjct:    16 DTSLAGDDLFAILESLEGAGEISPTAASTPKDGTTSSKELVKDQDYENSSPKRKKQRLET 75

Query:    78 NKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGD 137
              K +          ++E N  DGQQ+MSH+TVERNRRKQMNE+L+VLRSLMPCFYVKRGD
Sbjct:    76 RKEEDEEEEDGDGEAEEDNKQDGQQKMSHVTVERNRRKQMNEHLTVLRSLMPCFYVKRGD 135

Query:   138 QASIIGGVVDYINELQQVLQSLEAKKQRKVYCEV 171
             QASIIGGVV+YI+ELQQVLQSLEAKKQRK Y EV
Sbjct:   136 QASIIGGVVEYISELQQVLQSLEAKKQRKTYAEV 169

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0010374 "stomatal complex development" evidence=IMP

GO:0010103 "stomatal complex morphogenesis" evidence=RCA

GO:0042127 "regulation of cell proliferation" evidence=RCA

UNIPROTKB|Q6ETQ5 P0613F08.25 "Basic helix-loop-helix-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 347 (127.2 bits), Expect = 2.9e-50, Sum P(2) = 2.9e-50
 Identities = 78/145 (53%), Positives = 91/145 (62%)

Query:    76 PKNKRQKTAATSAVNSSDEA---NNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFY 132
             P  K+QK +++S+ + +  A    + DG  +MSHITVERNRRKQMNE+L+VLRSLMPCFY
Sbjct:   101 PAQKKQKGSSSSSSSPAALAAAVGDGDGAAKMSHITVERNRRKQMNEHLAVLRSLMPCFY 160

Query:   133 VKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCEVXXXXXXXXXXXXXXXXXX--- 189
             VKRGDQASIIGGVVDYI ELQQVL+SLEAKK RK Y +                      
Sbjct:   161 VKRGDQASIIGGVVDYIKELQQVLRSLEAKKNRKAYADQVLSPRPSPAAAALMVKPTPPI 220

Query:   190 ---XXXXXXXXXXISPRTPQPGSPY 211
                          ISPRTP PGSPY
Sbjct:   221 SPRFAAAAAAGVPISPRTPTPGSPY 245

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q653A4 OSJNBa0043B22.14 "Basic helix-loop-helix-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 307 (113.1 bits), Expect = 6.8e-49, Sum P(2) = 6.8e-49
 Identities = 65/92 (70%), Positives = 75/92 (81%)

Query:    79 KRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQ 138
             KR+K  +  + +++D A  T    + +HI VERNRRKQMNENL+VLRSLMPCFYVKRGDQ
Sbjct:   115 KRRKCCSPES-STTDVAAATT--PKTAHIAVERNRRKQMNENLAVLRSLMPCFYVKRGDQ 171

Query:   139 ASIIGGVVDYINELQQVLQSLEAKKQRKVYCE 170
             ASIIGGVVDYI ELQQVL SLEAKKQRKVY +
Sbjct:   172 ASIIGGVVDYIKELQQVLHSLEAKKQRKVYTD 203

GO:0005634 "nucleus" evidence=IC

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

 Score = 262 (97.3 bits), Expect = 1.5e-38, Sum P(2) = 1.5e-38
 Identities = 58/108 (53%), Positives = 79/108 (73%)

Query:    63 QESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLS 122
             +E  E   +T+   K+KR K A TS   +S+E  +    QRM+HI VERNRRKQMNE+L 
Sbjct:   163 EEDRENKNVTKKEVKSKR-KRARTS--KTSEEVES----QRMTHIAVERNRRKQMNEHLR 215

Query:   123 VLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKVYCE 170
             VLRSLMP  YV+RGDQASIIGG ++++ EL+Q+LQ LE++K+R++  E
Sbjct:   216 VLRSLMPGSYVQRGDQASIIGGAIEFVRELEQLLQCLESQKRRRILGE 263

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:2082400 MUTE "AT3G06120" [Arabidopsis thaliana (taxid:3702)]

 Score = 251 (93.4 bits), Expect = 6.4e-37, Sum P(2) = 6.4e-37
 Identities = 47/63 (74%), Positives = 57/63 (90%)

Query:   104 MSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKK 163
             MSHI VERNRR+QMNE+L  LRSL PCFY+KRGDQASIIGGV+++I ELQQ++Q LE+KK
Sbjct:     1 MSHIAVERNRRRQMNEHLKSLRSLTPCFYIKRGDQASIIGGVIEFIKELQQLVQVLESKK 60

Query:   164 QRK 166
             +RK
Sbjct:    61 RRK 63

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0010374 "stomatal complex development" evidence=IMP

UNIPROTKB|Q5KQG3 OSJNBb0086G17.12 "Putative uncharacterized protein OSJNBb0086G17.12" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 244 (91.0 bits), Expect = 2.4e-35, Sum P(2) = 2.4e-35
 Identities = 46/63 (73%), Positives = 56/63 (88%)

Query:   104 MSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKK 163
             MSHI VERNRR+QMN++L VLRSL P FY+KRGDQASIIGG +D+I ELQ +LQSLEA+K
Sbjct:     1 MSHIAVERNRRRQMNDHLKVLRSLTPAFYIKRGDQASIIGGAIDFIKELQTLLQSLEAQK 60

Query:   164 QRK 166
             +R+
Sbjct:    61 KRR 63

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q8H7N8 OJ1217B09.8 "BHLH transcription factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 241 (89.9 bits), Expect = 2.0e-30, Sum P(2) = 2.0e-30
 Identities = 55/127 (43%), Positives = 76/127 (59%)

Query:    40 DEAATAVSEARLVSQKSTSSSILQESDETDQLTETLPKNKRQKTAATSAVNSSDEANNTD 99
             D+   A  +   V+ K  S +  +      +  E +   +R K   T  V + +E     
Sbjct:    52 DQLQVASVDEWEVASKDNSDASTEGKAAAAERAEPVAAGRR-KRRRTKVVKNKEEIEC-- 108

Query:   100 GQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSL 159
               QRM+HI VERNRR+QMNE L+VLRSLMP  Y +RGDQASI+GG ++Y+ EL+Q+LQSL
Sbjct:   109 --QRMTHIAVERNRRRQMNEYLAVLRSLMPASYSQRGDQASIVGGAINYVKELEQLLQSL 166

Query:   160 EAKKQRK 166
             E +K  K
Sbjct:   167 EVQKSLK 173

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q6ZGS3 OJ1148_D05.9 "Putative basic-helix-loop-helix transcription factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 334 (122.6 bits), Expect = 3.0e-30, P = 3.0e-30
 Identities = 92/306 (30%), Positives = 141/306 (46%)

Query:    26 LFAIFESLDSVTPLDEAATAVSEARLVSQKSTSSSILQESDETDQLTETLPKNKRQKTAA 85
             ++  F +  + + L + A A  +A ++   +T       S       E  P  K+++  A
Sbjct:    18 IYDTFNASAAASFLFDNAAAFCDADILGATATGEKEATSSAAA-AAAEAAPPRKKRRRRA 76

Query:    86 TSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGV 145
              S    S E   T   QRM+HI VERNRR+QMNE L++LRSLMP  YV+RGDQASI+GG 
Sbjct:    77 KSC--KSREETET---QRMTHIAVERNRRRQMNEYLAILRSLMPEPYVQRGDQASIVGGA 131

Query:   146 VDYINELQQVLQSLEAKKQ-----RKVYCEVXXXXXXXXXXXXXXXXXXXXXXXXXXXXI 200
             ++++ EL+Q LQSLEA+K+      K  C+                              
Sbjct:   132 IEFVKELEQQLQSLEAQKRTLLPHHKARCDDATPMHNASGSNVGAGGCMEPTTTTSNCSS 191

Query:   201 SPRTPQPGSPYKPRLQQQGYL------SP---TKATXXXXXXXXXXXXXXXXXXXXXXLV 251
             S     P +   P  Q   Y       SP   T  T                      L 
Sbjct:   192 SVTEDAPSADAPPFAQFFAYPQYVWCHSPRDSTTTTTAASASASASASSSSPATVAAALQ 251

Query:   252 ANSKSAIADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHN 311
             +  +S +AD+EV     +  ++ +SPR PGQ +K+I+ L+ L   +LH+N++T+D  +  
Sbjct:   252 SEHRSGLADIEVSLVETHASVRVMSPRRPGQLLKMIAGLQALRLTVLHLNVTTLDSLVLY 311

Query:   312 SFTIKV 317
             + ++KV
Sbjct:   312 TLSVKV 317

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q7XLY9 OSJNBa0086O06.20 "OSJNBa0086O06.20 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 247 (92.0 bits), Expect = 6.8e-30, Sum P(2) = 6.8e-30
 Identities = 52/99 (52%), Positives = 72/99 (72%)

Query:    67 ETDQLTETLPK-NKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLR 125
             E DQL +   +  +R++     +  S ++A +    QRM+HI VERNRR+QMNE L+VLR
Sbjct:    61 EVDQLLKQAQQPGRRKRRRRARSCKSREDAES----QRMTHIAVERNRRRQMNEYLAVLR 116

Query:   126 SLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQ 164
             SLMP  YV RGDQASI+GG +D++ EL+Q+LQSLEA+K+
Sbjct:   117 SLMPESYVHRGDQASIVGGAIDFVKELEQLLQSLEAQKR 155

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2009537 AT1G22490 "AT1G22490" [Arabidopsis thaliana (taxid:3702)]

 Score = 244 (91.0 bits), Expect = 1.8e-29, Sum P(2) = 1.8e-29
 Identities = 49/90 (54%), Positives = 63/90 (70%)

Query:    76 PKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKR 135
             P   R+K   T    + +E  N    QRM+HI VERNRRKQMNE L+VLRSLMP  Y +R
Sbjct:    91 PPQHRRKRRRTRNCKNKEEIEN----QRMTHIAVERNRRKQMNEYLAVLRSLMPSSYAQR 146

Query:   136 GDQASIIGGVVDYINELQQVLQSLEAKKQR 165
             GDQASI+GG ++Y+ EL+ +LQS+E K+ R
Sbjct:   147 GDQASIVGGAINYVKELEHILQSMEPKRTR 176

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q700C7	SPCH_ARATH	No assigned EC number	0.5341	0.9531	0.8379	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	320
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	5e-13
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	7e-13
smart00353	53	smart00353, HLH, helix loop helix domain	3e-09

>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 = 62.6 bits (153), Expect = 5e-13
 Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 99  DGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYV-KRGDQASIIGGVVDYINELQQVLQ 157
              +R +H   ER RR+++N+    LRSL+P     K+  +A I+   VDYI  LQ++LQ
Sbjct: 1   RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60

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

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

 Score = 61.7 bits (151), Expect = 7e-13
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQ 153
           +R +H   ER RR ++N+    LR L+P    K+  +A I+   ++YI  LQ
Sbjct: 1   RRKAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHLQ 52

Length = 52

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

 Score = 51.8 bits (125), Expect = 3e-09
 Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 1/50 (2%)

Query: 110 ERNRRKQMNENLSVLRSLMP-CFYVKRGDQASIIGGVVDYINELQQVLQS 158
           ER RR+++NE    LRSL+P     K+  +A I+   ++YI  LQ+ LQ 
Sbjct: 4   ERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53

Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	320
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.44
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.42
smart00353	53	HLH helix loop helix domain.	99.37
KOG1318	411	consensus Helix loop helix transcription factor EB	99.19
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	98.64
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.38
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.23
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.22
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	98.16
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	98.15
KOG3960	284	consensus Myogenic helix-loop-helix transcription	98.12
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	98.08
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.99
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	97.97
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	97.95
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	97.92
KOG0561	373	consensus bHLH transcription factor [Transcription	97.86
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	97.69
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	97.48
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	97.35
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	97.32
PLN03217	93	transcription factor ATBS1; Provisional	97.31
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	97.26
KOG3910	632	consensus Helix loop helix transcription factor [T	97.24
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	96.64
PRK05007	884	PII uridylyl-transferase; Provisional	96.59
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	96.44
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	96.43
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	96.41
PRK00275	895	glnD PII uridylyl-transferase; Provisional	96.39
PRK04374	869	PII uridylyl-transferase; Provisional	96.25
PRK03059	856	PII uridylyl-transferase; Provisional	96.12
PRK03381	774	PII uridylyl-transferase; Provisional	96.11
PRK01759	854	glnD PII uridylyl-transferase; Provisional	96.02
PRK05092	931	PII uridylyl-transferase; Provisional	95.93
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	95.86
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	95.57
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	95.43
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	95.39
KOG3898	254	consensus Transcription factor NeuroD and related	95.38
PRK01759	854	glnD PII uridylyl-transferase; Provisional	95.21
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	95.14
PRK03381	774	PII uridylyl-transferase; Provisional	95.1
PRK05007	884	PII uridylyl-transferase; Provisional	95.05
PRK00194	90	hypothetical protein; Validated	94.99
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	94.97
PRK00275	895	glnD PII uridylyl-transferase; Provisional	94.85
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	94.82
PRK03059	856	PII uridylyl-transferase; Provisional	94.81
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	94.72
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	94.6
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	94.25
PRK05092	931	PII uridylyl-transferase; Provisional	94.19
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	94.05
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	93.97
PRK04435	147	hypothetical protein; Provisional	93.78
PRK04374	869	PII uridylyl-transferase; Provisional	93.75
cd02116	60	ACT ACT domains are commonly involved in specifica	93.49
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	93.26
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	92.74
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	92.61
KOG4395	285	consensus Transcription factor Atonal, contains HT	91.93
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	91.46
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	90.99
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	90.76
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	90.44
PRK08577	136	hypothetical protein; Provisional	90.42
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	89.38
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	88.78
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	88.78
PRK07334	403	threonine dehydratase; Provisional	88.59
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	87.7
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	87.45
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	86.26
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	86.23
TIGR00691	683	spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (	83.98
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	83.94
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	83.93
PRK10872	743	relA (p)ppGpp synthetase I/GTP pyrophosphokinase;	83.81
PRK11092	702	bifunctional (p)ppGpp synthetase II/ guanosine-3',	83.72
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	83.47
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	80.54
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	80.13

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

Probab=99.44  E-value=1.4e-13  Score=99.81  Aligned_cols=51  Identities=37%  Similarity=0.612  Sum_probs=48.1

Q ss_pred             ccchhHHHHHHHHHHHHHHHHHHhcCCCC---CCCCCChhhhHHHHHHHHHHHH
Q 042904          103 RMSHITVERNRRKQMNENLSVLRSLMPCF---YVKRGDQASIIGGVVDYINELQ  153 (320)
Q Consensus       103 r~~h~~~ER~RR~~in~~~~~LrslvP~~---~~~k~dKasIL~~AI~YIk~Lq  153 (320)
                      |..|+..||+||..||+.|..|+.+||..   ...|++|++||..||+||++||
T Consensus         2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq   55 (55)
T PF00010_consen    2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ   55 (55)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence            67899999999999999999999999996   4678999999999999999997

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

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

Probab=99.42  E-value=2.6e-13  Score=99.09  Aligned_cols=57  Identities=40%  Similarity=0.625  Sum_probs=51.8

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCChhhhHHHHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFY-VKRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~-~~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      ..+..|+..||+||++||+.|..|+++||..+ ..|++|++||..||+||+.|+.+++
T Consensus         3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~   60 (60)
T cd00083           3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ   60 (60)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            34779999999999999999999999999963 4789999999999999999998763

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=99.37  E-value=1.1e-12  Score=93.84  Aligned_cols=51  Identities=39%  Similarity=0.583  Sum_probs=46.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCCC-CCCCChhhhHHHHHHHHHHHHHHHH
Q 042904          107 ITVERNRRKQMNENLSVLRSLMPCFY-VKRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       107 ~~~ER~RR~~in~~~~~LrslvP~~~-~~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      +..||+||++||+.|..|+++||..+ ..+++|++||..||+||++|+.+++
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            46899999999999999999999753 6789999999999999999999875

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

Probab=99.19  E-value=3.4e-11  Score=118.97  Aligned_cols=61  Identities=36%  Similarity=0.564  Sum_probs=53.0

Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCChhhhHHHHHHHHHHHHHHHHHH
Q 042904           99 DGQQRMSHITVERNRRKQMNENLSVLRSLMPCFY--VKRGDQASIIGGVVDYINELQQVLQSL  159 (320)
Q Consensus        99 ~~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~--~~k~dKasIL~~AI~YIk~Lq~~v~~L  159 (320)
                      +..+|.+||++||+||++||+++.+|..|||.+.  ..|..|.+||..+++||++||+..++.
T Consensus       230 dr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~  292 (411)
T KOG1318|consen  230 DRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRA  292 (411)
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHH
Confidence            3444889999999999999999999999999973  235679999999999999999988743

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=98.64  E-value=4.3e-08  Score=87.57  Aligned_cols=65  Identities=23%  Similarity=0.358  Sum_probs=55.8

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHHhcCCCCC-----CCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 042904          102 QRMSHITVERNRRKQMNENLSVLRSLMPCFY-----VKRGDQASIIGGVVDYINELQQVLQSLEAKKQRK  166 (320)
Q Consensus       102 ~r~~h~~~ER~RR~~in~~~~~LrslvP~~~-----~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~  166 (320)
                      +|..|..+||+||+.||..+..|+.|||.+.     +.|+.||-||..+|+||.+|.++...-+.+...+
T Consensus        62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L  131 (229)
T KOG1319|consen   62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTL  131 (229)
T ss_pred             HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3679999999999999999999999999862     1378999999999999999998877766665543

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

Probab=98.38  E-value=1.5e-06  Score=80.71  Aligned_cols=65  Identities=17%  Similarity=0.316  Sum_probs=55.2

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCC-hhhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGD-QASIIGGVVDYINELQQVLQSLEAKKQR  165 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~d-KasIL~~AI~YIk~Lq~~v~~L~~~~~~  165 (320)
                      ..|..||.-||+||..|++.|..|+.+||.....+.. .++||+.|.+||+.|+.......+.+++
T Consensus        58 ~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~  123 (232)
T KOG2483|consen   58 SSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIED  123 (232)
T ss_pred             cchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHH
Confidence            4488999999999999999999999999997544444 6899999999999999887776655544

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

Probab=98.23  E-value=1.2e-06  Score=93.42  Aligned_cols=53  Identities=23%  Similarity=0.412  Sum_probs=49.0

Q ss_pred             ccchhHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCChhhhHHHHHHHHHHHHHH
Q 042904          103 RMSHITVERNRRKQMNENLSVLRSLMPCFY--VKRGDQASIIGGVVDYINELQQV  155 (320)
Q Consensus       103 r~~h~~~ER~RR~~in~~~~~LrslvP~~~--~~k~dKasIL~~AI~YIk~Lq~~  155 (320)
                      |.+|+.+||+||++||..+.+|.+|||.+.  ..|+||.+||..||.+|+.+++.
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            669999999999999999999999999872  37999999999999999999885

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

Probab=98.22  E-value=6.5e-07  Score=84.18  Aligned_cols=58  Identities=24%  Similarity=0.382  Sum_probs=50.4

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCC------CCCCChhhhHHHHHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFY------VKRGDQASIIGGVVDYINELQQVLQS  158 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~------~~k~dKasIL~~AI~YIk~Lq~~v~~  158 (320)
                      .++..|-+.||+||.+||+.|.+|+.|||...      ..|++||.||.-|++|+++|+...+.
T Consensus        31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   31 YRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             HhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            44678999999999999999999999999641      26889999999999999999986543

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

Probab=98.16  E-value=9.3e-06  Score=62.58  Aligned_cols=47  Identities=28%  Similarity=0.369  Sum_probs=45.0

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      -+|+|.++.|||+|.+|.++|..+||+|..|.|+|.++.+..+|.|.
T Consensus         2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~   48 (72)
T cd04895           2 TLVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVT   48 (72)
T ss_pred             EEEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEE
Confidence            37899999999999999999999999999999999999999999985

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.

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

Probab=98.15  E-value=9.6e-06  Score=62.99  Aligned_cols=46  Identities=17%  Similarity=0.428  Sum_probs=44.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +|+|.|+.|||+|.+|..+|-.++|+|.+|.|+|.++.+..+|.|+
T Consensus         3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~   48 (75)
T cd04897           3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIR   48 (75)
T ss_pred             EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEE
Confidence            6899999999999999999999999999999999999999999985

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.

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

Probab=98.12  E-value=5.5e-06  Score=77.21  Aligned_cols=66  Identities=24%  Similarity=0.333  Sum_probs=55.7

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRK  166 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~  166 (320)
                      .+|....++||+|=+|+|+.|..|+.-.-.-.+.+.-|+.||..||+||..||.-++++.+....+
T Consensus       117 DRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~  182 (284)
T KOG3960|consen  117 DRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGL  182 (284)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhh
Confidence            457889999999999999999999866543335788999999999999999999999888765543

>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=98.08  E-value=1.6e-05  Score=61.31  Aligned_cols=47  Identities=28%  Similarity=0.346  Sum_probs=44.4

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEEE
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNIST-VDETMHNSFTIK  316 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist-~~~~vl~tf~vK  316 (320)
                      ++|+|.|+.+||+|.+|..+|..++|.|++|.|+| .++.++++|.|.
T Consensus         1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~   48 (76)
T cd04927           1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFIT   48 (76)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEe
Confidence            47899999999999999999999999999999996 899999999985

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.

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

Probab=97.99  E-value=5.9e-06  Score=76.39  Aligned_cols=64  Identities=27%  Similarity=0.338  Sum_probs=55.6

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCChhhhHHHHHHHHHHHHHHHHHHHHHH
Q 042904          100 GQQRMSHITVERNRRKQMNENLSVLRSLMPCFY--VKRGDQASIIGGVVDYINELQQVLQSLEAKK  163 (320)
Q Consensus       100 ~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~--~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~  163 (320)
                      ..++..+|.+||+|=+.+|..|..||.+||...  .+|.+|+.+|.-||.||+.|++-++.-+...
T Consensus       107 ~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~  172 (228)
T KOG4029|consen  107 SAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL  172 (228)
T ss_pred             hhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence            345778899999999999999999999999984  5788999999999999999999876655433

>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=97.97  E-value=3.9e-05  Score=58.27  Aligned_cols=47  Identities=28%  Similarity=0.404  Sum_probs=43.6

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEEEEE
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-DETMHNSFTIK  316 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-~~~vl~tf~vK  316 (320)
                      ..|.|.|+.+||+|.+|..+|..++|+|+.|.|.|. ++.++.+|.+.
T Consensus         2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~   49 (73)
T cd04900           2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVL   49 (73)
T ss_pred             EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEE
Confidence            367899999999999999999999999999999877 79999999985

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.

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

Probab=97.95  E-value=3.4e-05  Score=59.97  Aligned_cols=46  Identities=17%  Similarity=0.147  Sum_probs=44.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE--eeCCeEEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNIS--TVDETMHNSFTIK  316 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anis--t~~~~vl~tf~vK  316 (320)
                      +|+|.|..|||+|.+|.++|..++|+|..|.|+  |.++.+..+|.+.
T Consensus         2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~   49 (75)
T cd04896           2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQ   49 (75)
T ss_pred             EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEe
Confidence            689999999999999999999999999999999  9999999999984

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.

