Citrus Sinensis ID: 024326

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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-------27
Protein Sequence
MLAMDPYFWSSCRNDNGVEILTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLFDSSLSSSSDYLW
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccHHHcccccccccccccEEEEEEccccccHHHHHHHHHHccccEEEEEEEEEccccEEEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHccccccccccEEEcccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEccccccccccEEccccEEEccccccccccccccccHcEEccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEEEccccccccEEEEEEEEEccccccHHHHHHHHHHHcccEEEEEEEEEccccEEEEEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccEEEEEccccccccccccc
Coil and Loop (DISEMBL)
mlamdpyfwsscrndngveiltdefvvnngfqgksrngssshsslvldseRGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTlrslipgatkmdKATLLTEVISQLKELDKNAMeategfliptdidevkveqqedgldgapysikaslccnykpglLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLfdsslssssdylw
Flexible Loop (DISEMBL)
MLAMDPYFWSSCRNDNGVEILTDEFVVNNGfqgksrngssshsslvldserGELVEANVKlqrkgvsedrsvaalknhieaernrrkringhldtlrslipgatkmdKATLLTEVISQLKELDKNAMEATEgfliptdidEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLlgarlsnkrrrvslfdsslssssdylw
Low Complexity Region (SEG)
MLAMDPYFWSSCRNDNGVEILTDEFVVNNGFQGKsrngssshsslvldsERGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVslfdsslssssdYLW
Disordered region (IsUnstruct)
*****PYFWSSCRNDNGVEILTDEFVVNNGF************************************************************HLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARL**********************
Disordered Region (DISOPRED)
****DPY******************************************************************************RKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKE****************************************LCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIR**************************LFDSSLS***DYLW
Disordered Region (DISEMBL)
MLAMDPYFWSSCRNDNGVEILTDEFVVNNGFQGK************LDSERGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVS**************
Disordered Region (DISPRO)
*****P******RNDNGVEILTDEFVVNN******************************************************NRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFS**************RRR****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLAMDPYFWSSCRNDNGVEILTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLFDSSLSSSSDYLW
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	269	2.2.26 [Sep-21-2011]
Q9S7Y1	368	Transcription factor bHLH	yes	no	0.810	0.592	0.369	5e-26
Q9LET0	230	Putative transcription fa	no	no	0.527	0.617	0.427	9e-25
Q9LS08	344	Transcription factor AIG1	no	no	0.646	0.505	0.369	3e-23
O80674	253	Transcription factor bHLH	no	no	0.602	0.640	0.375	5e-22
Q9XEF0	254	Transcription factor bHLH	no	no	0.650	0.688	0.351	1e-20
P0CB25	256	Transcription factor bHLH	no	no	0.460	0.484	0.340	2e-11
Q39204	623	Transcription factor MYC2	no	no	0.256	0.110	0.4	4e-08
Q9ZPY8	566	Transcription factor ABA-	no	no	0.171	0.081	0.543	8e-08
O49687	589	Transcription factor MYC4	no	no	0.420	0.191	0.304	1e-07
Q9LSE2	494	Transcription factor ICE1	no	no	0.475	0.259	0.281	1e-07

>sp|Q9S7Y1|BH030_ARATH Transcription factor bHLH30 OS=Arabidopsis thaliana GN=BHLH30 PE=1 SV=1

 Score =  118 bits (295), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 89/241 (36%), Positives = 136/241 (56%), Gaps = 23/241 (9%)

Query: 30  GFQGKSRNGSSSHSSL-VLDSERGELVEANV----------KLQRKGVSEDRSVAALKNH 78
           GF G +      H  L +L    G +V+A            K+  + + + +++AA K+H
Sbjct: 119 GFGGATSAAHHHHEQLRILSEALGPVVQAGSGPFGLQAELGKMTAQEIMDAKALAASKSH 178

Query: 79  IEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTD 138
            EAER RR+RIN HL  LRS++P  TK DKA+LL EVI  +KEL +     +E  L+PT+
Sbjct: 179 SEAERRRRERINNHLAKLRSILPNTTKTDKASLLAEVIQHVKELKRETSVISETNLVPTE 238

Query: 139 IDEVKV---EQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEG 195
            DE+ V   E++E G DG  + IKASLCC  +  LL D+ + L+A+ L  +KAEI T+ G
Sbjct: 239 SDELTVAFTEEEETG-DGR-FVIKASLCCEDRSDLLPDMIKTLKAMRLKTLKAEITTVGG 296

Query: 196 RMKNI-FVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRV 254
           R+KN+ FV            E C   + ++ +A+++V++K +  E    G   + KR+R+
Sbjct: 297 RVKNVLFVTGEESSGEEVEEEYC---IGTIEEALKAVMEKSNVEESSSSG---NAKRQRM 350

Query: 255 S 255
           S
Sbjct: 351 S 351

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LET0|BH107_ARATH Putative transcription factor bHLH107 OS=Arabidopsis thaliana GN=BHLH107 PE=2 SV=1

 Score =  114 bits (284), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 62/145 (42%), Positives = 93/145 (64%), Gaps = 3/145 (2%)

Query: 66  VSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKN 125
           V ED+++A+L+NH EAER RR RIN HL+ LR L+   +K DK+TLL +V+ ++KEL + 
Sbjct: 37  VYEDKALASLRNHKEAERKRRARINSHLNKLRKLLSCNSKTDKSTLLAKVVQRVKELKQQ 96

Query: 126 AMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSI--KASLCCNYKPGLLSDLRRVLEALHL 183
            +E T+   IP++ DE+ V   ED   G    I  K S CC  +P LL DL   L++L +
Sbjct: 97  TLEITDE-TIPSETDEISVLNIEDCSRGDDRRIIFKVSFCCEDRPELLKDLMETLKSLQM 155

Query: 184 SIVKAEIATLEGRMKNIFVMASCKE 208
             + A++ T+ GR +N+ V+A+ KE
Sbjct: 156 ETLFADMTTVGGRTRNVLVVAADKE 180

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LS08|BH032_ARATH Transcription factor AIG1 OS=Arabidopsis thaliana GN=BHLH32 PE=1 SV=1

 Score =  108 bits (271), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 71/192 (36%), Positives = 114/192 (59%), Gaps = 18/192 (9%)

Query: 60  KLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQL 119
           KL  + V + +++AA K+H EAER RR+RIN HL  LRS++P  TK DKA+LL EVI  +
Sbjct: 118 KLSAQEVMDAKALAASKSHSEAERRRRERINTHLAKLRSILPNTTKTDKASLLAEVIQHM 177

Query: 120 KELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLE 179
           KEL +   + T+ + +PT+ D++ V+   +  +G    I+AS CC  +  L+ D+   L+
Sbjct: 178 KELKRQTSQITDTYQVPTECDDLTVDSSYNDEEGN-LVIRASFCCQDRTDLMHDVINALK 236

Query: 180 ALHLSIVKAEIATLEGRMKNIFVMA---------SCKELNFENTEV--------CQSLVS 222
           +L L  +KAEIAT+ GR+KNI  ++              NF+  +V          + VS
Sbjct: 237 SLRLRTLKAEIATVGGRVKNILFLSREYDDEEDHDSYRRNFDGDDVEDYDEERMMNNRVS 296

Query: 223 SVHQAIRSVLDK 234
           S+ +A+++V++K
Sbjct: 297 SIEEALKAVIEK 308

Transcription factor required for MONOPTEROS-dependent root initiation in embryo. Transcriptionally controlled by MONOPTEROS.

Arabidopsis thaliana (taxid: 3702)

>sp|O80674|BH106_ARATH Transcription factor bHLH106 OS=Arabidopsis thaliana GN=BHLH106 PE=2 SV=1

 Score =  105 bits (261), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 66/176 (37%), Positives = 114/176 (64%), Gaps = 14/176 (7%)

Query: 66  VSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKN 125
           +++DR++AAL+NH EAER RR+RIN HL+ LR+++   +K DKATLL +V+ +++EL + 
Sbjct: 59  MAQDRALAALRNHKEAERRRRERINSHLNKLRNVLSCNSKTDKATLLAKVVQRVRELKQQ 118

Query: 126 AMEATEG--FLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHL 183
            +E ++    L+P++ DE+ V    D  +      KASLCC  +  LL DL  +L++L++
Sbjct: 119 TLETSDSDQTLLPSETDEISVLHFGDYSNDGHIIFKASLCCEDRSDLLPDLMEILKSLNM 178

Query: 184 SIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVH---QAIRSVLDKFS 236
             ++AE+ T+ GR +++ V+A+ KE++          V SVH    A++S+L++ S
Sbjct: 179 KTLRAEMVTIGGRTRSVLVVAADKEMHG---------VESVHFLQNALKSLLERSS 225

Arabidopsis thaliana (taxid: 3702)

>sp|Q9XEF0|BH051_ARATH Transcription factor bHLH51 OS=Arabidopsis thaliana GN=BHLH51 PE=2 SV=1

 Score =  100 bits (250), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 64/182 (35%), Positives = 104/182 (57%), Gaps = 7/182 (3%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLI 135
           ++H  AE+ RR RIN HL  LR L+P + K+DKA LL  VI Q+KEL + A E+     +
Sbjct: 65  RSHRLAEKRRRDRINSHLTALRKLVPNSDKLDKAALLATVIEQVKELKQKAAESPIFQDL 124

Query: 136 PTDIDEVKVEQQE-DGLDGAPYSI--KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT 192
           PT+ DEV V+ +     +    +I  KAS CC  +P  +S++ RVL  L L  ++AEI +
Sbjct: 125 PTEADEVTVQPETISDFESNTNTIIFKASFCCEDQPEAISEIIRVLTKLQLETIQAEIIS 184

Query: 193 LEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLG-ARLSNKR 251
           + GRM+  F++   K+ N   T    +   ++ Q++ S L++ +++        R+ +KR
Sbjct: 185 VGGRMRINFIL---KDSNCNETTNIAASAKALKQSLCSALNRITSSSTTTSSVCRIRSKR 241

Query: 252 RR 253
           +R
Sbjct: 242 QR 243

Arabidopsis thaliana (taxid: 3702)

>sp|P0CB25|BH131_ARATH Transcription factor bHLH131 OS=Arabidopsis thaliana GN=BHLH131 PE=2 SV=1

 Score = 70.1 bits (170), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 47/138 (34%), Positives = 73/138 (52%), Gaps = 14/138 (10%)

Query: 64  KGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELD 123
           K  +E + VAA K H +AER RR RIN    TLR+++P   K DKA++L E +    EL 
Sbjct: 83  KSKTESKEVAA-KKHSDAERRRRLRINSQFATLRTILPNLVKQDKASVLGETVRYFNELK 141

Query: 124 KNAMEATEGFLIPTDI---DEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEA 180
           K   +      IPT     D ++++   +  D A    +    C+ + GL+S++   ++A
Sbjct: 142 KMVQD------IPTTPSLEDNLRLDHCNNNRDLA----RVVFSCSDREGLMSEVAESMKA 191

Query: 181 LHLSIVKAEIATLEGRMK 198
           +    V+AEI T+ GR K
Sbjct: 192 VKAKAVRAEIMTVGGRTK 209

Arabidopsis thaliana (taxid: 3702)

>sp|Q39204|RAP1_ARATH Transcription factor MYC2 OS=Arabidopsis thaliana GN=RAP1 PE=1 SV=2

 Score = 58.5 bits (140), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 46/70 (65%), Gaps = 1/70 (1%)

Query: 77  NHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEA-TEGFLI 135
           NH+EAER RR+++N     LR+++P  +KMDKA+LL + I+ + EL    ++  +E   I
Sbjct: 452 NHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQI 511

Query: 136 PTDIDEVKVE 145
              ++EVK+E
Sbjct: 512 KNQLEEVKLE 521

Transcriptional activator. Common transcription factor of light, abscisic acid (ABA), and jasmonic acid (JA) signaling pathways. In cooperation with MYB2 is involved in the regulation of ABA-inducible genes under drought stress conditions. Binds to the MYC recognition site (5'-CACATG-3'), and to the G-box (5'-CACNTG-3') and Z-box (5'-ATACGTGT-3') of light-responsive promoters. Negative regulator of blue light-mediated photomorphogenic growth and blue- and far-red-light regulated gene expression. Positive regulator of lateral root formation.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZPY8|AIB_ARATH Transcription factor ABA-INDUCIBLE bHLH-TYPE OS=Arabidopsis thaliana GN=AIB PE=2 SV=2

 Score = 57.8 bits (138), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 25/46 (54%), Positives = 35/46 (76%)

Query: 77  NHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKEL 122
           NH+EAER RR+++N     LRS++P  +KMDKA+LL + IS +KEL
Sbjct: 395 NHVEAERQRREKLNQRFYALRSVVPNISKMDKASLLGDAISYIKEL 440

Transcription activator. Regulates positively abscisic acid (ABA) response. Confers drought tolerance and sensitivity to ABA.

Arabidopsis thaliana (taxid: 3702)

>sp|O49687|BH004_ARATH Transcription factor MYC4 OS=Arabidopsis thaliana GN=BHLH4 PE=2 SV=1

 Score = 57.4 bits (137), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 69/125 (55%), Gaps = 12/125 (9%)

Query: 54  LVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLT 113
           +VE   K +++G           NH+EAER RR+++N    +LR+++P  +KMDKA+LL 
Sbjct: 393 VVEPEKKPRKRGRKPANGREEPLNHVEAERQRREKLNQRFYSLRAVVPNVSKMDKASLLG 452

Query: 114 EVISQLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLD----GAPYSIKASLCCNYKPG 169
           + IS + EL K+ ++  E        D+ ++++Q D ++     A  S+K   C N +  
Sbjct: 453 DAISYISEL-KSKLQKAES-------DKEELQKQIDVMNKEAGNAKSSVKDRKCLNQESS 504

Query: 170 LLSDL 174
           +L ++
Sbjct: 505 VLIEM 509

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSE2|ICE1_ARATH Transcription factor ICE1 OS=Arabidopsis thaliana GN=SCRM PE=1 SV=1

 Score = 57.0 bits (136), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/167 (28%), Positives = 72/167 (43%), Gaps = 39/167 (23%)

Query: 78  HIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDK------NAMEAT- 130
           ++ AER RRK++N  L  LRS++P  +KMD+A++L + I  LKEL +      N +E+T 
Sbjct: 308 NLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIDYLKELLQRINDLHNELESTP 367

Query: 131 EGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLC--------------------------- 163
            G L PT      +      L      +K  LC                           
Sbjct: 368 PGSLPPTSSSFHPLTPTPQTLS---CRVKEELCPSSLPSPKGQQARVEVRLREGRAVNIH 424

Query: 164 --CNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKE 208
             C  +PGLL    + L+ L L + +A I+   G   ++F    C+E
Sbjct: 425 MFCGRRPGLLLATMKALDNLGLDVQQAVISCFNGFALDVFRAEQCQE 471

Transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. Binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA.

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	269
224145243	267	predicted protein [Populus trichocarpa]	0.988	0.996	0.651	8e-92
255568283	265	conserved hypothetical protein [Ricinus	0.936	0.950	0.623	1e-83
224135857	268	predicted protein [Populus trichocarpa]	0.944	0.947	0.619	1e-82
356543028	258	PREDICTED: transcription factor bHLH30-l	0.936	0.976	0.586	1e-77
356517428	259	PREDICTED: transcription factor bHLH30-l	0.899	0.934	0.591	9e-75
225446577	259	PREDICTED: transcription factor bHLH30 [	0.925	0.961	0.602	1e-72
388510320	243	unknown [Lotus japonicus]	0.873	0.967	0.602	2e-71
356542185	247	PREDICTED: transcription factor bHLH30-l	0.814	0.886	0.639	5e-71
449521136	252	PREDICTED: transcription factor bHLH30-l	0.888	0.948	0.622	1e-67
449463302	252	PREDICTED: transcription factor bHLH30-l	0.888	0.948	0.627	2e-67

>gi|224145243|ref|XP_002325576.1| predicted protein [Populus trichocarpa] gi|222862451|gb|EEE99957.1| predicted protein [Populus trichocarpa]

 Score =  342 bits (878), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 174/267 (65%), Positives = 213/267 (79%), Gaps = 1/267 (0%)

Query: 4   MDPYFWSSCR-NDNGVEILTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQ 62
           M+P  W+S R   +  E ++D F+VN G Q K+R G SS SSLVLD+ERGELVEA V+++
Sbjct: 1   MEPCSWNSTRVQASDFEGMSDGFLVNTGLQAKTRTGPSSTSSLVLDNERGELVEATVRME 60

Query: 63  RKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKEL 122
           RKGV+ +RS+AALKNH EAE+ RR RIN HLDTLRSL+PG  KMDKA+LL EVI+ LKEL
Sbjct: 61  RKGVAAERSIAALKNHSEAEKKRRARINAHLDTLRSLVPGTRKMDKASLLAEVIAHLKEL 120

Query: 123 DKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALH 182
            + A EA+EG L+P DIDEV+VEQQEDGL  APY I+AS+CC+ KPG+LSDLR+ L+ALH
Sbjct: 121 KRQATEASEGLLMPLDIDEVRVEQQEDGLLSAPYVIRASICCDCKPGILSDLRQALDALH 180

Query: 183 LSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFL 242
           L I+KAEIATLEGRMKN+FVM+SCKE +  + +V Q L  S+HQA RS+LDKFSA++EFL
Sbjct: 181 LIIMKAEIATLEGRMKNVFVMSSCKEGDSGDAKVHQFLAGSIHQAFRSILDKFSASQEFL 240

Query: 243 LGARLSNKRRRVSLFDSSLSSSSDYLW 269
           L + LSNKRRRV  F  SLSSSS  LW
Sbjct: 241 LKSTLSNKRRRVDSFKPSLSSSSGDLW 267

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568283|ref|XP_002525116.1| conserved hypothetical protein [Ricinus communis] gi|223535575|gb|EEF37243.1| conserved hypothetical protein [Ricinus communis]

 Score =  315 bits (807), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 157/252 (62%), Positives = 191/252 (75%)

Query: 18  VEILTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKN 77
           +E  +DE  +N  F+ K RNG  S SSLVLDS+RGELVEA V + +KGVS +RS  AL+N
Sbjct: 14  LEGFSDEVFMNTDFEAKIRNGLCSTSSLVLDSQRGELVEATVSVGKKGVSAERSTQALRN 73

Query: 78  HIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPT 137
           H EAER RR RIN HLDTLRSL+PGA KMDKA+LL EVI  +KEL   A   +EG L+P 
Sbjct: 74  HCEAERKRRARINAHLDTLRSLVPGAKKMDKASLLAEVIKYMKELKMTAAGVSEGLLMPM 133

Query: 138 DIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRM 197
           D+DEV+VE Q+D +DGAP  I+ SLCC+YKPGLLSDLRR L+ALHL ++++EIATLEGRM
Sbjct: 134 DVDEVRVEGQDDKVDGAPCMIRISLCCDYKPGLLSDLRRALDALHLIVMRSEIATLEGRM 193

Query: 198 KNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLF 257
           KN+ VM SCKE +   TEV + L  SV QAIRS+LDKFSA+ E  L + LS+KR+RVSLF
Sbjct: 194 KNVLVMTSCKEAHSGCTEVHKLLACSVQQAIRSILDKFSASHELSLKSTLSHKRQRVSLF 253

Query: 258 DSSLSSSSDYLW 269
           D   SSSS  +W
Sbjct: 254 DPHFSSSSGDIW 265

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135857|ref|XP_002327321.1| predicted protein [Populus trichocarpa] gi|222835691|gb|EEE74126.1| predicted protein [Populus trichocarpa]

 Score =  311 bits (798), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 158/255 (61%), Positives = 196/255 (76%), Gaps = 1/255 (0%)

Query: 4   MDPYFWSSCR-NDNGVEILTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQ 62
           M+P  W+S R      E ++D F+VN+  Q ++RNGS S SSLVLD+ERGELVEA V+++
Sbjct: 1   MEPCSWNSARVQAYACEGMSDVFLVNSRLQAETRNGSRSTSSLVLDNERGELVEATVRME 60

Query: 63  RKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKEL 122
           RKGVS ++S+AAL+NH EAER RR RIN HLDTLRSL+PG +KMDKA+LL EVIS LKEL
Sbjct: 61  RKGVSAEKSIAALRNHSEAERKRRARINAHLDTLRSLVPGTSKMDKASLLAEVISHLKEL 120

Query: 123 DKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALH 182
              A  A EG L+P DIDEV+VEQ+EDGL  AP  I+AS+CC+YKP +LS LR+ L+ALH
Sbjct: 121 KIQAAGAGEGLLMPLDIDEVRVEQEEDGLCSAPCLIRASICCDYKPEILSGLRQALDALH 180

Query: 183 LSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFL 242
           L I +AEIATLEGRM N+ VM+SCKE    +++V Q L  SVH+A RSVL+KFSA++EF 
Sbjct: 181 LMITRAEIATLEGRMMNVLVMSSCKEGLGGDSKVRQFLAGSVHKAFRSVLEKFSASQEFS 240

Query: 243 LGARLSNKRRRVSLF 257
           L   LSNKRRRV L 
Sbjct: 241 LKPTLSNKRRRVGLL 255

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543028|ref|XP_003539965.1| PREDICTED: transcription factor bHLH30-like [Glycine max]

 Score =  295 bits (756), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 152/259 (58%), Positives = 192/259 (74%), Gaps = 7/259 (2%)

Query: 2   LAMDPYFWSSCRNDNGVEILTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKL 61
           + M+ + W      +  +  +D F  +NG  G   +G  S  SLVLD ERGELVEA V+L
Sbjct: 1   MEMEDFLWGGGIAGDAPKRKSDGFEGSNGVIG---SGCGSSFSLVLDRERGELVEAPVRL 57

Query: 62  QRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKE 121
           +RKGVS +RS+ ALK+H EAER RR RIN HLDTLRS+IPGA KMDKA+LL EVI  LKE
Sbjct: 58  ERKGVSTERSIEALKSHSEAERKRRARINAHLDTLRSVIPGAMKMDKASLLGEVIRHLKE 117

Query: 122 LDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEAL 181
           L KNA +A EG +IP D DE+ VE+QE GL+G PYSI+ASLCC YKPGLLSD+++ L+AL
Sbjct: 118 LKKNAAQACEGLMIPKDNDEISVEEQEGGLNGFPYSIRASLCCEYKPGLLSDIKQALDAL 177

Query: 182 HLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEF 241
           HL I +A+IATLEGRMKN+FV+ S KE NFE+    Q L  SVHQA+++VL++FS +E+ 
Sbjct: 178 HLMITRADIATLEGRMKNVFVIISSKEQNFEDAAYRQFLAGSVHQALKAVLNRFSVSED- 236

Query: 242 LLGARLSNKRRRVSLFDSS 260
           +LG R   KRRR+S+F SS
Sbjct: 237 ILGTR---KRRRISIFSSS 252

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356517428|ref|XP_003527389.1| PREDICTED: transcription factor bHLH30-like [Glycine max]

 Score =  286 bits (731), Expect = 9e-75,   Method: Compositional matrix adjust.
 Identities = 145/245 (59%), Positives = 184/245 (75%), Gaps = 3/245 (1%)

Query: 2   LAMDPYFWSSCRNDNGVEILTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKL 61
           + M+ + W    +++  +  +D F  +NG  G    GSS   SLVLD ERGELVE  V+L
Sbjct: 1   MEMEDFLWGGGIDEDVTKRKSDGFEGSNGVIGSGWCGSSF--SLVLDRERGELVEEPVRL 58

Query: 62  QRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKE 121
           ++KGVS +RS+ ALK+H EAER RR RIN HLDTLRS+IPGA KMDKA+LL EVI  LKE
Sbjct: 59  EKKGVSTERSIEALKSHSEAERKRRARINAHLDTLRSVIPGAMKMDKASLLGEVIRHLKE 118

Query: 122 LDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEAL 181
           L KNA +A EG +IP D DE+ VE+QE GL+G PYSI+ASLCC YKPGLLSD+++ L+AL
Sbjct: 119 LKKNAAQACEGLMIPKDNDEISVEEQEGGLNGFPYSIRASLCCEYKPGLLSDIKQALDAL 178

Query: 182 HLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEF 241
           HL I +A+IATLEGRMKN+FV+ SCKE NFE+    Q L  SVHQA++SVL++FS +E+ 
Sbjct: 179 HLMITRADIATLEGRMKNVFVIISCKEQNFEDAAYRQFLAVSVHQALKSVLNRFSVSED- 237

Query: 242 LLGAR 246
           +LG R
Sbjct: 238 ILGTR 242

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446577|ref|XP_002280074.1| PREDICTED: transcription factor bHLH30 [Vitis vinifera]

 Score =  279 bits (713), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 150/249 (60%), Positives = 186/249 (74%)

Query: 21  LTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIE 80
            +D F  N+G+    R GSSS S LVLDSERGELV A  +L    V  ++++ ALKNH E
Sbjct: 11  FSDGFSENSGYGAIIRGGSSSSSLLVLDSERGELVRAPARLGPNEVKAEKAMVALKNHSE 70

Query: 81  AERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDID 140
           AER RR RIN HL TLR +IPG  KMDKA+LL EV+S LKEL ++A E ++GFL+P DID
Sbjct: 71  AERRRRGRINAHLATLRGIIPGTKKMDKASLLGEVVSHLKELKRSAAEISKGFLVPMDID 130

Query: 141 EVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNI 200
           EV+VEQQE GLD APYSIKASLCC+YKPG+LSDLRR L+ +HL  V+AEIATL GRMKN+
Sbjct: 131 EVRVEQQEGGLDEAPYSIKASLCCDYKPGVLSDLRRALDTVHLKTVRAEIATLGGRMKNV 190

Query: 201 FVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLFDSS 260
           FVM  CK+ N E+TE  +   +SVHQA+RSVLDKF A+++F   +  SNKR+R+S+F+SS
Sbjct: 191 FVMTGCKDGNLEDTETRKLHANSVHQALRSVLDKFPASQDFSSRSTSSNKRQRISIFNSS 250

Query: 261 LSSSSDYLW 269
            SS     W
Sbjct: 251 SSSPFGDFW 259

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388510320|gb|AFK43226.1| unknown [Lotus japonicus]

 Score =  275 bits (702), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 147/244 (60%), Positives = 189/244 (77%), Gaps = 9/244 (3%)

Query: 25  FVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIEAERN 84
           F V++G  G   +G +S SSLVLD ++GELVEA ++L+RKGVS +RS+ AL+NH EAER 
Sbjct: 9   FQVSSGVIG---SGYASSSSLVLDRDKGELVEAPMQLERKGVSPERSIEALRNHSEAERR 65

Query: 85  RRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKV 144
           RR RIN HLDTLR++IPGA KMDKA+LL EVI+ LKEL  NA +A+EG + P D DE++V
Sbjct: 66  RRARINAHLDTLRTVIPGANKMDKASLLAEVITHLKELKTNAAQASEGLMTPKDNDELRV 125

Query: 145 EQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA 204
            +QE GL+G PYSI+ASLCC Y+PGLLSD+R+ L+ALHL I +AEIATL GR+KN+FV+ 
Sbjct: 126 GEQEGGLNGFPYSIRASLCCEYRPGLLSDIRQALDALHLMITRAEIATLGGRVKNVFVII 185

Query: 205 SCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLFDSSLSSS 264
           SCKE NFE+ E  Q L  SVHQA+RSVLD+FS +++ L     S KRRR+S+F S  +S 
Sbjct: 186 SCKEQNFEDAEYRQFLAGSVHQALRSVLDRFSVSQDIL----ESRKRRRISIFSS--TSL 239

Query: 265 SDYL 268
            D+L
Sbjct: 240 EDFL 243

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356542185|ref|XP_003539550.1| PREDICTED: transcription factor bHLH30-like [Glycine max]

 Score =  273 bits (699), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 142/222 (63%), Positives = 176/222 (79%), Gaps = 3/222 (1%)

Query: 21  LTDEFVVNNGFQGKSRNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIE 80
           ++D F V+ G  G   NG  S SSLVLD E+GELVEA VKL+RKGVS +RS+ ALKNH E
Sbjct: 9   ISDGFQVSCGVIG---NGYGSSSSLVLDKEKGELVEAPVKLERKGVSPERSIEALKNHSE 65

Query: 81  AERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDID 140
           AER RR RIN HLDTLRS+IPGA K+DKATLL EVI  LK+L  NA +A+EG +IP D D
Sbjct: 66  AERRRRARINAHLDTLRSVIPGAKKLDKATLLGEVIRHLKDLKTNAAQASEGLMIPKDSD 125

Query: 141 EVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNI 200
           E+++E+QE GL+G PYSI+ASLCC YKPGLL+D+R+ L+ALHL I++AEIATL GRMKN+
Sbjct: 126 EIRIEEQEGGLNGFPYSIRASLCCEYKPGLLTDIRQALDALHLMIIRAEIATLGGRMKNV 185

Query: 201 FVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFL 242
           FV+ +CKE N E+ E  Q L  SVHQA+RSVLD+FS +++ L
Sbjct: 186 FVIINCKEQNVEDAEYRQFLAGSVHQALRSVLDRFSVSQDML 227

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449521136|ref|XP_004167587.1| PREDICTED: transcription factor bHLH30-like [Cucumis sativus]

 Score =  262 bits (669), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 152/244 (62%), Positives = 178/244 (72%), Gaps = 5/244 (2%)

Query: 29  NGFQGKS---RNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIEAERNR 85
           +GF   S   RNGS S SSLVLDSER ELVEA +KL+ KGV  +RS AALKNH EAER R
Sbjct: 11  DGFCANSASMRNGSVSTSSLVLDSERDELVEAPLKLESKGVPAERSAAALKNHSEAERRR 70

Query: 86  RKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVE 145
           R RIN HL  LRSL+PG  KMDKATLL EVIS L  L + A E ++  +IP + DE+ VE
Sbjct: 71  RARINDHLGILRSLVPGGKKMDKATLLAEVISHLNVLKRAAAEVSDAHIIPEESDEITVE 130

Query: 146 QQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMAS 205
           Q EDG +G PYSI+ASLCC+YKPGLL DLRR L AL L I +AEIATL GRMKN+FV+ S
Sbjct: 131 Q-EDGFNGVPYSIRASLCCDYKPGLLPDLRRALHALDLIIQRAEIATLNGRMKNVFVLTS 189

Query: 206 CKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLFDSSLSSSS 265
           CKE N E TE+ + L +SVHQAI+SVL+KFS  +EF       NKRRR+SLF++S SSS 
Sbjct: 190 CKEGNIETTELRRFLETSVHQAIKSVLNKFSDPQEFSF-MTFPNKRRRISLFNASSSSSM 248

Query: 266 DYLW 269
              W
Sbjct: 249 GDFW 252

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463302|ref|XP_004149373.1| PREDICTED: transcription factor bHLH30-like [Cucumis sativus]

 Score =  261 bits (667), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 153/244 (62%), Positives = 178/244 (72%), Gaps = 5/244 (2%)

Query: 29  NGFQGKS---RNGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIEAERNR 85
           +GF   S   RNGS S SSLVLDSER ELVEA +KL+ KGV  +RS AALKNH EAER R
Sbjct: 11  DGFCANSASMRNGSVSTSSLVLDSERDELVEAPLKLESKGVPAERSAAALKNHSEAERRR 70

Query: 86  RKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKVE 145
           R RIN HL  LRSL+PG  KMDKATLL EVIS L  L + A E ++  +IP + DE+ VE
Sbjct: 71  RARINDHLGILRSLVPGGKKMDKATLLAEVISHLNVLKRAAAEVSDAHIIPEESDEITVE 130

Query: 146 QQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMAS 205
           Q EDG +G PYSI+ASLCC+YKPGLL DLRR L AL L I +AEIATL GRMKN+FV+ S
Sbjct: 131 Q-EDGFNGVPYSIRASLCCDYKPGLLPDLRRALHALDLIIQRAEIATLNGRMKNVFVLTS 189

Query: 206 CKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLGARLSNKRRRVSLFDSSLSSSS 265
           CKE N E TE+ + L +SVHQAI+SVL+KFS  +EF       NKRRR+SLF+SS SSS 
Sbjct: 190 CKEGNIETTELRRFLETSVHQAIKSVLNKFSDPQEFSF-MTFPNKRRRISLFNSSSSSSM 248

Query: 266 DYLW 269
              W
Sbjct: 249 GDFW 252

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	269
TAIR|locus:2012393	368	AT1G68810 "AT1G68810" [Arabido	0.698	0.510	0.393	6.9e-31
TAIR|locus:2063203	253	AT2G41130 "AT2G41130" [Arabido	0.680	0.723	0.354	1.7e-27
UNIPROTKB|Q9FTQ1	267	P0665D10.21 "DNA binding prote	0.687	0.692	0.386	3.5e-27
TAIR|locus:2085964	344	BHLH32 "AT3G25710" [Arabidopsi	0.646	0.505	0.369	3.5e-27
TAIR|locus:2103560	230	AT3G56770 "AT3G56770" [Arabido	0.609	0.713	0.398	1.4e-25
UNIPROTKB|Q6ZA99	345	P0431A03.9 "Os08g0432800 prote	0.546	0.426	0.416	1.2e-24
UNIPROTKB|Q7F7Z2	258	Os01g0159800 "ESTs C26093(C116	0.646	0.674	0.366	2.6e-24
UNIPROTKB|Q6ESL3	363	OJ1294_G06.8 "DNA binding prot	0.241	0.179	0.507	1.1e-23
UNIPROTKB|Q6ZJC8	223	OJ1666_A04.16 "Os08g0477900 pr	0.635	0.766	0.367	4.8e-23
UNIPROTKB|Q75IR0	271	OSJNBb0099P06.13 "Putative unc	0.687	0.682	0.358	4.8e-23

TAIR|locus:2012393 AT1G68810 "AT1G68810" [Arabidopsis thaliana (taxid:3702)]

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 78/198 (39%), Positives = 125/198 (63%)

Query:    60 KLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQL 119
             K+  + + + +++AA K+H EAER RR+RIN HL  LRS++P  TK DKA+LL EVI  +
Sbjct:   160 KMTAQEIMDAKALAASKSHSEAERRRRERINNHLAKLRSILPNTTKTDKASLLAEVIQHV 219

Query:   120 KELDKNAMEATEGFLIPTDIDEVKV---EQQEDGLDGAPYSIKASLCCNYKPGLLSDLRR 176
             KEL +     +E  L+PT+ DE+ V   E++E G DG  + IKASLCC  +  LL D+ +
Sbjct:   220 KELKRETSVISETNLVPTESDELTVAFTEEEETG-DGR-FVIKASLCCEDRSDLLPDMIK 277

Query:   177 VLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFS 236
              L+A+ L  +KAEI T+ GR+KN+  +   +E + E  E  +  + ++ +A+++V++K +
Sbjct:   278 TLKAMRLKTLKAEITTVGGRVKNVLFVTG-EESSGEEVEE-EYCIGTIEEALKAVMEKSN 335

Query:   237 ATEEFLLGARLSNKRRRV 254
               E    G   + KR+R+
Sbjct:   336 VEESSSSG---NAKRQRM 350

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

TAIR|locus:2063203 AT2G41130 "AT2G41130" [Arabidopsis thaliana (taxid:3702)]

 Score = 308 (113.5 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 68/192 (35%), Positives = 123/192 (64%)

Query:    66 VSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKN 125
             +++DR++AAL+NH EAER RR+RIN HL+ LR+++   +K DKATLL +V+ +++EL + 
Sbjct:    59 MAQDRALAALRNHKEAERRRRERINSHLNKLRNVLSCNSKTDKATLLAKVVQRVRELKQQ 118

Query:   126 AMEATEG--FLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLEALHL 183
              +E ++    L+P++ DE+ V    D  +      KASLCC  +  LL DL  +L++L++
Sbjct:   119 TLETSDSDQTLLPSETDEISVLHFGDYSNDGHIIFKASLCCEDRSDLLPDLMEILKSLNM 178

Query:   184 SIVKAEIATLEGRMKNIFVMASCKELN-FENTEVCQSLVSSV-HQAIRSVLDKFSATEEF 241
               ++AE+ T+ GR +++ V+A+ KE++  E+    Q+ + S+  ++ +S++++ S     
Sbjct:   179 KTLRAEMVTIGGRTRSVLVVAADKEMHGVESVHFLQNALKSLLERSSKSLMERSSGG--- 235

Query:   242 LLGARLSNKRRR 253
               G    +KRRR
Sbjct:   236 --GGGERSKRRR 245

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009941 "chloroplast envelope" evidence=IDA

UNIPROTKB|Q9FTQ1 P0665D10.21 "DNA binding protein-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 75/194 (38%), Positives = 114/194 (58%)

Query:    65 GVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDK 124
             G  E+++  ALK+H EAER RR+RIN HL TLR+++P   KMDKA LL EV+  +K+L  
Sbjct:    69 GGREEKAAMALKSHSEAERRRRERINAHLATLRTMVPCTDKMDKAALLAEVVGHVKKLKS 128

Query:   125 NAMEATEGFLIPTDIDEVKVEQQE-DGLDG-APYSIKASLCCNYKPGLLSDLRRVLEALH 182
              A        +P+  DEV V++    G  G  P  ++A+L C+ +  L  D++R L+ L 
Sbjct:   129 AAARVGRRATVPSGADEVAVDEASATGGGGEGPLLLRATLSCDDRADLFVDVKRALQPLG 188

Query:   183 LSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFL 242
             L +V +E+ TL GR++  F++ SC            + ++SV  A++SVLDK S+  +F 
Sbjct:   189 LEVVGSEVTTLGGRVRLAFLV-SCGSRG----GAAAAAMASVRHALQSVLDKASSGFDFA 243

Query:   243 LGAR--LSNKRRRV 254
               A   L +KRR+V
Sbjct:   244 PRAASLLGSKRRKV 257

GO:0005634 "nucleus" evidence=IC

TAIR|locus:2085964 BHLH32 "AT3G25710" [Arabidopsis thaliana (taxid:3702)]

 Score = 305 (112.4 bits), Expect = 3.5e-27, P = 3.5e-27
 Identities = 71/192 (36%), Positives = 114/192 (59%)

Query:    60 KLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQL 119
             KL  + V + +++AA K+H EAER RR+RIN HL  LRS++P  TK DKA+LL EVI  +
Sbjct:   118 KLSAQEVMDAKALAASKSHSEAERRRRERINTHLAKLRSILPNTTKTDKASLLAEVIQHM 177

Query:   120 KELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVLE 179
             KEL +   + T+ + +PT+ D++ V+   +  +G    I+AS CC  +  L+ D+   L+
Sbjct:   178 KELKRQTSQITDTYQVPTECDDLTVDSSYNDEEGN-LVIRASFCCQDRTDLMHDVINALK 236

Query:   180 ALHLSIVKAEIATLEGRMKNIFVMA---------SCKELNFENTEV--------CQSLVS 222
             +L L  +KAEIAT+ GR+KNI  ++              NF+  +V          + VS
Sbjct:   237 SLRLRTLKAEIATVGGRVKNILFLSREYDDEEDHDSYRRNFDGDDVEDYDEERMMNNRVS 296

Query:   223 SVHQAIRSVLDK 234
             S+ +A+++V++K
Sbjct:   297 SIEEALKAVIEK 308

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:0005515 "protein binding" evidence=IPI

GO:0009718 "anthocyanin-containing compound biosynthetic process" evidence=IMP

GO:0016036 "cellular response to phosphate starvation" evidence=IMP

GO:0080147 "root hair cell development" evidence=IMP

GO:0048364 "root development" evidence=IEP

TAIR|locus:2103560 AT3G56770 "AT3G56770" [Arabidopsis thaliana (taxid:3702)]

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 69/173 (39%), Positives = 108/173 (62%)

Query:    66 VSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKN 125
             V ED+++A+L+NH EAER RR RIN HL+ LR L+   +K DK+TLL +V+ ++KEL + 
Sbjct:    37 VYEDKALASLRNHKEAERKRRARINSHLNKLRKLLSCNSKTDKSTLLAKVVQRVKELKQQ 96

Query:   126 AMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSI--KASLCCNYKPGLLSDLRRVLEALHL 183
              +E T+   IP++ DE+ V   ED   G    I  K S CC  +P LL DL   L++L +
Sbjct:    97 TLEITDE-TIPSETDEISVLNIEDCSRGDDRRIIFKVSFCCEDRPELLKDLMETLKSLQM 155

Query:   184 SIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFS 236
               + A++ T+ GR +N+ V+A+ KE +       QS V+ +  A++S+L++ S
Sbjct:   156 ETLFADMTTVGGRTRNVLVVAADKEHHG-----VQS-VNFLQNALKSLLERSS 202

GO:0003677 "DNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0010200 "response to chitin" evidence=IEP

UNIPROTKB|Q6ZA99 P0431A03.9 "Os08g0432800 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 281 (104.0 bits), Expect = 1.2e-24, P = 1.2e-24
 Identities = 67/161 (41%), Positives = 100/161 (62%)

Query:    60 KLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQL 119
             ++  K + + +++AA ++H EAER RR+RINGHL  LRSL+P  TK DKA+LL EVI  +
Sbjct:   107 RMTAKEIMDAKALAASRSHSEAERRRRQRINGHLARLRSLLPNTTKTDKASLLAEVIEHV 166

Query:   120 KELDKNA---ME--ATEG-------FLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYK 167
             KEL +     ME  A  G        L+PT+ DE++V+   D  +G     +ASLCC  +
Sbjct:   167 KELKRQTSAMMEDGAAGGEAAAAPVVLLPTEDDELEVDAAAD--EGGRLVARASLCCEDR 224

Query:   168 PGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKE 208
               L+  + R L AL L   +AEIATL GR++++ ++A+ +E
Sbjct:   225 ADLIPGIARALAALRLRARRAEIATLGGRVRSVLLIAAVEE 265

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q7F7Z2 Os01g0159800 "ESTs C26093(C11622)" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 70/191 (36%), Positives = 107/191 (56%)

Query:    74 ALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDKNAMEATEGF 133
             ALK H EAER RR+RIN HL TLR +IP   +MDKATLL  V+ Q+K+L + A E T+  
Sbjct:    65 ALKIHSEAERRRRERINAHLTTLRRMIPDTKQMDKATLLARVVDQVKDLKRKASEITQRT 124

Query:   134 LIPTDIDEVKVEQ-QEDGLDGAP--------YSIKASLCCNYKPGLLSDLRRVLEALHLS 184
              +P + +EV +E    D    A           IKAS+ C+ +P L++ +      L L 
Sbjct:   125 PLPPETNEVSIECFTGDAATAATTVAGNHKTLYIKASISCDDRPDLIAGITHAFHGLRLR 184

Query:   185 IVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATEEFLLG 244
              V+AE+ +L GR++++F++  C+E         +SL  +V QA+  V     A+ E + G
Sbjct:   185 TVRAEMTSLGGRVQHVFIL--CREEGIAGGVSLKSLKEAVRQALAKV-----ASPELVYG 237

Query:   245 A-RLSNKRRRV 254
             +    +KR+R+
Sbjct:   238 SSHFQSKRQRI 248

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q6ESL3 OJ1294_G06.8 "DNA binding protein-like" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 170 (64.9 bits), Expect = 1.1e-23, Sum P(3) = 1.1e-23
 Identities = 33/65 (50%), Positives = 48/65 (73%)

Query:    60 KLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQL 119
             ++  + + + +++AA ++H EAER RR+RINGHL  LRSL+P  TK DKA+LL EVI  +
Sbjct:    92 RVTAREIMDAKALAASRSHSEAERRRRQRINGHLARLRSLLPNTTKTDKASLLAEVIEHV 151

Query:   120 KELDK 124
             KEL +
Sbjct:   152 KELKR 156

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q6ZJC8 OJ1666_A04.16 "Os08g0477900 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 71/193 (36%), Positives = 112/193 (58%)

Query:    56 EANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEV 115
             E +    RKG S      A+++H EAER RR+RIN HL TLR+L+P A++MDKA LL EV
Sbjct:     6 ECSAAAVRKGGSP-----AVRSHSEAERKRRQRINAHLATLRTLVPSASRMDKAALLGEV 60

Query:   116 ISQLKELDKNAMEATEG--FLIPTDIDEVKVEQQEDG---LDGAPY-----------SIK 159
             +  ++EL   A +ATEG   ++P + DEV VE ++D     D   Y            ++
Sbjct:    61 VRHVRELRCRADDATEGADVVVPGEGDEVGVEDEDDDEGERDEGCYVVGGGDRRWRRRVR 120

Query:   160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQS 219
             A +CC  +PGL+SDL R + ++    V+AE+AT+ GR +++  +      +  + +   +
Sbjct:   121 AWVCCADRPGLMSDLGRAVRSVSARPVRAEVATVGGRTRSVLELDVVVASDAADNDRAVA 180

Query:   220 LVSSVHQAIRSVL 232
             L S++  A+R+VL
Sbjct:   181 L-SALRAALRTVL 192

GO:0005634 "nucleus" evidence=IC

UNIPROTKB|Q75IR0 OSJNBb0099P06.13 "Putative uncharacterized protein OSJNBb0099P06.13" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 266 (98.7 bits), Expect = 4.8e-23, P = 4.8e-23
 Identities = 70/195 (35%), Positives = 106/195 (54%)

Query:    65 GVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKELDK 124
             G S      A+  H EAER RR+RIN HL TLR ++P A +MDKATLL  V++Q+K L  
Sbjct:    57 GRSAAAQATAMTIHSEAERRRRERINAHLATLRRILPDAKQMDKATLLASVVNQVKHLKT 116

Query:   125 NAMEATE---GFLIPTDIDEVKVEQQEDG--LDGAPYSIKASLCCNYKPGLLSDLRRVLE 179
              A EAT       IP + +EV V+    G     A   ++A++ C+ +PGLL+D+     
Sbjct:   117 RATEATTPSTAATIPPEANEVTVQCYAGGEHTAAARTYVRATVSCDDRPGLLADIAATFR 176

Query:   180 ALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSATE 239
              L L  + A+++ L GR ++ FV+  C+E   E     ++    + +A+R  L K  A  
Sbjct:   177 RLRLRPLSADMSCLGGRTRHAFVL--CREEEEEEDAAAEA--RPLKEAVRQALAKV-ALP 231

Query:   240 EFLLGARLSNKRRRV 254
             E + G    +KR+R+
Sbjct:   232 ETVYGGGGRSKRQRL 246

GO:0005634 "nucleus" evidence=IC

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	269
cd00083	60	cd00083, HLH, Helix-loop-helix domain, found in sp	1e-10
pfam00010	52	pfam00010, HLH, Helix-loop-helix DNA-binding domai	8e-10
smart00353	53	smart00353, HLH, helix loop helix domain	6e-09
cd04899	70	cd04899, ACT_ACR-UUR-like_2, C-terminal ACT domain	4e-06
cd04873	70	cd04873, ACT_UUR-ACR-like, ACT domains of the bact	3e-05
cd04926	72	cd04926, ACT_ACR_4, C-terminal ACT domain, of a no	1e-04
COG2844	867	COG2844, GlnD, UTP:GlnB (protein PII) uridylyltran	2e-04
TIGR01693	850	TIGR01693, UTase_glnD, [Protein-PII] uridylyltrans	6e-04