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=97.92  E-value=5e-06  Score=89.14  Aligned_cols=66  Identities=24%  Similarity=0.468  Sum_probs=59.8

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 042904          100 GQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRK  166 (320)
Q Consensus       100 ~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~  166 (320)
                      +.+|.+||.+||+-|..||+++.+|+.+||.. .-|+.|.++|..||+||++|+...+.|+.+.+.+
T Consensus       274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~-~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l  339 (953)
T KOG2588|consen  274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGT-EAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASL  339 (953)
T ss_pred             CcccchhhHHHHHhhcchhHHHHHHHHhcCcc-HhhhhhhhhHHHHHHHHHHhhccccccchhhhhh
Confidence            47799999999999999999999999999986 4689999999999999999999998888766543

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=97.86  E-value=9.9e-06  Score=77.26  Aligned_cols=57  Identities=28%  Similarity=0.379  Sum_probs=49.7

Q ss_pred             ccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHH
Q 042904          103 RMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSL  159 (320)
Q Consensus       103 r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L  159 (320)
                      |...|.-||+|-.-||..|..||+|+|.....|.+||.||..+.+||.+|+.+--+|
T Consensus        61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence            446677799999999999999999999876779999999999999999998765444

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

Probab=97.69  E-value=0.00021  Score=54.59  Aligned_cols=46  Identities=13%  Similarity=0.260  Sum_probs=44.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +|+|.++.+||+|.+|..+|..+++.|+.|.+.+.++.++.+|.|.
T Consensus         2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~   47 (74)
T cd04925           2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVR   47 (74)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEE
Confidence            6899999999999999999999999999999999999999999985

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.

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

Probab=97.48  E-value=0.00059  Score=52.07  Aligned_cols=46  Identities=17%  Similarity=0.195  Sum_probs=42.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNIST-VDETMHNSFTIK  316 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist-~~~~vl~tf~vK  316 (320)
                      .|-|.|+.+||+|.+|..+|..++|.|+.|+|.+ .+|.++.+|.|.
T Consensus         3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~   49 (68)
T cd04928           3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVT   49 (68)
T ss_pred             EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEe
Confidence            5778999999999999999999999999999975 589999999885

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.

>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=97.35  E-value=0.0012  Score=48.79  Aligned_cols=47  Identities=21%  Similarity=0.372  Sum_probs=43.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      .|.|.|+.++|+|.+|+.+|.++++.|.++++.+.++.++..|.+.-
T Consensus         2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~   48 (70)
T cd04899           2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTD   48 (70)
T ss_pred             EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEEC
Confidence            58899999999999999999999999999999998889999998864

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.

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=97.32  E-value=0.00011  Score=64.08  Aligned_cols=64  Identities=25%  Similarity=0.331  Sum_probs=55.0

Q ss_pred             cccCCcccccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHH
Q 042904           93 DEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVL  156 (320)
Q Consensus        93 ~~~~~~~~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v  156 (320)
                      ...-++-..++..|+..||+|-..+|+.|..||.++|.....|.+|.-.|.-|..||..|-+-+
T Consensus        69 ~~~~dE~q~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl  132 (173)
T KOG4447|consen   69 IQSLDELQKQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVL  132 (173)
T ss_pred             hhhHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhcc
Confidence            3333344557999999999999999999999999999987788999999999999999987653

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.31  E-value=0.00064  Score=53.83  Aligned_cols=54  Identities=19%  Similarity=0.365  Sum_probs=45.2

Q ss_pred             HHHHHHHHHHHHhcCCCCCC----CCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          114 RKQMNENLSVLRSLMPCFYV----KRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       114 R~~in~~~~~LrslvP~~~~----~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      -++|++.+..|+.|+|....    .|..-+-+|.++..||+.|+++|..|-..+.++.
T Consensus        19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL   76 (93)
T PLN03217         19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL   76 (93)
T ss_pred             HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47899999999999998522    2344456899999999999999999999988754

>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=97.26  E-value=0.0017  Score=49.31  Aligned_cols=46  Identities=15%  Similarity=0.202  Sum_probs=42.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      .|.|.++.++|+|.+|..+|.++++.|+++.+.+.++.++.+|.+.
T Consensus         3 ri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~   48 (72)
T cd04926           3 RLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVT   48 (72)
T ss_pred             EEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEE
Confidence            5778889999999999999999999999999999888888888874

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=97.24  E-value=0.00042  Score=70.11  Aligned_cols=62  Identities=23%  Similarity=0.280  Sum_probs=50.7

Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHHhcCCCC-C-CCCCChhhhHHHHHHHHHHHHHHHHHHH
Q 042904           99 DGQQRMSHITVERNRRKQMNENLSVLRSLMPCF-Y-VKRGDQASIIGGVVDYINELQQVLQSLE  160 (320)
Q Consensus        99 ~~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~-~-~~k~dKasIL~~AI~YIk~Lq~~v~~L~  160 (320)
                      +..+|+.+|.+||-|-..||+.|++|..+.=-. . .+.-.|.-||..|+.-|-.|++||.+-.
T Consensus       523 EkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN  586 (632)
T KOG3910|consen  523 EKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN  586 (632)
T ss_pred             HHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc
Confidence            566789999999999999999999998876432 1 1223688899999999999999997643

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

Probab=96.64  E-value=0.013  Score=42.72  Aligned_cols=47  Identities=28%  Similarity=0.428  Sum_probs=42.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      .|.|.|+.++|+|.+|+.+|.++++.|.++.+.+.++.....|++.-
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~   48 (70)
T cd04873           2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTD   48 (70)
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEEC
Confidence            57889999999999999999999999999999988777777787753

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

>PRK05007 PII uridylyl-transferase; Provisional

Probab=96.59  E-value=0.0062  Score=66.74  Aligned_cols=50  Identities=16%  Similarity=0.333  Sum_probs=47.5

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          267 GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       267 g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +...+|+|.|..|||+|.+|.++|..++|+|.+|.|+|.++.+..+|.|.
T Consensus       806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~  855 (884)
T PRK05007        806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILA  855 (884)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEE
Confidence            45689999999999999999999999999999999999999999999985

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

Probab=96.44  E-value=0.023  Score=43.49  Aligned_cols=49  Identities=14%  Similarity=0.292  Sum_probs=42.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          269 NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       269 ~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      .++|.+.++.|||++..|..+|.+++..|+.++.++.++.+...+.+.+
T Consensus         2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~   50 (76)
T PF13740_consen    2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSI   50 (76)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEe
Confidence            5799999999999999999999999999999999999999777777665

>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=96.43  E-value=0.022  Score=40.96  Aligned_cols=38  Identities=18%  Similarity=0.335  Sum_probs=35.6

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCC
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDE  307 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~  307 (320)
                      +.|.|.|+.+||+|.+|..+|.++++.|.++.+.+..+
T Consensus         1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~   38 (66)
T PF01842_consen    1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKD   38 (66)
T ss_dssp             EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence            46889999999999999999999999999999998876

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 ....

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

Probab=96.41  E-value=0.027  Score=42.99  Aligned_cols=51  Identities=24%  Similarity=0.317  Sum_probs=43.0

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEEEEecC
Q 042904          269 NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV--DETMHNSFTIKVTK  319 (320)
Q Consensus       269 ~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~--~~~vl~tf~vKv~~  319 (320)
                      .+.|+|.+..++|+|.+|..+|.+.++.|.++++...  ++.....|+++|..
T Consensus         6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d   58 (80)
T PF13291_consen    6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKD   58 (80)
T ss_dssp             EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESS
T ss_pred             EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECC
Confidence            3788999999999999999999999999999999984  67888888888753

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=96.39  E-value=0.016  Score=63.77  Aligned_cols=58  Identities=21%  Similarity=0.408  Sum_probs=50.9

Q ss_pred             ceEEEEEe--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          259 ADVEVKFS--GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~~--g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +.|.+.-.  .+...|.|.+..+||+|.+|..+|..++|+|+.|.|+|.++.++.+|.|.
T Consensus       802 ~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~  861 (895)
T PRK00275        802 TQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFIT  861 (895)
T ss_pred             CEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEE
Confidence            44555432  35679999999999999999999999999999999999999999999986

>PRK04374 PII uridylyl-transferase; Provisional

Probab=96.25  E-value=0.02  Score=62.75  Aligned_cols=58  Identities=24%  Similarity=0.352  Sum_probs=51.2

Q ss_pred             ceEEEEEe--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          259 ADVEVKFS--GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~~--g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +.|.+...  ++-..|.|.+..+||+|.+|..+|..++|+|+.|.|+|.++.++.+|.|.
T Consensus       784 ~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~  843 (869)
T PRK04374        784 PRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQIT  843 (869)
T ss_pred             CeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEE
Confidence            45555432  35689999999999999999999999999999999999999999999986

>PRK03059 PII uridylyl-transferase; Provisional

Probab=96.12  E-value=0.023  Score=62.19  Aligned_cols=50  Identities=22%  Similarity=0.377  Sum_probs=47.0

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          267 GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       267 g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      ++...|.|.|+.+||+|.+|..+|..++|+|+.|.|+|.++.++.+|.|.
T Consensus       784 ~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~  833 (856)
T PRK03059        784 GQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLID  833 (856)
T ss_pred             CCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEc
Confidence            35689999999999999999999999999999999999999999999983

>PRK03381 PII uridylyl-transferase; Provisional

Probab=96.11  E-value=0.023  Score=61.55  Aligned_cols=49  Identities=16%  Similarity=0.324  Sum_probs=46.9

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          268 PNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       268 ~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +...|.|.|..+||+|.+|..+|..++|+|++|.|+|.++.++.+|.|.
T Consensus       706 ~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~  754 (774)
T PRK03381        706 DATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVT  754 (774)
T ss_pred             CeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEE
Confidence            4589999999999999999999999999999999999999999999986

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=96.02  E-value=0.019  Score=62.86  Aligned_cols=50  Identities=14%  Similarity=0.302  Sum_probs=47.2

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          267 GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       267 g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +.-.+|+|.+..+||+|.+|.++|.+++|+|..|.|+|.++.+..+|-|.
T Consensus       781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~  830 (854)
T PRK01759        781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILT  830 (854)
T ss_pred             CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEE
Confidence            34589999999999999999999999999999999999999999999985

>PRK05092 PII uridylyl-transferase; Provisional

Probab=95.93  E-value=0.034  Score=61.37  Aligned_cols=59  Identities=20%  Similarity=0.273  Sum_probs=51.2

Q ss_pred             ceEEEEEe--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          259 ADVEVKFS--GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       259 ~~VeV~~~--g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      +.|.+.-.  +....|.|.|..+||+|.+|..+|..+||+|.+|.|.|.++.++.+|.|.-
T Consensus       831 ~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d  891 (931)
T PRK05092        831 PRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTD  891 (931)
T ss_pred             CEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeC
Confidence            44555432  355899999999999999999999999999999999999999999999953

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

Probab=95.86  E-value=0.046  Score=41.91  Aligned_cols=48  Identities=13%  Similarity=0.277  Sum_probs=42.5

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      +.|.+.|+.+||++.+|-+.|.++|..|+.++....++..+..+.+.+
T Consensus         2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~   49 (77)
T cd04893           2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEG   49 (77)
T ss_pred             EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEe
Confidence            688999999999999999999999999999999998887666555554

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

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

Probab=95.57  E-value=0.026  Score=60.80  Aligned_cols=58  Identities=19%  Similarity=0.323  Sum_probs=51.4

Q ss_pred             ceEEEEE--eCCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          259 ADVEVKF--SGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~--~g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      |.|.+.-  ..+..+|++.+..|||+|..|-.+|..++|+|++|.|+|+|+.+..+|.|-
T Consensus       779 p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt  838 (867)
T COG2844         779 PRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVT  838 (867)
T ss_pred             CceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEe
Confidence            5666653  345689999999999999999999999999999999999999999998875

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=95.43  E-value=0.049  Score=59.44  Aligned_cols=51  Identities=20%  Similarity=0.304  Sum_probs=47.1

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE-eeCCeEEEEEEEEe
Q 042904          267 GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNIS-TVDETMHNSFTIKV  317 (320)
Q Consensus       267 g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anis-t~~~~vl~tf~vKv  317 (320)
                      .+...|.|.++.+||+|.+|..+|..++|+|+.|.|. +.++.++.+|.|+-
T Consensus       666 ~~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~  717 (850)
T TIGR01693       666 SGGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQD  717 (850)
T ss_pred             CCeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEEC
Confidence            4567899999999999999999999999999999998 77999999999974

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.