>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 = 55.3 bits (134), Expect = 1e-10
 Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKEL 122
           + H   ER RR+RIN   D LRSL+P      K+ KA +L + +  +K L
Sbjct: 6   EAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSL 55

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 = 53.2 bits (129), Expect = 8e-10
 Identities = 21/49 (42%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKEL 122
           K H E ER RR RIN   + LR L+P     K+ KA +L   I  +K L
Sbjct: 3   KAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIKHL 51

Length = 52

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

 Score = 50.7 bits (122), Expect = 6e-09
 Identities = 19/46 (41%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 80  EAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKEL 122
             ER RR++IN   D LRSL+P      K+ KA +L   I  +K L
Sbjct: 2   ARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSL 47

Length = 53

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

 Score = 43.2 bits (103), Expect = 4e-06
 Identities = 19/41 (46%), Positives = 27/41 (65%)

Query: 161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIF 201
            L    +PGLL+D+ RVL  L L+I  A+IATL  R +++F
Sbjct: 4   ELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVF 44

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

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

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 16/42 (38%), Positives = 24/42 (57%)

Query: 161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFV 202
            +    +PGLL+D+ RVL  L L+I  A I+T   R  ++F 
Sbjct: 4   EVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFY 45

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

>gnl|CDD|153198 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)

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 15/44 (34%), Positives = 24/44 (54%)

Query: 158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIF 201
           ++  L    + GLLSD+ RV     L++ +AEI+T      N+F
Sbjct: 2   VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVF 45

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. Length = 72

>gnl|CDD|225400 COG2844, GlnD, UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 167 KPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQ 226
           +PGLL+ L  V   L LS+  A+I T   R++++F++           E+ QSL+  + +
Sbjct: 801 RPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADGQALNA-ELRQSLLQRLLE 859

Query: 227 AIRSVLD 233
           A+    +
Sbjct: 860 ALLPNDE 866

Length = 867

>gnl|CDD|233534 TIGR01693, UTase_glnD, [Protein-PII] uridylyltransferase

 Score = 40.5 bits (95), Expect = 6e-04
 Identities = 40/194 (20%), Positives = 68/194 (35%), Gaps = 37/194 (19%)

Query: 44  SLVLDSERGELVEANVKLQRKGVSEDRSVAALKNH--IEAERNRRKRINGHLDTLRSLIP 101
           +  L      + +A V   + GV+ D  V          AER  ++ + G +D L  L  
Sbjct: 686 AGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGSPPAAERVFQELLQGLVDVLAGL-- 743

Query: 102 GATKMDKATLLTEVISQLKELDKNAMEATEGFLIPTDID------EVKVEQQEDGLDGAP 155
            A   D  +       +L+            F +P  +             +   LD   
Sbjct: 744 -AKDPDTISARRARRRRLQH-----------FAVPPRVTILNTASRKATIMEVRALD--- 788

Query: 156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTE 215
                      +PGLL+ + R LE L LSI  A+I T   + +++F +     L     E
Sbjct: 789 -----------RPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGLKL-TDE 836

Query: 216 VCQSLVSSVHQAIR 229
             Q L+  +  ++ 
Sbjct: 837 EEQRLLEVLAASVA 850

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 [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, Protein interactions]. Length = 850

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	269
cd00083	60	HLH Helix-loop-helix domain, found in specific DNA	99.46
PF00010	55	HLH: Helix-loop-helix DNA-binding domain only nucl	99.44
smart00353	53	HLH helix loop helix domain.	99.4
KOG1318	411	consensus Helix loop helix transcription factor EB	99.15
KOG1319	229	consensus bHLHZip transcription factor BIGMAX [Tra	99.14
cd04897	75	ACT_ACR_3 ACT domain-containing protein which is c	99.09
cd04896	75	ACT_ACR-like_3 ACT domain-containing protein which	98.99
cd04895	72	ACT_ACR_1 ACT domain-containing protein which is c	98.94
cd04927	76	ACT_ACR-like_2 Second ACT domain, of a novel type	98.83
cd04900	73	ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1,	98.83
cd04925	74	ACT_ACR_2 ACT domain-containing protein which is c	98.62
KOG4304	250	consensus Transcriptional repressors of the hairy/	98.6
KOG3561	803	consensus Aryl-hydrocarbon receptor nuclear transl	98.44
cd04928	68	ACT_TyrKc Uncharacterized, N-terminal ACT domain o	98.36
cd04926	72	ACT_ACR_4 C-terminal ACT domain, of a novel type o	98.23
cd04899	70	ACT_ACR-UUR-like_2 C-terminal ACT domains of the b	98.22
KOG0561	373	consensus bHLH transcription factor [Transcription	98.16
KOG2483	232	consensus Upstream transcription factor 2/L-myc-2	98.07
PRK05007	884	PII uridylyl-transferase; Provisional	98.04
KOG2588	953	consensus Predicted DNA-binding protein [Transcrip	98.02
PRK00275	895	glnD PII uridylyl-transferase; Provisional	98.0
PRK01759	854	glnD PII uridylyl-transferase; Provisional	97.89
cd04873	70	ACT_UUR-ACR-like ACT domains of the bacterial sign	97.86
KOG3960	284	consensus Myogenic helix-loop-helix transcription	97.79
PRK04374	869	PII uridylyl-transferase; Provisional	97.75
PLN03217	93	transcription factor ATBS1; Provisional	97.75
KOG4029	228	consensus Transcription factor HAND2/Transcription	97.61
PRK03059	856	PII uridylyl-transferase; Provisional	97.59
PRK05092	931	PII uridylyl-transferase; Provisional	97.56
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	97.47
PRK05007	884	PII uridylyl-transferase; Provisional	97.43
PRK01759	854	glnD PII uridylyl-transferase; Provisional	97.39
TIGR01693	850	UTase_glnD [Protein-PII] uridylyltransferase. This	97.38
PRK03381	774	PII uridylyl-transferase; Provisional	97.38
PF13740	76	ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.	97.36
PF01842	66	ACT: ACT domain; InterPro: IPR002912 The ACT domai	97.35
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	97.31
PRK00275	895	glnD PII uridylyl-transferase; Provisional	97.25
PRK03059	856	PII uridylyl-transferase; Provisional	97.11
cd04893	77	ACT_GcvR_1 ACT domains that comprise the Glycine C	97.1
PRK03381	774	PII uridylyl-transferase; Provisional	97.01
PRK05092	931	PII uridylyl-transferase; Provisional	97.0
PF13291	80	ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.	96.71
PRK04374	869	PII uridylyl-transferase; Provisional	96.65
cd04872	88	ACT_1ZPV ACT domain proteins similar to the yet un	96.16
PRK00194	90	hypothetical protein; Validated	96.11
cd04869	81	ACT_GcvR_2 ACT domains that comprise the Glycine C	96.07
cd04870	75	ACT_PSP_1 CT domains found N-terminal of phosphose	96.06
KOG3910	632	consensus Helix loop helix transcription factor [T	95.99
cd04875	74	ACT_F4HF-DF N-terminal ACT domain of formyltetrahy	95.96
cd04886	73	ACT_ThrD-II-like C-terminal ACT domain of biodegra	95.66
cd04887	74	ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-te	95.46
cd04888	76	ACT_PheB-BS C-terminal ACT domain of a small (~147	95.43
COG2844	867	GlnD UTP:GlnB (protein PII) uridylyltransferase [P	95.35
TIGR00655	280	PurU formyltetrahydrofolate deformylase. This mode	94.83
cd04894	69	ACT_ACR-like_1 ACT domain-containing protein which	94.81
PRK06027	286	purU formyltetrahydrofolate deformylase; Reviewed	94.51
KOG4447	173	consensus Transcription factor TWIST [Transcriptio	94.4
PRK13010	289	purU formyltetrahydrofolate deformylase; Reviewed	94.17
cd04877	74	ACT_TyrR N-terminal ACT domain of the TyrR protein	94.01
cd04876	71	ACT_RelA-SpoT ACT domain found C-terminal of the R	93.44
PRK13011	286	formyltetrahydrofolate deformylase; Reviewed	93.35
cd04881	79	ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-termin	93.05
KOG3898	254	consensus Transcription factor NeuroD and related	92.84
cd04880	75	ACT_AAAH-PDT-like ACT domain of the nonheme iron-d	92.79
cd04874	72	ACT_Af1403 N-terminal ACT domain of the yet unchar	92.67
cd02116	60	ACT ACT domains are commonly involved in specifica	92.61
PRK04435	147	hypothetical protein; Provisional	92.53
cd04879	71	ACT_3PGDH-like ACT_3PGDH-like CD includes the C-te	92.18
cd04889	56	ACT_PDH-BS-like C-terminal ACT domain of the monof	92.05
COG0788	287	PurU Formyltetrahydrofolate hydrolase [Nucleotide	91.73
KOG3560	712	consensus Aryl-hydrocarbon receptor [Transcription	91.62
PRK11589	190	gcvR glycine cleavage system transcriptional repre	91.3
PRK07334	403	threonine dehydratase; Provisional	91.3
KOG3559	598	consensus Transcriptional regulator SIM1 [Transcri	91.09
cd04905	80	ACT_CM-PDT C-terminal ACT domain of the bifunction	91.09
cd04878	72	ACT_AHAS N-terminal ACT domain of the Escherichia	90.82
KOG4395	285	consensus Transcription factor Atonal, contains HT	90.79
cd04909	69	ACT_PDH-BS C-terminal ACT domain of the monofuncti	90.04
KOG3558	768	consensus Hypoxia-inducible factor 1/Neuronal PAS	89.6
cd04908	66	ACT_Bt0572_1 N-terminal ACT domain of a novel prot	89.41
cd04903	71	ACT_LSD C-terminal ACT domain of the L-serine dehy	89.1
cd04884	72	ACT_CBS C-terminal ACT domain of the cystathionine	89.0
cd04883	72	ACT_AcuB C-terminal ACT domain of the Bacillus sub	88.92
PRK08577	136	hypothetical protein; Provisional	88.84
cd04882	65	ACT_Bt0572_2 C-terminal ACT domain of a novel prot	86.51
TIGR00119	157	acolac_sm acetolactate synthase, small subunit. ac	84.49
cd04931	90	ACT_PAH ACT domain of the nonheme iron-dependent a	84.15
cd04904	74	ACT_AAAH ACT domain of the nonheme iron-dependent,	83.53
PRK10872	743	relA (p)ppGpp synthetase I/GTP pyrophosphokinase;	83.5
PRK11895	161	ilvH acetolactate synthase 3 regulatory subunit; R	83.15
cd04929	74	ACT_TPH ACT domain of the nonheme iron-dependent a	82.91
COG3830	90	ACT domain-containing protein [Signal transduction	82.84
cd04885	68	ACT_ThrD-I Tandem C-terminal ACT domains of threon	82.03
cd04901	69	ACT_3PGDH C-terminal ACT (regulatory) domain of D-	81.84
cd04902	73	ACT_3PGDH-xct C-terminal ACT (regulatory) domain o	80.68
PRK11092	702	bifunctional (p)ppGpp synthetase II/ guanosine-3',	80.62
CHL00100	174	ilvH acetohydroxyacid synthase small subunit	80.14

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

Probab=99.46  E-value=1.8e-13  Score=96.46  Aligned_cols=53  Identities=38%  Similarity=0.557  Sum_probs=50.2

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHH
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNA  126 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~  126 (269)
                      ....|+..||+||++||+.|..|+++||..   .|+||++||..||+||+.|+.++
T Consensus         4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~   59 (60)
T cd00083           4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL   59 (60)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence            457899999999999999999999999988   89999999999999999999876

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

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

Probab=99.44  E-value=1.9e-13  Score=95.38  Aligned_cols=49  Identities=43%  Similarity=0.706  Sum_probs=46.4

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCC-----CccchhhHHHHHHHHHHHHH
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGA-----TKMDKATLLTEVISQLKELD  123 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~-----~k~dk~sil~~ai~yik~L~  123 (269)
                      +..|+..||+||++||+.|..|+.+||..     .|++|++||..||+||++||
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            47899999999999999999999999975     78999999999999999997

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

>smart00353 HLH helix loop helix domain

Probab=99.40  E-value=5.9e-13  Score=91.81  Aligned_cols=49  Identities=39%  Similarity=0.587  Sum_probs=45.7

Q ss_pred             hHHHHHHHHHHHHhHHHHHhhcCC---CCccchhhHHHHHHHHHHHHHHHHH
Q 024326           79 IEAERNRRKRINGHLDTLRSLIPG---ATKMDKATLLTEVISQLKELDKNAM  127 (269)
Q Consensus        79 ~~~Er~RR~~in~~~~~LrslvP~---~~k~dk~sil~~ai~yik~L~~~~~  127 (269)
                      +..||+||++||+.|..|+++||.   ..|++|++||.+||+||++|+++++
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            468999999999999999999994   5799999999999999999999876

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

Probab=99.15  E-value=6.5e-11  Score=112.48  Aligned_cols=59  Identities=34%  Similarity=0.485  Sum_probs=52.6

Q ss_pred             chHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHHHHHHHHHHH
Q 024326           71 SVAALKNHIEAERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLKELDKNAMEA  129 (269)
Q Consensus        71 ~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik~L~~~~~~l  129 (269)
                      ....+.+|+++|||||++||+++.+|..|||.+    .|..|.+||..+++||+.||+..++.
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            334568999999999999999999999999987    56779999999999999999987754

>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]

Probab=99.14  E-value=6.7e-11  Score=100.74  Aligned_cols=90  Identities=27%  Similarity=0.361  Sum_probs=65.7

Q ss_pred             CCCCCCCCcccccccchhhhhhhhccCCCCCcccchHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC-------Cccchh
Q 024326           37 NGSSSHSSLVLDSERGELVEANVKLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGA-------TKMDKA  109 (269)
Q Consensus        37 ~~~s~s~s~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-------~k~dk~  109 (269)
                      +.++.++..+.|.+..+...+..+...|.|       ++..|..+||+||+.||..+..|+.|||.+       .|+.||
T Consensus        32 GStsssSApNtdd~ds~~hS~a~k~syk~r-------rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA  104 (229)
T KOG1319|consen   32 GSTSASSAPNTDDEDSDYHSEAYKESYKDR-------RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKA  104 (229)
T ss_pred             CCCCCCCCCCCCcccccchhHHHHhhHHHH-------HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHH
Confidence            334455555555555443333223222222       347899999999999999999999999954       488899


Q ss_pred             hHHHHHHHHHHHHHHHHHHHhccC
Q 024326          110 TLLTEVISQLKELDKNAMEATEGF  133 (269)
Q Consensus       110 sil~~ai~yik~L~~~~~~l~~~~  133 (269)
                      .||..+|+||.+|++++.+.+++.
T Consensus       105 ~ILqksidyi~~L~~~k~kqe~e~  128 (229)
T KOG1319|consen  105 IILQKTIDYIQFLHKEKKKQEEEV  128 (229)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999988776653

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

Probab=99.09  E-value=1e-09  Score=81.55  Aligned_cols=71  Identities=14%  Similarity=0.226  Sum_probs=56.9

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHh
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLD  233 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~  233 (269)
                      .|+|.|++|||||.+|..+|-+++++|.+|.|+|.++++.++|++....+....++...    ..|+++|..+++
T Consensus         3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~kl~~~~~~----~~l~~~L~~al~   73 (75)
T cd04897           3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGRTLSTEGER----QRVIKCLEAAIE   73 (75)
T ss_pred             EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCCccCCHHHH----HHHHHHHHHHHh
Confidence            36788999999999999999999999999999999999999999986655544454443    455555555544

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

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

Probab=98.99  E-value=4.6e-09  Score=78.07  Aligned_cols=69  Identities=14%  Similarity=0.250  Sum_probs=55.2

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE--eeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHh
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA--TLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLD  233 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is--t~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~  233 (269)
                      ++|.|.+|||+|.+|.++|..+|++|..|.|+  |.|+++.++|++ .+.++...+++.    ...|+++|..+++
T Consensus         3 lev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv-~~~g~kl~d~~~----~~~L~~~L~~~l~   73 (75)
T cd04896           3 LQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV-QSDGKKIMDPKK----QAALCARLREEMV   73 (75)
T ss_pred             EEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE-eCCCCccCCHHH----HHHHHHHHHHHhc
Confidence            56889999999999999999999999999999  999999999999 555544444444    3455555555544

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.

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

Probab=98.94  E-value=7.3e-09  Score=76.42  Aligned_cols=62  Identities=23%  Similarity=0.315  Sum_probs=50.8

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHH
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSL  220 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l  220 (269)
                      .++|.+++|||+|.+|.++|.++||+|..|.|+|.|+++.++|++....+....+++..+.+
T Consensus         3 viev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~kl~d~~~~~~l   64 (72)
T cd04895           3 LVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGNKLTDDSLIAYI   64 (72)
T ss_pred             EEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCCCCCCHHHHHHH
Confidence            36788999999999999999999999999999999999999999985543333344443333

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.

>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=98.83  E-value=4.7e-08  Score=72.63  Aligned_cols=69  Identities=26%  Similarity=0.471  Sum_probs=52.6

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe-eCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHH
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT-LEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVL  232 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist-~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~  232 (269)
                      .++|.|+++||+|.+|..+|..+|++|+.|.|.| .+|+++++|+|.... +....+...    ..|+++|..++
T Consensus         2 ~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~~-~~~~~~~~~----~~l~~~L~~~L   71 (76)
T cd04927           2 LLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDAR-ELLHTKKRR----EETYDYLRAVL   71 (76)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCCC-CCCCCHHHH----HHHHHHHHHHH
Confidence            4678999999999999999999999999999995 899999999997443 222222333    44555555444

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.

>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=98.83  E-value=4.3e-08  Score=71.91  Aligned_cols=48  Identities=27%  Similarity=0.450  Sum_probs=43.9

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee-CCeEEEEEEEee
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL-EGRMKNIFVMAS  205 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~-~g~v~~vf~v~~  205 (269)
                      ..|.|.|+++||+|++|..+|..+|++|+.|.+.|. +|+++++|++..
T Consensus         2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~   50 (73)
T cd04900           2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLD   50 (73)
T ss_pred             EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEEC
Confidence            356788999999999999999999999999999877 799999999974

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

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

Probab=98.62  E-value=5.5e-07  Score=66.37  Aligned_cols=46  Identities=33%  Similarity=0.486  Sum_probs=43.7

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEee
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMAS  205 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~  205 (269)
                      ++|.++++||+|.+|..+|..+|++|+.|.+.|.++++.++|++..
T Consensus         3 ~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d   48 (74)
T cd04925           3 IELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRD   48 (74)
T ss_pred             EEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEc
Confidence            5688999999999999999999999999999999999999999974

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.

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

Probab=98.60  E-value=4.6e-08  Score=88.32  Aligned_cols=55  Identities=33%  Similarity=0.526  Sum_probs=48.5

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCC--------CCccchhhHHHHHHHHHHHHHHHHHH
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPG--------ATKMDKATLLTEVISQLKELDKNAME  128 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~--------~~k~dk~sil~~ai~yik~L~~~~~~  128 (269)
                      +..+|-+.||+||+|||+.|.+|+.|||.        ..|++||-||+-|++|+++|+...+.
T Consensus        32 rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~   94 (250)
T KOG4304|consen   32 RKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA   94 (250)
T ss_pred             hhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence            34778899999999999999999999993        27899999999999999999886543

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

Probab=98.44  E-value=2.1e-07  Score=95.22  Aligned_cols=51  Identities=27%  Similarity=0.487  Sum_probs=47.9

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHHHHHHH
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLKELDKN  125 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik~L~~~  125 (269)
                      +.+|+.+|||||+++|..+.+|.+|||.+    .|+||.+||.+||.+||.+++.
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            48899999999999999999999999975    6999999999999999988875

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

Probab=98.36  E-value=4.4e-06  Score=60.98  Aligned_cols=48  Identities=33%  Similarity=0.453  Sum_probs=43.2

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE-eeCCeEEEEEEEeee
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA-TLEGRMKNIFVMASC  206 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is-t~~g~v~~vf~v~~~  206 (269)
                      .|.|.|+++||+|.+|..+|..+||+|+.|++. +.+|.++++|.|...
T Consensus         3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~   51 (68)
T cd04928           3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGW   51 (68)
T ss_pred             EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecC
Confidence            456889999999999999999999999999996 679999999999743

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

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

Probab=98.23  E-value=1.2e-05  Score=58.77  Aligned_cols=48  Identities=31%  Similarity=0.475  Sum_probs=43.9

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEee
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMAS  205 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~  205 (269)
                      +++.|.+++++|+|.+|..+|.+++++|+++.+.+.++.+.++|++..
T Consensus         2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~   49 (72)
T cd04926           2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTD   49 (72)
T ss_pred             eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEEC
Confidence            356688999999999999999999999999999999899999999974

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.

>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=98.22  E-value=1.6e-05  Score=56.88  Aligned_cols=68  Identities=29%  Similarity=0.419  Sum_probs=52.2

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHH
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSV  231 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v  231 (269)
                      .+.|.+++++|+|.+|+.+|.+++++|.++++.+.++.+.++|++....... ...    .....|+++|..+
T Consensus         2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~~~~-~~~----~~~~~i~~~l~~~   69 (70)
T cd04899           2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDADGQP-LDP----ERQEALRAALGEA   69 (70)
T ss_pred             EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCCCCc-CCH----HHHHHHHHHHHhh
Confidence            3568899999999999999999999999999999888999999997533222 221    2344566666544

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.

>KOG0561 consensus bHLH transcription factor [Transcription]

Probab=98.16  E-value=2.3e-06  Score=78.10  Aligned_cols=57  Identities=26%  Similarity=0.414  Sum_probs=50.9

Q ss_pred             HHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--CccchhhHHHHHHHHHHHHHHHHHHH
Q 024326           73 AALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKELDKNAMEA  129 (269)
Q Consensus        73 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dk~sil~~ai~yik~L~~~~~~l  129 (269)
                      -++.--|.-||||-+-||..|..||+|+|..  .|++||+||+.+.+||.+|+.+..+|
T Consensus        59 mRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l  117 (373)
T KOG0561|consen   59 MRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL  117 (373)
T ss_pred             HHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence            4556778899999999999999999999974  89999999999999999999876554

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

Probab=98.07  E-value=8.9e-06  Score=72.66  Aligned_cols=60  Identities=13%  Similarity=0.363  Sum_probs=50.6

Q ss_pred             cchHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--Cccc-hhhHHHHHHHHHHHHHHHHHHH
Q 024326           70 RSVAALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMD-KATLLTEVISQLKELDKNAMEA  129 (269)
Q Consensus        70 ~~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~d-k~sil~~ai~yik~L~~~~~~l  129 (269)
                      .....+..||.-||+||+.|.+.|..|+.+||..  .+.. .++||..|+.||+.|+.+....
T Consensus        55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~  117 (232)
T KOG2483|consen   55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQ  117 (232)
T ss_pred             CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHH
Confidence            3445678999999999999999999999999976  3333 6899999999999999876543

>PRK05007 PII uridylyl-transferase; Provisional

Probab=98.04  E-value=2.6e-05  Score=82.02  Aligned_cols=72  Identities=24%  Similarity=0.395  Sum_probs=56.3

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHH
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVL  232 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~  232 (269)
                      ....++|.|.+|||+|++|.++|.++|++|.+|.|+|.++++.++|+|.... +...+++.    ...|+++|..++
T Consensus       807 ~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~~-g~~l~~~~----~~~l~~~L~~~l  878 (884)
T PRK05007        807 RRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATAD-RRALNEEL----QQELRQRLTEAL  878 (884)
T ss_pred             CeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcCC-CCcCCHHH----HHHHHHHHHHHH
Confidence            3456789999999999999999999999999999999999999999997543 33223333    455555555554

>KOG2588 consensus Predicted DNA-binding protein [Transcription]

Probab=98.02  E-value=2.3e-06  Score=88.21  Aligned_cols=58  Identities=24%  Similarity=0.427  Sum_probs=53.1

Q ss_pred             HHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC-CccchhhHHHHHHHHHHHHHHHHHHHh
Q 024326           73 AALKNHIEAERNRRKRINGHLDTLRSLIPGA-TKMDKATLLTEVISQLKELDKNAMEAT  130 (269)
Q Consensus        73 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dk~sil~~ai~yik~L~~~~~~l~  130 (269)
                      ..+.+||.+|||.|..||+++.+|+.+||+. .|+.|.++|..||+||++|+...+.+.
T Consensus       275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk  333 (953)
T KOG2588|consen  275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLK  333 (953)
T ss_pred             cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccc
Confidence            4468999999999999999999999999987 899999999999999999998776654

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=98.00  E-value=3.4e-05  Score=81.27  Aligned_cols=77  Identities=21%  Similarity=0.457  Sum_probs=58.1

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHh
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLD  233 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~  233 (269)
                      ...|.|.+.++||+|++|..+|..+||+|+.|.|+|.|+++.++|+|....+.....+...+.+.+.|.++|....+
T Consensus       814 ~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~~l~~~~~~~~l~~~L~~~L~~~~~  890 (895)
T PRK00275        814 VTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQPLSDPQLCSRLQDAICEQLDARNE  890 (895)
T ss_pred             eEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHhcccc
Confidence            35677999999999999999999999999999999999999999999854433333333444455555555544333

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=97.89  E-value=6e-05  Score=79.05  Aligned_cols=71  Identities=18%  Similarity=0.374  Sum_probs=55.5

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHH
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSV  231 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v  231 (269)
                      ....++|.+.+|||+|.+|.++|.++|++|..|.|+|.++++.++|+|....+....+.+     ...|+++|...
T Consensus       782 ~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~~~g~~l~~~~-----~~~l~~~L~~~  852 (854)
T PRK01759        782 EQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTNQQGQALDEEE-----RKALKSRLLSN  852 (854)
T ss_pred             CeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEECCCCCcCChHH-----HHHHHHHHHHH
Confidence            345678999999999999999999999999999999999999999999754433222221     25566665544

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

Probab=97.86  E-value=0.00023  Score=50.39  Aligned_cols=47  Identities=34%  Similarity=0.533  Sum_probs=41.6

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEee
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMAS  205 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~  205 (269)
                      .+.|.|++++|+|.+|+.+|.++++.|.++.+.+.++....+|.+..
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            35678999999999999999999999999999988778777888764

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

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

Probab=97.79  E-value=8.2e-05  Score=66.57  Aligned_cols=62  Identities=24%  Similarity=0.333  Sum_probs=52.0

Q ss_pred             chHHhhhhhHHHHHHHHHHHHhHHHHHh-hcCCC-CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           71 SVAALKNHIEAERNRRKRINGHLDTLRS-LIPGA-TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        71 ~~~~~~~h~~~Er~RR~~in~~~~~Lrs-lvP~~-~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      +..+++.-.+.||||=.|+|+.|.+|+. -.++. ..+-|.-||..||+||..||.-++++.+.
T Consensus       115 svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~  178 (284)
T KOG3960|consen  115 SVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQA  178 (284)
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            3455677889999999999999999954 44554 77899999999999999999999988543

>PRK04374 PII uridylyl-transferase; Provisional

Probab=97.75  E-value=0.00012  Score=76.84  Aligned_cols=71  Identities=27%  Similarity=0.411  Sum_probs=55.7

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHH
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVL  232 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~  232 (269)
                      ...|.|.+.++||+|++|..+|..+|++|+.|.|+|.|+++.++|+|....+.. .+..   + ...|+++|...+
T Consensus       796 ~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~~-~~~~---~-~~~l~~~L~~~l  866 (869)
T PRK04374        796 RTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDRP-LSES---A-RQALRDALCACL  866 (869)
T ss_pred             eEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCCc-CChH---H-HHHHHHHHHHHh
Confidence            456779999999999999999999999999999999999999999997543332 2221   1 256666666554

>PLN03217 transcription factor ATBS1; Provisional

Probab=97.75  E-value=6.7e-05  Score=56.46  Aligned_cols=47  Identities=21%  Similarity=0.412  Sum_probs=40.2

Q ss_pred             HHHHHhHHHHHhhcCCC------CccchhhHHHHHHHHHHHHHHHHHHHhccC
Q 024326           87 KRINGHLDTLRSLIPGA------TKMDKATLLTEVISQLKELDKNAMEATEGF  133 (269)
Q Consensus        87 ~~in~~~~~LrslvP~~------~k~dk~sil~~ai~yik~L~~~~~~l~~~~  133 (269)
                      ++||+.+..|+.|+|..      .|..-+-+|++|+.||+.|+.+|.+|.+.+
T Consensus        20 dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerL   72 (93)
T PLN03217         20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERL   72 (93)
T ss_pred             HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            67999999999999953      455566689999999999999999997653

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

Probab=97.61  E-value=6.5e-05  Score=66.98  Aligned_cols=61  Identities=25%  Similarity=0.304  Sum_probs=53.1

Q ss_pred             hHHhhhhhHHHHHHHHHHHHhHHHHHhhcCC----CCccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           72 VAALKNHIEAERNRRKRINGHLDTLRSLIPG----ATKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        72 ~~~~~~h~~~Er~RR~~in~~~~~LrslvP~----~~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      ..++..++..||+|=..+|..|..||.+||.    .+|..|..+|.-||.||++|+.-++.-+..
T Consensus       107 ~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~  171 (228)
T KOG4029|consen  107 SAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP  171 (228)
T ss_pred             hhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence            3456778888999999999999999999994    478999999999999999999988766543

>PRK03059 PII uridylyl-transferase; Provisional

Probab=97.59  E-value=0.00035  Score=73.35  Aligned_cols=48  Identities=33%  Similarity=0.507  Sum_probs=44.9

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      ...|.|.|+++||+|.+|..+|..+|++|+.|.|+|.|+++.++|+|.
T Consensus       786 ~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~  833 (856)
T PRK03059        786 YYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLID  833 (856)
T ss_pred             EEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEc
Confidence            345779999999999999999999999999999999999999999994

>PRK05092 PII uridylyl-transferase; Provisional

Probab=97.56  E-value=0.00046  Score=73.15  Aligned_cols=74  Identities=28%  Similarity=0.394  Sum_probs=59.0

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      ...|.|.|.++||+|.+|..+|..+|++|..|.|.|.++++.++|++....+.....+.    ....|+++|..++..
T Consensus       843 ~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~~i~~~~----~~~~l~~~L~~~L~~  916 (931)
T PRK05092        843 FTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGLKITNEA----RQAAIRRALLAALAE  916 (931)
T ss_pred             eEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCCcCCCHH----HHHHHHHHHHHHhcC
Confidence            35677999999999999999999999999999999999999999999755433323322    245677777777654

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=97.47  E-value=0.00074  Score=70.90  Aligned_cols=74  Identities=20%  Similarity=0.278  Sum_probs=57.2

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE-eeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA-TLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is-t~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      ...|.|.++++||+|.+|..+|..+||+|+.|.|. |.+|+++++|+|....+.....+    .....|.++|..++..
T Consensus       668 ~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~~~~~~----~~~~~i~~~L~~~L~~  742 (850)
T TIGR01693       668 GTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGSPPAAE----RVFQELLQGLVDVLAG  742 (850)
T ss_pred             eEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCCCCCcH----HHHHHHHHHHHHHHcC
Confidence            34577899999999999999999999999999998 88999999999985443322222    2344566666666655

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.

>PRK05007 PII uridylyl-transferase; Provisional

Probab=97.43  E-value=0.0012  Score=69.61  Aligned_cols=74  Identities=16%  Similarity=0.220  Sum_probs=55.5

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee-CCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhc
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL-EGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKF  235 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~-~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~  235 (269)
                      ...|.|+|++++|+|.+|..+|..+||+|+.|.|.|. +|+++++|+|....+... ..    .....|.++|..++...
T Consensus       701 ~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~~~-~~----~~~~~I~~~L~~aL~~~  775 (884)
T PRK05007        701 GTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGSPL-SQ----DRHQVIRKALEQALTQS  775 (884)
T ss_pred             eEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCCCC-CH----HHHHHHHHHHHHHHcCC
Confidence            3566789999999999999999999999999998755 569999999985433322 22    23445666666666543

>PRK01759 glnD PII uridylyl-transferase; Provisional

Probab=97.39  E-value=0.001  Score=69.93  Aligned_cols=72  Identities=19%  Similarity=0.264  Sum_probs=55.9

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe-eCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT-LEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist-~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      ..|.|.|+++||+|++|..+|..+||+|+.|.|.| .+|+++++|+|....+.. ...    .....|+++|..++..
T Consensus       678 t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~~-~~~----~~~~~l~~~L~~aL~~  750 (854)
T PRK01759        678 TEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGKL-LEF----DRRRQLEQALTKALNT  750 (854)
T ss_pred             EEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCCC-CCH----HHHHHHHHHHHHHHcC
Confidence            46678999999999999999999999999999976 899999999998543322 222    2334566666666654

>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase

Probab=97.38  E-value=0.00099  Score=69.95  Aligned_cols=70  Identities=24%  Similarity=0.371  Sum_probs=54.9

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHH
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSV  231 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v  231 (269)
                      ...+.|.|.++||+|.+|.++|..+|++|.+|.|+|.++++.++|++....+....+ +.    ...|+++|...
T Consensus       779 ~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~~~~~-~~----~~~l~~~L~~~  848 (850)
T TIGR01693       779 ATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGLKLTD-EE----EQRLLEVLAAS  848 (850)
T ss_pred             eEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCCCCCH-HH----HHHHHHHHHHH
Confidence            345779999999999999999999999999999999999999999997544333232 23    35555555543

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=97.38  E-value=0.00076  Score=70.16  Aligned_cols=65  Identities=25%  Similarity=0.367  Sum_probs=52.9

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHH
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAI  228 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL  228 (269)
                      ..|.|.|.++||+|.+|..+|..+|++|..|.|+|.|+++.++|+|....+....+     . ...|+++|
T Consensus       708 t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~~g~~~~~-----~-~~~l~~~L  772 (774)
T PRK03381        708 TVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGAAGGPLAD-----A-RAAVEQAV  772 (774)
T ss_pred             EEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECCCCCcCch-----H-HHHHHHHh
Confidence            56779999999999999999999999999999999999999999997544332222     1 45566655

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

Probab=97.36  E-value=0.0035  Score=46.14  Aligned_cols=66  Identities=17%  Similarity=0.312  Sum_probs=49.9

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      +.|++.+++|||++..|..+|.++|.+|..++.++.++.+..++.+....           .....|+.+|..+..+
T Consensus         3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~-----------~~~~~l~~~L~~l~~~   68 (76)
T PF13740_consen    3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPE-----------DSLERLESALEELAEE   68 (76)
T ss_dssp             EEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESH-----------HHHHHHHHHHHHHHHH
T ss_pred             EEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCc-----------ccHHHHHHHHHHHHHH
Confidence            45778999999999999999999999999999999999987777775431           2345666666666443

>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=97.35  E-value=0.0026  Score=44.29  Aligned_cols=37  Identities=16%  Similarity=0.334  Sum_probs=34.1

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCC
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEG  195 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g  195 (269)
                      .|.+.|+++||+|.+|..+|.++|++|.++.+.+.++
T Consensus         2 ~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~   38 (66)
T PF01842_consen    2 RVRVIVPDRPGILADVTEILADHGINIDSISQSSDKD   38 (66)
T ss_dssp             EEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence            4568899999999999999999999999999998877

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 ....

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

Probab=97.31  E-value=0.00085  Score=69.02  Aligned_cols=53  Identities=26%  Similarity=0.434  Sum_probs=47.7

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELN  210 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~  210 (269)
                      ..+++.+.+|||+|..|..+|.+++|+|++|.|+|+|.++.++|++.......
T Consensus       792 t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~~~  844 (867)
T COG2844         792 TVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADGQA  844 (867)
T ss_pred             eEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEecccccc
Confidence            34678899999999999999999999999999999999999999998655443

>PRK00275 glnD PII uridylyl-transferase; Provisional

Probab=97.25  E-value=0.0017  Score=68.53  Aligned_cols=51  Identities=10%  Similarity=0.153  Sum_probs=45.4

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEE-EeeCCeEEEEEEEeeecc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEI-ATLEGRMKNIFVMASCKE  208 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~i-st~~g~v~~vf~v~~~k~  208 (269)
                      +.|.|.|+++||+|.+|..+|..+|++|+.|.| ++.+|.++++|+|....+
T Consensus       705 t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g  756 (895)
T PRK00275        705 TQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDG  756 (895)
T ss_pred             EEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCC
Confidence            456688999999999999999999999999998 677899999999985443

>PRK03059 PII uridylyl-transferase; Provisional

Probab=97.11  E-value=0.0027  Score=66.78  Aligned_cols=72  Identities=15%  Similarity=0.260  Sum_probs=54.8

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEE-EeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEI-ATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~i-st~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      +.|.|+|+++||+|.+|..+|..+||+|+.|.| ++.+|.++++|.|....+. ....    .....|.++|.+++..
T Consensus       679 ~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~~~-~~~~----~~~~~i~~~l~~~l~~  751 (856)
T PRK03059        679 LQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPEED-VHYR----DIINLVEHELAERLAE  751 (856)
T ss_pred             EEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCCCC-CChH----HHHHHHHHHHHHHHcC
Confidence            466789999999999999999999999999999 5789999999999753222 1122    2344566666666544

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

Probab=97.10  E-value=0.0079  Score=44.40  Aligned_cols=66  Identities=15%  Similarity=0.288  Sum_probs=49.9

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      +.+.+.|+++||+..+|.+.|.++|..|+.++....++.+...+.+....           .-...|.++|..+-.+
T Consensus         2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~~-----------~~~~~l~~~l~~~~~~   67 (77)
T cd04893           2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGSW-----------DAIAKLEAALPGLARR   67 (77)
T ss_pred             EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEecc-----------ccHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999999999875555554321           1135566666665444

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

>PRK03381 PII uridylyl-transferase; Provisional

Probab=97.01  E-value=0.0037  Score=65.14  Aligned_cols=48  Identities=23%  Similarity=0.335  Sum_probs=45.0

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEee
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMAS  205 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~  205 (269)
                      +.|.|.|+++||++.+|..+|..+|++|+.|+|.|.+|.++++|.|..
T Consensus       600 ~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~  647 (774)
T PRK03381        600 VEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSP  647 (774)
T ss_pred             EEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEEC
Confidence            456789999999999999999999999999999999999999999974

>PRK05092 PII uridylyl-transferase; Provisional

Probab=97.00  E-value=0.0043  Score=65.84  Aligned_cols=71  Identities=23%  Similarity=0.315  Sum_probs=52.7

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe-eCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHH
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT-LEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVL  232 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist-~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~  232 (269)
                      +.|.|.|++++|+|.+|..+|..+|++|+.|.|.| .+|+++++|.|....+........    ...|.++|..++
T Consensus       733 t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g~~~~~~~~----~~~l~~~L~~~l  804 (931)
T PRK05092        733 TEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFGRDEDEPRR----LARLAKAIEDAL  804 (931)
T ss_pred             EEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCCCCCCCHHH----HHHHHHHHHHHH
Confidence            45678899999999999999999999999999876 799999999997433222122223    344555555554

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

Probab=96.71  E-value=0.018  Score=42.29  Aligned_cols=51  Identities=18%  Similarity=0.374  Sum_probs=40.2

Q ss_pred             ceeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee--CCeEEEEEEEee
Q 024326          155 PYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL--EGRMKNIFVMAS  205 (269)
Q Consensus       155 ~~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~--~g~v~~vf~v~~  205 (269)
                      .+.+.+.|.+.+++|+|.+|..++.+.++.|.+.++.+.  ++...-.|.+..
T Consensus         4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V   56 (80)
T PF13291_consen    4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEV   56 (80)
T ss_dssp             -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEE
T ss_pred             EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEE
Confidence            467888899999999999999999999999999999885  566655566654

>PRK04374 PII uridylyl-transferase; Provisional

Probab=96.65  E-value=0.013  Score=61.94  Aligned_cols=70  Identities=14%  Similarity=0.222  Sum_probs=53.8

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe-eCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT-LEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist-~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      +.|.|.|++++|+|.+|..+|..+|++|+.|.|.| .+|.++++|.|.......  . ..    ...|.++|..++..
T Consensus       691 ~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~--~-~~----~~~i~~~l~~~l~~  761 (869)
T PRK04374        691 LEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYA--D-GD----PQRLAAALRQVLAG  761 (869)
T ss_pred             EEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCC--h-HH----HHHHHHHHHHHHcC
Confidence            45678999999999999999999999999999975 799999999997433221  1 11    23366666666654

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

Probab=96.16  E-value=0.04  Score=41.41  Aligned_cols=46  Identities=13%  Similarity=0.330  Sum_probs=38.9

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      .+.+.|+++||++.+|.+.|-.+|++|...+..+.++.+.-.+.+.
T Consensus         3 vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~   48 (88)
T cd04872           3 VITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVD   48 (88)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEE
Confidence            4678899999999999999999999999999988877764444443

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.

>PRK00194 hypothetical protein; Validated

Probab=96.11  E-value=0.047  Score=41.05  Aligned_cols=46  Identities=17%  Similarity=0.354  Sum_probs=38.4

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEE
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVM  203 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v  203 (269)
                      +.+.+.|+++||++.+|.+.|.++|++|...+..+.++.+.-.+.+
T Consensus         4 ~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v   49 (90)
T PRK00194          4 AIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLV   49 (90)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEE
Confidence            4567899999999999999999999999999988877765433333

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

Probab=96.07  E-value=0.093  Score=38.31  Aligned_cols=35  Identities=17%  Similarity=0.368  Sum_probs=32.6

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE  194 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~  194 (269)
                      +.+.|+++||++.+|.+.|.++|++|...+..+.+
T Consensus         2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~   36 (81)
T cd04869           2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS   36 (81)
T ss_pred             EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence            45889999999999999999999999999998877

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

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

Probab=96.06  E-value=0.076  Score=38.68  Aligned_cols=45  Identities=27%  Similarity=0.374  Sum_probs=39.4

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      |++.+++|||+..++.++|.++|++|...+.++.++.+.-.+.+.
T Consensus         2 vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~   46 (75)
T cd04870           2 ITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQ   46 (75)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEE
Confidence            467899999999999999999999999999999998876566554

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.

>KOG3910 consensus Helix loop helix transcription factor [Transcription]

Probab=95.99  E-value=0.0069  Score=59.10  Aligned_cols=59  Identities=20%  Similarity=0.216  Sum_probs=49.2

Q ss_pred             cchHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHHHHHHHHHH
Q 024326           70 RSVAALKNHIEAERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLKELDKNAME  128 (269)
Q Consensus        70 ~~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik~L~~~~~~  128 (269)
                      |..++++..|..||-|=..||+.|++|..+.-.-    ..-.|.-||..||.-|-.|++||.+
T Consensus       522 REkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE  584 (632)
T KOG3910|consen  522 REKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE  584 (632)
T ss_pred             HHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence            4446778899999999999999999998876422    3335899999999999999999986

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

Probab=95.96  E-value=0.1  Score=37.76  Aligned_cols=33  Identities=21%  Similarity=0.411  Sum_probs=30.7

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT  192 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist  192 (269)
                      |.+.|+++||++.+|.+.|.++|+.|...+..+
T Consensus         2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~   34 (74)
T cd04875           2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFV   34 (74)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeee
Confidence            568899999999999999999999999998875

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.

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

Probab=95.66  E-value=0.15  Score=35.55  Aligned_cols=33  Identities=18%  Similarity=0.239  Sum_probs=29.0

Q ss_pred             EEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       161 ~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      .|.++++||.|.+|+++|.+.|++|.+.+....
T Consensus         2 ~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~   34 (73)
T cd04886           2 RVELPDRPGQLAKLLAVIAEAGANIIEVSHDRA   34 (73)
T ss_pred             EEEeCCCCChHHHHHHHHHHcCCCEEEEEEEec
Confidence            366899999999999999999999998887653

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.

>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=95.46  E-value=0.21  Score=35.65  Aligned_cols=45  Identities=11%  Similarity=0.106  Sum_probs=35.7

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC-CeEEEEEEEe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE-GRMKNIFVMA  204 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~-g~v~~vf~v~  204 (269)
                      +.+.+.++||+|.+|+.+|.+.|..|...++.... +.....|.++
T Consensus         2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ve   47 (74)
T cd04887           2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVD   47 (74)
T ss_pred             EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEE
Confidence            45779999999999999999999999999987654 5544444443

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.

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

Probab=95.43  E-value=0.13  Score=36.77  Aligned_cols=47  Identities=17%  Similarity=0.299  Sum_probs=36.5

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee-CCeEEEEEEEe
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL-EGRMKNIFVMA  204 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~-~g~v~~vf~v~  204 (269)
                      |++.+.+++++|+|.+|+++|.+.+.+|...+.... ++...-.|.+.
T Consensus         1 ~~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~   48 (76)
T cd04888           1 VTLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISID   48 (76)
T ss_pred             CEEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEE
Confidence            356688999999999999999999999999877543 35444445554

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.

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

Probab=95.35  E-value=0.072  Score=55.31  Aligned_cols=71  Identities=18%  Similarity=0.207  Sum_probs=52.6

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEE-EeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEI-ATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~i-st~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      .|.|.|+++|.+|..+..++...|++|+.|+| +|.+|+.+++|+|....+. ...+    .-...+.+.|..++..
T Consensus       686 eV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~~~~g~-~~~~----dr~~~~~~~l~~~l~s  757 (867)
T COG2844         686 EVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVLEPDGF-PVEE----DRRAALRGELIEALLS  757 (867)
T ss_pred             EEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEecCCCC-ccch----hHHHHHHHHHHHHHhc
Confidence            45588999999999999999999999999998 6889999999999744332 2222    2334444444444444

>TIGR00655 PurU formyltetrahydrofolate deformylase

Probab=94.83  E-value=0.33  Score=44.79  Aligned_cols=89  Identities=24%  Similarity=0.257  Sum_probs=56.2

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC--CeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHH-HHhhcc
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE--GRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRS-VLDKFS  236 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~--g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~-v~~k~~  236 (269)
                      +.+.|++++|+...|...|-++|..|+.++.+..+  |++.-.+.+.  ......       ....++++|.. +-++.+
T Consensus         3 itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~mr~~v~--~~~~~~-------~~~~l~~~l~~~~~~~~~   73 (280)
T TIGR00655         3 LLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFFMRVEFQ--LEGFRL-------EESSLLAAFKSALAEKFE   73 (280)
T ss_pred             EEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEEEEEEE--eCCCCC-------CHHHHHHHHHHHHHHHhC
Confidence            56889999999999999999999999999888743  5543222222  111001       14566677777 555444


Q ss_pred             cchhhhccccCCCCCceeeeccCCC
Q 024326          237 ATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       237 ~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      ..-...    ...++.|+-+|-|-+
T Consensus        74 l~i~l~----~~~~~~ki~vl~Sg~   94 (280)
T TIGR00655        74 MTWELI----LADKLKRVAILVSKE   94 (280)
T ss_pred             CEEEEe----cCCCCcEEEEEEcCC
Confidence            322211    134567888776544

This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.