>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=95.39  E-value=0.11  Score=38.63  Aligned_cols=47  Identities=15%  Similarity=0.263  Sum_probs=41.2

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEEEEEEec
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD-ETMHNSFTIKVT  318 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~-~~vl~tf~vKv~  318 (320)
                      |+|.+..+||+|.+|+.+|.+.+..|.++++.... +.....|++++.
T Consensus         2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~   49 (74)
T cd04887           2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAP   49 (74)
T ss_pred             EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcC
Confidence            78899999999999999999999999999998764 676677888774

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.

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

Probab=95.38  E-value=0.017  Score=54.66  Aligned_cols=58  Identities=24%  Similarity=0.333  Sum_probs=50.9

Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHH
Q 042904           99 DGQQRMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVL  156 (320)
Q Consensus        99 ~~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v  156 (320)
                      .-..|..-|..||+|--.+|+.|+.||.++|.. ...|+.|...|.-|-+||..|++-.
T Consensus        69 ~~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~  127 (254)
T KOG3898|consen   69 LTLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVL  127 (254)
T ss_pred             hhhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcccc
Confidence            445688999999999999999999999999953 4678999999999999999998653

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=95.21  E-value=0.066  Score=58.63  Aligned_cols=58  Identities=17%  Similarity=0.147  Sum_probs=50.2

Q ss_pred             ceEEEEE--eCCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEEE
Q 042904          259 ADVEVKF--SGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNIST-VDETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~--~g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist-~~~~vl~tf~vK  316 (320)
                      +.|.+.-  ..+...|.|.|+.+||+|.+|..+|..++|.|+.|.|.| .+|.++.+|.|.
T Consensus       665 ~~V~i~~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~  725 (854)
T PRK01759        665 LLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVT  725 (854)
T ss_pred             CEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEe
Confidence            4555543  245679999999999999999999999999999999976 899999999985

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=95.14  E-value=0.066  Score=58.44  Aligned_cols=51  Identities=20%  Similarity=0.323  Sum_probs=47.6

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          267 GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       267 g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      .+..+|.|.|..+||+|.+|.++|..++++|.++.|+|.++.+..+|.+..
T Consensus       777 ~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~  827 (850)
T TIGR01693       777 RKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTD  827 (850)
T ss_pred             CCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEEC
Confidence            356899999999999999999999999999999999999999999999864

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.

>PRK03381 PII uridylyl-transferase; Provisional

Probab=95.10  E-value=0.07  Score=57.85  Aligned_cols=58  Identities=16%  Similarity=0.172  Sum_probs=50.1

Q ss_pred             ceEEEEEe-CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          259 ADVEVKFS-GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~~-g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +-|.++-. .+.+.|.|.|+.+||++.+|..+|..+|+.|+.|+|.+.+|.++.+|.|.
T Consensus       588 ~~v~~~~~~~~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~  646 (774)
T PRK03381        588 VHVEIAPADPHMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVS  646 (774)
T ss_pred             CEEEEeeCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEE
Confidence            34444322 46689999999999999999999999999999999999999999999986

>PRK05007 PII uridylyl-transferase; Provisional

Probab=95.05  E-value=0.085  Score=58.00  Aligned_cols=58  Identities=16%  Similarity=0.118  Sum_probs=49.2

Q ss_pred             ceEEEEE--eCCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEEEEE
Q 042904          259 ADVEVKF--SGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-DETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~--~g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-~~~vl~tf~vK  316 (320)
                      +-|.+.-  ..+...|.|.|+.++|+|.+|..+|..++|+|+.|.|.|. +|.++.+|.|.
T Consensus       689 p~V~i~~~~~~~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~  749 (884)
T PRK05007        689 PLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVL  749 (884)
T ss_pred             CeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEE
Confidence            4455543  2467899999999999999999999999999999999765 56999999985

>PRK00194 hypothetical protein; Validated

Probab=94.99  E-value=0.073  Score=41.54  Aligned_cols=49  Identities=12%  Similarity=0.277  Sum_probs=42.0

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          269 NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       269 ~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      .+.|.|.|+.+||++.+|.+.|.++|+.|++.+..+.++...-.+.+.+
T Consensus         3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~   51 (90)
T PRK00194          3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDI   51 (90)
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEe
Confidence            5789999999999999999999999999999998887776555455544

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

Probab=94.97  E-value=0.12  Score=39.22  Aligned_cols=47  Identities=15%  Similarity=0.227  Sum_probs=38.7

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC------CeEEEEEEEEe
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD------ETMHNSFTIKV  317 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~------~~vl~tf~vKv  317 (320)
                      .|.|.|+.+||++.+|-+.|.++++.|.+.+..+.+      +.+.-.+.+.+
T Consensus         1 ~l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~   53 (81)
T cd04869           1 VVEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLAL   53 (81)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEec
Confidence            378999999999999999999999999999998876      44444444443

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

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=94.85  E-value=0.079  Score=58.32  Aligned_cols=49  Identities=10%  Similarity=0.196  Sum_probs=45.1

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEE-EeeCCeEEEEEEEE
Q 042904          268 PNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNI-STVDETMHNSFTIK  316 (320)
Q Consensus       268 ~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~ani-st~~~~vl~tf~vK  316 (320)
                      +-..|.|.|+.+||+|.+|+.+|..++|.|+.|.| |+-+|.++.+|.|.
T Consensus       703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~  752 (895)
T PRK00275        703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVL  752 (895)
T ss_pred             CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEe
Confidence            56899999999999999999999999999999998 56688999999984

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

Probab=94.82  E-value=0.14  Score=36.86  Aligned_cols=46  Identities=20%  Similarity=0.364  Sum_probs=37.2

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-----CCeEEEEEEEEe
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-----DETMHNSFTIKV  317 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-----~~~vl~tf~vKv  317 (320)
                      |.|.++.+||.|.+|+.+|.+.++.|.+.+....     .+.....|++++
T Consensus         1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~   51 (73)
T cd04886           1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLET   51 (73)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEe
Confidence            4678899999999999999999999998887654     355555666655

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.

>PRK03059 PII uridylyl-transferase; Provisional

Probab=94.81  E-value=0.089  Score=57.68  Aligned_cols=50  Identities=20%  Similarity=0.364  Sum_probs=46.0

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEE-EeeCCeEEEEEEEE
Q 042904          267 GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNI-STVDETMHNSFTIK  316 (320)
Q Consensus       267 g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~ani-st~~~~vl~tf~vK  316 (320)
                      .+...|-|.|+.+||+|.+|..+|..++|.|+.|.| ++.+|.++.+|.|-
T Consensus       676 ~~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~  726 (856)
T PRK03059        676 GEGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVL  726 (856)
T ss_pred             CCeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEe
Confidence            366899999999999999999999999999999999 46789999999984

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

Probab=94.72  E-value=0.08  Score=41.33  Aligned_cols=48  Identities=15%  Similarity=0.278  Sum_probs=41.8

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      +.|.+.|+.+||++..|.+.|-.+|+.|++.+..+.++.+.-.+.+.+
T Consensus         2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~   49 (88)
T cd04872           2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDI   49 (88)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEe
Confidence            679999999999999999999999999999999888777555555554

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.

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

Probab=94.60  E-value=0.12  Score=38.81  Aligned_cols=35  Identities=17%  Similarity=0.210  Sum_probs=32.4

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV  305 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~  305 (320)
                      .|.|.|+.+||++.+|.+.|.++|+.|++.+..+.
T Consensus         1 ii~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~   35 (74)
T cd04875           1 ILTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVD   35 (74)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeec
Confidence            37899999999999999999999999999998863

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.

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

Probab=94.25  E-value=0.21  Score=37.05  Aligned_cols=49  Identities=14%  Similarity=0.276  Sum_probs=40.5

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEEEEEec
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-DETMHNSFTIKVT  318 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-~~~vl~tf~vKv~  318 (320)
                      +.|.|.+..++|+|.+|+.+|.+++..|...+.+.. ++.....|++.+.
T Consensus         1 ~~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v~   50 (76)
T cd04888           1 VTLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDTS   50 (76)
T ss_pred             CEEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEcC
Confidence            357889999999999999999999999999987653 4666667777654

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.

>PRK05092 PII uridylyl-transferase; Provisional

Probab=94.19  E-value=0.18  Score=55.78  Aligned_cols=58  Identities=21%  Similarity=0.213  Sum_probs=49.8

Q ss_pred             ceEEEEEe--CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEEE
Q 042904          259 ADVEVKFS--GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNIST-VDETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~~--g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist-~~~~vl~tf~vK  316 (320)
                      +.|.++..  .+...|.|.|+.++|+|.+|..+|..++++|+.|.|.| .+++++.+|.|.
T Consensus       720 ~~v~~~~~~~~~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~  780 (931)
T PRK05092        720 LATEVRPDPARGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQ  780 (931)
T ss_pred             cEEEEEecCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEE
Confidence            44555443  35789999999999999999999999999999999976 689999999885

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

Probab=94.05  E-value=0.27  Score=33.94  Aligned_cols=46  Identities=24%  Similarity=0.327  Sum_probs=37.6

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEEEEEEe
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD-ETMHNSFTIKV  317 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~-~~vl~tf~vKv  317 (320)
                      |++.|..++|.+.+|++.|.+++++|.+..+...+ +.....|++++
T Consensus         1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~   47 (71)
T cd04876           1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEV   47 (71)
T ss_pred             CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEE
Confidence            46789999999999999999999999999887655 55545566654

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

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

Probab=93.97  E-value=0.22  Score=37.76  Aligned_cols=47  Identities=17%  Similarity=0.360  Sum_probs=40.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      +|.+.++.|||++.+|.++|.++++.|.+.+.++.++.+...|.+.+
T Consensus         1 ~vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~   47 (75)
T cd04870           1 LITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQI   47 (75)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEc
Confidence            47899999999999999999999999999998888887555555554

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.