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

Probab=94.81  E-value=0.19  Score=36.09  Aligned_cols=45  Identities=24%  Similarity=0.332  Sum_probs=37.9

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      |.|.||++.|+--+|.+.+-+.||.|....++|-|.--.-+|-+.
T Consensus         3 itvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv   47 (69)
T cd04894           3 ITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVV   47 (69)
T ss_pred             EEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEe
Confidence            568899999999999999999999999999999777544445444

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.

>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed

Probab=94.51  E-value=0.55  Score=43.35  Aligned_cols=92  Identities=18%  Similarity=0.222  Sum_probs=59.1

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe--eCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT--LEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist--~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      .+.|++.|++|||+..+|.++|.++|++|...+.++  .+|.+.-.+.+.....     +..    ...|+++|..+-+.
T Consensus         6 ~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~-----~~~----~~~L~~~L~~l~~~   76 (286)
T PRK06027          6 RYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGL-----IFN----LETLRADFAALAEE   76 (286)
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCC-----CCC----HHHHHHHHHHHHHH
Confidence            455778999999999999999999999999999998  7775322222221010     111    45666666666555


Q ss_pred             cccchhhhccccCCCCCceeeeccCCC
Q 024326          235 FSATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       235 ~~~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      ....-...    ...++.|+-+|-|.+
T Consensus        77 l~l~i~l~----~~~~~~ri~vl~Sg~   99 (286)
T PRK06027         77 FEMDWRLL----DSAERKRVVILVSKE   99 (286)
T ss_pred             hCCEEEEc----ccccCcEEEEEEcCC
Confidence            44322111    234667888886544

>KOG4447 consensus Transcription factor TWIST [Transcription]

Probab=94.40  E-value=0.03  Score=46.86  Aligned_cols=54  Identities=22%  Similarity=0.215  Sum_probs=47.7

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--CccchhhHHHHHHHHHHHHHHHHH
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKELDKNAM  127 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dk~sil~~ai~yik~L~~~~~  127 (269)
                      ++.-|+..||+|=..+|+.|..||.++|..  .|.+|.--|.-|..||-.|-+-.+
T Consensus        78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~vl~  133 (173)
T KOG4447|consen   78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQVLQ  133 (173)
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhccc
Confidence            557899999999999999999999999965  788898899999999998876443

>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed

Probab=94.17  E-value=0.46  Score=44.04  Aligned_cols=92  Identities=18%  Similarity=0.249  Sum_probs=56.6

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE--eeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA--TLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKF  235 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is--t~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~  235 (269)
                      +.|.+.|++++|+...|...|-++|++|+.++-.  +..+.++-.+.+. +.....       .....++++|..+-.+.
T Consensus        10 ~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~-~~~~~~-------~~~~~l~~~l~~l~~~l   81 (289)
T PRK13010         10 YVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFH-AQSAEA-------ASVDTFRQEFQPVAEKF   81 (289)
T ss_pred             EEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEE-cCCCCC-------CCHHHHHHHHHHHHHHh
Confidence            4577999999999999999999999999999885  3333332111111 110000       11456777777766554


Q ss_pred             ccchhhhccccCCCCCceeeeccCCC
Q 024326          236 SATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       236 ~~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      +..-...    ...++.|+-+|-|-+
T Consensus        82 ~l~~~i~----~~~~~~kiavl~Sg~  103 (289)
T PRK13010         82 DMQWAIH----PDGQRPKVVIMVSKF  103 (289)
T ss_pred             CCeEEEe----cCCCCeEEEEEEeCC
Confidence            4432211    134567888886554

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

Probab=94.01  E-value=0.43  Score=34.52  Aligned_cols=36  Identities=19%  Similarity=0.405  Sum_probs=32.0

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGR  196 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~  196 (269)
                      +.|.|.+++|+|.+|+.++.+.+..|...++.+. +.
T Consensus         3 l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~   38 (74)
T cd04877           3 LEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GR   38 (74)
T ss_pred             EEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-Ce
Confidence            5677999999999999999999999999998765 44

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

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

Probab=93.44  E-value=0.99  Score=30.00  Aligned_cols=43  Identities=21%  Similarity=0.347  Sum_probs=33.5

Q ss_pred             EEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC-CeEEEEEEE
Q 024326          161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE-GRMKNIFVM  203 (269)
Q Consensus       161 ~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~-g~v~~vf~v  203 (269)
                      .+.+++++|.+.+|++.|.++++++....+...+ +.....+.+
T Consensus         2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~   45 (71)
T cd04876           2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTL   45 (71)
T ss_pred             EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEE
Confidence            4668899999999999999999999999887655 433333334

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

>PRK13011 formyltetrahydrofolate deformylase; Reviewed

Probab=93.35  E-value=1.1  Score=41.52  Aligned_cols=92  Identities=12%  Similarity=0.119  Sum_probs=54.5

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhccc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSA  237 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~~~  237 (269)
                      +.|.+.|+++||+..+|.+.|.+++++|...+..+-.+.-...+.+...-..+ .+       ...|+++|..+-+....
T Consensus         8 ~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~~-~~-------~~~L~~~L~~l~~~l~l   79 (286)
T PRK13011          8 FVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEG-LD-------EDALRAGFAPIAARFGM   79 (286)
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCC-CC-------HHHHHHHHHHHHHHhCc
Confidence            45678899999999999999999999999998863222212223332211111 11       45566666665444332


Q ss_pred             chhhhccccCCCCCceeeeccCCC
Q 024326          238 TEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       238 ~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      .-...    ...++.|+-+|-|.+
T Consensus        80 ~i~i~----~~~~~~ri~vl~Sg~   99 (286)
T PRK13011         80 QWELH----DPAARPKVLIMVSKF   99 (286)
T ss_pred             EEEEe----ecccCceEEEEEcCC
Confidence            21111    134456888886553

>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=93.05  E-value=0.91  Score=31.88  Aligned_cols=34  Identities=24%  Similarity=0.308  Sum_probs=29.9

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      +.+.+.+++|+|.+|+..|.+.+..|...+..+.
T Consensus         3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~   36 (79)
T cd04881           3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEA   36 (79)
T ss_pred             EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEccc
Confidence            4577899999999999999999999999887654

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.

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

Probab=92.84  E-value=0.11  Score=47.31  Aligned_cols=53  Identities=26%  Similarity=0.330  Sum_probs=46.3

Q ss_pred             HHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHH
Q 024326           73 AALKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKN  125 (269)
Q Consensus        73 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~  125 (269)
                      ..+..-|..||+|--.+|+.|..||.++|..   .|+.|.-.|.-|-.||..|++-
T Consensus        71 ~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~  126 (254)
T KOG3898|consen   71 LRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV  126 (254)
T ss_pred             hhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence            3457778999999999999999999999953   8889999999999999988754

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

Probab=92.79  E-value=1.6  Score=31.40  Aligned_cols=45  Identities=18%  Similarity=0.200  Sum_probs=35.0

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCC-eEEEEEEEeee
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEG-RMKNIFVMASC  206 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g-~v~~vf~v~~~  206 (269)
                      +..+++||.|.+|++.+..+|+.+.+.......+ .-.+.|++...
T Consensus         4 ~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~   49 (75)
T cd04880           4 FSLKNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFE   49 (75)
T ss_pred             EEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEE
Confidence            4457799999999999999999999998876554 34455666543

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

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

Probab=92.67  E-value=0.7  Score=32.02  Aligned_cols=35  Identities=26%  Similarity=0.263  Sum_probs=30.7

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      .+.+.+++++|.|.++++.|.+.+..|.+.+....
T Consensus         2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~   36 (72)
T cd04874           2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIE   36 (72)
T ss_pred             eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEecc
Confidence            35577999999999999999999999998887665

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.

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

Probab=92.61  E-value=0.97  Score=28.37  Aligned_cols=34  Identities=26%  Similarity=0.355  Sum_probs=29.8

Q ss_pred             EEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC
Q 024326          161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE  194 (269)
Q Consensus       161 ~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~  194 (269)
                      .+.|++++|.+.+|+..|...++.+.........
T Consensus         2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~   35 (60)
T cd02116           2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG   35 (60)
T ss_pred             EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence            4678899999999999999999999999876643

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

>PRK04435 hypothetical protein; Provisional

Probab=92.53  E-value=1.2  Score=37.09  Aligned_cols=50  Identities=22%  Similarity=0.255  Sum_probs=38.8

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe-eCCeEEEEEEEee
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT-LEGRMKNIFVMAS  205 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist-~~g~v~~vf~v~~  205 (269)
                      ..+.+.+.+++++|+|.+|+++|.+.+.+|...+... .+|...-+|.+..
T Consensus        68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVev  118 (147)
T PRK04435         68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDT  118 (147)
T ss_pred             cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEe
Confidence            3566778899999999999999999999999988754 3565544555543

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

Probab=92.18  E-value=0.62  Score=31.95  Aligned_cols=44  Identities=14%  Similarity=0.260  Sum_probs=35.6

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC--CeEEEEEEE
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE--GRMKNIFVM  203 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~--g~v~~vf~v  203 (269)
                      +.+..++++|++.+|++.|.+.++.|.+..+....  +.....|.+
T Consensus         2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v   47 (71)
T cd04879           2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV   47 (71)
T ss_pred             EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc
Confidence            44678999999999999999999999999887654  555445555

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=92.05  E-value=0.78  Score=31.01  Aligned_cols=43  Identities=21%  Similarity=0.267  Sum_probs=34.6

Q ss_pred             EEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC-CeEEEEEEE
Q 024326          161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE-GRMKNIFVM  203 (269)
Q Consensus       161 ~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~-g~v~~vf~v  203 (269)
                      .+..+++||.|.++++.|.+.+..|....+...+ +.....|.+
T Consensus         2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v   45 (56)
T cd04889           2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIF   45 (56)
T ss_pred             EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEE
Confidence            3568999999999999999999999888876655 555555555

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

>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]

Probab=91.73  E-value=1.2  Score=40.74  Aligned_cols=90  Identities=16%  Similarity=0.207  Sum_probs=56.9

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhcccc
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSAT  238 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~~~~  238 (269)
                      .+.++|++++|+...|-..|.+.|..|+.++-.+  +.....|.+...-..... +    .....++++|..+-+++...
T Consensus         9 ~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf~--D~~~g~FFmR~~f~~~~~-~----~~~~~l~~~f~~~a~~f~m~   81 (287)
T COG0788           9 ILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQFD--DPETGRFFMRVEFEGEGG-P----LDREALRAAFAPLAEEFGMD   81 (287)
T ss_pred             EEEEecCCCCCcHHHHHHHHHHcCCceeeccccc--ccccCeEEEEEEEecCCC-c----ccHHHHHHHHHHHHHhhCce
Confidence            4568899999999999999999999999987663  222222333322211111 1    22566777777776666643


Q ss_pred             hhhhccccCCCCCceeeeccC
Q 024326          239 EEFLLGARLSNKRRRVSLFDS  259 (269)
Q Consensus       239 ~~~~~~~~~~~kr~r~~~~~~  259 (269)
                      -.    -....+|.|+-++-|
T Consensus        82 ~~----~~~~~~~~ri~i~VS   98 (287)
T COG0788          82 WR----LHDAAQRKRIAILVS   98 (287)
T ss_pred             eE----EeccccCceEEEEEe
Confidence            22    123677777876643

>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]

Probab=91.62  E-value=0.15  Score=50.74  Aligned_cols=41  Identities=37%  Similarity=0.600  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHH
Q 024326           80 EAERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLK  120 (269)
Q Consensus        80 ~~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik  120 (269)
                      ---||-|+|+|.-|..|.+|+|-.    .|+||.|||.=+|.|++
T Consensus        31 NPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr   75 (712)
T KOG3560|consen   31 NPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR   75 (712)
T ss_pred             CcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence            345778999999999999999953    99999999999999986

>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional

Probab=91.30  E-value=0.86  Score=39.67  Aligned_cols=48  Identities=15%  Similarity=0.262  Sum_probs=42.3

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEE
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVM  203 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v  203 (269)
                      -.+.|++.+++|||+...|.++|.++|..|..++.+..+|.+.-++.+
T Consensus         7 ~~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lv   54 (190)
T PRK11589          7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLL   54 (190)
T ss_pred             cEEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEE
Confidence            346678999999999999999999999999999999999987555555

>PRK07334 threonine dehydratase; Provisional

Probab=91.30  E-value=1.6  Score=42.07  Aligned_cols=49  Identities=12%  Similarity=0.169  Sum_probs=39.3

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee-----CCeEEEEEEEe
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL-----EGRMKNIFVMA  204 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~-----~g~v~~vf~v~  204 (269)
                      +.+.+.|.+.+|+|+|.+|+.+|.+.+.+|.+.++.+.     ++...-.|.+.
T Consensus       325 y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~  378 (403)
T PRK07334        325 RLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIE  378 (403)
T ss_pred             CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEE
Confidence            56788899999999999999999999999999998754     45543344443

>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]

Probab=91.09  E-value=0.23  Score=47.86  Aligned_cols=41  Identities=37%  Similarity=0.478  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHHH
Q 024326           81 AERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLKE  121 (269)
Q Consensus        81 ~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik~  121 (269)
                      +-|.||++-|--|.+|..++|-.    ...||++|+.=|..|||.
T Consensus         8 aA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm   52 (598)
T KOG3559|consen    8 AARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM   52 (598)
T ss_pred             HHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence            56899999999999999999964    669999999999999984

>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=91.09  E-value=3.7  Score=29.89  Aligned_cols=45  Identities=22%  Similarity=0.299  Sum_probs=34.9

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCC-eEEEEEEEeee
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEG-RMKNIFVMASC  206 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g-~v~~vf~v~~~  206 (269)
                      +.-++++|.|.+|++.+.++|+.+.+.......+ ...++|++...
T Consensus         6 ~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~   51 (80)
T cd04905           6 FTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFE   51 (80)
T ss_pred             EEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEE
Confidence            4457899999999999999999999998766533 44466776543

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

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

Probab=90.82  E-value=3  Score=28.51  Aligned_cols=45  Identities=16%  Similarity=0.280  Sum_probs=34.7

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee--CCeEEEEEEEe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL--EGRMKNIFVMA  204 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~--~g~v~~vf~v~  204 (269)
                      +.+.+.+++|+|.+|+..|.+.+..+...+..+.  ++.....|.+.
T Consensus         3 l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~   49 (72)
T cd04878           3 LSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVE   49 (72)
T ss_pred             EEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEE
Confidence            3466889999999999999999999999887764  34444444443

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

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

Probab=90.79  E-value=0.42  Score=43.23  Aligned_cols=54  Identities=22%  Similarity=0.214  Sum_probs=46.5

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHHH
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNAM  127 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~~  127 (269)
                      ++..-+..||+|-..+|..|..||.+||..   .|++|-.-|+.|-.||--|-....
T Consensus       174 rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~  230 (285)
T KOG4395|consen  174 RRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD  230 (285)
T ss_pred             hhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence            345678899999999999999999999965   778888899999999998776553

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

Probab=90.04  E-value=4.3  Score=28.33  Aligned_cols=34  Identities=21%  Similarity=0.379  Sum_probs=29.4

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      +.+.++++||.|.++++.|.++|++|........
T Consensus         4 ~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~   37 (69)
T cd04909           4 LYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI   37 (69)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence            4567999999999999999999999988766554

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.

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

Probab=89.60  E-value=0.34  Score=49.42  Aligned_cols=42  Identities=33%  Similarity=0.513  Sum_probs=37.8

Q ss_pred             hHHHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHH
Q 024326           79 IEAERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLK  120 (269)
Q Consensus        79 ~~~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik  120 (269)
                      .-+-|-||.|-|+-|.+|..+||-.    ..+|||+|+.=||.|++
T Consensus        51 RdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLR   96 (768)
T KOG3558|consen   51 RDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLR   96 (768)
T ss_pred             hhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHH
Confidence            3577899999999999999999943    77899999999999998

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

Probab=89.41  E-value=2.1  Score=30.06  Aligned_cols=44  Identities=23%  Similarity=0.306  Sum_probs=34.9

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      ++.|..+++||.|.+|++.|.+.|+.|.+.-+...++.  .++.+.
T Consensus         3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~--~~~rl~   46 (66)
T cd04908           3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEF--GILRLI   46 (66)
T ss_pred             EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCC--CEEEEE
Confidence            45677899999999999999999999998877665553  345553

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.

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

Probab=89.10  E-value=2.1  Score=29.30  Aligned_cols=32  Identities=19%  Similarity=0.340  Sum_probs=28.7

Q ss_pred             EEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe
Q 024326          161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT  192 (269)
Q Consensus       161 ~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist  192 (269)
                      .+.+++++|.|.+|+..|.+++.+|.......
T Consensus         3 ~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~   34 (71)
T cd04903           3 IVVHKDKPGAIAKVTSVLADHEINIAFMRVSR   34 (71)
T ss_pred             EEEeCCCCChHHHHHHHHHHcCcCeeeeEEEe
Confidence            46789999999999999999999999887765

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.

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

Probab=89.00  E-value=3.3  Score=29.46  Aligned_cols=34  Identities=21%  Similarity=0.216  Sum_probs=28.9

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      +.+.-+++||.|.++++.|.++|..|++......
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            3456789999999999999999999998876654

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.

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

Probab=88.92  E-value=6  Score=27.67  Aligned_cols=45  Identities=18%  Similarity=0.294  Sum_probs=33.3

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee--CCeEEEEEEE
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL--EGRMKNIFVM  203 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~--~g~v~~vf~v  203 (269)
                      ++.+..+++||.|.++++.|.+.++.|.+......  ++...-+|.+
T Consensus         3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v   49 (72)
T cd04883           3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRV   49 (72)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEE
Confidence            55677899999999999999999999987754332  3444334444

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.

>PRK08577 hypothetical protein; Provisional

Probab=88.84  E-value=4.9  Score=32.66  Aligned_cols=38  Identities=21%  Similarity=0.422  Sum_probs=33.0

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE  194 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~  194 (269)
                      .+.+.+.+.+++|+|.+|++.|.+++.++.+.+..+..
T Consensus        56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~   93 (136)
T PRK08577         56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELK   93 (136)
T ss_pred             EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEec
Confidence            45677889999999999999999999999988876653

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

Probab=86.51  E-value=2.6  Score=28.79  Aligned_cols=33  Identities=18%  Similarity=0.157  Sum_probs=27.4

Q ss_pred             EEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       161 ~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      .+.-+++||.|.+++..|.+.|+.|.+......
T Consensus         3 ~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~   35 (65)
T cd04882           3 AVEVPDKPGGLHEILQILSEEGINIEYMYAFVE   35 (65)
T ss_pred             EEEeCCCCcHHHHHHHHHHHCCCChhheEEEcc
Confidence            355689999999999999999999987765443

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.

>TIGR00119 acolac_sm acetolactate synthase, small subunit

Probab=84.49  E-value=6.9  Score=33.05  Aligned_cols=44  Identities=18%  Similarity=0.273  Sum_probs=35.1

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC--CeEEEEEEE
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE--GRMKNIFVM  203 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~--g~v~~vf~v  203 (269)
                      +.+.-+++||.|.+|...|...|+.|.+..+...+  +...-++.+
T Consensus         4 isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V   49 (157)
T TIGR00119         4 LSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVV   49 (157)
T ss_pred             EEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEE
Confidence            45778999999999999999999999999887654  444444444

acetohydroxyacid synthase is a synonym.

>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH)

Probab=84.15  E-value=12  Score=28.57  Aligned_cols=44  Identities=14%  Similarity=0.170  Sum_probs=35.5

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCe-EEEEEEEee
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGR-MKNIFVMAS  205 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~-v~~vf~v~~  205 (269)
                      +..+++||.|.+++..+...|+.+.+...-...+. --+.|++..
T Consensus        19 f~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDi   63 (90)
T cd04931          19 FSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINL   63 (90)
T ss_pred             EEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEE
Confidence            55688999999999999999999999998765433 346777764

ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.

>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH)

Probab=83.53  E-value=9.6  Score=27.54  Aligned_cols=45  Identities=11%  Similarity=0.158  Sum_probs=35.6

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCe-EEEEEEEeee
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGR-MKNIFVMASC  206 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~-v~~vf~v~~~  206 (269)
                      +..+++||-|.+++..+...|+.+.+.+.-...+. --+.|++...
T Consensus         5 f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~   50 (74)
T cd04904           5 FSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCE   50 (74)
T ss_pred             EEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEE
Confidence            34577999999999999999999999998765543 3466777643

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. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy

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

Probab=83.50  E-value=7.9  Score=40.54  Aligned_cols=50  Identities=16%  Similarity=0.258  Sum_probs=40.6

Q ss_pred             ceeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee--CCeEEEEEEEe
Q 024326          155 PYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL--EGRMKNIFVMA  204 (269)
Q Consensus       155 ~~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~--~g~v~~vf~v~  204 (269)
                      .+.+.|.|.+.+++|+|.+|..+|.+.++.|..+++.+.  ++...-.|.++
T Consensus       664 ~~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~~~~~~~~ie  715 (743)
T PRK10872        664 GYSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQLATIDMTIE  715 (743)
T ss_pred             eeEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCCEEEEEEEEE
Confidence            356788899999999999999999999999999998765  45544445554

>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed

Probab=83.15  E-value=8.9  Score=32.52  Aligned_cols=44  Identities=20%  Similarity=0.292  Sum_probs=35.0

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC--CeEEEEEEE
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE--GRMKNIFVM  203 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~--g~v~~vf~v  203 (269)
                      +.+.-+++||.|.+|...|...|+.|.+..+...+  +...-++.+
T Consensus         5 IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V   50 (161)
T PRK11895          5 LSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVT   50 (161)
T ss_pred             EEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEE
Confidence            55778999999999999999999999999887554  444444444

>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes

Probab=82.91  E-value=15  Score=26.81  Aligned_cols=43  Identities=14%  Similarity=0.182  Sum_probs=34.3

Q ss_pred             EcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCe-EEEEEEEee
Q 024326          163 CCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGR-MKNIFVMAS  205 (269)
Q Consensus       163 ~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~-v~~vf~v~~  205 (269)
                      .-+++||.|.+++..+...|+.+.+.+.-...+. --+.|++..
T Consensus         6 ~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~   49 (74)
T cd04929           6 SLKNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDC   49 (74)
T ss_pred             EcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEE
Confidence            3477899999999999999999999998765333 456677764

ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.

>COG3830 ACT domain-containing protein [Signal transduction mechanisms]

Probab=82.84  E-value=3  Score=32.09  Aligned_cols=47  Identities=15%  Similarity=0.302  Sum_probs=39.9

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      +.|++.-.+|+|+...|..+|-++|..|+..+=+-.+|++.-.+.+.
T Consensus         4 avITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~lV~   50 (90)
T COG3830           4 AVITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLVD   50 (90)
T ss_pred             EEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeEEc
Confidence            45678899999999999999999999999998888888875555554

>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase)

Probab=82.03  E-value=13  Score=26.22  Aligned_cols=31  Identities=16%  Similarity=0.230  Sum_probs=26.5

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      +.=+++||-|.++++.|.. +.+|+..+....
T Consensus         3 v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~   33 (68)
T cd04885           3 VTFPERPGALKKFLELLGP-PRNITEFHYRNQ   33 (68)
T ss_pred             EECCCCCCHHHHHHHHhCC-CCcEEEEEEEcC
Confidence            4568999999999999999 999998877654

This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.

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

Probab=81.84  E-value=1.3  Score=30.94  Aligned_cols=43  Identities=14%  Similarity=0.166  Sum_probs=32.3

Q ss_pred             EEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEE
Q 024326          161 SLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVM  203 (269)
Q Consensus       161 ~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v  203 (269)
                      -+.+.+++|+|.+|+..|.+.+..|...+....++...-.|.+
T Consensus         3 ~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~   45 (69)
T cd04901           3 LHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDI   45 (69)
T ss_pred             EEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEc
Confidence            3568999999999999999999999777655444554333333

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

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

Probab=80.68  E-value=6  Score=27.57  Aligned_cols=42  Identities=12%  Similarity=0.302  Sum_probs=33.0

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe--eCCeEEEEEEE
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIAT--LEGRMKNIFVM  203 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist--~~g~v~~vf~v  203 (269)
                      +..++++|.+.+|.+.|.+.|+.|.+.....  .++....+|.+
T Consensus         4 v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v   47 (73)
T cd04902           4 VRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSV   47 (73)
T ss_pred             EEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEe
Confidence            4688999999999999999999998776654  35666545555

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

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

Probab=80.62  E-value=11  Score=39.19  Aligned_cols=50  Identities=10%  Similarity=0.152  Sum_probs=40.2

Q ss_pred             ceeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCC-eEEEEEEEe
Q 024326          155 PYSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEG-RMKNIFVMA  204 (269)
Q Consensus       155 ~~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g-~v~~vf~v~  204 (269)
                      .+.+.|.|.+.+++|+|.+|+.+|.+.++.|.++++.+.++ .+.-.|.+.
T Consensus       624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ie  674 (702)
T PRK11092        624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGRVYSAFIRLT  674 (702)
T ss_pred             eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCCEEEEEEEEE
Confidence            35678889999999999999999999999999999877654 433334444

>CHL00100 ilvH acetohydroxyacid synthase small subunit

Probab=80.14  E-value=14  Score=31.75  Aligned_cols=33  Identities=12%  Similarity=0.234  Sum_probs=29.9

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT  192 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist  192 (269)
                      +.+..+++||+|.+|...|...|++|.+.++..
T Consensus         5 isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~   37 (174)
T CHL00100          5 LSVLVEDESGVLTRIAGLFARRGFNIESLAVGP   37 (174)
T ss_pred             EEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeE
Confidence            567789999999999999999999999988865

---

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	269
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	1e-07
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	4e-07
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	4e-07
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	6e-07
4f3l_A	361	Mclock, circadian locomoter output cycles protein	6e-07
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	5e-06
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	6e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	1e-04
1a0a_A	63	BHLH, protein (phosphate system positive regulator	5e-04

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

 Score = 47.4 bits (113), Expect = 1e-07
 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 77  NHIEAERNRRKRINGHLDTLRSLIPG-ATKMDKATLLTEVISQLKELDK 124
            H   E+  R  IN  +  L+ L+ G   K++K+ +L + I  ++ L  
Sbjct: 9   AHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQH 57

>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 = 45.8 bits (109), Expect = 4e-07
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPG--ATKMDKATLLTEVISQLKELDKNAMEATEGF 133
            +H   ER RR  I     +LR  +P     K  +A +L +    ++ + +      +  
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ-- 61

Query: 134 LIPTDIDEVKVEQQE 148
               DID++K +   
Sbjct: 62  ----DIDDLKRQNAL 72

>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 = 45.8 bits (109), Expect = 4e-07
 Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 6/52 (11%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPG---ATKMDKATLL---TEVISQLKE 121
           + H   ER RR  +      LR  IP      K  K  +L   T  I  ++ 
Sbjct: 8   RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQA 59

>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 = 45.4 bits (108), Expect = 6e-07
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPG--ATKMDKATLLTEVISQLKEL 122
            +H   ER RR  I     +LR  +P     K  +A +L +    ++ +
Sbjct: 14  AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYM 62

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

 Score = 48.8 bits (116), Expect = 6e-07
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 66  VSEDR-SVAALKNHIEAERNRRKRINGHLDTLRSLIPG-ATKMDKATLLTEVISQLK 120
           V ED    A   +  ++E+ RR + N  +  L S++PG A KMDK+T+L + I  L+
Sbjct: 3   VEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLR 59

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

 Score = 46.2 bits (109), Expect = 5e-06
 Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 5/92 (5%)

Query: 67  SEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPG----ATKMDKATLLTEVISQLKEL 122
            + R   A + H + E+ RR ++N  +D L SL+P     + K+DK T+L   +  +K L
Sbjct: 6   HQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTL 65

Query: 123 DKNAMEATEGFLIPTDIDEVKVEQQE-DGLDG 153
                  TE    PT + + +++       DG
Sbjct: 66  RGATNPYTEANYKPTFLSDDELKHLILRAADG 97

>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 = 41.9 bits (99), Expect = 6e-06
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 6/56 (10%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPG------ATKMDKATLLTEVISQLKELDKN 125
             H E ER RR +IN  +  L  +IP        +   K  +L++    ++EL ++
Sbjct: 7   AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQS 62

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

 Score = 45.6 bits (107), Expect = 9e-06
 Identities = 45/283 (15%), Positives = 88/283 (31%), Gaps = 54/283 (19%)

Query: 8   FWSSCR-NDNGVEILTDEFVVNN-GF---QGKSRNGSSSHSSLVLDSERGELVEANVKLQ 62
           FW+     +  V+   +E +  N  F     K+     S  + +   +R  L   N    
Sbjct: 68  FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA 127

Query: 63  RKGVSEDRSVAALKNHI-EAERNRRKRINGHLDTLRSLIPGATKMDKATLLTEVISQLKE 121
           +  VS  +    L+  + E    +   I+G        + G+    K  +  +V    K 
Sbjct: 128 KYNVSRLQPYLKLRQALLELRPAKNVLIDG--------VLGS---GKTWVALDVCLSYKV 176

Query: 122 LDKNAMEATEGF---LIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRVL 178
             K   +    F   L   +  E  +E  +             L     P   S      
Sbjct: 177 QCKMDFKI---FWLNLKNCNSPETVLEMLQK------------LLYQIDPNWTS------ 215

Query: 179 EALHLSIVKAEIATLEGRMKNIFVMASCKE-L----NFENTEV-------CQSLVSSVHQ 226
            + H S +K  I +++  ++ +      +  L    N +N +        C+ L+++  +
Sbjct: 216 RSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK 275

Query: 227 AIRSVLDKFSATEEFLLGARLS-NKRRRVSLFDSSLSSSSDYL 268
            +   L   + T   L    ++       SL    L      L
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL 318

>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 = 39.8 bits (92), Expect = 7e-04
 Identities = 42/307 (13%), Positives = 71/307 (23%), Gaps = 112/307 (36%)

Query: 3   AMDPYFWSSCRND--NGVEILTDEFV-----VNN--------------------GFQGKS 35
           +M    +   R+   N  ++     V                            G  GK+
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS-GKT 164

Query: 36  RNGSSSHSSLVLDSERGELVEAN---------------------------VKLQRKGVSE 68
                    + LD      V+                              ++     S 
Sbjct: 165 --------WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR 216

Query: 69  DRSVAALKNHIEAERNRRKRINGHLDTLRSLI-------PGATK-MD---KATLLTEVIS 117
               + +K  I + +   +R+         L+         A    +   K  LLT   +
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCK-ILLT---T 272

Query: 118 QLKELDKNAMEATEGFLIPTDIDEVKVEQQEDGLDGAPYSIKASLCCNYKPGLLSDLRRV 177
           +     K   +    FL       + ++     L         SL   Y      DL R 
Sbjct: 273 R----FKQVTD----FLSAATTTHISLDHHSMTLT-PDEVK--SLLLKYLDCRPQDLPR- 320

Query: 178 LEA-----LHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVL 232
            E        LSI+   I        N       K +N +           +   I S L
Sbjct: 321 -EVLTTNPRRLSIIAESIRDGLATWDNW------KHVNCDK----------LTTIIESSL 363

Query: 233 DKFSATE 239
           +     E
Sbjct: 364 NVLEPAE 370

>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 = 39.0 bits (91), Expect = 1e-04
 Identities = 11/34 (32%), Positives = 17/34 (50%)

Query: 77  NHIEAERNRRKRINGHLDTLRSLIPGATKMDKAT 110
            H E E+NRR  +   L+ L+ L+P      + T
Sbjct: 4   THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHT 37

>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 = 36.7 bits (85), Expect = 5e-04
 Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 7/56 (12%)

Query: 77  NHIEAERNRRKRINGHLDTLRSLIPGATKMD-------KATLLTEVISQLKELDKN 125
           +H  AE+ RR R+   L  L SLIP   K         KAT +      ++ L +N
Sbjct: 5   SHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQN 60

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	269
1am9_A	82	Srebp-1A, protein (sterol regulatory element bindi	99.67
4h10_B	71	Circadian locomoter output cycles protein kaput; B	99.63
1hlo_A	80	Protein (transcription factor MAX); transcriptiona	99.56
1a0a_A	63	BHLH, protein (phosphate system positive regulator	99.56
4ati_A	118	MITF, microphthalmia-associated transcription fact	99.56
1an4_A	65	Protein (upstream stimulatory factor); protein-DNA	99.55
1nkp_B	83	MAX protein, MYC proto-oncogene protein; transcrip	99.55
4h10_A	73	ARYL hydrocarbon receptor nuclear translocator-LI	99.54
1nkp_A	88	C-MYC, MYC proto-oncogene protein; transcription,	99.53
3u5v_A	76	Protein MAX, transcription factor E2-alpha chimer;	99.45
1nlw_A	80	MAD protein, MAX dimerizer; transcription factor,	99.45
1mdy_A	68	Protein (MYOD BHLH domain); protein-DNA complex, t	99.28
2ql2_B	60	Neurod1, neurogenic differentiation factor 1; basi	99.23
4f3l_A	361	Mclock, circadian locomoter output cycles protein	99.02
4f3l_B	387	BMAL1B; BHLH, PAS, circadian rhythm proteins, tran	98.95
2lfh_A	68	DNA-binding protein inhibitor ID-3; structural gen	98.79
4ath_A	83	MITF, microphthalmia-associated transcription fact	98.77
4aya_A	97	DNA-binding protein inhibitor ID-2; cell cycle; 2.	98.3
1zpv_A	91	ACT domain protein; structural genomics, PSI, prot	96.98
1u8s_A	192	Glycine cleavage system transcriptional repressor,	96.68
2ko1_A	88	CTR148A, GTP pyrophosphokinase; homodimer, alpha+b	96.29
2nyi_A	195	Unknown protein; protein structure initiative, PSI	96.08
2nyi_A	195	Unknown protein; protein structure initiative, PSI	95.46
1u8s_A	192	Glycine cleavage system transcriptional repressor,	94.32
3o1l_A	302	Formyltetrahydrofolate deformylase; structural gen	94.19
3obi_A	288	Formyltetrahydrofolate deformylase; structural gen	94.07
3n0v_A	286	Formyltetrahydrofolate deformylase; formyl transfe	94.02
3lou_A	292	Formyltetrahydrofolate deformylase; structural gen	92.92
3nrb_A	287	Formyltetrahydrofolate deformylase; N-terminal ACT	92.2
3p96_A	415	Phosphoserine phosphatase SERB; ssgcid, structural	91.57
2f1f_A	164	Acetolactate synthase isozyme III small subunit; f	90.61
2jhe_A	190	Transcription regulator TYRR; aromatic hydrocarbon	90.37
2pc6_A	165	Probable acetolactate synthase isozyme III (small;	90.14
1y7p_A	223	Hypothetical protein AF1403; structural genomics,	87.1
2fgc_A	193	Acetolactate synthase, small subunit; regulatory s	84.69

>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=8.5e-17  Score=120.57  Aligned_cols=60  Identities=22%  Similarity=0.375  Sum_probs=56.6

Q ss_pred             HHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC-CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           73 AALKNHIEAERNRRKRINGHLDTLRSLIPGA-TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        73 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      ..+.+|+.+||+||++||++|.+|+++||+. .|+||++||.+||+||++|+.+++.|+.+
T Consensus         5 ~rr~~H~~~ErrRR~~in~~f~~L~~lvP~~~~k~~Ka~IL~~Ai~YI~~Lq~~~~~L~~e   65 (82)
T 1am9_A            5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE   65 (82)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4568999999999999999999999999987 99999999999999999999999999765

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

Probab=99.63  E-value=6.2e-16  Score=112.41  Aligned_cols=59  Identities=29%  Similarity=0.393  Sum_probs=54.0

Q ss_pred             hHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC-CccchhhHHHHHHHHHHHHHHHHHHHh
Q 024326           72 VAALKNHIEAERNRRKRINGHLDTLRSLIPGA-TKMDKATLLTEVISQLKELDKNAMEAT  130 (269)
Q Consensus        72 ~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dk~sil~~ai~yik~L~~~~~~l~  130 (269)
                      ...+.+|+.+||+||++||++|.+|++|||.. .|+||++||++||+||++||+++.=|+
T Consensus         6 ~~kR~~Hn~iErrRRd~IN~~i~eL~~LvP~~~~K~dK~sIL~~aI~yik~Lq~~~~~~~   65 (71)
T 4h10_B            6 KAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKEITAWLE   65 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSCCCHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             hHHhhhhhHHHhhHHHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhhhHHH
Confidence            44568999999999999999999999999965 799999999999999999999987664

>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=99.56  E-value=5.1e-15  Score=110.30  Aligned_cols=61  Identities=20%  Similarity=0.363  Sum_probs=56.4

Q ss_pred             hHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           72 VAALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        72 ~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      ...+.+|+.+||+||.+||+.|..|+++||..  .|++|++||..||+||++|++++++|+.+
T Consensus        10 ~~~R~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~L~~e   72 (80)
T 1hlo_A           10 ADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD   72 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHCcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34568999999999999999999999999975  79999999999999999999999999764

>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=99.56  E-value=3.9e-16  Score=111.29  Aligned_cols=52  Identities=33%  Similarity=0.457  Sum_probs=47.5

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCC-------CccchhhHHHHHHHHHHHHHHHH
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGA-------TKMDKATLLTEVISQLKELDKNA  126 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~-------~k~dk~sil~~ai~yik~L~~~~  126 (269)
                      +.+|+.+||+||++||+.|.+|++|||..       .+.+||+||+.||+||++||+++
T Consensus         3 r~~H~~aEr~RR~rIn~~~~~L~~LlP~~~~~~~~~~k~sKa~iL~~Ai~YIk~Lq~~~   61 (63)
T 1a0a_A            3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             ccchhHHHHHHHHHHHHHHHHHHHHCCCcccccccCCcccHHHHHHHHHHHHHHHHHHh
Confidence            37899999999999999999999999954       56779999999999999999865

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

Probab=99.56  E-value=4.8e-15  Score=118.28  Aligned_cols=58  Identities=29%  Similarity=0.467  Sum_probs=51.8

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      +.+|+.+||+||++||++|.+|++|||.+    .|++|++||.+||+||++||++++.|+++
T Consensus        28 r~~Hn~~ERrRR~~In~~~~~L~~lvP~~~~~~~k~~Ka~IL~~aieYIk~Lq~~~~~l~~~   89 (118)
T 4ati_A           28 KDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKDL   89 (118)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHSCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHhhccCccccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47999999999999999999999999976    47889999999999999999999999764

>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=99.55  E-value=5.3e-16  Score=111.19  Aligned_cols=52  Identities=29%  Similarity=0.487  Sum_probs=48.2

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCCC------ccchhhHHHHHHHHHHHHHHHH
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGAT------KMDKATLLTEVISQLKELDKNA  126 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~~------k~dk~sil~~ai~yik~L~~~~  126 (269)
                      +.+|+.+||+||++||+.|.+|++|||.+.      |++|++||.+||+||++||++.
T Consensus         6 r~~H~~~Er~RR~~in~~~~~L~~lvP~~~~~~~~~k~~Ka~IL~~ai~YI~~Lq~~~   63 (65)
T 1an4_A            6 RAQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CCSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHhhchHHHHHHHHHHHHHHHHHHHCcCcccccccCCCCHHHHHHHHHHHHHHHHHHh
Confidence            378999999999999999999999999764      7899999999999999999865

>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=99.55  E-value=6.9e-15  Score=110.28  Aligned_cols=59  Identities=20%  Similarity=0.376  Sum_probs=54.4

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      .+.+|+..||+||.+||+.|..|+++||..  .|++|++||.+||+||++|+.++++|+.+
T Consensus         2 rR~~hn~~Er~RR~~in~~f~~Lr~lvP~~~~~k~sK~~iL~~Ai~YI~~L~~~~~~l~~e   62 (83)
T 1nkp_B            2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD   62 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHhhhHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357999999999999999999999999974  89999999999999999999999888654

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

Probab=99.54  E-value=3.1e-15  Score=109.54  Aligned_cols=53  Identities=34%  Similarity=0.559  Sum_probs=48.9

Q ss_pred             hHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHHHHHH
Q 024326           72 VAALKNHIEAERNRRKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLKELDK  124 (269)
Q Consensus        72 ~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik~L~~  124 (269)
                      ..++.+|+.+||+||++||+.|.+|++|||.+    .|+||++||+.||+||+.|+.
T Consensus         7 ~~rR~~H~~~ERrRR~rIN~~l~eL~~LvP~~~~~~~KldKasIL~~tV~ylk~l~~   63 (73)
T 4h10_A            7 KNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRG   63 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTCSSCCCHHHHHHHHHHHHHHHSC
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHhc
Confidence            34568999999999999999999999999965    799999999999999999975

>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=99.53  E-value=1.2e-14  Score=110.26  Aligned_cols=60  Identities=20%  Similarity=0.283  Sum_probs=54.5

Q ss_pred             hHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHHHHHhc
Q 024326           72 VAALKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNAMEATE  131 (269)
Q Consensus        72 ~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~~~l~~  131 (269)
                      ...+..|+..||+||..||+.|..|+++||..   .|++|++||.+||+||++|+.+.+.+..
T Consensus         4 ~~~R~~Hn~~ER~RR~~ln~~f~~Lr~~vP~~~~~~K~sK~~iL~~A~~YI~~L~~~~~~l~~   66 (88)
T 1nkp_A            4 NVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS   66 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            34578999999999999999999999999975   6999999999999999999999887654

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

Probab=99.45  E-value=4.9e-14  Score=103.92  Aligned_cols=58  Identities=22%  Similarity=0.302  Sum_probs=49.7

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCC---CCcc-chhhHHHHHHHHHHHHHHHHHHHhc
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPG---ATKM-DKATLLTEVISQLKELDKNAMEATE  131 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~---~~k~-dk~sil~~ai~yik~L~~~~~~l~~  131 (269)
                      .+.+|+..||+||..||+.|.+|+.+||.   ..|. +|++||..||+||+.||+++++++.
T Consensus         5 rR~~hN~~ER~Rr~~IN~~f~~Lr~~vP~~~~~~K~~sK~~IL~~AieYI~~Lq~~l~e~~~   66 (76)
T 3u5v_A            5 KRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNL   66 (76)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             HHhhchHHHhhhHHHHHHHHHHHHHHcCCCCCccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            45889999999999999999999999994   3555 7999999999999999999999875

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

Probab=99.45  E-value=1.5e-13  Score=102.35  Aligned_cols=58  Identities=28%  Similarity=0.437  Sum_probs=53.1

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      +..|+..||+||..||+.|..|+++||..   .|++|++||.+|++||++|+.+.++|..+
T Consensus         2 R~~HN~~ER~RR~~lk~~f~~Lr~~vP~~~~~~k~sk~~iL~kA~~yI~~L~~~~~~l~~e   62 (80)
T 1nlw_A            2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ   62 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999964   78899999999999999999999887654

>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=99.28  E-value=4.1e-12  Score=91.63  Aligned_cols=56  Identities=20%  Similarity=0.291  Sum_probs=50.9

Q ss_pred             chHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--CccchhhHHHHHHHHHHHHHHHH
Q 024326           71 SVAALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKELDKNA  126 (269)
Q Consensus        71 ~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dk~sil~~ai~yik~L~~~~  126 (269)
                      ....+..|+..||+|+..||+.|..||.+||..  .|++|+.||..||+||.+|++.+
T Consensus         9 ~~~rR~~aN~rER~R~~~iN~af~~LR~~iP~~~~~KlSKi~tLr~Ai~YI~~L~~~L   66 (68)
T 1mdy_A            9 NADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL   66 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             chhhhhHhhHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence            345678999999999999999999999999964  79999999999999999999765

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

Probab=99.23  E-value=1.2e-11  Score=87.06  Aligned_cols=53  Identities=26%  Similarity=0.287  Sum_probs=48.8

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHHH
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNAM  127 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~~  127 (269)
                      +..|+..||+|+..||+.|..||.+||..   .|++|..+|..||+||..|++.++
T Consensus         3 R~~~N~rER~R~~~iN~af~~LR~~lP~~~~~~klSKi~tLr~Ai~YI~~L~~~L~   58 (60)
T 2ql2_B            3 RMKANARERNRMHGLNAALDNLRKVVPCYSKTQKLSKIETLRLAKNYIWALSEILR   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSSSCCSSSCCCHHHHHHHHHHHHHHHHHHTT
T ss_pred             cchhhHHHHHHHHHHHHHHHHHHHHccCCCCcCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            56799999999999999999999999965   689999999999999999998753

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

Probab=99.02  E-value=1.8e-10  Score=107.02  Aligned_cols=53  Identities=30%  Similarity=0.471  Sum_probs=43.2

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcC-CCCccchhhHHHHHHHHHHHHHHHH
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIP-GATKMDKATLLTEVISQLKELDKNA  126 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP-~~~k~dk~sil~~ai~yik~L~~~~  126 (269)
                      .+.+|+.+||+||++||+.|.+|++||| ...|+||++||..||.|||.|+...
T Consensus        12 ~~~~~~~~e~~rr~~~n~~~~~l~~~~p~~~~~~dk~~il~~~~~~~~~~~~~~   65 (361)
T 4f3l_A           12 KRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETT   65 (361)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHTCCSSSCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHhhc
Confidence            3478999999999999999999999999 5589999999999999999998753

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

Probab=98.95  E-value=6.7e-10  Score=104.31  Aligned_cols=53  Identities=34%  Similarity=0.557  Sum_probs=48.9

Q ss_pred             HHhhhhhHHHHHHHHHHHHhHHHHHhhcC----CCCccchhhHHHHHHHHHHHHHHH
Q 024326           73 AALKNHIEAERNRRKRINGHLDTLRSLIP----GATKMDKATLLTEVISQLKELDKN  125 (269)
Q Consensus        73 ~~~~~h~~~Er~RR~~in~~~~~LrslvP----~~~k~dk~sil~~ai~yik~L~~~  125 (269)
                      ..+.+|+.+||+||++||+.|.+|++|||    ...|+||++||..||.|||.|+..
T Consensus        12 ~~~~~~~~~ek~rR~~~n~~~~~L~~l~p~~~~~~~k~dk~~il~~~~~~l~~~~~~   68 (387)
T 4f3l_B           12 NAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMKTLRGA   68 (387)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHCSSCCCHHHHHHHHHHHHHHHHCC
T ss_pred             hhcccccchhhcchHHHHHHHHHHHHhcCCCCccccccCHHHHHHHHHHHHHHhhcc
Confidence            34689999999999999999999999999    568999999999999999999853