>PRK04435 hypothetical protein; Provisional

Probab=93.78  E-value=0.35  Score=41.93  Aligned_cols=54  Identities=17%  Similarity=0.273  Sum_probs=46.6

Q ss_pred             EeCCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEEEec
Q 042904          265 FSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNIST-VDETMHNSFTIKVT  318 (320)
Q Consensus       265 ~~g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist-~~~~vl~tf~vKv~  318 (320)
                      ..|+.+.|.+.+..++|+|.+|+++|.+.+..|++.+.+. .++....+|++.+.
T Consensus        65 ~~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs  119 (147)
T PRK04435         65 VKGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTS  119 (147)
T ss_pred             CCCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeC
Confidence            4578899999999999999999999999999999998765 46777777888764

>PRK04374 PII uridylyl-transferase; Provisional

Probab=93.75  E-value=0.21  Score=54.92  Aligned_cols=50  Identities=16%  Similarity=0.283  Sum_probs=46.1

Q ss_pred             CCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEe-eCCeEEEEEEEE
Q 042904          267 GPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNIST-VDETMHNSFTIK  316 (320)
Q Consensus       267 g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist-~~~~vl~tf~vK  316 (320)
                      .+...|-|.|+.++|+|.+|..+|..++|.|+.|.|.| .+|.++.+|.|.
T Consensus       688 ~~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~  738 (869)
T PRK04374        688 NDALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVL  738 (869)
T ss_pred             CCeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEe
Confidence            35689999999999999999999999999999999986 689999999985

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

Probab=93.49  E-value=0.38  Score=31.34  Aligned_cols=35  Identities=26%  Similarity=0.432  Sum_probs=31.2

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD  306 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~  306 (320)
                      |.+.|+.++|.+.+|+.+|...++.|...+.....
T Consensus         1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (60)
T cd02116           1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG   35 (60)
T ss_pred             CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence            56888999999999999999999999999987653

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

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

Probab=93.26  E-value=0.34  Score=36.52  Aligned_cols=37  Identities=11%  Similarity=0.170  Sum_probs=33.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCe
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDET  308 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~  308 (320)
                      .|+|.|..++|+|.+|+.+|.+++..|.+.++.+- +.
T Consensus         2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~   38 (74)
T cd04877           2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GR   38 (74)
T ss_pred             EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-Ce
Confidence            58899999999999999999999999999999765 55

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

>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=92.74  E-value=0.46  Score=34.68  Aligned_cols=47  Identities=21%  Similarity=0.198  Sum_probs=37.8

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-C-CeEEEEEEEE
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-D-ETMHNSFTIK  316 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-~-~~vl~tf~vK  316 (320)
                      ++|+|.+..++|+|.+|+..|.+.+..|.+.+.... + +.....|.++
T Consensus         1 ~yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~   49 (79)
T cd04881           1 YYLRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTH   49 (79)
T ss_pred             CEEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEc
Confidence            478999999999999999999999999999987665 3 5444444443

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.

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

Probab=92.61  E-value=0.69  Score=33.25  Aligned_cols=45  Identities=9%  Similarity=0.066  Sum_probs=35.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD-ETMHNSFTI  315 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~-~~vl~tf~v  315 (320)
                      .|.+.++.++|.|.+|+..|.+.++.|.+.+....+ +.....|.+
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i~~   47 (72)
T cd04874           2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYMEL   47 (72)
T ss_pred             eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEEEE
Confidence            578899999999999999999999999998887653 443333433

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.

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

Probab=91.93  E-value=0.28  Score=46.42  Aligned_cols=56  Identities=23%  Similarity=0.253  Sum_probs=47.8

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVL  156 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v  156 (320)
                      -+|..-+..||+|-..||..|+.||..||.. ..+|.+|-..|.-|-.||--|-..+
T Consensus       173 ~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l  229 (285)
T KOG4395|consen  173 HRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL  229 (285)
T ss_pred             hhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence            3467789999999999999999999999986 3567889999999999998776554

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

Probab=91.46  E-value=1.3  Score=31.60  Aligned_cols=47  Identities=13%  Similarity=0.191  Sum_probs=38.6

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEEEEe
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV--DETMHNSFTIKV  317 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~--~~~vl~tf~vKv  317 (320)
                      .|.+.+..++|+|.+|+..|.+.++.|...+....  ++.....|.+++
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~   50 (72)
T cd04878           2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEG   50 (72)
T ss_pred             EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEEC
Confidence            46788899999999999999999999999988764  455566666654

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

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

Probab=90.99  E-value=0.95  Score=32.14  Aligned_cols=45  Identities=16%  Similarity=0.231  Sum_probs=37.6

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC--CeEEEEEEEE
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD--ETMHNSFTIK  316 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~--~~vl~tf~vK  316 (320)
                      +.|.+..++|++.+|+..|.+.++.|.+.++....  +.....|+++
T Consensus         2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~   48 (71)
T cd04879           2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVD   48 (71)
T ss_pred             EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcC
Confidence            56788999999999999999999999999987654  6666666653

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

>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=90.76  E-value=1  Score=31.67  Aligned_cols=46  Identities=15%  Similarity=0.208  Sum_probs=37.4

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEEEEEEe
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD-ETMHNSFTIKV  317 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~-~~vl~tf~vKv  317 (320)
                      |.+..+.+||.|.+|++.|.+.++.|.+..+...+ +..+..|.+..
T Consensus         1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~~   47 (56)
T cd04889           1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFSD   47 (56)
T ss_pred             CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEECC
Confidence            45678999999999999999999999888887655 66666666543

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

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

Probab=90.44  E-value=1.4  Score=32.99  Aligned_cols=46  Identities=9%  Similarity=0.170  Sum_probs=36.4

Q ss_pred             EEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCC-eEEEEEEEEec
Q 042904          273 KTVSPRIPGQAVKIISALEDLAFEILHVNISTVDE-TMHNSFTIKVT  318 (320)
Q Consensus       273 kI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~-~vl~tf~vKv~  318 (320)
                      -+..+.+||.|.+|+..|..+++.+++.......+ .--|.|.+.+.
T Consensus         3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~   49 (75)
T cd04880           3 VFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFE   49 (75)
T ss_pred             EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEE
Confidence            34456789999999999999999999998876644 44567777664

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

>PRK08577 hypothetical protein; Provisional

Probab=90.42  E-value=1.9  Score=36.54  Aligned_cols=51  Identities=18%  Similarity=0.255  Sum_probs=41.4

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC--CeEEEEEEEEec
Q 042904          268 PNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD--ETMHNSFTIKVT  318 (320)
Q Consensus       268 ~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~--~~vl~tf~vKv~  318 (320)
                      +.+.|.|.+..++|+|.+|+++|.+++..+.+.+..+..  +...-.|++.+.
T Consensus        55 ~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~  107 (136)
T PRK08577         55 KLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLS  107 (136)
T ss_pred             cEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeC
Confidence            478999999999999999999999999999998887653  444445555553

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

Probab=89.38  E-value=1.6  Score=31.12  Aligned_cols=44  Identities=23%  Similarity=0.313  Sum_probs=34.5

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEEE
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTV--DETMHNSFTI  315 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~--~~~vl~tf~v  315 (320)
                      |.+.+..++|.+.+|+..|.++++.|.+.+....  ++.....|.+
T Consensus         2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v   47 (71)
T cd04903           2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEV   47 (71)
T ss_pred             EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEe
Confidence            6788999999999999999999999998887653  3443333443

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.

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

Probab=88.78  E-value=1.4  Score=33.47  Aligned_cols=46  Identities=13%  Similarity=0.128  Sum_probs=40.3

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      +|.|.|+.+.|+--+|++.+=++||.|....++|-+..-+-.|-|.
T Consensus         2 vitvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv   47 (69)
T cd04894           2 VITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVV   47 (69)
T ss_pred             EEEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEe
Confidence            6899999999999999999999999999999999887655555553

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.

>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=88.78  E-value=2.8  Score=31.89  Aligned_cols=48  Identities=10%  Similarity=0.223  Sum_probs=37.6

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEEEEEEec
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD-ETMHNSFTIKVT  318 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~-~~vl~tf~vKv~  318 (320)
                      .|.+.-+.++|.|.+|+..|.++++.+++....... +...+.|.+.+.
T Consensus         3 sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~   51 (80)
T cd04905           3 SIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFE   51 (80)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEE
Confidence            344555778999999999999999999999877653 455577777664

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

>PRK07334 threonine dehydratase; Provisional

Probab=88.59  E-value=1.9  Score=43.02  Aligned_cols=49  Identities=12%  Similarity=0.209  Sum_probs=43.0

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-----CCeEEEEEEEEec
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-----DETMHNSFTIKVT  318 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-----~~~vl~tf~vKv~  318 (320)
                      +.|+|.+..++|+|.+|+.+|.+.++.|.++++.+.     ++...-.|+++|.
T Consensus       327 v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~  380 (403)
T PRK07334        327 ARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETR  380 (403)
T ss_pred             EEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeC
Confidence            899999999999999999999999999999998764     5676667777764

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

Probab=87.70  E-value=1.5  Score=47.67  Aligned_cols=58  Identities=17%  Similarity=0.176  Sum_probs=49.7

Q ss_pred             ceEEEEEeCCeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEE-eeCCeEEEEEEEE
Q 042904          259 ADVEVKFSGPNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNIS-TVDETMHNSFTIK  316 (320)
Q Consensus       259 ~~VeV~~~g~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anis-t~~~~vl~tf~vK  316 (320)
                      ..+.++...+...|-|.|+.+|.++..|+.++...|++|+.|+|- +-+|.++.+|.|-
T Consensus       674 v~~~~r~~~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~  732 (867)
T COG2844         674 VLISVRPHSGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVL  732 (867)
T ss_pred             eeeeecccCCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEe
Confidence            344445556778999999999999999999999999999999995 5689999999775

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

Probab=87.45  E-value=3.4  Score=30.12  Aligned_cols=36  Identities=22%  Similarity=0.317  Sum_probs=31.6

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV  305 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~  305 (320)
                      +.+.+.++.+||.|.+|+..|.++++.|........
T Consensus         2 ~~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~   37 (69)
T cd04909           2 YDLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI   37 (69)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence            457888999999999999999999999998876654

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.

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=86.26  E-value=0.69  Score=40.74  Aligned_cols=46  Identities=20%  Similarity=0.258  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHH
Q 042904          109 VERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQ  154 (320)
Q Consensus       109 ~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~  154 (320)
                      .||.|-+++|+.|.-|+.|+|.....++.+.--|.-+-+||.+|.+
T Consensus        29 ~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~dE   74 (173)
T KOG4447|consen   29 KERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSLDE   74 (173)
T ss_pred             HHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhHHH
Confidence            6999999999999999999999755555544446666666665543

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

Probab=86.23  E-value=2.1  Score=30.44  Aligned_cols=44  Identities=18%  Similarity=0.169  Sum_probs=33.5

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC--CeEEEEEEE
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD--ETMHNSFTI  315 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~--~~vl~tf~v  315 (320)
                      |.+.-+.+||.|.+|+..|.+.++.|.+.......  +.....|.+
T Consensus         2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~v   47 (65)
T cd04882           2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRT   47 (65)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEe
Confidence            56677899999999999999999999877765443  444444444

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.

>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family

Probab=83.98  E-value=5.3  Score=42.97  Aligned_cols=61  Identities=11%  Similarity=0.181  Sum_probs=49.9

Q ss_pred             ceEEEEEeCC-----eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCeEEEEEEEEecC
Q 042904          259 ADVEVKFSGP-----NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-DETMHNSFTIKVTK  319 (320)
Q Consensus       259 ~~VeV~~~g~-----~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-~~~vl~tf~vKv~~  319 (320)
                      .-|.|+....     .+.|+|.+..++|+|.+|+.+|.+.+..|.++++.+. +++..-.|+++|..
T Consensus       595 r~I~v~W~~~~~~~f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~~~~~~~~~ieV~~  661 (683)
T TIGR00691       595 KIIEVEWNASKPRRFIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGKREAILNITVEIKN  661 (683)
T ss_pred             cEEEEEecCCCCceeEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCEEEEEEEEEECC
Confidence            3577777432     4689999999999999999999999999999999876 46766678887753

(p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.