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

Probab=98.79  E-value=7.4e-10  Score=79.19  Aligned_cols=46  Identities=26%  Similarity=0.434  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHH
Q 024326           79 IEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDK  124 (269)
Q Consensus        79 ~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~  124 (269)
                      ++.||+|+..||+.|..||.+||..   .|++|..+|.-||+||..||.
T Consensus        19 ~erER~Rm~~lN~aF~~LR~~VP~~p~~kKLSKiEtLr~Ai~YI~~Lq~   67 (68)
T 2lfh_A           19 AEEPLSLLDDMNHCYSRLRELVPGVPRGTQLSQVEILQRVIDYILDLQV   67 (68)
T ss_dssp             BCCCSCSSSHHHHHHHHHHHHCCCCCTTCCCCHHHHHHHHHHHHHHHHC
T ss_pred             cHHHHHHHHHHHHHHHHHHHHCCCCCCCCCccHHHHHHHHHHHHHHHHc
Confidence            3678999999999999999999965   789999999999999999984

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

Probab=98.77  E-value=8.8e-09  Score=76.44  Aligned_cols=46  Identities=26%  Similarity=0.511  Sum_probs=41.5

Q ss_pred             HHHHHHhHHHHHhhcCCC----CccchhhHHHHHHHHHHHHHHHHHHHhc
Q 024326           86 RKRINGHLDTLRSLIPGA----TKMDKATLLTEVISQLKELDKNAMEATE  131 (269)
Q Consensus        86 R~~in~~~~~LrslvP~~----~k~dk~sil~~ai~yik~L~~~~~~l~~  131 (269)
                      |..||+++.+|..|||.+    .|.+|++||..||+||++||++.+.+.+
T Consensus         4 R~nIN~~I~EL~~LiP~~~~~~~k~nKg~IL~ksvdYI~~Lq~e~~r~~e   53 (83)
T 4ath_A            4 RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKD   53 (83)
T ss_dssp             HHHHHHHHHHHHHHSCCCCCTTCCCSHHHHHHHHHHHHHHHHHTHHHHHH
T ss_pred             hhhHHHhhhhhhccCCCCCCcccCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            789999999999999964    6789999999999999999998877654

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

Probab=98.30  E-value=1.1e-06  Score=67.05  Aligned_cols=50  Identities=20%  Similarity=0.269  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHHHHHh
Q 024326           81 AERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNAMEAT  130 (269)
Q Consensus        81 ~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~~~l~  130 (269)
                      .||.|-..+|+.|..||.+||..   .|+.|..+|.-||+||..|++-+++-.
T Consensus        32 ~~r~Rm~~lN~AF~~LR~~vP~~p~~kKLSKIETLRlAi~YI~~Lq~~L~~~~   84 (97)
T 4aya_A           32 DPMSLLYNMNDCYSKLKELVPSIPQNKKVSKMEILQHVIDYILDLQIALDSHL   84 (97)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTSCSSSCCCHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             cHHHHHHHHHHHHHHHHHHCCCCCCCCcccHHHHHHHHHHHHHHHHHHHhcCC
Confidence            35778889999999999999964   789999999999999999999887643

>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=96.98  E-value=0.013  Score=42.72  Aligned_cols=47  Identities=15%  Similarity=0.210  Sum_probs=39.9

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEE
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVM  203 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v  203 (269)
                      .+.+.+.|+++||++.+|..+|.+.|..|.+.+..+.++...-.+.+
T Consensus         5 ~~~l~v~~~DrpGila~vt~~la~~~~NI~~i~~~~~~~~~~~~i~v   51 (91)
T 1zpv_A            5 KAIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVV   51 (91)
T ss_dssp             EEEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEE
T ss_pred             eEEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEeEEEcCEEEEEEEE
Confidence            45677899999999999999999999999999998877765444444

>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=96.68  E-value=0.015  Score=48.68  Aligned_cols=47  Identities=13%  Similarity=0.332  Sum_probs=40.7

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      +.|.|.|+++||++.+|..+|.++|++|+.+++.+..|.+.-.+.+.
T Consensus         7 ~~itv~~~DrpGiva~vt~~La~~g~NI~d~~~~~~~~~f~~~~~v~   53 (192)
T 1u8s_A            7 LVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLIS   53 (192)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEE
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHHCCCCEEeeeeeecCCceEEEEEEe
Confidence            45779999999999999999999999999999998888775555553

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

Probab=96.29  E-value=0.03  Score=40.15  Aligned_cols=48  Identities=10%  Similarity=0.219  Sum_probs=38.9

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEE
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVM  203 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v  203 (269)
                      +.+.+.+.++++||+|.+|..+|.+.|+.|.+.++.+.++....++.+
T Consensus         4 ~~~~l~v~~~Dr~G~L~~I~~~la~~~inI~~i~~~~~~~~~~~~i~v   51 (88)
T 2ko1_A            4 FLAGIRIVGEDKNGMTNQITGVISKFDTNIRTIVLNAKDGIFTCNLMI   51 (88)
T ss_dssp             EEEEEEEEEECCTTHHHHHHHHHTTSSSCEEEEEEEECSSEEEEEEEE
T ss_pred             EEEEEEEEEECCCcHHHHHHHHHHHCCCCeEEEEEEEcCCEEEEEEEE
Confidence            456777889999999999999999999999999998777633333333

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

Probab=96.08  E-value=0.02  Score=48.21  Aligned_cols=48  Identities=19%  Similarity=0.353  Sum_probs=40.8

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      .+.|.|.|+++||++..|..+|.++|+.|+.+++.+..|.+.-.+.+.
T Consensus         5 ~~~ltv~~~DrpGiva~vs~~La~~g~NI~da~q~~~~~~f~m~~~v~   52 (195)
T 2nyi_A            5 SFVVSVAGSDRVGIVHDFSWALKNISANVESSRMACLGGDFAMIVLVS   52 (195)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEE
T ss_pred             EEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEEeEEECCeEEEEEEEE
Confidence            356779999999999999999999999999999998888764455553

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

Probab=95.46  E-value=0.069  Score=44.91  Aligned_cols=38  Identities=21%  Similarity=0.195  Sum_probs=34.7

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE  194 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~  194 (269)
                      ...+.|.|+++||++..|...|-++|+.|..++..+.+
T Consensus        93 ~~iltv~g~DrpGiva~Vt~~La~~g~nI~~~~~~t~~  130 (195)
T 2nyi_A           93 EYELYVEGPDSEGIVEAVTAVLAKKGANIVELETETLP  130 (195)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEEE
T ss_pred             EEEEEEEeCCCcCHHHHHHHHHHHcCCCEEEceeeecc
Confidence            35577899999999999999999999999999998876

>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=94.32  E-value=0.25  Score=40.99  Aligned_cols=39  Identities=13%  Similarity=0.297  Sum_probs=35.1

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE  194 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~  194 (269)
                      ....+.+.|+++||++.+|.+.|.+.|++|..+...+.+
T Consensus        92 ~~~~l~v~~~D~~Gil~~v~~~l~~~~~nI~~~~~~t~~  130 (192)
T 1u8s_A           92 YTVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTIS  130 (192)
T ss_dssp             EEEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEEC
T ss_pred             ceEEEEEEeCCCccHHHHHHHHHHHcCCcHHHhhhhccc
Confidence            456678899999999999999999999999999988775

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

Probab=94.19  E-value=0.26  Score=44.66  Aligned_cols=91  Identities=15%  Similarity=0.195  Sum_probs=56.5

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee--CCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL--EGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKF  235 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~--~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~  235 (269)
                      +.+.+.|++++|+...|...|-+.|..|+.++....  .|+++  +.+.........+       ...|+++|..+-+++
T Consensus        23 ~iLtv~c~DrpGIVa~VS~~La~~g~NI~d~~q~~d~~~g~Ff--Mr~~~~~~~~~~~-------~~~L~~~l~~la~~l   93 (302)
T 3o1l_A           23 FRLVIACPDRVGIVAKVSNFLASHNGWITEASHHSDNLSGWFF--MRHEIRADTLPFD-------LDGFREAFTPIAEEF   93 (302)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHHTTCCEEEEEEEEETTTTEEE--EEEEEEGGGSSSC-------HHHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCCEEEeeEEecCCCCeEE--EEEEEecCCCCCC-------HHHHHHHHHHHHHHh
Confidence            457799999999999999999999999999988754  45542  2332221110011       355666666655544


Q ss_pred             ccchhhhccccCCCCCceeeeccCCC
Q 024326          236 SATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       236 ~~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      ...-...    ...++.|+-+|-|-+
T Consensus        94 ~m~~~l~----~~~~~~ri~vl~Sg~  115 (302)
T 3o1l_A           94 SMDWRIT----DSAQKKRVVLMASRE  115 (302)
T ss_dssp             TCEEEEE----ETTSCCEEEEEECSC
T ss_pred             CCeeeec----ccCCCcEEEEEEeCC
Confidence            3322111    134567888776544

>3obi_A Formyltetrahydrofolate deformylase; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.95A {Rhodopseudomonas palustris}

Probab=94.07  E-value=0.26  Score=44.21  Aligned_cols=91  Identities=20%  Similarity=0.221  Sum_probs=56.1

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE--eeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA--TLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKF  235 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is--t~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~  235 (269)
                      +.+.+.|++++|+...|...|-++|..|..++..  ...|.++-.+.+..  .....+       ...|+++|..+-+++
T Consensus         7 ~iLtv~g~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ffmr~~~~~--~~~~~~-------~~~L~~~f~~la~~~   77 (288)
T 3obi_A            7 YVLTLSCPDRAGIVSAVSTFLFENGQNILDAQQYNDTESGHFFMRVVFNA--AAKVIP-------LASLRTGFGVIAAKF   77 (288)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHHTTEEEEEEEEEEETTTTEEEEEEEEEE--SSCCCC-------HHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCcEEeeeeeecCCCCceEEEEEEEc--CCCCCC-------HHHHHHHHHHHHHHc
Confidence            4577899999999999999999999999998875  33554422222211  110011       355666666665554


Q ss_pred             ccchhhhccccCCCCCceeeeccCCC
Q 024326          236 SATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       236 ~~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      ...-...    ...++.|+-+|-|-+
T Consensus        78 ~m~~~l~----~~~~~~ri~vl~Sg~   99 (288)
T 3obi_A           78 TMGWHMR----DRETRRKVMLLVSQS   99 (288)
T ss_dssp             TCEEEEE----ETTSCEEEEEEECSC
T ss_pred             CCEEEee----ccCCCcEEEEEEcCC
Confidence            4332211    134567888876543

>3n0v_A Formyltetrahydrofolate deformylase; formyl transferase, ACT domain, structural genomics, joint C structural genomics, JCSG; HET: MSE; 2.25A {Pseudomonas putida}

Probab=94.02  E-value=0.41  Score=42.94  Aligned_cols=90  Identities=13%  Similarity=0.104  Sum_probs=56.6

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE--eeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA--TLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKF  235 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is--t~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~  235 (269)
                      +.+.+.|++++|+...|...|-++|..|..++..  ...|+++  +.+....... .+       ...|+++|..+-++.
T Consensus         9 ~vLtv~c~DrpGIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ff--mr~~~~~~~~-~~-------~~~L~~~f~~la~~l   78 (286)
T 3n0v_A            9 WILTADCPSMLGTVDVVTRYLFEQRCYVTEHHSFDDRQSGRFF--IRVEFRQPDD-FD-------EAGFRAGLAERSEAF   78 (286)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEE--EEEEEECCSS-CC-------HHHHHHHHHHHHGGG
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHHCCCCeeeeeeeccCCCCeeE--EEEEEecCCC-CC-------HHHHHHHHHHHHHHc
Confidence            4567899999999999999999999999998877  3445442  2222221111 11       356666776665544


Q ss_pred             ccchhhhccccCCCCCceeeeccCCC
Q 024326          236 SATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       236 ~~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      ...-...    ...++.|+-+|-|-+
T Consensus        79 ~m~~~l~----~~~~~~ri~vl~Sg~  100 (286)
T 3n0v_A           79 GMAFELT----APNHRPKVVIMVSKA  100 (286)
T ss_dssp             TCEEEEE----CTTCCCEEEEEESSC
T ss_pred             CCEEEee----cCCCCcEEEEEEeCC
Confidence            4322211    245567888775543

>3lou_A Formyltetrahydrofolate deformylase; structural genomics, JOI for structural genomics, JCSG, protein structure initiative hydrolase; HET: MSE; 1.90A {Burkholderia mallei}

Probab=92.92  E-value=0.6  Score=41.94  Aligned_cols=91  Identities=13%  Similarity=0.178  Sum_probs=55.6

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE--eeCCeEEEEEEEeeecc--cccchhhhHHHHHHHHHHHHHHHHh
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA--TLEGRMKNIFVMASCKE--LNFENTEVCQSLVSSVHQAIRSVLD  233 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is--t~~g~v~~vf~v~~~k~--~~~~~~~~~~~l~~~v~qaL~~v~~  233 (269)
                      +.+.+.|++++|+..+|...|-++|+.|..++..  ...|+++  +.+.....  ....+       ...|+++|..+-+
T Consensus        11 ~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ff--mr~~~~~~~~~~~~~-------~~~L~~~f~~la~   81 (292)
T 3lou_A           11 FVLTLSCPSAAGQVAAVVGLLDRHRCYVDELTVFDDDLSARFF--VRCVFHATDDADALR-------VDALRREFEPIAE   81 (292)
T ss_dssp             EEEEEEEESCSCHHHHHHHHHHHTTEEEEEEEEEEETTTTEEE--EEEEEEECC----CC-------HHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEeeEEEecCCCCceE--EEEEEEccCcccCCC-------HHHHHHHHHHHHH
Confidence            4577899999999999999999999999998887  3455542  22221111  00011       3556666666555


Q ss_pred             hcccchhhhccccCCCCCceeeeccCCC
Q 024326          234 KFSATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       234 k~~~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      ++...-...    ...++.|+-+|-|-+
T Consensus        82 ~~~m~~~l~----~~~~~~ri~vl~Sg~  105 (292)
T 3lou_A           82 RFRMQWAIH----DVAARPKVLIMVSKL  105 (292)
T ss_dssp             HHTCEEEEE----ETTSCCEEEEEECSC
T ss_pred             hcCcEEEee----ccCCCCEEEEEEcCC
Confidence            444322211    134567888876543

>3nrb_A Formyltetrahydrofolate deformylase; N-terminal ACT domain, structural genomics, joint center for structural genomics, JCSG; HET: MSE FLC; 2.05A {Pseudomonas putida}

Probab=92.20  E-value=0.74  Score=41.24  Aligned_cols=89  Identities=22%  Similarity=0.299  Sum_probs=56.0

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEE--eeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhc
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIA--TLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKF  235 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~is--t~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~  235 (269)
                      +.+.+.|++++|+...|...|-++|..|+.++..  ...|+++  +.+......  ..       ...|+++|..+-+++
T Consensus         8 ~vLtv~c~Dr~GIVa~Vs~~La~~g~NI~d~~q~~d~~~g~Ff--mr~~~~~~~--~~-------~~~L~~~f~~la~~~   76 (287)
T 3nrb_A            8 YVLSLACQDAPGIVSEVSTFLFNNGANIVEAEQFNDEDSSKFF--MRVSVEIPV--AG-------VNDFNSAFGKVVEKY   76 (287)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTTTEEE--EEEEEECCC------------CHHHHHHHHHHGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCCEEeeeeeecCCCCeEE--EEEEEEcCC--CC-------HHHHHHHHHHHHHHc
Confidence            4577899999999999999999999999998875  3355442  222222111  00       236777777665554


Q ss_pred             ccchhhhccccCCCCCceeeeccCCC
Q 024326          236 SATEEFLLGARLSNKRRRVSLFDSSL  261 (269)
Q Consensus       236 ~~~~~~~~~~~~~~kr~r~~~~~~~~  261 (269)
                      ...-...    ...++.|+-+|-|-+
T Consensus        77 ~m~~~l~----~~~~~~ri~vl~Sg~   98 (287)
T 3nrb_A           77 NAEWWFR----PRTDRKKVVIMVSKF   98 (287)
T ss_dssp             TCEEEEE----ETTCCCEEEEEECSC
T ss_pred             CCeeEee----ccCCCcEEEEEEeCC
Confidence            4432211    234567888876544

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

Probab=91.57  E-value=1.1  Score=41.16  Aligned_cols=72  Identities=13%  Similarity=0.200  Sum_probs=50.4

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhcc
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFS  236 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~~  236 (269)
                      .+.|++.|++|||+...|...|-++|..|+.++-...+|++.-.+.+....     ..    .-...|+.+|..+-.+..
T Consensus        12 ~~~lt~~g~Dr~Giv~~vs~~l~~~~~nI~d~~q~~~~~~f~~~~~~~~~~-----~~----~~~~~l~~~l~~~~~~~~   82 (415)
T 3p96_A           12 SVLITVTGVDQPGVTATLFEVLSRHGVELLNVEQVVIRHRLTLGVLVCCPA-----DV----ADGPALRHDVEAAIRKVG   82 (415)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHTTTTCEEEEEEEEEETTEEEEEEEEEECH-----HH----HTSHHHHHHHHHHHHHTT
T ss_pred             eEEEEEEcCCCCCHHHHHHHHHHHCCCCEEEeeeEEECCEeEEEEEEEecC-----Cc----CCHHHHHHHHHHHHHHcC
Confidence            356789999999999999999999999999999998888764333332111     00    012456666666655544


Q ss_pred             c
Q 024326          237 A  237 (269)
Q Consensus       237 ~  237 (269)
                      .
T Consensus        83 ~   83 (415)
T 3p96_A           83 L   83 (415)
T ss_dssp             C
T ss_pred             e
Confidence            4

>2f1f_A Acetolactate synthase isozyme III small subunit; ferredoxin fold, ACT domain, transferase; HET: P33 1PE; 1.75A {Escherichia coli} SCOP: d.58.18.6 d.58.18.6

Probab=90.61  E-value=0.76  Score=37.84  Aligned_cols=46  Identities=13%  Similarity=0.087  Sum_probs=36.2

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC--CeEEEEEEEe
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE--GRMKNIFVMA  204 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~--g~v~~vf~v~  204 (269)
                      .+++..+++||+|.+|...|...|..|.+.++.+..  +...-+|.+.
T Consensus         5 ~IsV~v~NrpGvLarIt~lfs~rg~NI~Sl~v~~t~d~~~sriti~V~   52 (164)
T 2f1f_A            5 ILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTV   52 (164)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHTTTCCCSEEEEEECSCSSEEEEEEEEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCeeeceeeecCCCCEEEEEEEEe
Confidence            456778999999999999999999999999987544  4444444553

>2jhe_A Transcription regulator TYRR; aromatic hydrocarbons catabolism, TYRR protei nucleotide-binding, transcription regulation, activator; HET: PG4; 2.30A {Escherichia coli}

Probab=90.37  E-value=0.64  Score=37.02  Aligned_cols=37  Identities=24%  Similarity=0.441  Sum_probs=33.1

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCe
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGR  196 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~  196 (269)
                      +|.|.|.+|+|+|.+|+++|.+.++++..+++.+. |.
T Consensus         2 ~~~v~~~dr~g~l~~i~~~l~~~~~ni~~~~~~~~-g~   38 (190)
T 2jhe_A            2 RLEVFCEDRLGLTRELLDLLVLRGIDLRGIEIDPI-GR   38 (190)
T ss_dssp             EEEEEECSCTTHHHHHHHHHHHTTCCEEEEEEETT-TE
T ss_pred             EEEEEEecCCcHHHHHHHHHHHcCCCeEEEEEecC-CE
Confidence            46688999999999999999999999999999766 44

>2pc6_A Probable acetolactate synthase isozyme III (small; regulatory subunit, structural genomi protein structure initiative; HET: MSE; 2.50A {Nitrosomonas europaea atcc 19718} SCOP: d.58.18.6 d.58.18.6

Probab=90.14  E-value=1  Score=37.19  Aligned_cols=46  Identities=22%  Similarity=0.190  Sum_probs=36.4

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC--CeEEEEEEEe
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE--GRMKNIFVMA  204 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~--g~v~~vf~v~  204 (269)
                      .+++..+++||.|.+|...|...|..|.+.++....  +...-++.+.
T Consensus         6 ~IsV~veNrpGvL~rI~~lfs~rg~NI~Sl~v~~t~d~g~sritivV~   53 (165)
T 2pc6_A            6 IISLLMENEAGALSRVAGLFSARGYNIESLSVAPTEDPTLSRMTLVTN   53 (165)
T ss_dssp             EEEEEEECSTTHHHHHHHHHHHHTCCCCEEEEEECSSTTEEEEEEEEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCcEEEEEEEecCCCCEEEEEEEEe
Confidence            466788999999999999999999999999887443  5454445553

>1y7p_A Hypothetical protein AF1403; structural genomics, protein structure initiative, PSI, alpha-beta-alpha sandwich; HET: RIP; 1.90A {Archaeoglobus fulgidus} SCOP: c.23.1.7 d.58.18.12

Probab=87.10  E-value=1.4  Score=38.19  Aligned_cols=38  Identities=18%  Similarity=0.165  Sum_probs=30.0

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeC
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLE  194 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~  194 (269)
                      .+.+.|.+.+|+|+|.+|+.+|-+.+..|.+.+..+..
T Consensus         4 ~VtL~I~a~DRpGLLsDIt~vLAe~kiNIltIn~~~~~   41 (223)
T 1y7p_A            4 LRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIK   41 (223)
T ss_dssp             CEEEEEEEECCTTHHHHHHHHCC----CEEEEEEEECC
T ss_pred             eEEEEEEEcCCCCHHHHHHHHHHHcCCCceEEEEEccc
Confidence            35667889999999999999999999999999998764

>2fgc_A Acetolactate synthase, small subunit; regulatory subunit, structural genomi protein structure initiative; 2.30A {Thermotoga maritima} SCOP: d.58.18.6 d.58.18.6

Probab=84.69  E-value=3.1  Score=35.13  Aligned_cols=47  Identities=13%  Similarity=0.270  Sum_probs=36.3

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe-eC-CeEEEEEEEe
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT-LE-GRMKNIFVMA  204 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist-~~-g~v~~vf~v~  204 (269)
                      -.+++..+++||.|.+|...|...|+.|.+..+.. -+ +...-++++.
T Consensus        30 ~~LsVlVeN~pGvLaRItglfsrRG~NI~SLtV~~ted~gisRitIvV~   78 (193)
T 2fgc_A           30 HLVSMLVHNKPGVMRKVANLFARRGFNISSITVGESETPGLSRLVIMVK   78 (193)
T ss_dssp             EEEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEECSSTTEEEEEEEEE
T ss_pred             EEEEEEECCCChHHHHHHHHHHHCCceEEEEEeeccCCCCEEEEEEEEE
Confidence            35667889999999999999999999999988863 33 4444444553

---

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	269
d1a0aa_	63	a.38.1.1 (A:) Pho4 B/HLH domain {Baker's yeast (Sa	2e-09
d1mdya_	68	a.38.1.1 (A:) Myod B/HLH domain {Mouse (Mus muscul	3e-09
d1an4a_	65	a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapien	5e-09
d1nkpb_	83	a.38.1.1 (B:) Max protein {Human (Homo sapiens) [T	1e-08
d1nlwa_	79	a.38.1.1 (A:) Mad protein {Human (Homo sapiens) [T	4e-08
d1am9a_	80	a.38.1.1 (A:) SREBP-1a {Human (Homo sapiens) [TaxI	2e-07
d1nkpa_	88	a.38.1.1 (A:) Myc proto-oncogene protein {Human (H	3e-07
d1uklc_	61	a.38.1.1 (C:) SREBP-2 {Human (Homo sapiens) [TaxId	1e-06