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

Probab=83.94  E-value=5.6  Score=29.01  Aligned_cols=38  Identities=18%  Similarity=0.292  Sum_probs=32.5

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCe
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDET  308 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~  308 (320)
                      .|.|..+.+||.|.+|+++|.+.++.|.+..+....+.
T Consensus         3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~   40 (66)
T cd04908           3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEF   40 (66)
T ss_pred             EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCC
Confidence            46778899999999999999999999998887665553

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.

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=83.93  E-value=0.86  Score=47.45  Aligned_cols=39  Identities=28%  Similarity=0.474  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHHHHhcCCCC--CCCCCChhhhHHHHHHHHH
Q 042904          112 NRRKQMNENLSVLRSLMPCF--YVKRGDQASIIGGVVDYIN  150 (320)
Q Consensus       112 ~RR~~in~~~~~LrslvP~~--~~~k~dKasIL~~AI~YIk  150 (320)
                      +-|+++|.-|+.|.+|+|-.  .++|.||.|||.-++.|++
T Consensus        35 RHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   35 RHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             hHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            35899999999999999964  3579999999999999986

>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional

Probab=83.81  E-value=5.5  Score=43.36  Aligned_cols=61  Identities=15%  Similarity=0.209  Sum_probs=49.8

Q ss_pred             ceEEEEEeCC-----eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEEEEecC
Q 042904          259 ADVEVKFSGP-----NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV--DETMHNSFTIKVTK  319 (320)
Q Consensus       259 ~~VeV~~~g~-----~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~--~~~vl~tf~vKv~~  319 (320)
                      .-|+|++...     .+.|.|.+..++|+|.+|..+|.+.++.|.++++.+.  +++..-.|+++|..
T Consensus       651 R~I~V~W~~~~~~~~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~~~~~~~~ieV~~  718 (743)
T PRK10872        651 RIVDAVWGESYSSGYSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQLATIDMTIEIYN  718 (743)
T ss_pred             eEEEeEecCCCCceeEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCCEEEEEEEEEECC
Confidence            3577877532     3689999999999999999999999999999999765  46766678888753

>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional

Probab=83.72  E-value=5.5  Score=43.08  Aligned_cols=61  Identities=11%  Similarity=0.100  Sum_probs=49.5

Q ss_pred             ceEEEEEeCC-----eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC-CeEEEEEEEEecC
Q 042904          259 ADVEVKFSGP-----NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD-ETMHNSFTIKVTK  319 (320)
Q Consensus       259 ~~VeV~~~g~-----~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~-~~vl~tf~vKv~~  319 (320)
                      .-|+|+....     .+.|+|.+..++|+|.+|+.+|.+.++.|.++++.+.+ ++..-.|+++|..
T Consensus       611 r~i~v~W~~~~~~~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ieV~~  677 (702)
T PRK11092        611 KFMAVEWDKETEQEFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGRVYSAFIRLTARD  677 (702)
T ss_pred             eeEEeEECCCCCceeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCCEEEEEEEEEECC
Confidence            3577877532     46899999999999999999999999999999987765 5655668887753

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

Probab=83.47  E-value=7.6  Score=28.24  Aligned_cols=46  Identities=20%  Similarity=0.344  Sum_probs=35.8

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee--CCeEEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV--DETMHNSFTIK  316 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~--~~~vl~tf~vK  316 (320)
                      .|.+..+.+||.|.+|+..|.+.++.|.+......  ++.....|.+.
T Consensus         3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~   50 (72)
T cd04883           3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQ   50 (72)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEe
Confidence            57778899999999999999999999998765433  34555556554

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.

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

Probab=80.54  E-value=1.3  Score=47.39  Aligned_cols=44  Identities=30%  Similarity=0.398  Sum_probs=37.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHhcCCCC--CCCCCChhhhHHHHHHHHH
Q 042904          107 ITVERNRRKQMNENLSVLRSLMPCF--YVKRGDQASIIGGVVDYIN  150 (320)
Q Consensus       107 ~~~ER~RR~~in~~~~~LrslvP~~--~~~k~dKasIL~~AI~YIk  150 (320)
                      .-+-|-||.|=|+-|++|..+||-.  -....|||+|+.-||-|++
T Consensus        51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH
Confidence            3456889999999999999999942  1346799999999999986

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

Probab=80.13  E-value=9.2  Score=28.22  Aligned_cols=34  Identities=12%  Similarity=0.244  Sum_probs=29.4

Q ss_pred             EEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 042904          272 LKTVSPRIPGQAVKIISALEDLAFEILHVNISTV  305 (320)
Q Consensus       272 IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~  305 (320)
                      +.+.-+.+||.|.+++..|.++|..|++......
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            4566688999999999999999999999877654

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.

---

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	320
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	2e-11
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	4e-11
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	1e-10
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	1e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-09
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	9e-08
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	4e-07
1a0a_A	63	BHLH, protein (phosphate system positive regulator	5e-05
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	8e-05

>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 = 58.1 bits (141), Expect = 2e-11
 Identities = 15/75 (20%), Positives = 33/75 (44%)

Query: 91  SSDEANNTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYIN 150
           + D    +D  +R  H  +ER RR  + ++   LR  +P    ++  +A I+    +YI 
Sbjct: 1   NDDIEVESDADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQ 60

Query: 151 ELQQVLQSLEAKKQR 165
            +++   + +     
Sbjct: 61  YMRRKNHTHQQDIDD 75

>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 = 57.4 bits (139), Expect = 4e-11
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 100 GQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSL 159
           G++R +H  +E+  R  +N+ +  L+ L+     K  ++++++   +DYI  LQ   Q L
Sbjct: 4   GEKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKL-NKSAVLRKAIDYIRFLQHSNQKL 62

Query: 160 EAKKQR 165
           + +   
Sbjct: 63  KQENLS 68

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

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 99  DGQQRMSHITVERNRRKQMNENLSVLRSLMP-CFYVKRGDQASIIGGVVDYINELQQVLQ 157
              +R +H  +ER RR ++  +   LR  +P     ++  +  I+     YI  +Q   Q
Sbjct: 3   MNVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQ 62

Query: 158 SLEAKKQR 165
            L +++  
Sbjct: 63  KLISEEDL 70

>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 = 55.8 bits (135), Expect = 1e-10
 Identities = 13/64 (20%), Positives = 29/64 (45%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEA 161
           +R  H  +ER RR  + ++   LR  +P    ++  +A I+    +YI  +++   + + 
Sbjct: 2   KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ 61

Query: 162 KKQR 165
               
Sbjct: 62  DIDD 65

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

 Score = 56.0 bits (134), Expect = 7e-09
 Identities = 63/372 (16%), Positives = 116/372 (31%), Gaps = 93/372 (25%)

Query: 7   DTLSEY---FFDEGETNLAEDDLFAIF--ESLDSVTPLDEAATAVSEARLV------SQK 55
           D LS +   F D  +    +D   +I   E +D +     +  AVS    +       Q+
Sbjct: 20  DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHII---MSKDAVSGTLRLFWTLLSKQE 76

Query: 56  STSSSILQESDETDQ--LTETLPKNKRQKTAATSAVNSSDEANNTDGQQRMSHITVERNR 113
                 ++E    +   L   +   +RQ +  T       +    D Q   +   V  +R
Sbjct: 77  EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQ-VFAKYNV--SR 133

Query: 114 RKQMNENLSVLRSLMPCFYVKRGDQASII---GG------VVDYINELQQVLQSLEAKKQ 164
            +   +    L  L P   V       +I    G       +D       V  S + + +
Sbjct: 134 LQPYLKLRQALLELRPAKNV-------LIDGVLGSGKTWVALD-------VCLSYKVQCK 179

Query: 165 R--KVY------CEVLSPRLVSSPRPSPLSPRKPPLSPRLNLPISPRTPQPGSPYKPR-- 214
              K++      C   SP  V       L    P  + R +   + +        + R  
Sbjct: 180 MDFKIFWLNLKNCN--SPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237

Query: 215 LQQQGY---L-------SPT--KATNNNSVEPSPCSS--STSSIDSINELVANSKSAIAD 260
           L+ + Y   L       +     A N +      C    +T      + L A + + I+ 
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNLS------CKILLTTRFKQVTDFLSAATTTHISL 291

Query: 261 VEVK--FSGP---NLLLKTVSPRI---PGQAVKI-------ISAL--EDLA-FE-ILHVN 301
                  +     +LLLK +  R    P + +         I+    + LA ++   HVN
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVN 351

Query: 302 ISTVDETMHNSF 313
              +   + +S 
Sbjct: 352 CDKLTTIIESSL 363

>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 = 47.9 bits (114), Expect = 9e-08
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 103 RMSHITVERNRRKQMNENLSVLRSLMPCFY-VKRGDQASIIGGVVDYINELQQVLQSLEA 161
           R +H  +E+NRR  +  +L  L+ L+P      R    S++     +I +L+   +    
Sbjct: 2   RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH 61

Query: 162 KKQR 165
           +  +
Sbjct: 62  QIDQ 65

>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 = 45.4 bits (108), Expect = 4e-07
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 99  DGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQ----ASIIGGVVDYINELQQ 154
           D ++R  H  VER RR ++N  +  L  ++P   ++          I+    DYI EL+Q
Sbjct: 2   DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ 61

>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 = 39.4 bits (92), Expect = 5e-05
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQ-----ASIIGGVVDYINELQQ 154
           +R SH   E+ RR ++   L  L SL+P  + ++        A+ +     YI  LQQ
Sbjct: 2   KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQ 59

>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* Length = 68

 Score = 39.3 bits (92), Expect = 8e-05
 Identities = 14/57 (24%), Positives = 25/57 (43%)

Query: 101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQ 157
            +R +    ER R  ++NE    L+        +R  +  I+   + YI  LQ +L+
Sbjct: 11  DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR 67

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	320
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.67
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.63
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.63
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.59
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.58
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.58
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.57
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.55
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.53
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.48
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.42
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.35
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.32
4f3l_A	361	Mclock, circadian locomoter output cycles protein	98.94
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.81
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.75
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.66
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.42
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	96.25
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	95.34
2nyi_A	195	Unknown protein; protein structure initiative, PSI	93.32
1u8s_A	192	Glycine cleavage system transcriptional repressor,	91.21
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	87.51

>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=99.67  E-value=6.5e-17  Score=126.14  Aligned_cols=66  Identities=21%  Similarity=0.357  Sum_probs=61.2

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      .+|.+|+.+||+||++||++|..|++|||.. ..|+||++||.+||+||++||.+++.|+.+.+.+.
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~-~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e~~~L~   70 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGT-EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS-SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4588999999999999999999999999985 48999999999999999999999999999887654

>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=99.63  E-value=2.5e-16  Score=122.04  Aligned_cols=69  Identities=20%  Similarity=0.408  Sum_probs=63.3

Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904           99 DGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus        99 ~~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      ...+|.+|+.+||+||..||+.|..|+++||.....|++|++||..||+||++|+++++.|+.+++.+.
T Consensus         9 ~~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e~~~L~   77 (80)
T 1hlo_A            9 DADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   77 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTHH
T ss_pred             hHHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345688999999999999999999999999987557999999999999999999999999999988653

>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=99.63  E-value=4.5e-16  Score=121.32  Aligned_cols=66  Identities=20%  Similarity=0.396  Sum_probs=60.8

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       102 ~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      +|.+|+.+||+||..||+.|..|+++||.+...|++|++||..||+||++|+++++.|+.+++.+.
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e~~~L~   67 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999986568999999999999999999999999998887654

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

Probab=99.59  E-value=8.6e-16  Score=116.63  Aligned_cols=61  Identities=25%  Similarity=0.453  Sum_probs=55.8

Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHH
Q 042904           99 DGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLE  160 (320)
Q Consensus        99 ~~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~  160 (320)
                      +...|.+|+.+||+||++||+.|..|++|||.. ..|+||++||..||+||++||+++.-|+
T Consensus         5 ~~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~-~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            5 DKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGN-ARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSC-CSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hhHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCC-CCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            456689999999999999999999999999974 4799999999999999999999987765

>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=99.58  E-value=7.1e-16  Score=114.90  Aligned_cols=58  Identities=29%  Similarity=0.459  Sum_probs=51.7

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHHhcCCCCCC----CCCChhhhHHHHHHHHHHHHHHHH
Q 042904          100 GQQRMSHITVERNRRKQMNENLSVLRSLMPCFYV----KRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       100 ~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~----~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      +.++.+|+.+||+||.+||+.|..|++|||.+..    .|++|++||..||+||++||++.+
T Consensus         3 ~~rr~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~~   64 (65)
T 1an4_A            3 EKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSNH   64 (65)
T ss_dssp             CCCCCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTTC
T ss_pred             HHHHHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHhc
Confidence            3458899999999999999999999999998743    378999999999999999998753

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

Probab=99.58  E-value=3e-15  Score=124.27  Aligned_cols=64  Identities=30%  Similarity=0.431  Sum_probs=53.5

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCChhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFY--VKRGDQASIIGGVVDYINELQQVLQSLEAKKQ  164 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~--~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~  164 (320)
                      ..+.+|+.+||+||++||++|..|++|||.+.  ..|++|++||.+||+||++||++++.|+.+..
T Consensus        26 ~kr~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~~~   91 (118)
T 4ati_A           26 QKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLEN   91 (118)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            44789999999999999999999999999863  34789999999999999999999999987544

>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=99.57  E-value=3.2e-15  Score=118.07  Aligned_cols=66  Identities=23%  Similarity=0.351  Sum_probs=59.4

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRK  166 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~  166 (320)
                      ..|..|+..||+||..||+.|..|+++||.. ...|++|++||.+||+||++|+.+.+.|..+++.+
T Consensus         5 ~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~~~~~L   71 (88)
T 1nkp_A            5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL   71 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3588999999999999999999999999985 24699999999999999999999999988776654

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

Probab=99.55  E-value=1.2e-14  Score=112.78  Aligned_cols=65  Identities=22%  Similarity=0.242  Sum_probs=59.7

Q ss_pred             ccchhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          103 RMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       103 r~~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      |..||..||+||..||+.|..|+++||.. ...|.+|++||..|++||++|+++.+.|..+++.+.
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e~~~L~   67 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67999999999999999999999999975 357889999999999999999999999999887654

>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=99.53  E-value=1.5e-15  Score=112.96  Aligned_cols=56  Identities=30%  Similarity=0.412  Sum_probs=49.9

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHHhcCCCCC-----CCCCChhhhHHHHHHHHHHHHHHHH
Q 042904          102 QRMSHITVERNRRKQMNENLSVLRSLMPCFY-----VKRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       102 ~r~~h~~~ER~RR~~in~~~~~LrslvP~~~-----~~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      +|.+|+.+||+||++||+.|..|++|||.++     ..+.+|++||..||+||++||++++
T Consensus         2 kr~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~~   62 (63)
T 1a0a_A            2 KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGS   62 (63)
T ss_dssp             CTTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCSC
T ss_pred             cccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHhh
Confidence            4789999999999999999999999999641     3578899999999999999998753

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

Probab=99.48  E-value=9.8e-15  Score=112.32  Aligned_cols=60  Identities=23%  Similarity=0.364  Sum_probs=49.2

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCC-CCCCCC-ChhhhHHHHHHHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPC-FYVKRG-DQASIIGGVVDYINELQQVLQSLE  160 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~-~~~~k~-dKasIL~~AI~YIk~Lq~~v~~L~  160 (320)
                      .+|..|+..||+||..||+.|..|+.+||. ....|. +|++||..||+||+.||+++++++
T Consensus         4 ~rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~   65 (76)
T 3u5v_A            4 DKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN   65 (76)
T ss_dssp             -----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred             hHHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHh
Confidence            458899999999999999999999999994 334555 799999999999999999998764

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

Probab=99.42  E-value=4.4e-14  Score=107.86  Aligned_cols=54  Identities=26%  Similarity=0.434  Sum_probs=48.8

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCC--CCCCChhhhHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFY--VKRGDQASIIGGVVDYINELQQ  154 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~--~~k~dKasIL~~AI~YIk~Lq~  154 (320)
                      .+|.+|+.+||+||++||+.|..|++|||.+.  ..|+||++||..||+||+.|+.
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            45789999999999999999999999999741  3699999999999999999874

>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=99.35  E-value=6.1e-13  Score=100.20  Aligned_cols=57  Identities=25%  Similarity=0.352  Sum_probs=52.2

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      .+|..|+..||+|+..||+.|..||.+||.....|++|+.||..||+||..|++.++
T Consensus        11 ~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L~   67 (68)
T 1mdy_A           11 DRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             hhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHc
Confidence            348899999999999999999999999998766799999999999999999998653

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

Probab=99.32  E-value=1.5e-12  Score=95.73  Aligned_cols=56  Identities=29%  Similarity=0.504  Sum_probs=51.0

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHHH
Q 042904          102 QRMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       102 ~r~~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      +|..|+..||+|+..||+.|..||.+||.. ...|++|+.||..||+||..|++.++
T Consensus         2 rR~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            2 RRMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            477899999999999999999999999986 35789999999999999999998764

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

Probab=98.94  E-value=5.7e-10  Score=107.01  Aligned_cols=55  Identities=22%  Similarity=0.439  Sum_probs=42.7

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHH
Q 042904          100 GQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQV  155 (320)
Q Consensus       100 ~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~  155 (320)
                      ..+|.+|+.+||+||++||+.|.+|++|||.. ..|+||++||..||.||+.|+..
T Consensus        10 ~~~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~-~~~~dk~~il~~~~~~~~~~~~~   64 (361)
T 4f3l_A           10 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPGN-ARKMDKSTVLQKSIDFLRKHKET   64 (361)
T ss_dssp             ---------CHHHHHHHHHHHHHHHHHTCCSS-SCCCCHHHHHHHHHHHHHHHHHH
T ss_pred             chhhhhhhHHHHHHHHHHHHHHHHHHHhCCCC-CCCcCHHHHHHHHHHHHHHHHhh
Confidence            44578999999999999999999999999943 67999999999999999999754

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

Probab=98.81  E-value=1.1e-09  Score=82.09  Aligned_cols=50  Identities=30%  Similarity=0.317  Sum_probs=43.9

Q ss_pred             chhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHH
Q 042904          105 SHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQ  154 (320)
Q Consensus       105 ~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~  154 (320)
                      .-+..||+|+..||+.|..||.+||.. ...|++|+.||.-||+||..||.
T Consensus        17 ~a~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           17 PAAEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             CCBCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             CccHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            334568999999999999999999986 35689999999999999999984

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

Probab=98.75  E-value=4.8e-09  Score=101.74  Aligned_cols=53  Identities=26%  Similarity=0.445  Sum_probs=47.9

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHHhcCCCC--CCCCCChhhhHHHHHHHHHHHHH
Q 042904          102 QRMSHITVERNRRKQMNENLSVLRSLMPCF--YVKRGDQASIIGGVVDYINELQQ  154 (320)
Q Consensus       102 ~r~~h~~~ER~RR~~in~~~~~LrslvP~~--~~~k~dKasIL~~AI~YIk~Lq~  154 (320)
                      .|.+|+.+||+||++||+.|.+|++|||.+  ...|+||++||..||.|||.|+.
T Consensus        13 ~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~   67 (387)
T 4f3l_B           13 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   67 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHC
T ss_pred             hcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhc
Confidence            377999999999999999999999999942  15799999999999999999874

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

Probab=98.66  E-value=4.5e-08  Score=76.01  Aligned_cols=52  Identities=29%  Similarity=0.401  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHhcCCCC--CCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 042904          114 RKQMNENLSVLRSLMPCF--YVKRGDQASIIGGVVDYINELQQVLQSLEAKKQR  165 (320)
Q Consensus       114 R~~in~~~~~LrslvP~~--~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~  165 (320)
                      |..||++|.+|..|||.+  ...|.+|++||..|++||++||+.++.+..+..+
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e~e~r   57 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDLENR   57 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999975  2457899999999999999999999888765543

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

Probab=98.42  E-value=3.7e-07  Score=72.88  Aligned_cols=49  Identities=31%  Similarity=0.394  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHHH
Q 042904          109 VERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       109 ~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      .||.|-..||+.|..||.+||.. ...|++|+.+|.-||+||..|++.++
T Consensus        32 ~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~   81 (97)
T 4aya_A           32 DPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALD   81 (97)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHh
Confidence            36889999999999999999976 35789999999999999999998763

>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=96.25  E-value=0.027  Score=42.46  Aligned_cols=50  Identities=12%  Similarity=0.230  Sum_probs=43.3

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEec
Q 042904          269 NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKVT  318 (320)
Q Consensus       269 ~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv~  318 (320)
                      .+.|.|.|+.+||++.+|..+|-+.+..|.+.+....++...-.|.+.+.
T Consensus         5 ~~~l~v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v~~~   54 (91)
T 1zpv_A            5 KAIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSSD   54 (91)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEES
T ss_pred             eEEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEEEeC
Confidence            47899999999999999999999999999999998887776666666553

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

Probab=95.34  E-value=0.074  Score=39.40  Aligned_cols=49  Identities=14%  Similarity=0.164  Sum_probs=41.1

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          269 NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       269 ~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      .+.|+|.+..+||+|.+|..+|.+.++.|.++++...++.....|.+.+
T Consensus         5 ~~~l~v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v~~   53 (88)
T 2ko1_A            5 LAGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMIFV   53 (88)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEEEE
T ss_pred             EEEEEEEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEEEE
Confidence            3678899999999999999999999999999999877665445555554

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

Probab=93.32  E-value=0.24  Score=43.07  Aligned_cols=39  Identities=15%  Similarity=0.193  Sum_probs=36.6

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 042904          268 PNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD  306 (320)
Q Consensus       268 ~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~  306 (320)
                      ..+.|.|.|+.+||++..|..+|-++|+.|++++..+.+
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            458999999999999999999999999999999999876

>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=91.21  E-value=0.59  Score=40.08  Aligned_cols=38  Identities=11%  Similarity=0.084  Sum_probs=35.4

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeC
Q 042904          269 NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVD  306 (320)
Q Consensus       269 ~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~  306 (320)
                      .+.|.|.|+.+||++.+|..+|.++++.|..+...+.+
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            47899999999999999999999999999999998775

>3p96_A Phosphoserine phosphatase SERB; ssgcid, structural genomics, structural genomics center for infectious disease, hydrolas; 2.05A {Mycobacterium avium}

Probab=87.51  E-value=1.7  Score=41.41  Aligned_cols=49  Identities=14%  Similarity=0.270  Sum_probs=42.0

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEE
Q 042904          268 PNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIK  316 (320)
Q Consensus       268 ~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vK  316 (320)
                      ..++|.+.|+.|||+...|...|-++|..|+.++-...++..+-.+.+.
T Consensus        11 ~~~~lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~   59 (415)
T 3p96_A           11 VSVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVC   59 (415)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEE
T ss_pred             CeEEEEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEE
Confidence            4578999999999999999999999999999999998888754444443

---

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	320
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	2e-15
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	1e-14
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	2e-14
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	2e-13
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	5e-13
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	1e-12
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	3e-12
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-09

>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 = 68.4 bits (167), Expect = 2e-15
 Identities = 13/65 (20%), Positives = 29/65 (44%)