>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 = 50.6 bits (121), Expect = 2e-09
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPGA-------TKMDKATLLTEVISQLKELDKN 125
           ++H  AE+ RR R+   L  L SLIP             KAT +      ++ L +N
Sbjct: 4   ESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQN 60

>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 = 50.3 bits (120), Expect = 3e-09
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 6/67 (8%)

Query: 60  KLQRKGVSEDRSVAALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVIS 117
           +L+RK  + DR  A        ER R  ++N   +TL+         ++ K  +L   I 
Sbjct: 2   ELKRKTTNADRRKA----ATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIR 57

Query: 118 QLKELDK 124
            ++ L  
Sbjct: 58  YIEGLQA 64

>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 = 49.4 bits (118), Expect = 5e-09
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 6/53 (11%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIP------GATKMDKATLLTEVISQLKEL 122
             H E ER RR +IN  +  L  +IP        +   K  +L++    ++EL
Sbjct: 7   AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQEL 59

>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 = 48.7 bits (116), Expect = 1e-08
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 8/75 (10%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPG--ATKMDKATLLTEVISQLKELDKNAMEATEGF 133
            +H   ER RR  I     +LR  +P     K  +A +L +    ++ + +      +  
Sbjct: 4   AHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQ-- 61

Query: 134 LIPTDIDEVKVEQQE 148
               DID++K +   
Sbjct: 62  ----DIDDLKRQNAL 72

>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 = 47.2 bits (112), Expect = 4e-08
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 9/75 (12%)

Query: 77  NHIEAERNRRKRINGHLDTLRSLIPG---ATKMDKATLLTEVISQLKELDKNAMEATEGF 133
            H E E+NRR  +   L+ L+ L+P    +++    +LLT+    +K+L+ +  +A    
Sbjct: 4   THNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVH-- 61

Query: 134 LIPTDIDEVKVEQQE 148
                ID+++ EQ+ 
Sbjct: 62  ----QIDQLQREQRH 72

>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 = 45.7 bits (108), Expect = 2e-07
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIPGA-TKMDKATLLTEVISQLKELDK 124
             H   E+  R  IN  +  L+ L+ G   K++K+ +L + I  ++ L  
Sbjct: 8   TAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQH 57

>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 = 45.3 bits (107), Expect = 3e-07
 Identities = 13/76 (17%), Positives = 27/76 (35%), Gaps = 9/76 (11%)

Query: 76  KNHIEAERNRRKRINGHLDTLRSLIP---GATKMDKATLLTEVISQLKELDKNAMEATEG 132
           + H   ER RR  +      LR  IP      K  K  +L +  + +  +     +    
Sbjct: 8   RTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLIS- 66

Query: 133 FLIPTDIDEVKVEQQE 148
                + D ++  +++
Sbjct: 67  -----EEDLLRKRREQ 77

>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 = 42.8 bits (101), Expect = 1e-06
 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 7/67 (10%)

Query: 86  RKRINGHLDTLRSLIPGAT-KMDKATLLTEVISQLKELDKNAMEATEGFLIPTDIDEVKV 144
           R  IN  +  L+ L+ G   KM K+ +L + I  +K L +   +  +      +   +K+
Sbjct: 1   RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQ------ENMVLKL 54

Query: 145 EQQEDGL 151
             Q++ L
Sbjct: 55  ANQKNKL 61

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	269
d1am9a_	80	SREBP-1a {Human (Homo sapiens) [TaxId: 9606]}	99.6
d1mdya_	68	Myod B/HLH domain {Mouse (Mus musculus) [TaxId: 10	99.58
d1a0aa_	63	Pho4 B/HLH domain {Baker's yeast (Saccharomyces ce	99.55
d1nlwa_	79	Mad protein {Human (Homo sapiens) [TaxId: 9606]}	99.55
d1nkpb_	83	Max protein {Human (Homo sapiens) [TaxId: 9606]}	99.52
d1nkpa_	88	Myc proto-oncogene protein {Human (Homo sapiens) [	99.51
d1an4a_	65	Usf B/HLH domain {Human (Homo sapiens) [TaxId: 960	99.44
d1uklc_	61	SREBP-2 {Human (Homo sapiens) [TaxId: 9606]}	99.39
d1u8sa1	86	putative transcriptional repressor VC2159 {Vibrio	97.36
d1zpva1	83	UPF0237 protein SP0238 {Streptococcus pneumoniae [	97.28
d1u8sa2	93	putative transcriptional repressor VC2159 {Vibrio	95.82
d1y7pa2	77	Hypothetical protein AF1403, N-terminal domain {Ar	94.11
d2f06a1	71	Hypothetical protein BT0572 {Bacteroides thetaiota	92.93
d2f06a2	70	Hypothetical protein BT0572 {Bacteroides thetaiota	92.93
d1sc6a3	84	Phosphoglycerate dehydrogenase, regulatory (C-term	90.32
d1phza1	97	Phenylalanine hydroxylase N-terminal domain {Rat (	86.07
d2qmwa2	80	Prephenate dehydratase C-terminal domain {Staphylo	83.06
d1ygya3	78	Phosphoglycerate dehydrogenase, regulatory (C-term	82.45
d2fgca2	78	Acetolactate synthase small subunit, IlvH {Thermot	81.0

>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=99.60  E-value=7.5e-16  Score=113.03  Aligned_cols=60  Identities=22%  Similarity=0.375  Sum_probs=55.6

Q ss_pred             HHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC-CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           73 AALKNHIEAERNRRKRINGHLDTLRSLIPGA-TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        73 ~~~~~h~~~Er~RR~~in~~~~~LrslvP~~-~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      ..+.+|+.+||+||++||+.|..|++|||+. .|++|++||.+||+||++|+.+++.|..+
T Consensus         5 ~kR~~H~~~Er~RR~~in~~~~~L~~llP~~~~k~~K~~iL~~a~~yI~~L~~~~~~L~~e   65 (80)
T d1am9a_           5 EKRTAHNAIEKRYRSSINDKIIELKDLVVGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQE   65 (80)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4568999999999999999999999999976 79999999999999999999999988764

>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=99.58  E-value=7.8e-16  Score=109.64  Aligned_cols=58  Identities=19%  Similarity=0.271  Sum_probs=52.1

Q ss_pred             cchHHhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--CccchhhHHHHHHHHHHHHHHHHH
Q 024326           70 RSVAALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKELDKNAM  127 (269)
Q Consensus        70 ~~~~~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dk~sil~~ai~yik~L~~~~~  127 (269)
                      .....+..|+..||+||.+||+.|..|+++||..  .|++|++||..||+||++||+.++
T Consensus         8 ~~~~rR~~hn~~Er~Rr~~in~~~~~L~~llP~~~~~k~sK~~iL~~Ai~YI~~Lq~~l~   67 (68)
T d1mdya_           8 TNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALLR   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCTTSCCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHhh
Confidence            3445678999999999999999999999999975  688999999999999999998764

>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=99.55  E-value=8e-16  Score=107.95  Aligned_cols=52  Identities=33%  Similarity=0.464  Sum_probs=48.0

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCC-------CCccchhhHHHHHHHHHHHHHHHH
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPG-------ATKMDKATLLTEVISQLKELDKNA  126 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~-------~~k~dk~sil~~ai~yik~L~~~~  126 (269)
                      +.+|+.+||+||++||+.|..|++|||.       ..|++|++||+.||+||++||+++
T Consensus         3 R~~H~~~Er~RR~~in~~~~~L~~llP~~~~~~~~~~k~sKa~iL~~Av~yI~~Lq~~v   61 (63)
T d1a0aa_           3 RESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNG   61 (63)
T ss_dssp             TTGGGGGTHHHHHHHHHHHHHHHHTSCHHHHTSSCCCCSCTTHHHHHHHHHHHHHHTCS
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHCCCcccccCCcccccHHHHHHHHHHHHHHHHHhh
Confidence            3689999999999999999999999994       478999999999999999999765

>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=99.55  E-value=4.3e-15  Score=108.56  Aligned_cols=58  Identities=28%  Similarity=0.437  Sum_probs=53.3

Q ss_pred             hhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           75 LKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        75 ~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      +..|+.+||+||++||+.|..|+++||..   .|++|++||..||+||++|+.+++.+..+
T Consensus         2 R~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~   62 (79)
T d1nlwa_           2 RSTHNEMEKNRRAHLRLSLEKLKGLVPLGPDSSRHTTLSLLTKAKLHIKKLEDSDRKAVHQ   62 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSSCCCSSSCCCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhCccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            46899999999999999999999999964   68999999999999999999999887653

>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=99.52  E-value=7.2e-15  Score=108.33  Aligned_cols=59  Identities=20%  Similarity=0.376  Sum_probs=53.9

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCCC--CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPGA--TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~--~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      .+.+|+.+||+||++||+.|..|+++||..  .|++|++||..||+||++|+.+++.|..+
T Consensus         2 rR~~Hn~~Er~RR~~in~~f~~L~~llP~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~   62 (83)
T d1nkpb_           2 KRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHTHQQD   62 (83)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSGGGTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999953  78999999999999999999999887653

>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=99.51  E-value=1.1e-14  Score=108.42  Aligned_cols=59  Identities=20%  Similarity=0.295  Sum_probs=54.1

Q ss_pred             HhhhhhHHHHHHHHHHHHhHHHHHhhcCCC---CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           74 ALKNHIEAERNRRKRINGHLDTLRSLIPGA---TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        74 ~~~~h~~~Er~RR~~in~~~~~LrslvP~~---~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      .+..|+.+||+||++||+.|..|+++||+.   .|++|++||..||+||++|+.++++|..+
T Consensus         6 rR~~Hn~~Er~RR~~in~~f~~Lr~llP~~~~~~k~sK~~iL~~A~~yI~~L~~~~~~l~~~   67 (88)
T d1nkpa_           6 KRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISE   67 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTCGGGTTCTTCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999964   68999999999999999999999888653

>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=99.44  E-value=1.6e-14  Score=101.85  Aligned_cols=51  Identities=29%  Similarity=0.511  Sum_probs=47.2

Q ss_pred             hhhhHHHHHHHHHHHHhHHHHHhhcCCC------CccchhhHHHHHHHHHHHHHHHH
Q 024326           76 KNHIEAERNRRKRINGHLDTLRSLIPGA------TKMDKATLLTEVISQLKELDKNA  126 (269)
Q Consensus        76 ~~h~~~Er~RR~~in~~~~~LrslvP~~------~k~dk~sil~~ai~yik~L~~~~  126 (269)
                      .+|+.+||+||++||+.|..|+++||..      .|++|++||..||+||++||++.
T Consensus         7 ~~H~~~Er~RR~~in~~f~~L~~lvP~~~~~~~~~k~sK~~iL~~av~yI~~Lq~~~   63 (65)
T d1an4a_           7 AQHNEVERRRRDKINNWIVQLSKIIPDSSMESTKSGQSKGGILSKASDYIQELRQSN   63 (65)
T ss_dssp             CSSHHHHHHHHHHHHHHHHHHHHHSCCCCCCSSTTCCCTTTTTTTTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcccccccCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence            6899999999999999999999999954      58999999999999999998753

>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=6.9e-14  Score=97.28  Aligned_cols=47  Identities=28%  Similarity=0.420  Sum_probs=44.0

Q ss_pred             HHHHHHhHHHHHhhcCCC-CccchhhHHHHHHHHHHHHHHHHHHHhcc
Q 024326           86 RKRINGHLDTLRSLIPGA-TKMDKATLLTEVISQLKELDKNAMEATEG  132 (269)
Q Consensus        86 R~~in~~~~~LrslvP~~-~k~dk~sil~~ai~yik~L~~~~~~l~~~  132 (269)
                      |++||++|.+|+++||+. .|+||++||.+||+||++||+++++|+++
T Consensus         1 R~~in~~f~~L~~lvP~~~~K~~Ka~iL~~Ai~YI~~Lq~~~~~L~~e   48 (61)
T d1uklc_           1 RSSINDKIIELKDLVMGTDAKMHKSGVLRKAIDYIKYLQQVNHKLRQE   48 (61)
T ss_dssp             CCCHHHHHHHHHHHHSCSSCCCCTTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHhhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            678999999999999986 69999999999999999999999999765

>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=97.36  E-value=0.0013  Score=46.87  Aligned_cols=67  Identities=12%  Similarity=0.270  Sum_probs=52.5

Q ss_pred             eEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhh
Q 024326          157 SIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDK  234 (269)
Q Consensus       157 ~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k  234 (269)
                      .+.|.+.|++|||++.+|...|-+.|..|..++..+.++.+...+.+....           .-...++.+|.++-++
T Consensus         5 ~~vitv~G~DrpGiva~vt~~l~~~g~NI~d~~~~~~~~~~~~~~~v~~~~-----------~~~~~l~~~L~~l~~~   71 (86)
T d1u8sa1           5 HLVITAVGTDRPGICNEVVRLVTQAGCNIIDSRIAMFGKEFTLLMLISGSP-----------SNITRVETTLPLLGQQ   71 (86)
T ss_dssp             EEEEEEEEECCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEEECH-----------HHHHHHHHHHHHHHHH
T ss_pred             EEEEEEEeCCCChHHHHHHHHHHHCCCeEEEeEeEEECCeeEEEEEEEcCc-----------ccHHHHHHHHHHHHHH
Confidence            456789999999999999999999999999999999999987666665321           1134566666666554

>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=97.28  E-value=0.0021  Score=45.18  Aligned_cols=47  Identities=15%  Similarity=0.217  Sum_probs=40.3

Q ss_pred             EEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEEe
Q 024326          158 IKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVMA  204 (269)
Q Consensus       158 V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v~  204 (269)
                      +.|++.|++|||++.+|...|.++|..|...+-.+.++.+.-.+.+.
T Consensus         3 ~vitv~g~DrpGiVa~vt~~l~~~g~NI~d~~q~~~~~~f~~~~~v~   49 (83)
T d1zpva1           3 AIITVVGKDKSGIVAGVSGKIAELGLNIDDISQTVLDEYFTMMAVVS   49 (83)
T ss_dssp             EEEEEEESCCTTHHHHHHHHHHHTTCEEEEEEEEEETTEEEEEEEEE
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCeEEEEEeEEeCCEEEEEEEEE
Confidence            34678899999999999999999999999999998888765555554

>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=95.82  E-value=0.067  Score=37.92  Aligned_cols=38  Identities=13%  Similarity=0.303  Sum_probs=33.4

Q ss_pred             eeEEEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          156 YSIKASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       156 ~~V~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      ..|.|.|.|++|||++.+|...|-++|+.|...+..+.
T Consensus         5 ~tv~v~v~g~DrpGIV~~it~~la~~~~nI~~l~t~~~   42 (93)
T d1u8sa2           5 YTVEVYVESDDKLGLTEKFTQFFAQRQIGMASLSAQTI   42 (93)
T ss_dssp             EEEEEEEEESCCTTHHHHHHHHHHHTTCCEEEEEEEEE
T ss_pred             eEEEEEEEECCCCCHHHHHHHHHHHcCCCchhhhcccc
Confidence            45677788999999999999999999999999887654

>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=94.11  E-value=0.025  Score=39.10  Aligned_cols=33  Identities=21%  Similarity=0.206  Sum_probs=26.5

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIAT  192 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist  192 (269)
                      |.|.|.+|+|+|.+|..++-+.+..|.+++..+
T Consensus         4 i~i~~~Dr~GlL~di~~~ia~~~~NI~~i~~~~   36 (77)
T d1y7pa2           4 LRIIAENKIGVLRDLTTIIAEEGGNITFAQTFL   36 (77)
T ss_dssp             EEEEEECCTTHHHHHHHHCC----CEEEEEEEE
T ss_pred             EEEEEecCCChHHHHHHHHHHcCCCeEEEEeec
Confidence            568899999999999999999999999998765

>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=92.93  E-value=0.2  Score=33.81  Aligned_cols=44  Identities=16%  Similarity=0.128  Sum_probs=36.6

Q ss_pred             EEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEE
Q 024326          160 ASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVM  203 (269)
Q Consensus       160 I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v  203 (269)
                      |.|..+++||.|.+++++|.+.|+.|...-.....++..-+|.+
T Consensus         2 iaV~v~d~pG~L~~v~~~L~~~~InI~~~y~~~~~~~~~~vl~v   45 (71)
T d2f06a1           2 VGISCPNVPGALAKVLGFLSAEGVFIEYMYSFANNNVANVVIRP   45 (71)
T ss_dssp             EEEEEESSTTHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEE
T ss_pred             EEEEecCCccHHHHHHHHHHHCCCCEEEEEEEcCCCcEEEEEEE
Confidence            45678999999999999999999999998888777876544444

>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=92.93  E-value=0.22  Score=33.63  Aligned_cols=43  Identities=19%  Similarity=0.087  Sum_probs=36.4

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEE
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIF  201 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf  201 (269)
                      .++|..+++||.|.++...|...|+.|....+....+....-+
T Consensus         5 QisV~~eNkpG~L~~v~~~~~~~~inI~sl~v~~t~~~~i~Ri   47 (70)
T d2f06a2           5 QLSIFLENKSGRLTEVTEVLAKENINLSALCIAENADFGILRG   47 (70)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHTTCCEEEEEEEECSSCEEEEE
T ss_pred             EEEEEEeCCCcHHHHHHHHHHHCCCCEEEEEEeecCCCCEEEE
Confidence            3678899999999999999999999999999887777654333

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

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

Probab=90.32  E-value=0.92  Score=31.07  Aligned_cols=45  Identities=13%  Similarity=0.209  Sum_probs=35.2

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCeEEEEEEE
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGRMKNIFVM  203 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~v~~vf~v  203 (269)
                      ++.+.-.++||+|.+|...|-+.|+.|........++.-..+..+
T Consensus        13 rl~i~~~d~PGvla~I~~~l~~~~iNI~~~~~~~~~~~~~a~~~i   57 (84)
T d1sc6a3          13 RLMHIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQMGYVVIDI   57 (84)
T ss_dssp             EEEEEEESCTTHHHHHHHHHHHTTCEEEEEEEEECSSEEEEEEEE
T ss_pred             EEEEEeCCcCCHHHHHHHHHHHcCCCHHHhccccCCCCcEEEEEE
Confidence            444567899999999999999999999998887776654333333

>d1phza1 d.58.18.3 (A:19-115) Phenylalanine hydroxylase N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phenylalanine metabolism regulatory domain
domain: Phenylalanine hydroxylase N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=86.07  E-value=1.1  Score=31.91  Aligned_cols=66  Identities=15%  Similarity=0.134  Sum_probs=45.8

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCe-EEEEEEEeeecccccchhhhHHHHHHHHHHHHHHHHhhcccc
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGR-MKNIFVMASCKELNFENTEVCQSLVSSVHQAIRSVLDKFSAT  238 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~-v~~vf~v~~~k~~~~~~~~~~~~l~~~v~qaL~~v~~k~~~~  238 (269)
                      +..+++||.|.+++..+...|+.+.+.++-...+. --|.|++...  +. .        -..+..+|..+...++..
T Consensus        21 f~~~~~pGaL~~vL~~f~~~~INLt~IeSRP~~~~~~~Y~F~id~e--g~-~--------~~~i~~~l~~L~~~~~~~   87 (97)
T d1phza1          21 FSLKEEVGALAKVLRLFEENDINLTHIESRPSRLNKDEYEFFTYLD--KR-T--------KPVLGSIIKSLRNDIGAT   87 (97)
T ss_dssp             EEEECCTTHHHHHHHHHHTTTCCTTSEEEEECSSCTTEEEEEECBC--GG-G--------HHHHHHHHHHHHHTTCCC
T ss_pred             EEeCCCCCHHHHHHHHHHHCCCCEEEEEeeccCCCCceEEEEEEcc--cC-C--------hHHHHHHHHHHHHhhCcE
Confidence            55778999999999999999999998888655443 3567888532  21 1        134566666665555543

>d2qmwa2 d.58.18.3 (A:185-264) Prephenate dehydratase C-terminal domain {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phenylalanine metabolism regulatory domain
domain: Prephenate dehydratase C-terminal domain
species: Staphylococcus aureus [TaxId: 1280]

Probab=83.06  E-value=2.2  Score=28.98  Aligned_cols=43  Identities=19%  Similarity=0.267  Sum_probs=35.2

Q ss_pred             EcCCCCCHHHHHHHHHHhcCCeEEEEEEEeeCCe-EEEEEEEee
Q 024326          163 CCNYKPGLLSDLRRVLEALHLSIVKAEIATLEGR-MKNIFVMAS  205 (269)
Q Consensus       163 ~c~~r~glL~~Il~aLe~LgL~V~~a~ist~~g~-v~~vf~v~~  205 (269)
                      .-.++||.|.+++..+.+.|+.+.+.+.-...+. --|.|++..
T Consensus         8 ~~~d~pGaL~~vL~~F~~~~INLt~IeSRP~~~~~~~Y~F~id~   51 (80)
T d2qmwa2           8 PMHDKPGLLASVLNTFALFNINLSWIESRPLKTQLGMYRFFVQA   51 (80)
T ss_dssp             ESSCCTTHHHHHHHHHHTTTCCEEEEEEEECSSSTTCEEEEEEE
T ss_pred             eCCCCCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEE
Confidence            3467999999999999999999999998766654 356688864

>d1ygya3 d.58.18.1 (A:452-529) Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: ACT-like
family: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
domain: Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.45  E-value=2.5  Score=28.40  Aligned_cols=36  Identities=17%  Similarity=0.252  Sum_probs=30.2

Q ss_pred             EEcCCCCCHHHHHHHHHHhcCCeEEEEEEEe--eCCeE
Q 024326          162 LCCNYKPGLLSDLRRVLEALHLSIVKAEIAT--LEGRM  197 (269)
Q Consensus       162 I~c~~r~glL~~Il~aLe~LgL~V~~a~ist--~~g~v  197 (269)
                      +.-.++||++.+|-..|-+.|+.|....+++  .+|..
T Consensus         8 i~~~D~PGvi~~I~~~l~~~~iNI~~m~~~~~~~g~~a   45 (78)
T d1ygya3           8 IHYVDRPGALGKIGTLLGTAGVNIQAAQLSEDAEGPGA   45 (78)
T ss_dssp             EEESCCTTHHHHHHHHHHHTTCCEEEEEEEECSSSSCE
T ss_pred             EEeCCcCCHHHHHHHHHHhcCcChhhheeeecCCCCeE
Confidence            5578999999999999999999999988764  34444

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

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

Probab=81.00  E-value=2.4  Score=28.82  Aligned_cols=35  Identities=14%  Similarity=0.299  Sum_probs=30.6

Q ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCeEEEEEEEee
Q 024326          159 KASLCCNYKPGLLSDLRRVLEALHLSIVKAEIATL  193 (269)
Q Consensus       159 ~I~I~c~~r~glL~~Il~aLe~LgL~V~~a~ist~  193 (269)
                      .+.+..+++||+|.+|...+...|..|.+.++...
T Consensus         5 tisvlv~n~pGvL~Ri~~lF~rRg~NI~SL~v~~t   39 (78)
T d2fgca2           5 LVSMLVHNKPGVMRKVANLFARRGFNISSITVGES   39 (78)
T ss_dssp             EEEEEEECCTTHHHHHHHHHHTTTCEEEEEEEEEC
T ss_pred             EEEEEEeCCCcHHHHHHHHHhhCCcceEEEEEeec
Confidence            45677899999999999999999999998888643