Query: 101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLE 160
            +R  H  +ER RR  + ++   LR  +P    ++  +A I+    +YI  +++   + +
Sbjct: 1   DKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQ 60

Query: 161 AKKQR 165
                
Sbjct: 61  QDIDD 65

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

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

 Score = 66.5 bits (162), Expect = 1e-14
 Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFY-VKRGDQASIIGGVVDYINELQQVLQSLE 160
           +R +H  +ER RR ++  +   LR  +P     ++  +  I+     YI  +Q   Q L 
Sbjct: 6   KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLI 65

Query: 161 AKKQR 165
           +++  
Sbjct: 66  SEEDL 70

>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 = 65.3 bits (159), Expect = 2e-14
 Identities = 15/61 (24%), Positives = 27/61 (44%)

Query: 97  NTDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVL 156
            T+  +R +    ER R  ++NE    L+        +R  +  I+   + YI  LQ +L
Sbjct: 7   TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL 66

Query: 157 Q 157
           +
Sbjct: 67  R 67

>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 = 15/68 (22%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 98  TDGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQ 157
           + G++R +H  +E+  R  +N+ +  L+ L+      + ++++++   +DYI  LQ   Q
Sbjct: 2   SRGEKRTAHNAIEKRYRSSINDKIIELKDLVVGTE-AKLNKSAVLRKAIDYIRFLQHSNQ 60

Query: 158 SLEAKKQR 165
            L+ +   
Sbjct: 61  KLKQENLS 68

>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 = 61.5 bits (149), Expect = 5e-13
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 103 RMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVLQSLEA 161
           R +H  +E+NRR  +  +L  L+ L+P      R    S++     +I +L+   +    
Sbjct: 2   RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH 61

Query: 162 KKQR 165
           +  +
Sbjct: 62  QIDQ 65

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

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

 Score = 59.9 bits (145), Expect = 1e-12
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 5/62 (8%)

Query: 102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRG-----DQASIIGGVVDYINELQQVL 156
           +R SH   E+ RR ++   L  L SL+P  + ++       +A+ +     YI  LQQ  
Sbjct: 2   KRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG 61

Query: 157 QS 158
            +
Sbjct: 62  ST 63

>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 = 58.6 bits (142), Expect = 3e-12
 Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 99  DGQQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQ----ASIIGGVVDYINELQQ 154
           D ++R  H  VER RR ++N  +  L  ++P   ++          I+    DYI EL+Q
Sbjct: 2   DEKRRAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQ 61

Query: 155 VLQ 157
              
Sbjct: 62  SNH 64

>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 = 51.7 bits (124), Expect = 1e-09
 Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 114 RKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQR 165
           R  +N+ +  L+ L+     K   ++ ++   +DYI  LQQV   L  +   
Sbjct: 1   RSSINDKIIELKDLVMGTDAKM-HKSGVLRKAIDYIKYLQQVNHKLRQENMV 51

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	320
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.61
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.59
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.57
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.55
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.54
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.49
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.39
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	96.32
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	96.31
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	92.88
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	92.66
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	92.14
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	91.26

>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=99.61  E-value=3.3e-16  Score=119.51  Aligned_cols=66  Identities=21%  Similarity=0.357  Sum_probs=60.7

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      .+|..|+.+||+||.+||+.|..|++|||.. ..|++|++||..||+||++|+++++.|..+...+.
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~-~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e~~~lk   70 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGT-EAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLR   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCS-SCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999999999986 57999999999999999999999999998887643

>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=99.60  E-value=5.5e-16  Score=118.87  Aligned_cols=66  Identities=20%  Similarity=0.396  Sum_probs=60.8

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          102 QRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       102 ~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      +|..|+.+||+||.+||+.|..|+++||..+..|++|++||..||+||++|+++++.|..+.+.+.
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~   67 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQDIDDLK   67 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999986668999999999999999999999999998877644

>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=99.59  E-value=1.3e-15  Score=115.66  Aligned_cols=65  Identities=22%  Similarity=0.242  Sum_probs=59.5

Q ss_pred             ccchhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          103 RMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       103 r~~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      |..|+..||+||.+||+.|..|+++||.. ...|++|++||..||+||+.|+.+++.|..+++.+.
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~L~   67 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQIDQLQ   67 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67999999999999999999999999976 346899999999999999999999999998887654

>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=99.57  E-value=6.4e-16  Score=114.67  Aligned_cols=57  Identities=25%  Similarity=0.352  Sum_probs=52.6

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHH
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQ  157 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~  157 (320)
                      .+|..|+..||+||.+||+.|..|++|||.++..|++|++||..||+||++||+.++
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            347899999999999999999999999999866789999999999999999998764

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

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

Probab=99.55  E-value=2.9e-15  Score=116.02  Aligned_cols=67  Identities=22%  Similarity=0.336  Sum_probs=60.1

Q ss_pred             ccccchhHHHHHHHHHHHHHHHHHHhcCCCC-CCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          101 QQRMSHITVERNRRKQMNENLSVLRSLMPCF-YVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       101 ~~r~~h~~~ER~RR~~in~~~~~LrslvP~~-~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      .+|..|+.+||+||+.||+.|..|+++||.+ ...|++|++||..||+||+.|+++++.|..+++.+.
T Consensus         5 ~rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~~~~l~   72 (88)
T d1nkpa_           5 VKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLLR   72 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999999975 246799999999999999999999999998877643

>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=99.54  E-value=1.6e-15  Score=110.71  Aligned_cols=55  Identities=31%  Similarity=0.387  Sum_probs=49.8

Q ss_pred             cccchhHHHHHHHHHHHHHHHHHHhcCCCC-----CCCCCChhhhHHHHHHHHHHHHHHH
Q 042904          102 QRMSHITVERNRRKQMNENLSVLRSLMPCF-----YVKRGDQASIIGGVVDYINELQQVL  156 (320)
Q Consensus       102 ~r~~h~~~ER~RR~~in~~~~~LrslvP~~-----~~~k~dKasIL~~AI~YIk~Lq~~v  156 (320)
                      +|..|+.+||+||++||+.|..|++|||.+     ...|++|++||..||+||++||+++
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            477999999999999999999999999942     3578999999999999999999865

>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=99.49  E-value=5.1e-15  Score=108.69  Aligned_cols=57  Identities=30%  Similarity=0.441  Sum_probs=50.8

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHHHhcCCCCC----CCCCChhhhHHHHHHHHHHHHHHH
Q 042904          100 GQQRMSHITVERNRRKQMNENLSVLRSLMPCFY----VKRGDQASIIGGVVDYINELQQVL  156 (320)
Q Consensus       100 ~~~r~~h~~~ER~RR~~in~~~~~LrslvP~~~----~~k~dKasIL~~AI~YIk~Lq~~v  156 (320)
                      +.+|.+|+.+||+||..||+.|..|++|||.++    ..|++|++||..||+||++||++.
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            345889999999999999999999999999753    348999999999999999999764

>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=99.39  E-value=8.5e-14  Score=100.87  Aligned_cols=53  Identities=23%  Similarity=0.325  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHhcCCCCCCCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 042904          114 RKQMNENLSVLRSLMPCFYVKRGDQASIIGGVVDYINELQQVLQSLEAKKQRKV  167 (320)
Q Consensus       114 R~~in~~~~~LrslvP~~~~~k~dKasIL~~AI~YIk~Lq~~v~~L~~~~~~~~  167 (320)
                      |++||++|..||++||++ ..|+||++||.+||+||+.||++++.|+++...+.
T Consensus         1 R~~in~~f~~L~~lvP~~-~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e~~~L~   53 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGT-DAKMHKSGVLRKAIDYIKYLQQVNHKLRQENMVLK   53 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCS-SCCCCTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCC-CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999986 46999999999999999999999999999887654

>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=96.32  E-value=0.01  Score=43.66  Aligned_cols=50  Identities=14%  Similarity=0.266  Sum_probs=45.2

Q ss_pred             CeEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          268 PNLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       268 ~~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      ..++|.+.|+.+||++.+|..+|-+.|..|+.++....++.....+.+.+
T Consensus         4 ~~~vitv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~   53 (86)
T d1u8sa1           4 QHLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISG   53 (86)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             cEEEEEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEc
Confidence            35889999999999999999999999999999999999998777776664

>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=96.31  E-value=0.011  Score=42.87  Aligned_cols=48  Identities=13%  Similarity=0.234  Sum_probs=42.5

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEEEe
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTIKV  317 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~vKv  317 (320)
                      ++|.+.|+.|||++..|..+|-++|..|++++-.+.++...-.+.+.+
T Consensus         3 ~vitv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~~   50 (83)
T d1zpva1           3 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVSS   50 (83)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEEE
Confidence            689999999999999999999999999999999988887655666654

>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=92.88  E-value=0.024  Score=40.95  Aligned_cols=48  Identities=6%  Similarity=0.026  Sum_probs=33.9

Q ss_pred             EEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee-CCe--EEEEEEEEe
Q 042904          270 LLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV-DET--MHNSFTIKV  317 (320)
Q Consensus       270 v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~-~~~--vl~tf~vKv  317 (320)
                      +-|+|.|..|+|+|.+|..+|-+.+..|++++..+. +|.  +..+|.++.
T Consensus         2 ~~i~i~~~Dr~GlL~di~~~ia~~~~NI~~i~~~~~~~g~~~~~~~i~v~~   52 (77)
T d1y7pa2           2 RGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEI   52 (77)
T ss_dssp             EEEEEEEECCTTHHHHHHHHCC----CEEEEEEEECCSSTTTTEEEEEEEE
T ss_pred             eeEEEEEecCCChHHHHHHHHHHcCCCeEEEEeeccCCCeEEEEEEEEEEc
Confidence            358999999999999999999999999999998753 333  234555543

>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=92.66  E-value=0.17  Score=37.22  Aligned_cols=37  Identities=11%  Similarity=0.081  Sum_probs=33.4

Q ss_pred             eEEEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEee
Q 042904          269 NLLLKTVSPRIPGQAVKIISALEDLAFEILHVNISTV  305 (320)
Q Consensus       269 ~v~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~  305 (320)
                      .+.|.|.|+.|||++.+|-..|-++++.|.+.+-.+.
T Consensus         6 tv~v~v~g~DrpGIV~~it~~la~~~~nI~~l~t~~~   42 (93)
T d1u8sa2           6 TVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTI   42 (93)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEE
T ss_pred             EEEEEEEECCCCCHHHHHHHHHHHcCCCchhhhcccc
Confidence            3678899999999999999999999999999987664

>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=92.14  E-value=0.3  Score=34.35  Aligned_cols=45  Identities=13%  Similarity=0.161  Sum_probs=38.1

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFTI  315 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~v  315 (320)
                      +|.|..+.+||.|.+++++|.+.++.|....+....+..+-.|.+
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            467888999999999999999999999999988777876544443

>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=91.26  E-value=0.4  Score=33.74  Aligned_cols=44  Identities=9%  Similarity=0.006  Sum_probs=37.7

Q ss_pred             EEEEEcCCCCChHHHHHHHHHhCCceEEEEEEEeeCCeEEEEEE
Q 042904          271 LLKTVSPRIPGQAVKIISALEDLAFEILHVNISTVDETMHNSFT  314 (320)
Q Consensus       271 ~IkI~c~rr~glL~~Im~aLE~L~LdV~~anist~~~~vl~tf~  314 (320)
                      .|.|..+.+||.|.+|...|...|+.|...++....+.-+.-|.
T Consensus         5 QisV~~eNkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Rii   48 (70)
T d2f06a2           5 QLSIFLENKSGRLTEVTEVLAKENINLSALCIAENADFGILRGI   48 (70)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEEE
Confidence            47889999999999999999999999999999877766554443